Starting phenix.real_space_refine on Wed Apr 30 20:14:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7psl_13613/04_2025/7psl_13613.cif Found real_map, /net/cci-nas-00/data/ceres_data/7psl_13613/04_2025/7psl_13613.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7psl_13613/04_2025/7psl_13613.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7psl_13613/04_2025/7psl_13613.map" model { file = "/net/cci-nas-00/data/ceres_data/7psl_13613/04_2025/7psl_13613.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7psl_13613/04_2025/7psl_13613.cif" } resolution = 3.3 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= 0.070 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 34 5.16 5 C 6190 2.51 5 N 1634 2.21 5 O 1750 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 9612 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4756 Classifications: {'peptide': 600} Link IDs: {'PTRANS': 17, 'TRANS': 582} Chain: "A" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 50 Unusual residues: {'LOP': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B Time building chain proxies: 9.59, per 1000 atoms: 1.00 Number of scatterers: 9612 At special positions: 0 Unit cell: (109.647, 76.167, 142.29, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 34 16.00 P 4 15.00 O 1750 8.00 N 1634 7.00 C 6190 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.38 Conformation dependent library (CDL) restraints added in 1.4 seconds 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2244 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 6 sheets defined 68.4% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 92 through 99 Processing helix chain 'A' and resid 104 through 140 removed outlier: 3.916A pdb=" N ARG A 108 " --> pdb=" O ASN A 104 " (cutoff:3.500A) Proline residue: A 129 - end of helix Processing helix chain 'A' and resid 151 through 199 removed outlier: 4.073A pdb=" N THR A 157 " --> pdb=" O ALA A 153 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASN A 185 " --> pdb=" O LYS A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 209 removed outlier: 3.630A pdb=" N ARG A 209 " --> pdb=" O TRP A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 234 Processing helix chain 'A' and resid 236 through 254 removed outlier: 3.626A pdb=" N PHE A 254 " --> pdb=" O LEU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 304 removed outlier: 4.178A pdb=" N ALA A 259 " --> pdb=" O GLY A 255 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA A 294 " --> pdb=" O ALA A 290 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN A 304 " --> pdb=" O ASP A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 311 removed outlier: 3.726A pdb=" N PHE A 311 " --> pdb=" O ALA A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 365 Processing helix chain 'A' and resid 366 through 368 No H-bonds generated for 'chain 'A' and resid 366 through 368' Processing helix chain 'A' and resid 371 through 387 removed outlier: 3.527A pdb=" N LEU A 375 " --> pdb=" O THR A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 412 removed outlier: 3.942A pdb=" N LEU A 392 " --> pdb=" O PRO A 388 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ARG A 397 " --> pdb=" O GLY A 393 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ASP A 398 " --> pdb=" O SER A 394 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LYS A 400 " --> pdb=" O TYR A 396 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N GLN A 401 " --> pdb=" O ARG A 397 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU A 412 " --> pdb=" O THR A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 483 Processing helix chain 'A' and resid 504 through 510 Processing helix chain 'A' and resid 526 through 532 Processing helix chain 'A' and resid 538 through 549 Processing helix chain 'A' and resid 551 through 556 Processing helix chain 'A' and resid 574 through 590 Processing helix chain 'A' and resid 604 through 619 Processing helix chain 'A' and resid 632 through 636 Processing helix chain 'A' and resid 655 through 661 Processing helix chain 'A' and resid 665 through 691 removed outlier: 3.800A pdb=" N GLU A 669 " --> pdb=" O SER A 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 99 Processing helix chain 'B' and resid 104 through 140 removed outlier: 3.916A pdb=" N ARG B 108 " --> pdb=" O ASN B 104 " (cutoff:3.500A) Proline residue: B 129 - end of helix Processing helix chain 'B' and resid 151 through 199 removed outlier: 4.074A pdb=" N THR B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASN B 185 " --> pdb=" O LYS B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 209 removed outlier: 3.629A pdb=" N ARG B 209 " --> pdb=" O TRP B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 234 Processing helix chain 'B' and resid 236 through 254 removed outlier: 3.626A pdb=" N PHE B 254 " --> pdb=" O LEU B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 304 removed outlier: 4.179A pdb=" N ALA B 259 " --> pdb=" O GLY B 255 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA B 294 " --> pdb=" O ALA B 290 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASN B 304 " --> pdb=" O ASP B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 311 removed outlier: 3.726A pdb=" N PHE B 311 " --> pdb=" O ALA B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 365 Processing helix chain 'B' and resid 366 through 368 No H-bonds generated for 'chain 'B' and resid 366 through 368' Processing helix chain 'B' and resid 371 through 387 removed outlier: 3.527A pdb=" N LEU B 375 " --> pdb=" O THR B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 412 removed outlier: 3.942A pdb=" N LEU B 392 " --> pdb=" O PRO B 388 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ARG B 397 " --> pdb=" O GLY B 393 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ASP B 398 " --> pdb=" O SER B 394 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LYS B 400 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N GLN B 401 " --> pdb=" O ARG B 397 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU B 412 " --> pdb=" O THR B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 483 Processing helix chain 'B' and resid 504 through 510 Processing helix chain 'B' and resid 526 through 532 Processing helix chain 'B' and resid 538 through 549 Processing helix chain 'B' and resid 551 through 556 Processing helix chain 'B' and resid 574 through 590 Processing helix chain 'B' and resid 604 through 619 Processing helix chain 'B' and resid 632 through 636 Processing helix chain 'B' and resid 655 through 661 Processing helix chain 'B' and resid 665 through 691 removed outlier: 3.800A pdb=" N GLU B 669 " --> pdb=" O SER B 665 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 438 through 439 Processing sheet with id=AA2, first strand: chain 'A' and resid 441 through 443 removed outlier: 7.148A pdb=" N PHE A 443 " --> pdb=" O LYS A 453 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N LYS A 453 " --> pdb=" O PHE A 443 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 512 through 515 removed outlier: 7.026A pdb=" N THR A 465 " --> pdb=" O TYR A 628 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ALA A 466 " --> pdb=" O ILE A 643 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N LEU A 645 " --> pdb=" O ALA A 466 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL A 468 " --> pdb=" O LEU A 645 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 438 through 439 Processing sheet with id=AA5, first strand: chain 'B' and resid 441 through 443 removed outlier: 7.148A pdb=" N PHE B 443 " --> pdb=" O LYS B 453 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N LYS B 453 " --> pdb=" O PHE B 443 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 512 through 515 removed outlier: 7.026A pdb=" N THR B 465 " --> pdb=" O TYR B 628 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ALA B 466 " --> pdb=" O ILE B 643 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N LEU B 645 " --> pdb=" O ALA B 466 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N VAL B 468 " --> pdb=" O LEU B 645 " (cutoff:3.500A) 637 hydrogen bonds defined for protein. 1881 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: 2.77 Time building geometry restraints manager: 2.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1552 1.31 - 1.43: 2487 1.43 - 1.56: 5683 1.56 - 1.68: 4 1.68 - 1.81: 62 Bond restraints: 9788 Sorted by residual: bond pdb=" C24 LOP B 701 " pdb=" O6 LOP B 701 " ideal model delta sigma weight residual 1.325 1.397 -0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" C24 LOP A 701 " pdb=" O6 LOP A 701 " ideal model delta sigma weight residual 1.325 1.397 -0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" C6 LOP A 701 " pdb=" O5 LOP A 701 " ideal model delta sigma weight residual 1.331 1.400 -0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" C6 LOP B 701 " pdb=" O5 LOP B 701 " ideal model delta sigma weight residual 1.331 1.400 -0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" O3 PO4 A 702 " pdb=" P PO4 A 702 " ideal model delta sigma weight residual 1.569 1.519 0.050 2.00e-02 2.50e+03 6.23e+00 ... (remaining 9783 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 13055 2.26 - 4.52: 145 4.52 - 6.79: 16 6.79 - 9.05: 6 9.05 - 11.31: 4 Bond angle restraints: 13226 Sorted by residual: angle pdb=" N ILE B 526 " pdb=" CA ILE B 526 " pdb=" C ILE B 526 " ideal model delta sigma weight residual 113.42 108.14 5.28 1.17e+00 7.31e-01 2.04e+01 angle pdb=" N ILE A 526 " pdb=" CA ILE A 526 " pdb=" C ILE A 526 " ideal model delta sigma weight residual 113.42 108.14 5.28 1.17e+00 7.31e-01 2.04e+01 angle pdb=" N ILE B 154 " pdb=" CA ILE B 154 " pdb=" C ILE B 154 " ideal model delta sigma weight residual 112.96 109.16 3.80 1.00e+00 1.00e+00 1.44e+01 angle pdb=" N ILE A 154 " pdb=" CA ILE A 154 " pdb=" C ILE A 154 " ideal model delta sigma weight residual 112.96 109.16 3.80 1.00e+00 1.00e+00 1.44e+01 angle pdb=" O3 LOP A 701 " pdb=" P1 LOP A 701 " pdb=" O4 LOP A 701 " ideal model delta sigma weight residual 120.67 109.36 11.31 3.00e+00 1.11e-01 1.42e+01 ... (remaining 13221 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 5158 17.54 - 35.07: 574 35.07 - 52.61: 134 52.61 - 70.14: 24 70.14 - 87.68: 4 Dihedral angle restraints: 5894 sinusoidal: 2420 harmonic: 3474 Sorted by residual: dihedral pdb=" CA ASP A 374 " pdb=" CB ASP A 374 " pdb=" CG ASP A 374 " pdb=" OD1 ASP A 374 " ideal model delta sinusoidal sigma weight residual -30.00 -89.21 59.21 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CA ASP B 374 " pdb=" CB ASP B 374 " pdb=" CG ASP B 374 " pdb=" OD1 ASP B 374 " ideal model delta sinusoidal sigma weight residual -30.00 -89.18 59.18 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CA ARG B 484 " pdb=" C ARG B 484 " pdb=" N PHE B 485 " pdb=" CA PHE B 485 " ideal model delta harmonic sigma weight residual 180.00 164.32 15.68 0 5.00e+00 4.00e-02 9.83e+00 ... (remaining 5891 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1096 0.039 - 0.078: 329 0.078 - 0.116: 83 0.116 - 0.155: 14 0.155 - 0.194: 2 Chirality restraints: 1524 Sorted by residual: chirality pdb=" C4 LOP B 701 " pdb=" C3 LOP B 701 " pdb=" C5 LOP B 701 " pdb=" O5 LOP B 701 " both_signs ideal model delta sigma weight residual False -2.34 -2.53 0.19 2.00e-01 2.50e+01 9.39e-01 chirality pdb=" C4 LOP A 701 " pdb=" C3 LOP A 701 " pdb=" C5 LOP A 701 " pdb=" O5 LOP A 701 " both_signs ideal model delta sigma weight residual False -2.34 -2.53 0.19 2.00e-01 2.50e+01 9.17e-01 chirality pdb=" CA PRO A 129 " pdb=" N PRO A 129 " pdb=" C PRO A 129 " pdb=" CB PRO A 129 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.13 2.00e-01 2.50e+01 4.54e-01 ... (remaining 1521 not shown) Planarity restraints: 1664 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 128 " -0.023 5.00e-02 4.00e+02 3.44e-02 1.89e+00 pdb=" N PRO A 129 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 129 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 129 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 128 " 0.023 5.00e-02 4.00e+02 3.40e-02 1.85e+00 pdb=" N PRO B 129 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO B 129 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 129 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 387 " -0.019 5.00e-02 4.00e+02 2.87e-02 1.32e+00 pdb=" N PRO A 388 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 388 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 388 " -0.016 5.00e-02 4.00e+02 ... (remaining 1661 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2326 2.79 - 3.32: 9919 3.32 - 3.84: 15409 3.84 - 4.37: 17523 4.37 - 4.90: 31515 Nonbonded interactions: 76692 Sorted by model distance: nonbonded pdb=" OD1 ASP A 499 " pdb=" N ILE A 500 " model vdw 2.258 3.120 nonbonded pdb=" OD1 ASP B 499 " pdb=" N ILE B 500 " model vdw 2.259 3.120 nonbonded pdb=" NZ LYS A 531 " pdb=" O ILE A 535 " model vdw 2.297 3.120 nonbonded pdb=" NZ LYS B 531 " pdb=" O ILE B 535 " model vdw 2.297 3.120 nonbonded pdb=" O THR A 273 " pdb=" OG1 THR A 277 " model vdw 2.311 3.040 ... (remaining 76687 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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=0.94 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: 102.030 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 27.580 Find NCS groups from input model: 0.160 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: 0.010 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: 133.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 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 0.072 9788 Z= 0.266 Angle : 0.649 11.311 13226 Z= 0.342 Chirality : 0.040 0.194 1524 Planarity : 0.003 0.034 1664 Dihedral : 15.096 87.681 3650 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % 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: -3.04 (0.22), residues: 1196 helix: -0.93 (0.17), residues: 778 sheet: -3.80 (0.67), residues: 56 loop : -4.02 (0.27), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 279 HIS 0.002 0.001 HIS B 656 PHE 0.012 0.001 PHE A 132 TYR 0.008 0.001 TYR B 310 ARG 0.002 0.000 ARG A 280 Details of bonding type rmsd hydrogen bonds : bond 0.10273 ( 637) hydrogen bonds : angle 5.28085 ( 1881) covalent geometry : bond 0.00638 ( 9788) covalent geometry : angle 0.64925 (13226) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 ARG cc_start: 0.8202 (ttp80) cc_final: 0.7884 (ttp80) REVERT: A 649 ARG cc_start: 0.7714 (mtt180) cc_final: 0.7013 (mtp-110) REVERT: A 665 SER cc_start: 0.8387 (m) cc_final: 0.8121 (p) REVERT: A 668 ARG cc_start: 0.8517 (mtp180) cc_final: 0.8178 (mtm180) REVERT: B 312 ASN cc_start: 0.8628 (m110) cc_final: 0.8422 (m110) REVERT: B 668 ARG cc_start: 0.8484 (mtp180) cc_final: 0.8130 (mtm180) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.3088 time to fit residues: 54.6541 Evaluate side-chains 100 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 GLN A 196 GLN A 346 GLN A 606 HIS B 127 GLN B 196 GLN B 346 GLN ** B 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 606 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.179268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.132358 restraints weight = 10172.192| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.53 r_work: 0.3398 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 9788 Z= 0.168 Angle : 0.559 7.584 13226 Z= 0.290 Chirality : 0.041 0.227 1524 Planarity : 0.003 0.035 1664 Dihedral : 8.219 56.760 1378 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.87 % Allowed : 10.37 % Favored : 88.76 % 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 (0.24), residues: 1196 helix: 0.96 (0.18), residues: 786 sheet: -3.83 (0.65), residues: 56 loop : -3.17 (0.29), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 279 HIS 0.005 0.001 HIS B 197 PHE 0.020 0.002 PHE A 132 TYR 0.031 0.002 TYR A 310 ARG 0.003 0.000 ARG B 632 Details of bonding type rmsd hydrogen bonds : bond 0.05400 ( 637) hydrogen bonds : angle 4.06168 ( 1881) covalent geometry : bond 0.00394 ( 9788) covalent geometry : angle 0.55876 (13226) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 127 time to evaluate : 1.574 Fit side-chains revert: symmetry clash REVERT: A 97 ARG cc_start: 0.8210 (ttp80) cc_final: 0.7892 (tmm160) REVERT: A 216 ARG cc_start: 0.6918 (ttp80) cc_final: 0.6614 (ttp80) REVERT: A 588 LEU cc_start: 0.7359 (mt) cc_final: 0.7043 (mp) REVERT: A 594 MET cc_start: 0.7642 (mmt) cc_final: 0.7197 (mmt) REVERT: A 662 MET cc_start: 0.6919 (mtp) cc_final: 0.6693 (ptp) REVERT: A 668 ARG cc_start: 0.8666 (mtp180) cc_final: 0.8219 (mtm180) REVERT: B 148 VAL cc_start: 0.8654 (p) cc_final: 0.8448 (m) REVERT: B 668 ARG cc_start: 0.8599 (mtp180) cc_final: 0.8121 (mtm180) outliers start: 9 outliers final: 7 residues processed: 133 average time/residue: 0.2470 time to fit residues: 45.2277 Evaluate side-chains 117 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 110 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 390 ASN Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 390 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 65 optimal weight: 0.4980 chunk 16 optimal weight: 1.9990 chunk 119 optimal weight: 20.0000 chunk 18 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 42 optimal weight: 0.1980 chunk 26 optimal weight: 0.5980 chunk 44 optimal weight: 0.0060 chunk 12 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 312 ASN ** 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 = 0.4060 r_free = 0.4060 target = 0.181525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.134448 restraints weight = 10292.344| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.56 r_work: 0.3419 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9788 Z= 0.123 Angle : 0.510 7.837 13226 Z= 0.263 Chirality : 0.039 0.229 1524 Planarity : 0.003 0.027 1664 Dihedral : 7.771 55.984 1378 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.07 % Allowed : 12.60 % Favored : 86.34 % 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: 0.33 (0.26), residues: 1196 helix: 1.71 (0.19), residues: 798 sheet: -3.78 (0.52), residues: 80 loop : -2.65 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 279 HIS 0.005 0.001 HIS A 606 PHE 0.018 0.001 PHE A 532 TYR 0.037 0.002 TYR B 310 ARG 0.006 0.000 ARG A 632 Details of bonding type rmsd hydrogen bonds : bond 0.04875 ( 637) hydrogen bonds : angle 3.73955 ( 1881) covalent geometry : bond 0.00269 ( 9788) covalent geometry : angle 0.50969 (13226) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 121 time to evaluate : 1.084 Fit side-chains revert: symmetry clash REVERT: A 216 ARG cc_start: 0.6926 (ttp80) cc_final: 0.6549 (ttp80) REVERT: A 594 MET cc_start: 0.7470 (mmt) cc_final: 0.7227 (mmt) REVERT: A 668 ARG cc_start: 0.8677 (mtp180) cc_final: 0.8265 (mtm180) REVERT: B 97 ARG cc_start: 0.8144 (tmm160) cc_final: 0.7829 (ttp80) REVERT: B 148 VAL cc_start: 0.8670 (p) cc_final: 0.8409 (m) REVERT: B 216 ARG cc_start: 0.6937 (ttp80) cc_final: 0.6468 (ttp80) REVERT: B 594 MET cc_start: 0.7441 (mmt) cc_final: 0.7149 (mmt) REVERT: B 668 ARG cc_start: 0.8645 (mtp180) cc_final: 0.8325 (mtp180) outliers start: 11 outliers final: 8 residues processed: 126 average time/residue: 0.2361 time to fit residues: 41.9740 Evaluate side-chains 116 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 108 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 390 ASN Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 390 ASN Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 659 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 116 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 115 optimal weight: 0.6980 chunk 47 optimal weight: 4.9990 chunk 59 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 HIS B 235 HIS B 312 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.169954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.120162 restraints weight = 10615.666| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.48 r_work: 0.3234 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 9788 Z= 0.285 Angle : 0.662 9.528 13226 Z= 0.342 Chirality : 0.045 0.240 1524 Planarity : 0.004 0.033 1664 Dihedral : 8.162 59.143 1378 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.84 % Allowed : 15.02 % Favored : 83.14 % 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: -0.12 (0.25), residues: 1196 helix: 1.25 (0.19), residues: 794 sheet: -3.50 (0.68), residues: 56 loop : -2.70 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 100 HIS 0.004 0.001 HIS B 197 PHE 0.021 0.003 PHE A 132 TYR 0.039 0.002 TYR B 310 ARG 0.006 0.000 ARG A 632 Details of bonding type rmsd hydrogen bonds : bond 0.06196 ( 637) hydrogen bonds : angle 4.12216 ( 1881) covalent geometry : bond 0.00698 ( 9788) covalent geometry : angle 0.66232 (13226) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 146 time to evaluate : 0.968 Fit side-chains revert: symmetry clash REVERT: A 216 ARG cc_start: 0.6980 (ttp80) cc_final: 0.6541 (ttp80) REVERT: A 594 MET cc_start: 0.7741 (mmt) cc_final: 0.7170 (mmt) REVERT: B 97 ARG cc_start: 0.8286 (tmm160) cc_final: 0.7980 (ttp80) REVERT: B 148 VAL cc_start: 0.8661 (p) cc_final: 0.8404 (m) REVERT: B 216 ARG cc_start: 0.6972 (ttp80) cc_final: 0.6495 (ttp80) REVERT: B 594 MET cc_start: 0.7581 (mmt) cc_final: 0.7152 (mmt) REVERT: B 668 ARG cc_start: 0.8635 (mtp180) cc_final: 0.8205 (mtp180) outliers start: 19 outliers final: 13 residues processed: 160 average time/residue: 0.2131 time to fit residues: 47.6633 Evaluate side-chains 147 residues out of total 1032 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 134 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain B residue 659 LEU 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: 63.2934 > 50: distance: 15 - 19: 20.377 distance: 19 - 20: 22.580 distance: 19 - 137: 19.638 distance: 20 - 21: 15.091 distance: 20 - 23: 43.911 distance: 21 - 22: 36.441 distance: 21 - 26: 6.427 distance: 22 - 134: 22.076 distance: 23 - 24: 36.581 distance: 23 - 25: 33.289 distance: 26 - 27: 27.963 distance: 27 - 28: 17.872 distance: 27 - 30: 21.285 distance: 28 - 29: 13.702 distance: 28 - 33: 23.532 distance: 30 - 31: 15.876 distance: 30 - 32: 8.645 distance: 33 - 34: 22.468 distance: 34 - 35: 28.259 distance: 34 - 37: 25.320 distance: 35 - 36: 22.795 distance: 35 - 44: 36.412 distance: 37 - 38: 18.313 distance: 38 - 39: 18.373 distance: 38 - 40: 16.910 distance: 39 - 41: 15.398 distance: 40 - 42: 12.688 distance: 41 - 43: 7.108 distance: 42 - 43: 7.680 distance: 44 - 45: 43.848 distance: 45 - 46: 55.873 distance: 46 - 47: 12.367 distance: 46 - 48: 57.109 distance: 48 - 49: 22.088 distance: 49 - 52: 16.368 distance: 50 - 51: 49.650 distance: 50 - 60: 34.518 distance: 52 - 53: 26.173 distance: 53 - 54: 8.117 distance: 53 - 55: 12.930 distance: 54 - 56: 15.078 distance: 55 - 57: 7.419 distance: 56 - 58: 11.075 distance: 57 - 58: 14.067 distance: 58 - 59: 21.205 distance: 60 - 61: 14.839 distance: 61 - 62: 43.313 distance: 61 - 64: 14.608 distance: 62 - 63: 28.206 distance: 62 - 70: 34.347 distance: 64 - 65: 23.162 distance: 65 - 66: 33.031 distance: 65 - 67: 19.415 distance: 66 - 68: 12.442 distance: 67 - 69: 35.025 distance: 68 - 69: 10.697 distance: 70 - 71: 33.929 distance: 70 - 76: 41.435 distance: 71 - 72: 43.147 distance: 71 - 74: 15.977 distance: 72 - 73: 18.135 distance: 72 - 77: 11.129 distance: 74 - 75: 21.556 distance: 75 - 76: 27.630 distance: 77 - 78: 12.193 distance: 78 - 79: 20.403 distance: 78 - 81: 19.503 distance: 79 - 80: 10.945 distance: 79 - 85: 13.112 distance: 81 - 82: 11.737 distance: 82 - 83: 20.663 distance: 82 - 84: 9.514 distance: 85 - 86: 3.946 distance: 86 - 87: 27.488 distance: 86 - 89: 9.737 distance: 87 - 88: 16.125 distance: 87 - 96: 30.359 distance: 89 - 90: 12.449 distance: 91 - 92: 9.570 distance: 93 - 94: 4.204 distance: 93 - 95: 3.133 distance: 97 - 98: 9.448 distance: 97 - 100: 21.715 distance: 98 - 99: 5.371 distance: 98 - 105: 30.788 distance: 100 - 101: 11.693 distance: 101 - 102: 11.826 distance: 102 - 103: 7.565 distance: 103 - 104: 6.836