Starting phenix.real_space_refine (version: 1.21rc1) on Tue Oct 3 05:13:43 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ooy_17033/10_2023/8ooy_17033.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ooy_17033/10_2023/8ooy_17033.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ooy_17033/10_2023/8ooy_17033.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ooy_17033/10_2023/8ooy_17033.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ooy_17033/10_2023/8ooy_17033.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ooy_17033/10_2023/8ooy_17033.pdb" } resolution = 4.0 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= 0.001 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: 6 Type Number sf(0) Gaussians P 51 5.49 5 Mg 1 5.21 5 S 15 5.16 5 C 3520 2.51 5 N 1029 2.21 5 O 1212 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 493": "OE1" <-> "OE2" Residue "A ASP 548": "OD1" <-> "OD2" Residue "A GLU 611": "OE1" <-> "OE2" Residue "A GLU 615": "OE1" <-> "OE2" Residue "A GLU 629": "OE1" <-> "OE2" Residue "A TYR 814": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 5828 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 604, 4782 Classifications: {'peptide': 604} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 575} Chain: "T" Number of atoms: 536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 536 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "P" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 366 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "D" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 143 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.64, per 1000 atoms: 0.62 Number of scatterers: 5828 At special positions: 0 Unit cell: (89.452, 96.14, 78.584, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 15 16.00 P 51 15.00 Mg 1 11.99 O 1212 8.00 N 1029 7.00 C 3520 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 - 3.50 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: 3.37 Conformation dependent library (CDL) restraints added in 887.9 milliseconds 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1140 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 4 sheets defined 62.7% alpha, 5.6% beta 23 base pairs and 39 stacking pairs defined. Time for finding SS restraints: 2.29 Creating SS restraints... Processing helix chain 'A' and resid 335 through 348 removed outlier: 3.673A pdb=" N LYS A 348 " --> pdb=" O ALA A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 410 removed outlier: 3.604A pdb=" N LEU A 402 " --> pdb=" O ARG A 398 " (cutoff:3.500A) Proline residue: A 407 - end of helix Processing helix chain 'A' and resid 420 through 430 removed outlier: 3.605A pdb=" N ASP A 424 " --> pdb=" O ASN A 420 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY A 426 " --> pdb=" O LYS A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 450 Processing helix chain 'A' and resid 457 through 466 removed outlier: 3.944A pdb=" N GLU A 463 " --> pdb=" O ASP A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 478 removed outlier: 4.045A pdb=" N ILE A 476 " --> pdb=" O THR A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 489 removed outlier: 3.647A pdb=" N GLN A 488 " --> pdb=" O THR A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 519 Proline residue: A 514 - end of helix removed outlier: 3.555A pdb=" N HIS A 519 " --> pdb=" O ASP A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 529 Processing helix chain 'A' and resid 532 through 544 removed outlier: 4.405A pdb=" N VAL A 536 " --> pdb=" O PRO A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 575 removed outlier: 3.831A pdb=" N LEU A 552 " --> pdb=" O ASP A 548 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N GLU A 557 " --> pdb=" O HIS A 553 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU A 558 " --> pdb=" O ASN A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 594 removed outlier: 3.628A pdb=" N LEU A 586 " --> pdb=" O SER A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 619 Processing helix chain 'A' and resid 621 through 640 removed outlier: 4.032A pdb=" N LYS A 625 " --> pdb=" O TYR A 621 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU A 636 " --> pdb=" O GLY A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 647 removed outlier: 3.799A pdb=" N LEU A 646 " --> pdb=" O ASP A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 679 removed outlier: 3.877A pdb=" N ILE A 679 " --> pdb=" O LEU A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 692 Processing helix chain 'A' and resid 708 through 719 Processing helix chain 'A' and resid 720 through 730 Processing helix chain 'A' and resid 732 through 743 Processing helix chain 'A' and resid 745 through 749 Processing helix chain 'A' and resid 750 through 767 Processing helix chain 'A' and resid 769 through 778 Processing helix chain 'A' and resid 780 through 795 Processing helix chain 'A' and resid 795 through 812 removed outlier: 3.734A pdb=" N LEU A 799 " --> pdb=" O TYR A 795 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS A 810 " --> pdb=" O ARG A 806 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU A 811 " --> pdb=" O ALA A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 871 removed outlier: 3.743A pdb=" N ALA A 838 " --> pdb=" O ALA A 834 " (cutoff:3.500A) Proline residue: A 847 - end of helix Processing helix chain 'A' and resid 892 through 906 removed outlier: 3.570A pdb=" N ALA A 897 " --> pdb=" O VAL A 893 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LYS A 898 " --> pdb=" O ASP A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 928 Processing sheet with id=AA1, first strand: chain 'A' and resid 330 through 332 removed outlier: 3.620A pdb=" N TYR A 382 " --> pdb=" O VAL A 331 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N VAL A 379 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE A 375 " --> pdb=" O VAL A 379 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 351 through 353 removed outlier: 6.262A pdb=" N PHE A 352 " --> pdb=" O VAL A 417 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LYS A 416 " --> pdb=" O PHE A 440 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 658 through 660 removed outlier: 3.587A pdb=" N SER A 670 " --> pdb=" O HIS A 660 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 699 through 702 252 hydrogen bonds defined for protein. 735 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 59 hydrogen bonds 118 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 39 stacking parallelities Total time for adding SS restraints: 2.20 Time building geometry restraints manager: 3.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1534 1.33 - 1.45: 1226 1.45 - 1.57: 3153 1.57 - 1.69: 99 1.69 - 1.81: 29 Bond restraints: 6041 Sorted by residual: bond pdb=" N VAL A 663 " pdb=" CA VAL A 663 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.48e+00 bond pdb=" N THR A 664 " pdb=" CA THR A 664 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.27e-02 6.20e+03 6.88e+00 bond pdb=" N VAL A 504 " pdb=" CA VAL A 504 " ideal model delta sigma weight residual 1.461 1.489 -0.028 1.17e-02 7.31e+03 5.56e+00 bond pdb=" N ASP A 501 " pdb=" CA ASP A 501 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.17e-02 7.31e+03 5.41e+00 bond pdb=" N THR A 485 " pdb=" CA THR A 485 " ideal model delta sigma weight residual 1.456 1.483 -0.027 1.25e-02 6.40e+03 4.83e+00 ... (remaining 6036 not shown) Histogram of bond angle deviations from ideal: 98.15 - 105.31: 297 105.31 - 112.48: 3175 112.48 - 119.64: 2085 119.64 - 126.80: 2641 126.80 - 133.96: 193 Bond angle restraints: 8391 Sorted by residual: angle pdb=" CA THR A 664 " pdb=" C THR A 664 " pdb=" O THR A 664 " ideal model delta sigma weight residual 121.56 117.76 3.80 1.09e+00 8.42e-01 1.21e+01 angle pdb=" CA LEU A 506 " pdb=" C LEU A 506 " pdb=" O LEU A 506 " ideal model delta sigma weight residual 120.90 117.30 3.60 1.07e+00 8.73e-01 1.13e+01 angle pdb=" C ASN A 554 " pdb=" N HIS A 555 " pdb=" CA HIS A 555 " ideal model delta sigma weight residual 120.28 125.04 -4.76 1.44e+00 4.82e-01 1.09e+01 angle pdb=" N ILE A 529 " pdb=" CA ILE A 529 " pdb=" C ILE A 529 " ideal model delta sigma weight residual 112.12 109.38 2.74 8.40e-01 1.42e+00 1.06e+01 angle pdb=" N THR A 505 " pdb=" CA THR A 505 " pdb=" C THR A 505 " ideal model delta sigma weight residual 111.11 107.33 3.78 1.20e+00 6.94e-01 9.94e+00 ... (remaining 8386 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.28: 2863 17.28 - 34.57: 368 34.57 - 51.85: 192 51.85 - 69.13: 65 69.13 - 86.41: 7 Dihedral angle restraints: 3495 sinusoidal: 1732 harmonic: 1763 Sorted by residual: dihedral pdb=" CA VAL A 815 " pdb=" C VAL A 815 " pdb=" N GLU A 816 " pdb=" CA GLU A 816 " ideal model delta harmonic sigma weight residual -180.00 -160.15 -19.85 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA ASP A 892 " pdb=" CB ASP A 892 " pdb=" CG ASP A 892 " pdb=" OD1 ASP A 892 " ideal model delta sinusoidal sigma weight residual -30.00 -85.98 55.98 1 2.00e+01 2.50e-03 1.06e+01 dihedral pdb=" CB GLU A 917 " pdb=" CG GLU A 917 " pdb=" CD GLU A 917 " pdb=" OE1 GLU A 917 " ideal model delta sinusoidal sigma weight residual 0.00 86.41 -86.41 1 3.00e+01 1.11e-03 1.00e+01 ... (remaining 3492 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 694 0.042 - 0.083: 179 0.083 - 0.125: 64 0.125 - 0.167: 5 0.167 - 0.208: 2 Chirality restraints: 944 Sorted by residual: chirality pdb=" CA VAL A 663 " pdb=" N VAL A 663 " pdb=" C VAL A 663 " pdb=" CB VAL A 663 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA ILE A 779 " pdb=" N ILE A 779 " pdb=" C ILE A 779 " pdb=" CB ILE A 779 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.71e-01 chirality pdb=" CG LEU A 636 " pdb=" CB LEU A 636 " pdb=" CD1 LEU A 636 " pdb=" CD2 LEU A 636 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 6.85e-01 ... (remaining 941 not shown) Planarity restraints: 913 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 521 " 0.030 5.00e-02 4.00e+02 4.54e-02 3.30e+00 pdb=" N PRO A 522 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 522 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 522 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 779 " 0.029 5.00e-02 4.00e+02 4.31e-02 2.98e+00 pdb=" N PRO A 780 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 780 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 780 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 901 " -0.008 2.00e-02 2.50e+03 1.53e-02 2.33e+00 pdb=" C HIS A 901 " 0.026 2.00e-02 2.50e+03 pdb=" O HIS A 901 " -0.010 2.00e-02 2.50e+03 pdb=" N GLN A 902 " -0.009 2.00e-02 2.50e+03 ... (remaining 910 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 60 2.59 - 3.17: 5044 3.17 - 3.75: 10010 3.75 - 4.32: 13143 4.32 - 4.90: 20807 Nonbonded interactions: 49064 Sorted by model distance: nonbonded pdb=" OD1 ASP A 355 " pdb="MG MG A1001 " model vdw 2.016 2.170 nonbonded pdb=" OD1 ASN A 524 " pdb=" ND2 ASN A 528 " model vdw 2.201 2.520 nonbonded pdb=" NE2 HIS A 555 " pdb=" OE2 GLU A 685 " model vdw 2.206 2.520 nonbonded pdb=" OE1 GLU A 729 " pdb=" NZ LYS A 731 " model vdw 2.214 2.520 nonbonded pdb=" OG1 THR A 817 " pdb=" OG1 THR A 851 " model vdw 2.231 2.440 ... (remaining 49059 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=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: 0.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.710 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 22.760 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 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 : 0.004 0.039 6041 Z= 0.219 Angle : 0.681 7.727 8391 Z= 0.395 Chirality : 0.043 0.208 944 Planarity : 0.004 0.045 913 Dihedral : 19.973 86.412 2355 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 0.79 % Allowed : 0.39 % Favored : 98.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.97 (0.35), residues: 602 helix: 0.59 (0.30), residues: 315 sheet: -3.34 (0.66), residues: 47 loop : -1.70 (0.40), residues: 240 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 73 time to evaluate : 0.675 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 76 average time/residue: 0.1618 time to fit residues: 16.8521 Evaluate side-chains 53 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.547 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 53 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 32 optimal weight: 0.5980 chunk 25 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 785 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.0913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6041 Z= 0.196 Angle : 0.598 8.041 8391 Z= 0.319 Chirality : 0.041 0.246 944 Planarity : 0.005 0.054 913 Dihedral : 21.718 66.276 1160 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.97 % Allowed : 7.48 % Favored : 90.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.57 (0.35), residues: 602 helix: 0.89 (0.29), residues: 325 sheet: -3.26 (0.64), residues: 49 loop : -1.52 (0.42), residues: 228 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 58 time to evaluate : 0.608 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 65 average time/residue: 0.1506 time to fit residues: 13.8471 Evaluate side-chains 54 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 48 time to evaluate : 0.603 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0566 time to fit residues: 1.4125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 31 optimal weight: 0.0070 chunk 17 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 56 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 45 optimal weight: 0.0570 overall best weight: 0.5116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6041 Z= 0.167 Angle : 0.556 7.613 8391 Z= 0.298 Chirality : 0.038 0.159 944 Planarity : 0.004 0.051 913 Dihedral : 21.601 63.647 1160 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.98 % Allowed : 11.42 % Favored : 87.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.27 (0.36), residues: 602 helix: 1.09 (0.29), residues: 326 sheet: -3.10 (0.65), residues: 49 loop : -1.32 (0.44), residues: 227 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 66 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 69 average time/residue: 0.1561 time to fit residues: 15.0768 Evaluate side-chains 56 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 53 time to evaluate : 0.623 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0575 time to fit residues: 1.1307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 56 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 6 optimal weight: 0.0980 chunk 27 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 60 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6041 Z= 0.178 Angle : 0.553 8.675 8391 Z= 0.293 Chirality : 0.039 0.167 944 Planarity : 0.004 0.050 913 Dihedral : 21.677 62.735 1160 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.57 % Allowed : 14.76 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.07 (0.35), residues: 602 helix: 1.19 (0.29), residues: 326 sheet: -3.03 (0.65), residues: 43 loop : -1.18 (0.43), residues: 233 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 57 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 61 average time/residue: 0.1850 time to fit residues: 15.2186 Evaluate side-chains 55 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 51 time to evaluate : 0.457 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1550 time to fit residues: 1.4996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 50 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 54 optimal weight: 0.0770 chunk 15 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 overall best weight: 2.1544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 899 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 6041 Z= 0.312 Angle : 0.625 8.671 8391 Z= 0.332 Chirality : 0.042 0.169 944 Planarity : 0.005 0.048 913 Dihedral : 21.902 73.287 1160 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.36 % Allowed : 16.73 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.39 (0.35), residues: 602 helix: 0.94 (0.29), residues: 326 sheet: -3.17 (0.61), residues: 44 loop : -1.35 (0.43), residues: 232 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 54 time to evaluate : 0.625 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 63 average time/residue: 0.1650 time to fit residues: 14.4050 Evaluate side-chains 55 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 49 time to evaluate : 0.607 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0564 time to fit residues: 1.4077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 0.2980 chunk 12 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 15 optimal weight: 7.9990 chunk 60 optimal weight: 6.9990 chunk 50 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 20 optimal weight: 0.4980 chunk 32 optimal weight: 0.0040 chunk 58 optimal weight: 3.9990 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 507 GLN ** A 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6041 Z= 0.173 Angle : 0.570 8.295 8391 Z= 0.300 Chirality : 0.039 0.164 944 Planarity : 0.004 0.048 913 Dihedral : 21.904 74.743 1160 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.57 % Allowed : 18.11 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.10 (0.36), residues: 602 helix: 1.16 (0.29), residues: 327 sheet: -3.11 (0.60), residues: 44 loop : -1.17 (0.43), residues: 231 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1204 Ramachandran restraints generated. 602 Oldfield, 0 Emsley, 602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 58 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 63 average time/residue: 0.1577 time to fit residues: 13.7182 Evaluate side-chains 58 residues out of total 508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 54 time to evaluate : 0.610 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0635 time to fit residues: 1.2135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/modules/cctbx_project/iotbx/cli_parser.py", line 881, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.4233 > 50: distance: 24 - 28: 10.567 distance: 28 - 29: 7.291 distance: 29 - 30: 18.198 distance: 29 - 32: 11.366 distance: 30 - 31: 28.348 distance: 30 - 36: 18.839 distance: 32 - 33: 22.053 distance: 32 - 34: 33.877 distance: 33 - 35: 8.821 distance: 36 - 37: 18.029 distance: 37 - 38: 15.475 distance: 37 - 40: 21.298 distance: 38 - 39: 22.430 distance: 38 - 41: 14.227 distance: 41 - 42: 15.013 distance: 41 - 47: 10.168 distance: 42 - 43: 9.558 distance: 42 - 45: 19.861 distance: 43 - 44: 8.337 distance: 43 - 48: 12.854 distance: 45 - 46: 10.829 distance: 46 - 47: 19.669 distance: 48 - 49: 6.338 distance: 49 - 50: 5.265 distance: 49 - 52: 5.830 distance: 50 - 51: 8.555 distance: 50 - 57: 13.629 distance: 52 - 53: 14.986 distance: 53 - 54: 14.874 distance: 54 - 55: 8.529 distance: 54 - 56: 17.692 distance: 57 - 58: 12.914 distance: 58 - 59: 8.191 distance: 58 - 61: 9.167 distance: 59 - 60: 23.058 distance: 59 - 65: 15.942 distance: 61 - 62: 5.791 distance: 62 - 63: 6.075 distance: 62 - 64: 4.872 distance: 65 - 66: 13.843 distance: 66 - 67: 14.131 distance: 66 - 69: 14.005 distance: 67 - 68: 18.721 distance: 67 - 77: 11.260 distance: 69 - 70: 7.177 distance: 70 - 71: 14.563 distance: 70 - 72: 12.109 distance: 71 - 73: 19.752 distance: 72 - 74: 18.177 distance: 73 - 75: 11.984 distance: 74 - 75: 15.777 distance: 75 - 76: 9.142 distance: 77 - 78: 21.036 distance: 77 - 152: 19.252 distance: 78 - 79: 9.352 distance: 78 - 81: 5.253 distance: 79 - 80: 18.958 distance: 79 - 84: 19.253 distance: 80 - 149: 8.931 distance: 81 - 82: 12.110 distance: 81 - 83: 23.632 distance: 84 - 85: 11.379 distance: 85 - 86: 15.694 distance: 85 - 88: 14.928 distance: 86 - 87: 24.118 distance: 86 - 92: 19.117 distance: 88 - 89: 21.073 distance: 88 - 90: 27.785 distance: 89 - 91: 15.885 distance: 92 - 93: 27.120 distance: 92 - 135: 12.599 distance: 93 - 94: 17.620 distance: 93 - 96: 13.909 distance: 94 - 95: 20.706 distance: 94 - 99: 15.170 distance: 95 - 132: 23.427 distance: 96 - 97: 17.480 distance: 96 - 98: 5.127 distance: 99 - 100: 9.006 distance: 100 - 101: 13.824 distance: 100 - 103: 4.401 distance: 101 - 102: 14.402 distance: 101 - 105: 13.196 distance: 103 - 104: 9.917