Starting phenix.real_space_refine on Wed May 21 09:35:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vl6_21231/05_2025/6vl6_21231.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vl6_21231/05_2025/6vl6_21231.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vl6_21231/05_2025/6vl6_21231.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vl6_21231/05_2025/6vl6_21231.map" model { file = "/net/cci-nas-00/data/ceres_data/6vl6_21231/05_2025/6vl6_21231.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vl6_21231/05_2025/6vl6_21231.cif" } resolution = 4.6 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 13788 2.51 5 N 3564 2.21 5 O 4116 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 132 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 21504 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 981 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "B" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 811 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Restraints were copied for chains: O, N, Q, P, S, R, U, T, W, V, X, C, E, D, G, F, I, H, K, J, M, L Time building chain proxies: 6.30, per 1000 atoms: 0.29 Number of scatterers: 21504 At special positions: 0 Unit cell: (162.15, 158.7, 156.4, 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 36 16.00 O 4116 8.00 N 3564 7.00 C 13788 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: 5.06 Conformation dependent library (CDL) restraints added in 2.4 seconds 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4944 Finding SS restraints... Secondary structure from input PDB file: 156 helices and 0 sheets defined 90.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.73 Creating SS restraints... Processing helix chain 'A' and resid 5 through 20 Processing helix chain 'A' and resid 22 through 36 Processing helix chain 'A' and resid 40 through 55 Processing helix chain 'A' and resid 56 through 71 Processing helix chain 'A' and resid 74 through 88 Processing helix chain 'A' and resid 90 through 105 Processing helix chain 'A' and resid 108 through 122 Processing helix chain 'B' and resid 3 through 16 Processing helix chain 'B' and resid 18 through 33 Processing helix chain 'B' and resid 36 through 50 Processing helix chain 'B' and resid 52 through 67 Processing helix chain 'B' and resid 70 through 84 Processing helix chain 'B' and resid 86 through 99 Processing helix chain 'C' and resid 5 through 20 Processing helix chain 'C' and resid 22 through 36 Processing helix chain 'C' and resid 40 through 55 Processing helix chain 'C' and resid 56 through 71 Processing helix chain 'C' and resid 74 through 88 Processing helix chain 'C' and resid 90 through 105 Processing helix chain 'C' and resid 108 through 122 Processing helix chain 'N' and resid 3 through 16 Processing helix chain 'N' and resid 18 through 33 Processing helix chain 'N' and resid 36 through 50 Processing helix chain 'N' and resid 52 through 67 Processing helix chain 'N' and resid 70 through 84 Processing helix chain 'N' and resid 86 through 99 Processing helix chain 'D' and resid 5 through 20 Processing helix chain 'D' and resid 22 through 36 Processing helix chain 'D' and resid 40 through 55 Processing helix chain 'D' and resid 56 through 71 Processing helix chain 'D' and resid 74 through 88 Processing helix chain 'D' and resid 90 through 105 Processing helix chain 'D' and resid 108 through 122 Processing helix chain 'O' and resid 3 through 16 Processing helix chain 'O' and resid 18 through 33 Processing helix chain 'O' and resid 36 through 50 Processing helix chain 'O' and resid 52 through 67 Processing helix chain 'O' and resid 70 through 84 Processing helix chain 'O' and resid 86 through 99 Processing helix chain 'E' and resid 5 through 20 Processing helix chain 'E' and resid 22 through 36 Processing helix chain 'E' and resid 40 through 55 Processing helix chain 'E' and resid 56 through 71 Processing helix chain 'E' and resid 74 through 88 Processing helix chain 'E' and resid 90 through 105 Processing helix chain 'E' and resid 108 through 122 Processing helix chain 'P' and resid 3 through 16 Processing helix chain 'P' and resid 18 through 33 Processing helix chain 'P' and resid 36 through 50 Processing helix chain 'P' and resid 52 through 67 Processing helix chain 'P' and resid 70 through 84 Processing helix chain 'P' and resid 86 through 99 Processing helix chain 'F' and resid 5 through 20 Processing helix chain 'F' and resid 22 through 36 Processing helix chain 'F' and resid 40 through 55 Processing helix chain 'F' and resid 56 through 71 Processing helix chain 'F' and resid 74 through 88 Processing helix chain 'F' and resid 90 through 105 Processing helix chain 'F' and resid 108 through 122 Processing helix chain 'Q' and resid 3 through 16 Processing helix chain 'Q' and resid 18 through 33 Processing helix chain 'Q' and resid 36 through 50 Processing helix chain 'Q' and resid 52 through 67 Processing helix chain 'Q' and resid 70 through 84 Processing helix chain 'Q' and resid 86 through 99 Processing helix chain 'G' and resid 5 through 20 Processing helix chain 'G' and resid 22 through 36 Processing helix chain 'G' and resid 40 through 55 Processing helix chain 'G' and resid 56 through 71 Processing helix chain 'G' and resid 74 through 88 Processing helix chain 'G' and resid 90 through 105 Processing helix chain 'G' and resid 108 through 122 Processing helix chain 'R' and resid 3 through 16 Processing helix chain 'R' and resid 18 through 33 Processing helix chain 'R' and resid 36 through 50 Processing helix chain 'R' and resid 52 through 67 Processing helix chain 'R' and resid 70 through 84 Processing helix chain 'R' and resid 86 through 99 Processing helix chain 'H' and resid 5 through 20 Processing helix chain 'H' and resid 22 through 36 Processing helix chain 'H' and resid 40 through 55 Processing helix chain 'H' and resid 56 through 71 Processing helix chain 'H' and resid 74 through 88 Processing helix chain 'H' and resid 90 through 105 Processing helix chain 'H' and resid 108 through 122 Processing helix chain 'S' and resid 3 through 16 Processing helix chain 'S' and resid 18 through 33 Processing helix chain 'S' and resid 36 through 50 Processing helix chain 'S' and resid 52 through 67 Processing helix chain 'S' and resid 70 through 84 Processing helix chain 'S' and resid 86 through 99 Processing helix chain 'I' and resid 5 through 20 Processing helix chain 'I' and resid 22 through 36 Processing helix chain 'I' and resid 40 through 55 Processing helix chain 'I' and resid 56 through 71 Processing helix chain 'I' and resid 74 through 88 Processing helix chain 'I' and resid 90 through 105 Processing helix chain 'I' and resid 108 through 122 Processing helix chain 'T' and resid 3 through 16 Processing helix chain 'T' and resid 18 through 33 Processing helix chain 'T' and resid 36 through 50 Processing helix chain 'T' and resid 52 through 67 Processing helix chain 'T' and resid 70 through 84 Processing helix chain 'T' and resid 86 through 99 Processing helix chain 'J' and resid 5 through 20 Processing helix chain 'J' and resid 22 through 36 Processing helix chain 'J' and resid 40 through 55 Processing helix chain 'J' and resid 56 through 71 Processing helix chain 'J' and resid 74 through 88 Processing helix chain 'J' and resid 90 through 105 Processing helix chain 'J' and resid 108 through 122 Processing helix chain 'U' and resid 3 through 16 Processing helix chain 'U' and resid 18 through 33 Processing helix chain 'U' and resid 36 through 50 Processing helix chain 'U' and resid 52 through 67 Processing helix chain 'U' and resid 70 through 84 Processing helix chain 'U' and resid 86 through 99 Processing helix chain 'K' and resid 5 through 20 Processing helix chain 'K' and resid 22 through 36 Processing helix chain 'K' and resid 40 through 55 Processing helix chain 'K' and resid 56 through 71 Processing helix chain 'K' and resid 74 through 88 Processing helix chain 'K' and resid 90 through 105 Processing helix chain 'K' and resid 108 through 122 Processing helix chain 'V' and resid 3 through 16 Processing helix chain 'V' and resid 18 through 33 Processing helix chain 'V' and resid 36 through 50 Processing helix chain 'V' and resid 52 through 67 Processing helix chain 'V' and resid 70 through 84 Processing helix chain 'V' and resid 86 through 99 Processing helix chain 'L' and resid 5 through 20 Processing helix chain 'L' and resid 22 through 36 Processing helix chain 'L' and resid 40 through 55 Processing helix chain 'L' and resid 56 through 71 Processing helix chain 'L' and resid 74 through 88 Processing helix chain 'L' and resid 90 through 105 Processing helix chain 'L' and resid 108 through 122 Processing helix chain 'W' and resid 3 through 16 Processing helix chain 'W' and resid 18 through 33 Processing helix chain 'W' and resid 36 through 50 Processing helix chain 'W' and resid 52 through 67 Processing helix chain 'W' and resid 70 through 84 Processing helix chain 'W' and resid 86 through 99 Processing helix chain 'M' and resid 5 through 20 Processing helix chain 'M' and resid 22 through 36 Processing helix chain 'M' and resid 40 through 55 Processing helix chain 'M' and resid 56 through 71 Processing helix chain 'M' and resid 74 through 88 Processing helix chain 'M' and resid 90 through 105 Processing helix chain 'M' and resid 108 through 122 Processing helix chain 'X' and resid 3 through 16 Processing helix chain 'X' and resid 18 through 33 Processing helix chain 'X' and resid 36 through 50 Processing helix chain 'X' and resid 52 through 67 Processing helix chain 'X' and resid 70 through 84 Processing helix chain 'X' and resid 86 through 99 1764 hydrogen bonds defined for protein. 5292 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: 7.09 Time building geometry restraints manager: 5.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4212 1.32 - 1.44: 6379 1.44 - 1.56: 11225 1.56 - 1.68: 84 1.68 - 1.81: 72 Bond restraints: 21972 Sorted by residual: bond pdb=" NE1 TRP O 40 " pdb=" CE2 TRP O 40 " ideal model delta sigma weight residual 1.370 1.326 0.044 1.10e-02 8.26e+03 1.58e+01 bond pdb=" NE1 TRP U 40 " pdb=" CE2 TRP U 40 " ideal model delta sigma weight residual 1.370 1.327 0.043 1.10e-02 8.26e+03 1.56e+01 bond pdb=" NE1 TRP Q 40 " pdb=" CE2 TRP Q 40 " ideal model delta sigma weight residual 1.370 1.327 0.043 1.10e-02 8.26e+03 1.56e+01 bond pdb=" NE1 TRP N 40 " pdb=" CE2 TRP N 40 " ideal model delta sigma weight residual 1.370 1.327 0.043 1.10e-02 8.26e+03 1.56e+01 bond pdb=" NE1 TRP B 40 " pdb=" CE2 TRP B 40 " ideal model delta sigma weight residual 1.370 1.327 0.043 1.10e-02 8.26e+03 1.55e+01 ... (remaining 21967 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 23496 1.64 - 3.27: 5137 3.27 - 4.91: 888 4.91 - 6.55: 155 6.55 - 8.18: 48 Bond angle restraints: 29724 Sorted by residual: angle pdb=" C ASP S 33 " pdb=" N PRO S 34 " pdb=" CA PRO S 34 " ideal model delta sigma weight residual 119.82 128.00 -8.18 9.80e-01 1.04e+00 6.97e+01 angle pdb=" C ASP T 33 " pdb=" N PRO T 34 " pdb=" CA PRO T 34 " ideal model delta sigma weight residual 119.82 128.00 -8.18 9.80e-01 1.04e+00 6.96e+01 angle pdb=" C ASP N 33 " pdb=" N PRO N 34 " pdb=" CA PRO N 34 " ideal model delta sigma weight residual 119.82 127.99 -8.17 9.80e-01 1.04e+00 6.95e+01 angle pdb=" C ASP R 33 " pdb=" N PRO R 34 " pdb=" CA PRO R 34 " ideal model delta sigma weight residual 119.82 127.99 -8.17 9.80e-01 1.04e+00 6.95e+01 angle pdb=" C ASP W 33 " pdb=" N PRO W 34 " pdb=" CA PRO W 34 " ideal model delta sigma weight residual 119.82 127.98 -8.16 9.80e-01 1.04e+00 6.93e+01 ... (remaining 29719 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.11: 12386 17.11 - 34.22: 539 34.22 - 51.33: 107 51.33 - 68.43: 48 68.43 - 85.54: 12 Dihedral angle restraints: 13092 sinusoidal: 5196 harmonic: 7896 Sorted by residual: dihedral pdb=" CB MET L 17 " pdb=" CG MET L 17 " pdb=" SD MET L 17 " pdb=" CE MET L 17 " ideal model delta sinusoidal sigma weight residual 60.00 99.36 -39.36 3 1.50e+01 4.44e-03 6.97e+00 dihedral pdb=" CB MET F 17 " pdb=" CG MET F 17 " pdb=" SD MET F 17 " pdb=" CE MET F 17 " ideal model delta sinusoidal sigma weight residual 60.00 99.35 -39.35 3 1.50e+01 4.44e-03 6.97e+00 dihedral pdb=" CB MET J 17 " pdb=" CG MET J 17 " pdb=" SD MET J 17 " pdb=" CE MET J 17 " ideal model delta sinusoidal sigma weight residual 60.00 99.35 -39.35 3 1.50e+01 4.44e-03 6.97e+00 ... (remaining 13089 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1719 0.065 - 0.130: 773 0.130 - 0.195: 398 0.195 - 0.260: 49 0.260 - 0.325: 25 Chirality restraints: 2964 Sorted by residual: chirality pdb=" CA ASN E 80 " pdb=" N ASN E 80 " pdb=" C ASN E 80 " pdb=" CB ASN E 80 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" CA ASN J 80 " pdb=" N ASN J 80 " pdb=" C ASN J 80 " pdb=" CB ASN J 80 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" CA ASN K 80 " pdb=" N ASN K 80 " pdb=" C ASN K 80 " pdb=" CB ASN K 80 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.61e+00 ... (remaining 2961 not shown) Planarity restraints: 3888 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR V 59 " -0.044 2.00e-02 2.50e+03 2.22e-02 9.84e+00 pdb=" CG TYR V 59 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR V 59 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR V 59 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR V 59 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR V 59 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR V 59 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR V 59 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR R 59 " 0.044 2.00e-02 2.50e+03 2.21e-02 9.75e+00 pdb=" CG TYR R 59 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR R 59 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR R 59 " -0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR R 59 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR R 59 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR R 59 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR R 59 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR T 59 " -0.044 2.00e-02 2.50e+03 2.21e-02 9.73e+00 pdb=" CG TYR T 59 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR T 59 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR T 59 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR T 59 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR T 59 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR T 59 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR T 59 " -0.024 2.00e-02 2.50e+03 ... (remaining 3885 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.92: 10121 2.92 - 3.42: 23687 3.42 - 3.91: 39439 3.91 - 4.41: 49797 4.41 - 4.90: 71062 Nonbonded interactions: 194106 Sorted by model distance: nonbonded pdb=" NZ LYS D 99 " pdb=" OD2 ASP O 88 " model vdw 2.431 3.120 nonbonded pdb=" NZ LYS C 99 " pdb=" OD2 ASP N 88 " model vdw 2.431 3.120 nonbonded pdb=" NZ LYS L 99 " pdb=" OD2 ASP W 88 " model vdw 2.431 3.120 nonbonded pdb=" NZ LYS A 99 " pdb=" OD2 ASP B 88 " model vdw 2.431 3.120 nonbonded pdb=" NZ LYS H 99 " pdb=" OD2 ASP S 88 " model vdw 2.431 3.120 ... (remaining 194101 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: 0.18 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'O' selection = chain 'N' selection = chain 'Q' selection = chain 'P' selection = chain 'S' selection = chain 'R' selection = chain 'U' selection = chain 'T' selection = chain 'W' selection = chain 'V' selection = chain 'X' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'M' selection = chain 'L' } Set up NCS constraints Number of NCS constrained groups: 2 pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'O' selection = chain 'N' selection = chain 'Q' selection = chain 'P' selection = chain 'S' selection = chain 'R' selection = chain 'U' selection = chain 'T' selection = chain 'W' selection = chain 'V' selection = chain 'X' } pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'M' selection = chain 'L' } Set refine NCS operators NCS operators will be refined. 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: 7.060 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: 0.020 Extract box with map and model: 0.760 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 38.670 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 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 : 0.019 0.086 21972 Z= 1.051 Angle : 1.456 8.182 29724 Z= 1.015 Chirality : 0.089 0.325 2964 Planarity : 0.008 0.041 3888 Dihedral : 11.376 85.543 8148 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 0.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % 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: 0.45 (0.14), residues: 2592 helix: 0.53 (0.09), residues: 2412 sheet: None (None), residues: 0 loop : -1.42 (0.43), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.006 TRP B 40 TYR 0.044 0.008 TYR V 59 ARG 0.006 0.001 ARG R 32 Details of bonding type rmsd hydrogen bonds : bond 0.13473 ( 1764) hydrogen bonds : angle 5.34972 ( 5292) covalent geometry : bond 0.01867 (21972) covalent geometry : angle 1.45581 (29724) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5184 Ramachandran restraints generated. 2592 Oldfield, 0 Emsley, 2592 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 74 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.084 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 11 GLU cc_start: 0.8865 (mt-10) cc_final: 0.8664 (mt-10) REVERT: B 33 ASP cc_start: 0.9175 (t0) cc_final: 0.8910 (t0) REVERT: B 36 ASN cc_start: 0.9184 (t0) cc_final: 0.8950 (t0) REVERT: B 67 ASP cc_start: 0.9240 (t0) cc_final: 0.9023 (t0) REVERT: B 86 LYS cc_start: 0.9005 (mptt) cc_final: 0.8735 (mmtt) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.3235 time to fit residues: 10.3726 Evaluate side-chains 17 residues out of total 74 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.083 Evaluate side-chains 38 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.103 Fit side-chains revert: symmetry clash REVERT: A 10 MET cc_start: 0.9149 (mmt) cc_final: 0.8679 (mtm) REVERT: A 32 LEU cc_start: 0.9706 (mt) cc_final: 0.9105 (tp) REVERT: A 108 ASN cc_start: 0.9462 (t0) cc_final: 0.8999 (t0) REVERT: A 110 ASP cc_start: 0.9268 (m-30) cc_final: 0.8932 (p0) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.2130 time to fit residues: 8.5573 Evaluate side-chains 14 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 1.9990 chunk 191 optimal weight: 2.9990 chunk 105 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 128 optimal weight: 0.8980 chunk 102 optimal weight: 0.5980 chunk 197 optimal weight: 0.4980 chunk 76 optimal weight: 1.9990 chunk 120 optimal weight: 0.0370 chunk 147 optimal weight: 8.9990 chunk 228 optimal weight: 0.1980 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 50 GLN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.033673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2468 r_free = 0.2468 target = 0.027430 restraints weight = 6122.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2514 r_free = 0.2514 target = 0.028600 restraints weight = 3468.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2547 r_free = 0.2547 target = 0.029490 restraints weight = 2257.951| |-----------------------------------------------------------------------------| r_work (final): 0.2523 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.033349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2514 r_free = 0.2514 target = 0.026587 restraints weight = 6745.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2559 r_free = 0.2559 target = 0.027884 restraints weight = 4041.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2591 r_free = 0.2591 target = 0.028858 restraints weight = 2723.172| |-----------------------------------------------------------------------------| r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.4152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21972 Z= 0.161 Angle : 0.601 5.191 29724 Z= 0.324 Chirality : 0.041 0.147 2964 Planarity : 0.005 0.033 3888 Dihedral : 3.857 12.343 3072 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 0.60 % Allowed : 2.38 % Favored : 97.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.14), residues: 2592 helix: 1.11 (0.09), residues: 2436 sheet: None (None), residues: 0 loop : -1.85 (0.51), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP U 74 TYR 0.016 0.002 TYR C 64 ARG 0.005 0.000 ARG O 32 Details of bonding type rmsd hydrogen bonds : bond 0.04929 ( 1764) hydrogen bonds : angle 3.74829 ( 5292) covalent geometry : bond 0.00334 (21972) covalent geometry : angle 0.60107 (29724) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4934 Ramachandran restraints generated. 2467 Oldfield, 0 Emsley, 2467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4934 Ramachandran restraints generated. 2467 Oldfield, 0 Emsley, 2467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 74 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.095 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 11 GLU cc_start: 0.9088 (mt-10) cc_final: 0.8636 (mm-30) REVERT: Q 18 GLU cc_start: 0.8790 (tp30) cc_final: 0.8385 (tp30) REVERT: Q 33 ASP cc_start: 0.9108 (t0) cc_final: 0.8714 (t0) REVERT: Q 36 ASN cc_start: 0.8734 (t0) cc_final: 0.8142 (t0) REVERT: Q 38 GLU cc_start: 0.8839 (pm20) cc_final: 0.8568 (pm20) REVERT: Q 69 GLU cc_start: 0.9343 (mm-30) cc_final: 0.9110 (mp0) REVERT: Q 70 ASN cc_start: 0.8697 (t0) cc_final: 0.8316 (t0) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.2442 time to fit residues: 6.4422 Evaluate side-chains 17 residues out of total 74 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.099 Evaluate side-chains 33 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 0.120 Fit side-chains REVERT: I 10 MET cc_start: 0.9323 (mmt) cc_final: 0.8969 (mtm) REVERT: I 32 LEU cc_start: 0.9885 (mt) cc_final: 0.9613 (mt) REVERT: I 37 ASP cc_start: 0.9487 (t0) cc_final: 0.9284 (t0) REVERT: I 42 GLU cc_start: 0.9613 (mt-10) cc_final: 0.9406 (mp0) REVERT: I 108 ASN cc_start: 0.9232 (t0) cc_final: 0.8270 (t0) REVERT: I 110 ASP cc_start: 0.8678 (m-30) cc_final: 0.8234 (p0) outliers start: 1 outliers final: 0 residues processed: 32 average time/residue: 0.1334 time to fit residues: 4.7442 Evaluate side-chains 22 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 104 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 246 optimal weight: 0.3980 chunk 251 optimal weight: 1.9990 chunk 43 optimal weight: 0.0770 chunk 60 optimal weight: 0.0370 chunk 110 optimal weight: 0.0980 chunk 176 optimal weight: 0.0040 chunk 7 optimal weight: 0.0670 overall best weight: 0.0566 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.032267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2438 r_free = 0.2438 target = 0.026599 restraints weight = 6536.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2479 r_free = 0.2479 target = 0.027650 restraints weight = 3578.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2508 r_free = 0.2508 target = 0.028429 restraints weight = 2325.257| |-----------------------------------------------------------------------------| r_work (final): 0.2489 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.032319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2464 r_free = 0.2464 target = 0.025576 restraints weight = 6783.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2513 r_free = 0.2513 target = 0.026789 restraints weight = 4214.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.2553 r_free = 0.2553 target = 0.027815 restraints weight = 2929.178| |-----------------------------------------------------------------------------| r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.4847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21972 Z= 0.145 Angle : 0.784 18.602 29724 Z= 0.354 Chirality : 0.043 0.245 2964 Planarity : 0.004 0.031 3888 Dihedral : 4.109 14.958 3072 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % 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: 0.72 (0.15), residues: 2592 helix: 0.74 (0.09), residues: 2436 sheet: None (None), residues: 0 loop : -2.39 (0.51), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 78 TYR 0.029 0.002 TYR I 57 ARG 0.003 0.001 ARG O 32 Details of bonding type rmsd hydrogen bonds : bond 0.04382 ( 1764) hydrogen bonds : angle 3.64629 ( 5292) covalent geometry : bond 0.00310 (21972) covalent geometry : angle 0.78434 (29724) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4742 Ramachandran restraints generated. 2371 Oldfield, 0 Emsley, 2371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4742 Ramachandran restraints generated. 2371 Oldfield, 0 Emsley, 2371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 74 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 11 GLU cc_start: 0.9105 (mt-10) cc_final: 0.8760 (mt-10) REVERT: N 18 GLU cc_start: 0.8882 (tp30) cc_final: 0.8526 (tp30) REVERT: N 23 ILE cc_start: 0.9708 (pt) cc_final: 0.9380 (mt) REVERT: N 33 ASP cc_start: 0.8995 (t0) cc_final: 0.8661 (t0) REVERT: N 36 ASN cc_start: 0.8596 (t0) cc_final: 0.8048 (t0) REVERT: N 38 GLU cc_start: 0.8867 (pm20) cc_final: 0.8497 (pm20) REVERT: N 52 ASP cc_start: 0.8209 (t0) cc_final: 0.7923 (t0) REVERT: N 70 ASN cc_start: 0.8665 (t0) cc_final: 0.8042 (t0) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.2214 time to fit residues: 5.8504 Evaluate side-chains 21 residues out of total 74 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.086 Evaluate side-chains 32 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.105 Fit side-chains revert: symmetry clash REVERT: I 10 MET cc_start: 0.9405 (mmt) cc_final: 0.8766 (mtm) REVERT: I 32 LEU cc_start: 0.9852 (mt) cc_final: 0.9413 (tp) REVERT: I 34 LEU cc_start: 0.9286 (mt) cc_final: 0.9050 (mt) REVERT: I 37 ASP cc_start: 0.9489 (t0) cc_final: 0.9142 (t0) REVERT: I 58 ASP cc_start: 0.9580 (p0) cc_final: 0.9265 (p0) REVERT: I 68 LEU cc_start: 0.9747 (pp) cc_final: 0.9338 (mt) REVERT: I 108 ASN cc_start: 0.9272 (t0) cc_final: 0.8264 (t0) REVERT: I 110 ASP cc_start: 0.8887 (m-30) cc_final: 0.8447 (p0) REVERT: I 113 GLU cc_start: 0.9601 (tt0) cc_final: 0.9298 (tm-30) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.1017 time to fit residues: 3.6850 Evaluate side-chains 23 residues out of total 94 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 704, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 801, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 400, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 133, in refine refine_sites = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 434, in __init__ ignore_line_search_failed_maxfev=True)) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 459, in compute_functional_and_gradients x=self.x) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 248, in target_and_gradients grad = g_data) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 112, in restraints_target_and_grads compute_gradients = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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: 71.97 > 50: distance: 0 - 1: 39.845 distance: 1 - 2: 57.129 distance: 1 - 4: 39.126 distance: 2 - 3: 38.972 distance: 4 - 5: 56.267 distance: 6 - 7: 39.201 distance: 7 - 8: 39.718 distance: 9 - 10: 68.987 distance: 11 - 12: 56.969 distance: 13 - 14: 56.330 distance: 14 - 15: 57.740 distance: 14 - 17: 55.514 distance: 15 - 16: 39.120 distance: 15 - 22: 39.249 distance: 16 - 49: 41.661 distance: 17 - 18: 39.021 distance: 18 - 19: 38.854 distance: 19 - 20: 40.560 distance: 19 - 21: 57.372 distance: 22 - 23: 40.792 distance: 23 - 24: 39.665 distance: 23 - 26: 40.134 distance: 24 - 25: 40.341 distance: 25 - 54: 53.711 distance: 26 - 27: 41.124 distance: 27 - 28: 57.204 distance: 27 - 29: 56.301 distance: 28 - 30: 57.063 distance: 29 - 31: 39.795 distance: 30 - 32: 39.053 distance: 31 - 32: 57.321 distance: 32 - 33: 39.643 distance: 34 - 35: 40.380 distance: 35 - 38: 39.720 distance: 36 - 37: 56.585 distance: 36 - 41: 56.625 distance: 37 - 62: 3.265 distance: 38 - 39: 40.670 distance: 38 - 40: 55.472 distance: 41 - 42: 39.559 distance: 42 - 43: 40.497 distance: 44 - 70: 59.735 distance: 45 - 46: 56.366 distance: 45 - 47: 68.979 distance: 46 - 48: 55.697 distance: 49 - 50: 39.718 distance: 50 - 51: 40.458 distance: 51 - 52: 40.938 distance: 55 - 56: 69.197 distance: 55 - 58: 38.656 distance: 56 - 57: 40.544 distance: 56 - 62: 39.719 distance: 58 - 59: 40.446 distance: 58 - 60: 68.238 distance: 59 - 61: 40.135 distance: 62 - 63: 41.376 distance: 63 - 64: 38.919 distance: 63 - 66: 39.706 distance: 64 - 70: 56.611 distance: 66 - 67: 40.980 distance: 66 - 68: 40.569 distance: 67 - 69: 55.535 distance: 70 - 71: 38.981 distance: 71 - 72: 40.466 distance: 72 - 73: 39.542