Starting phenix.real_space_refine on Sat Sep 28 21:59:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gi2_40060/09_2024/8gi2_40060.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gi2_40060/09_2024/8gi2_40060.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gi2_40060/09_2024/8gi2_40060.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gi2_40060/09_2024/8gi2_40060.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gi2_40060/09_2024/8gi2_40060.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gi2_40060/09_2024/8gi2_40060.cif" } resolution = 3.0 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= 0.003 sd= 0.124 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 60 5.16 5 C 12780 2.51 5 N 3400 2.21 5 O 4580 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 20820 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1041 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 144} Restraints were copied for chains: C, B, E, D, G, F, I, H, K, J, M, L, O, N, Q, P, S, R, T Time building chain proxies: 5.31, per 1000 atoms: 0.26 Number of scatterers: 20820 At special positions: 0 Unit cell: (117.72, 117.72, 197.64, 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 60 16.00 O 4580 8.00 N 3400 7.00 C 12780 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: 5.50 Conformation dependent library (CDL) restraints added in 2.9 seconds 5800 Ramachandran restraints generated. 2900 Oldfield, 0 Emsley, 2900 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5200 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 40 sheets defined 19.0% alpha, 23.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.11 Creating SS restraints... Processing helix chain 'A' and resid 19 through 46 removed outlier: 3.630A pdb=" N VAL A 25 " --> pdb=" O PRO A 21 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE A 34 " --> pdb=" O ALA A 30 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP A 45 " --> pdb=" O ALA A 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 46 removed outlier: 3.630A pdb=" N VAL B 25 " --> pdb=" O PRO B 21 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE B 34 " --> pdb=" O ALA B 30 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP B 45 " --> pdb=" O ALA B 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 46 removed outlier: 3.629A pdb=" N VAL C 25 " --> pdb=" O PRO C 21 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE C 34 " --> pdb=" O ALA C 30 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP C 45 " --> pdb=" O ALA C 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 46 removed outlier: 3.630A pdb=" N VAL D 25 " --> pdb=" O PRO D 21 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE D 34 " --> pdb=" O ALA D 30 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP D 45 " --> pdb=" O ALA D 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 46 removed outlier: 3.630A pdb=" N VAL E 25 " --> pdb=" O PRO E 21 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE E 34 " --> pdb=" O ALA E 30 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP E 45 " --> pdb=" O ALA E 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 46 removed outlier: 3.630A pdb=" N VAL F 25 " --> pdb=" O PRO F 21 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE F 34 " --> pdb=" O ALA F 30 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP F 45 " --> pdb=" O ALA F 41 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 46 removed outlier: 3.630A pdb=" N VAL G 25 " --> pdb=" O PRO G 21 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ILE G 34 " --> pdb=" O ALA G 30 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP G 45 " --> pdb=" O ALA G 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 46 removed outlier: 3.630A pdb=" N VAL H 25 " --> pdb=" O PRO H 21 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE H 34 " --> pdb=" O ALA H 30 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP H 45 " --> pdb=" O ALA H 41 " (cutoff:3.500A) Processing helix chain 'I' and resid 19 through 46 removed outlier: 3.630A pdb=" N VAL I 25 " --> pdb=" O PRO I 21 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE I 34 " --> pdb=" O ALA I 30 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP I 45 " --> pdb=" O ALA I 41 " (cutoff:3.500A) Processing helix chain 'J' and resid 19 through 46 removed outlier: 3.629A pdb=" N VAL J 25 " --> pdb=" O PRO J 21 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE J 34 " --> pdb=" O ALA J 30 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP J 45 " --> pdb=" O ALA J 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 46 removed outlier: 3.629A pdb=" N VAL K 25 " --> pdb=" O PRO K 21 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE K 34 " --> pdb=" O ALA K 30 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP K 45 " --> pdb=" O ALA K 41 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 46 removed outlier: 3.630A pdb=" N VAL L 25 " --> pdb=" O PRO L 21 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE L 34 " --> pdb=" O ALA L 30 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP L 45 " --> pdb=" O ALA L 41 " (cutoff:3.500A) Processing helix chain 'M' and resid 19 through 46 removed outlier: 3.630A pdb=" N VAL M 25 " --> pdb=" O PRO M 21 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE M 34 " --> pdb=" O ALA M 30 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP M 45 " --> pdb=" O ALA M 41 " (cutoff:3.500A) Processing helix chain 'N' and resid 19 through 46 removed outlier: 3.630A pdb=" N VAL N 25 " --> pdb=" O PRO N 21 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE N 34 " --> pdb=" O ALA N 30 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP N 45 " --> pdb=" O ALA N 41 " (cutoff:3.500A) Processing helix chain 'O' and resid 19 through 46 removed outlier: 3.630A pdb=" N VAL O 25 " --> pdb=" O PRO O 21 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE O 34 " --> pdb=" O ALA O 30 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP O 45 " --> pdb=" O ALA O 41 " (cutoff:3.500A) Processing helix chain 'P' and resid 19 through 46 removed outlier: 3.629A pdb=" N VAL P 25 " --> pdb=" O PRO P 21 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE P 34 " --> pdb=" O ALA P 30 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP P 45 " --> pdb=" O ALA P 41 " (cutoff:3.500A) Processing helix chain 'Q' and resid 19 through 46 removed outlier: 3.630A pdb=" N VAL Q 25 " --> pdb=" O PRO Q 21 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE Q 34 " --> pdb=" O ALA Q 30 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP Q 45 " --> pdb=" O ALA Q 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 19 through 46 removed outlier: 3.629A pdb=" N VAL R 25 " --> pdb=" O PRO R 21 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE R 34 " --> pdb=" O ALA R 30 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP R 45 " --> pdb=" O ALA R 41 " (cutoff:3.500A) Processing helix chain 'S' and resid 19 through 46 removed outlier: 3.630A pdb=" N VAL S 25 " --> pdb=" O PRO S 21 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE S 34 " --> pdb=" O ALA S 30 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP S 45 " --> pdb=" O ALA S 41 " (cutoff:3.500A) Processing helix chain 'T' and resid 19 through 46 removed outlier: 3.630A pdb=" N VAL T 25 " --> pdb=" O PRO T 21 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE T 34 " --> pdb=" O ALA T 30 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP T 45 " --> pdb=" O ALA T 41 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'A' and resid 58 through 63 Processing sheet with id=2, first strand: chain 'A' and resid 82 through 87 removed outlier: 6.279A pdb=" N ALA A 140 " --> pdb=" O GLN A 150 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N GLN A 150 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ILE A 142 " --> pdb=" O ARG A 148 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ARG A 148 " --> pdb=" O ILE A 142 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'B' and resid 58 through 63 Processing sheet with id=4, first strand: chain 'B' and resid 82 through 87 removed outlier: 6.280A pdb=" N ALA B 140 " --> pdb=" O GLN B 150 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N GLN B 150 " --> pdb=" O ALA B 140 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ILE B 142 " --> pdb=" O ARG B 148 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ARG B 148 " --> pdb=" O ILE B 142 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'C' and resid 58 through 63 Processing sheet with id=6, first strand: chain 'C' and resid 82 through 87 removed outlier: 6.279A pdb=" N ALA C 140 " --> pdb=" O GLN C 150 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N GLN C 150 " --> pdb=" O ALA C 140 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ILE C 142 " --> pdb=" O ARG C 148 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ARG C 148 " --> pdb=" O ILE C 142 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'D' and resid 58 through 63 Processing sheet with id=8, first strand: chain 'D' and resid 82 through 87 removed outlier: 6.279A pdb=" N ALA D 140 " --> pdb=" O GLN D 150 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N GLN D 150 " --> pdb=" O ALA D 140 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ILE D 142 " --> pdb=" O ARG D 148 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ARG D 148 " --> pdb=" O ILE D 142 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'E' and resid 58 through 63 Processing sheet with id=10, first strand: chain 'E' and resid 82 through 87 removed outlier: 6.279A pdb=" N ALA E 140 " --> pdb=" O GLN E 150 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N GLN E 150 " --> pdb=" O ALA E 140 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ILE E 142 " --> pdb=" O ARG E 148 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ARG E 148 " --> pdb=" O ILE E 142 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'F' and resid 58 through 63 Processing sheet with id=12, first strand: chain 'F' and resid 82 through 87 removed outlier: 6.279A pdb=" N ALA F 140 " --> pdb=" O GLN F 150 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N GLN F 150 " --> pdb=" O ALA F 140 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ILE F 142 " --> pdb=" O ARG F 148 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ARG F 148 " --> pdb=" O ILE F 142 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'G' and resid 58 through 63 Processing sheet with id=14, first strand: chain 'G' and resid 82 through 87 removed outlier: 6.280A pdb=" N ALA G 140 " --> pdb=" O GLN G 150 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N GLN G 150 " --> pdb=" O ALA G 140 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ILE G 142 " --> pdb=" O ARG G 148 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ARG G 148 " --> pdb=" O ILE G 142 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'H' and resid 58 through 63 Processing sheet with id=16, first strand: chain 'H' and resid 82 through 87 removed outlier: 6.279A pdb=" N ALA H 140 " --> pdb=" O GLN H 150 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N GLN H 150 " --> pdb=" O ALA H 140 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ILE H 142 " --> pdb=" O ARG H 148 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ARG H 148 " --> pdb=" O ILE H 142 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'I' and resid 58 through 63 Processing sheet with id=18, first strand: chain 'I' and resid 82 through 87 removed outlier: 6.279A pdb=" N ALA I 140 " --> pdb=" O GLN I 150 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N GLN I 150 " --> pdb=" O ALA I 140 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ILE I 142 " --> pdb=" O ARG I 148 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ARG I 148 " --> pdb=" O ILE I 142 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'J' and resid 58 through 63 Processing sheet with id=20, first strand: chain 'J' and resid 82 through 87 removed outlier: 6.280A pdb=" N ALA J 140 " --> pdb=" O GLN J 150 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N GLN J 150 " --> pdb=" O ALA J 140 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ILE J 142 " --> pdb=" O ARG J 148 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ARG J 148 " --> pdb=" O ILE J 142 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'K' and resid 58 through 63 Processing sheet with id=22, first strand: chain 'K' and resid 82 through 87 removed outlier: 6.279A pdb=" N ALA K 140 " --> pdb=" O GLN K 150 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N GLN K 150 " --> pdb=" O ALA K 140 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ILE K 142 " --> pdb=" O ARG K 148 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ARG K 148 " --> pdb=" O ILE K 142 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'L' and resid 58 through 63 Processing sheet with id=24, first strand: chain 'L' and resid 82 through 87 removed outlier: 6.279A pdb=" N ALA L 140 " --> pdb=" O GLN L 150 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N GLN L 150 " --> pdb=" O ALA L 140 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ILE L 142 " --> pdb=" O ARG L 148 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ARG L 148 " --> pdb=" O ILE L 142 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'M' and resid 58 through 63 Processing sheet with id=26, first strand: chain 'M' and resid 82 through 87 removed outlier: 6.280A pdb=" N ALA M 140 " --> pdb=" O GLN M 150 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N GLN M 150 " --> pdb=" O ALA M 140 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ILE M 142 " --> pdb=" O ARG M 148 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ARG M 148 " --> pdb=" O ILE M 142 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'N' and resid 58 through 63 Processing sheet with id=28, first strand: chain 'N' and resid 82 through 87 removed outlier: 6.280A pdb=" N ALA N 140 " --> pdb=" O GLN N 150 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N GLN N 150 " --> pdb=" O ALA N 140 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ILE N 142 " --> pdb=" O ARG N 148 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ARG N 148 " --> pdb=" O ILE N 142 " (cutoff:3.500A) Processing sheet with id=29, first strand: chain 'O' and resid 58 through 63 Processing sheet with id=30, first strand: chain 'O' and resid 82 through 87 removed outlier: 6.280A pdb=" N ALA O 140 " --> pdb=" O GLN O 150 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N GLN O 150 " --> pdb=" O ALA O 140 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ILE O 142 " --> pdb=" O ARG O 148 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ARG O 148 " --> pdb=" O ILE O 142 " (cutoff:3.500A) Processing sheet with id=31, first strand: chain 'P' and resid 58 through 63 Processing sheet with id=32, first strand: chain 'P' and resid 82 through 87 removed outlier: 6.279A pdb=" N ALA P 140 " --> pdb=" O GLN P 150 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N GLN P 150 " --> pdb=" O ALA P 140 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ILE P 142 " --> pdb=" O ARG P 148 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ARG P 148 " --> pdb=" O ILE P 142 " (cutoff:3.500A) Processing sheet with id=33, first strand: chain 'Q' and resid 58 through 63 Processing sheet with id=34, first strand: chain 'Q' and resid 82 through 87 removed outlier: 6.279A pdb=" N ALA Q 140 " --> pdb=" O GLN Q 150 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N GLN Q 150 " --> pdb=" O ALA Q 140 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ILE Q 142 " --> pdb=" O ARG Q 148 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ARG Q 148 " --> pdb=" O ILE Q 142 " (cutoff:3.500A) Processing sheet with id=35, first strand: chain 'R' and resid 58 through 63 Processing sheet with id=36, first strand: chain 'R' and resid 82 through 87 removed outlier: 6.279A pdb=" N ALA R 140 " --> pdb=" O GLN R 150 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N GLN R 150 " --> pdb=" O ALA R 140 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ILE R 142 " --> pdb=" O ARG R 148 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ARG R 148 " --> pdb=" O ILE R 142 " (cutoff:3.500A) Processing sheet with id=37, first strand: chain 'S' and resid 58 through 63 Processing sheet with id=38, first strand: chain 'S' and resid 82 through 87 removed outlier: 6.279A pdb=" N ALA S 140 " --> pdb=" O GLN S 150 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N GLN S 150 " --> pdb=" O ALA S 140 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ILE S 142 " --> pdb=" O ARG S 148 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ARG S 148 " --> pdb=" O ILE S 142 " (cutoff:3.500A) Processing sheet with id=39, first strand: chain 'T' and resid 58 through 63 Processing sheet with id=40, first strand: chain 'T' and resid 82 through 87 removed outlier: 6.278A pdb=" N ALA T 140 " --> pdb=" O GLN T 150 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N GLN T 150 " --> pdb=" O ALA T 140 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ILE T 142 " --> pdb=" O ARG T 148 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ARG T 148 " --> pdb=" O ILE T 142 " (cutoff:3.500A) 860 hydrogen bonds defined for protein. 2340 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: 5.40 Time building geometry restraints manager: 6.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4140 1.32 - 1.44: 4500 1.44 - 1.56: 12200 1.56 - 1.68: 0 1.68 - 1.80: 120 Bond restraints: 20960 Sorted by residual: bond pdb=" CA TYR F 127 " pdb=" CB TYR F 127 " ideal model delta sigma weight residual 1.530 1.454 0.076 1.51e-02 4.39e+03 2.51e+01 bond pdb=" CA TYR I 127 " pdb=" CB TYR I 127 " ideal model delta sigma weight residual 1.530 1.454 0.076 1.51e-02 4.39e+03 2.51e+01 bond pdb=" CA TYR O 127 " pdb=" CB TYR O 127 " ideal model delta sigma weight residual 1.530 1.454 0.076 1.51e-02 4.39e+03 2.50e+01 bond pdb=" CA TYR G 127 " pdb=" CB TYR G 127 " ideal model delta sigma weight residual 1.530 1.454 0.076 1.51e-02 4.39e+03 2.50e+01 bond pdb=" CA TYR J 127 " pdb=" CB TYR J 127 " ideal model delta sigma weight residual 1.530 1.454 0.076 1.51e-02 4.39e+03 2.50e+01 ... (remaining 20955 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 26632 1.55 - 3.11: 1332 3.11 - 4.66: 316 4.66 - 6.22: 200 6.22 - 7.77: 100 Bond angle restraints: 28580 Sorted by residual: angle pdb=" N TYR T 127 " pdb=" CA TYR T 127 " pdb=" C TYR T 127 " ideal model delta sigma weight residual 112.93 106.41 6.52 1.12e+00 7.97e-01 3.39e+01 angle pdb=" N TYR J 127 " pdb=" CA TYR J 127 " pdb=" C TYR J 127 " ideal model delta sigma weight residual 112.93 106.42 6.51 1.12e+00 7.97e-01 3.37e+01 angle pdb=" N TYR E 127 " pdb=" CA TYR E 127 " pdb=" C TYR E 127 " ideal model delta sigma weight residual 112.93 106.43 6.50 1.12e+00 7.97e-01 3.37e+01 angle pdb=" N TYR O 127 " pdb=" CA TYR O 127 " pdb=" C TYR O 127 " ideal model delta sigma weight residual 112.93 106.43 6.50 1.12e+00 7.97e-01 3.37e+01 angle pdb=" N TYR M 127 " pdb=" CA TYR M 127 " pdb=" C TYR M 127 " ideal model delta sigma weight residual 112.93 106.43 6.50 1.12e+00 7.97e-01 3.36e+01 ... (remaining 28575 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.62: 11317 12.62 - 25.24: 763 25.24 - 37.85: 220 37.85 - 50.47: 80 50.47 - 63.09: 60 Dihedral angle restraints: 12440 sinusoidal: 4260 harmonic: 8180 Sorted by residual: dihedral pdb=" N SER S 131 " pdb=" C SER S 131 " pdb=" CA SER S 131 " pdb=" CB SER S 131 " ideal model delta harmonic sigma weight residual 122.80 114.20 8.60 0 2.50e+00 1.60e-01 1.18e+01 dihedral pdb=" N SER T 131 " pdb=" C SER T 131 " pdb=" CA SER T 131 " pdb=" CB SER T 131 " ideal model delta harmonic sigma weight residual 122.80 114.20 8.60 0 2.50e+00 1.60e-01 1.18e+01 dihedral pdb=" N SER R 131 " pdb=" C SER R 131 " pdb=" CA SER R 131 " pdb=" CB SER R 131 " ideal model delta harmonic sigma weight residual 122.80 114.20 8.60 0 2.50e+00 1.60e-01 1.18e+01 ... (remaining 12437 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2206 0.038 - 0.077: 935 0.077 - 0.115: 360 0.115 - 0.153: 119 0.153 - 0.191: 40 Chirality restraints: 3660 Sorted by residual: chirality pdb=" CA SER K 130 " pdb=" N SER K 130 " pdb=" C SER K 130 " pdb=" CB SER K 130 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.14e-01 chirality pdb=" CA SER Q 130 " pdb=" N SER Q 130 " pdb=" C SER Q 130 " pdb=" CB SER Q 130 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.06e-01 chirality pdb=" CA SER R 130 " pdb=" N SER R 130 " pdb=" C SER R 130 " pdb=" CB SER R 130 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.05e-01 ... (remaining 3657 not shown) Planarity restraints: 3760 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN Q 117 " 0.018 2.00e-02 2.50e+03 3.71e-02 1.38e+01 pdb=" C ASN Q 117 " -0.064 2.00e-02 2.50e+03 pdb=" O ASN Q 117 " 0.025 2.00e-02 2.50e+03 pdb=" N ALA Q 118 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN N 117 " 0.018 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C ASN N 117 " -0.064 2.00e-02 2.50e+03 pdb=" O ASN N 117 " 0.025 2.00e-02 2.50e+03 pdb=" N ALA N 118 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN M 117 " -0.018 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C ASN M 117 " 0.064 2.00e-02 2.50e+03 pdb=" O ASN M 117 " -0.025 2.00e-02 2.50e+03 pdb=" N ALA M 118 " -0.021 2.00e-02 2.50e+03 ... (remaining 3757 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.18: 29 2.18 - 2.86: 8124 2.86 - 3.54: 27383 3.54 - 4.22: 47858 4.22 - 4.90: 83245 Nonbonded interactions: 166639 Sorted by model distance: nonbonded pdb=" OE2 GLU M 146 " pdb=" OE1 GLU T 64 " model vdw 1.504 3.040 nonbonded pdb=" OE2 GLU I 146 " pdb=" OE1 GLU O 64 " model vdw 1.505 3.040 nonbonded pdb=" OE1 GLU A 64 " pdb=" OE2 GLU E 146 " model vdw 1.505 3.040 nonbonded pdb=" OE2 GLU J 146 " pdb=" OE1 GLU P 64 " model vdw 1.505 3.040 nonbonded pdb=" OE2 GLU A 146 " pdb=" OE1 GLU R 64 " model vdw 1.505 3.040 ... (remaining 166634 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.720 Check model and map are aligned: 0.140 Set scattering table: 0.220 Process input model: 37.950 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.080 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:11.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 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 : 0.008 0.076 20960 Z= 0.504 Angle : 0.975 7.771 28580 Z= 0.613 Chirality : 0.052 0.191 3660 Planarity : 0.004 0.037 3760 Dihedral : 11.484 63.089 7240 Min Nonbonded Distance : 1.504 Molprobity Statistics. All-atom Clashscore : 31.63 Ramachandran Plot: Outliers : 0.69 % Allowed : 12.97 % Favored : 86.34 % Rotamer: Outliers : 3.45 % Allowed : 4.31 % Favored : 92.24 % 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: -3.41 (0.14), residues: 2900 helix: -1.19 (0.24), residues: 560 sheet: -0.76 (0.17), residues: 940 loop : -3.96 (0.10), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 82 PHE 0.003 0.001 PHE P 159 TYR 0.007 0.001 TYR H 127 ARG 0.001 0.000 ARG J 148 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5800 Ramachandran restraints generated. 2900 Oldfield, 0 Emsley, 2900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5800 Ramachandran restraints generated. 2900 Oldfield, 0 Emsley, 2900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 726 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 646 time to evaluate : 2.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8090 (mt-10) REVERT: A 127 TYR cc_start: 0.6109 (OUTLIER) cc_final: 0.5314 (t80) REVERT: C 127 TYR cc_start: 0.6253 (OUTLIER) cc_final: 0.4616 (t80) REVERT: D 127 TYR cc_start: 0.6130 (OUTLIER) cc_final: 0.4625 (t80) REVERT: E 124 VAL cc_start: 0.5185 (OUTLIER) cc_final: 0.4607 (p) REVERT: F 124 VAL cc_start: 0.4596 (OUTLIER) cc_final: 0.4235 (p) REVERT: F 143 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7979 (mt-10) REVERT: G 96 TYR cc_start: 0.6763 (t80) cc_final: 0.6061 (t80) REVERT: G 127 TYR cc_start: 0.6532 (OUTLIER) cc_final: 0.5026 (t80) REVERT: H 63 ASP cc_start: 0.8019 (t0) cc_final: 0.7777 (t0) REVERT: H 96 TYR cc_start: 0.6884 (t80) cc_final: 0.6599 (t80) REVERT: H 112 ASP cc_start: 0.7873 (m-30) cc_final: 0.7494 (m-30) REVERT: H 127 TYR cc_start: 0.6473 (OUTLIER) cc_final: 0.5030 (t80) REVERT: J 63 ASP cc_start: 0.8323 (t0) cc_final: 0.8081 (t0) REVERT: J 73 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8032 (mt-10) REVERT: K 96 TYR cc_start: 0.7253 (t80) cc_final: 0.7021 (t80) REVERT: K 127 TYR cc_start: 0.6151 (OUTLIER) cc_final: 0.4957 (t80) REVERT: M 28 MET cc_start: 0.8702 (mmt) cc_final: 0.8447 (mmt) REVERT: M 73 GLU cc_start: 0.8307 (mt-10) cc_final: 0.8076 (mt-10) REVERT: M 96 TYR cc_start: 0.7146 (t80) cc_final: 0.6869 (t80) REVERT: M 127 TYR cc_start: 0.5940 (OUTLIER) cc_final: 0.5358 (t80) REVERT: N 63 ASP cc_start: 0.7739 (t0) cc_final: 0.7380 (t70) REVERT: N 127 TYR cc_start: 0.5964 (OUTLIER) cc_final: 0.5196 (t80) REVERT: O 127 TYR cc_start: 0.5923 (OUTLIER) cc_final: 0.5266 (t80) REVERT: P 129 LEU cc_start: 0.6516 (mt) cc_final: 0.6263 (mt) REVERT: R 127 TYR cc_start: 0.6191 (OUTLIER) cc_final: 0.4805 (t80) REVERT: R 129 LEU cc_start: 0.6056 (mt) cc_final: 0.5738 (mt) REVERT: S 94 THR cc_start: 0.6564 (t) cc_final: 0.6323 (m) REVERT: S 127 TYR cc_start: 0.6009 (OUTLIER) cc_final: 0.4818 (t80) REVERT: T 127 TYR cc_start: 0.5893 (OUTLIER) cc_final: 0.4274 (t80) outliers start: 80 outliers final: 44 residues processed: 706 average time/residue: 1.0078 time to fit residues: 829.1387 Evaluate side-chains 626 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 568 time to evaluate : 2.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 119 ASN Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 127 TYR Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 127 TYR Chi-restraints excluded: chain D residue 119 ASN Chi-restraints excluded: chain D residue 127 TYR Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain E residue 119 ASN Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 127 TYR Chi-restraints excluded: chain F residue 119 ASN Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain G residue 119 ASN Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 127 TYR Chi-restraints excluded: chain G residue 131 SER Chi-restraints excluded: chain H residue 119 ASN Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 127 TYR Chi-restraints excluded: chain I residue 119 ASN Chi-restraints excluded: chain I residue 127 TYR Chi-restraints excluded: chain J residue 119 ASN Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 127 TYR Chi-restraints excluded: chain K residue 119 ASN Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 127 TYR Chi-restraints excluded: chain L residue 119 ASN Chi-restraints excluded: chain L residue 124 VAL Chi-restraints excluded: chain L residue 127 TYR Chi-restraints excluded: chain L residue 131 SER Chi-restraints excluded: chain M residue 119 ASN Chi-restraints excluded: chain M residue 127 TYR Chi-restraints excluded: chain N residue 119 ASN Chi-restraints excluded: chain N residue 127 TYR Chi-restraints excluded: chain O residue 119 ASN Chi-restraints excluded: chain O residue 127 TYR Chi-restraints excluded: chain O residue 131 SER Chi-restraints excluded: chain P residue 119 ASN Chi-restraints excluded: chain P residue 127 TYR Chi-restraints excluded: chain Q residue 119 ASN Chi-restraints excluded: chain Q residue 127 TYR Chi-restraints excluded: chain Q residue 131 SER Chi-restraints excluded: chain R residue 119 ASN Chi-restraints excluded: chain R residue 127 TYR Chi-restraints excluded: chain R residue 131 SER Chi-restraints excluded: chain S residue 64 GLU Chi-restraints excluded: chain S residue 119 ASN Chi-restraints excluded: chain S residue 127 TYR Chi-restraints excluded: chain T residue 119 ASN Chi-restraints excluded: chain T residue 127 TYR Chi-restraints excluded: chain T residue 131 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 236 optimal weight: 4.9990 chunk 212 optimal weight: 0.9980 chunk 117 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 143 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 chunk 219 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 133 optimal weight: 8.9990 chunk 163 optimal weight: 0.9980 chunk 254 optimal weight: 0.9980 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 ASN B 126 ASN C 126 ASN E 59 ASN I 126 ASN J 126 ASN L 55 GLN L 126 ASN M 82 HIS M 126 ASN N 126 ASN O 69 ASN P 69 ASN P 126 ASN Q 69 ASN R 69 ASN R 126 ASN T 69 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20960 Z= 0.166 Angle : 0.642 12.701 28580 Z= 0.328 Chirality : 0.048 0.145 3660 Planarity : 0.003 0.021 3760 Dihedral : 6.797 78.654 3120 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 6.47 % Allowed : 14.40 % Favored : 79.14 % 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: -2.47 (0.15), residues: 2900 helix: 0.37 (0.23), residues: 560 sheet: -0.26 (0.18), residues: 960 loop : -3.73 (0.11), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS O 82 PHE 0.019 0.001 PHE T 42 TYR 0.007 0.001 TYR F 127 ARG 0.001 0.000 ARG B 148 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5800 Ramachandran restraints generated. 2900 Oldfield, 0 Emsley, 2900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5800 Ramachandran restraints generated. 2900 Oldfield, 0 Emsley, 2900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 572 time to evaluate : 2.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8393 (mt-10) cc_final: 0.8053 (mt-10) REVERT: A 143 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7922 (mt-10) REVERT: C 96 TYR cc_start: 0.7092 (t80) cc_final: 0.6605 (t80) REVERT: C 127 TYR cc_start: 0.6039 (OUTLIER) cc_final: 0.4760 (t80) REVERT: D 31 ILE cc_start: 0.8988 (mt) cc_final: 0.8679 (mp) REVERT: D 143 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7847 (mt-10) REVERT: E 162 LYS cc_start: 0.8258 (mtmt) cc_final: 0.7784 (mtpt) REVERT: F 64 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8202 (mt-10) REVERT: F 143 GLU cc_start: 0.8224 (mt-10) cc_final: 0.8018 (mt-10) REVERT: H 63 ASP cc_start: 0.8102 (t0) cc_final: 0.7862 (t0) REVERT: H 73 GLU cc_start: 0.8354 (mt-10) cc_final: 0.8104 (mt-10) REVERT: H 112 ASP cc_start: 0.7903 (m-30) cc_final: 0.7506 (m-30) REVERT: I 90 ASP cc_start: 0.6511 (t0) cc_final: 0.6252 (t0) REVERT: J 44 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8574 (mt) REVERT: J 63 ASP cc_start: 0.8341 (t0) cc_final: 0.8129 (t0) REVERT: J 73 GLU cc_start: 0.8466 (mt-10) cc_final: 0.8103 (mt-10) REVERT: K 31 ILE cc_start: 0.9056 (mp) cc_final: 0.8849 (mp) REVERT: K 96 TYR cc_start: 0.7210 (t80) cc_final: 0.6806 (t80) REVERT: K 127 TYR cc_start: 0.5736 (OUTLIER) cc_final: 0.4937 (t80) REVERT: M 73 GLU cc_start: 0.8357 (mt-10) cc_final: 0.8114 (mt-10) REVERT: M 108 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8756 (mt) REVERT: N 81 ASP cc_start: 0.8274 (m-30) cc_final: 0.7889 (m-30) REVERT: N 127 TYR cc_start: 0.5398 (OUTLIER) cc_final: 0.4845 (t80) REVERT: O 96 TYR cc_start: 0.7512 (t80) cc_final: 0.6737 (t80) REVERT: O 127 TYR cc_start: 0.5683 (OUTLIER) cc_final: 0.4777 (t80) REVERT: R 63 ASP cc_start: 0.8379 (t0) cc_final: 0.8131 (t0) REVERT: R 127 TYR cc_start: 0.5706 (OUTLIER) cc_final: 0.4481 (t80) REVERT: S 94 THR cc_start: 0.6789 (t) cc_final: 0.6583 (m) REVERT: S 127 TYR cc_start: 0.5827 (OUTLIER) cc_final: 0.4704 (t80) outliers start: 150 outliers final: 62 residues processed: 629 average time/residue: 1.1533 time to fit residues: 829.2104 Evaluate side-chains 606 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 535 time to evaluate : 2.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 127 TYR Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 127 TYR Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 127 TYR Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 127 TYR Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 127 TYR Chi-restraints excluded: chain G residue 133 GLU Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 127 TYR Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 127 TYR Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 44 LEU Chi-restraints excluded: chain J residue 45 ASP Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 127 TYR Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 26 ILE Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 127 TYR Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 127 TYR Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 127 TYR Chi-restraints excluded: chain M residue 133 GLU Chi-restraints excluded: chain N residue 50 VAL Chi-restraints excluded: chain N residue 127 TYR Chi-restraints excluded: chain N residue 144 GLU Chi-restraints excluded: chain O residue 50 VAL Chi-restraints excluded: chain O residue 89 ILE Chi-restraints excluded: chain O residue 127 TYR Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 127 TYR Chi-restraints excluded: chain Q residue 46 LEU Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 127 TYR Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain R residue 61 GLU Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 127 TYR Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 127 TYR Chi-restraints excluded: chain S residue 144 GLU Chi-restraints excluded: chain T residue 23 ILE Chi-restraints excluded: chain T residue 50 VAL Chi-restraints excluded: chain T residue 127 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 141 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 211 optimal weight: 6.9990 chunk 173 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 254 optimal weight: 0.9980 chunk 275 optimal weight: 6.9990 chunk 226 optimal weight: 3.9990 chunk 252 optimal weight: 7.9990 chunk 86 optimal weight: 3.9990 chunk 204 optimal weight: 7.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 119 ASN E 59 ASN L 55 GLN L 93 GLN P 119 ASN Q 119 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 20960 Z= 0.233 Angle : 0.658 15.619 28580 Z= 0.326 Chirality : 0.048 0.159 3660 Planarity : 0.003 0.025 3760 Dihedral : 6.153 54.251 3060 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 7.46 % Allowed : 15.22 % Favored : 77.33 % 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: -1.94 (0.15), residues: 2900 helix: 0.72 (0.22), residues: 580 sheet: -0.04 (0.18), residues: 960 loop : -3.30 (0.12), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS Q 82 PHE 0.011 0.002 PHE J 42 TYR 0.008 0.001 TYR K 96 ARG 0.001 0.000 ARG B 148 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5800 Ramachandran restraints generated. 2900 Oldfield, 0 Emsley, 2900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5800 Ramachandran restraints generated. 2900 Oldfield, 0 Emsley, 2900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 731 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 558 time to evaluate : 2.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ILE cc_start: 0.9154 (OUTLIER) cc_final: 0.8940 (mp) REVERT: A 73 GLU cc_start: 0.8380 (mt-10) cc_final: 0.8076 (mt-10) REVERT: A 127 TYR cc_start: 0.5363 (OUTLIER) cc_final: 0.4866 (t80) REVERT: A 143 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7979 (mt-10) REVERT: B 103 THR cc_start: 0.6182 (OUTLIER) cc_final: 0.5687 (p) REVERT: C 103 THR cc_start: 0.5999 (OUTLIER) cc_final: 0.5260 (p) REVERT: C 127 TYR cc_start: 0.6035 (OUTLIER) cc_final: 0.5208 (t80) REVERT: C 133 GLU cc_start: 0.7348 (mt-10) cc_final: 0.7133 (mt-10) REVERT: D 31 ILE cc_start: 0.8991 (mt) cc_final: 0.8689 (mp) REVERT: D 127 TYR cc_start: 0.5775 (OUTLIER) cc_final: 0.4818 (t80) REVERT: D 143 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7959 (mt-10) REVERT: E 26 ILE cc_start: 0.8999 (OUTLIER) cc_final: 0.8739 (mm) REVERT: E 162 LYS cc_start: 0.8324 (mtmt) cc_final: 0.7778 (mtpt) REVERT: F 64 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8243 (mt-10) REVERT: H 63 ASP cc_start: 0.8128 (t0) cc_final: 0.7898 (t0) REVERT: H 73 GLU cc_start: 0.8346 (mt-10) cc_final: 0.8076 (mt-10) REVERT: I 90 ASP cc_start: 0.6560 (t0) cc_final: 0.6232 (t0) REVERT: I 144 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7645 (tt0) REVERT: J 44 LEU cc_start: 0.8949 (mp) cc_final: 0.8742 (mt) REVERT: J 63 ASP cc_start: 0.8449 (t0) cc_final: 0.8240 (t0) REVERT: J 73 GLU cc_start: 0.8437 (mt-10) cc_final: 0.8087 (mt-10) REVERT: K 96 TYR cc_start: 0.7551 (t80) cc_final: 0.6695 (t80) REVERT: K 127 TYR cc_start: 0.5770 (OUTLIER) cc_final: 0.5048 (t80) REVERT: M 53 GLU cc_start: 0.8054 (tp30) cc_final: 0.7830 (tp30) REVERT: M 73 GLU cc_start: 0.8393 (mt-10) cc_final: 0.8185 (mt-10) REVERT: M 108 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8833 (mt) REVERT: N 61 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7206 (mt-10) REVERT: N 96 TYR cc_start: 0.7391 (t80) cc_final: 0.6801 (t80) REVERT: N 127 TYR cc_start: 0.5479 (OUTLIER) cc_final: 0.4950 (t80) REVERT: N 143 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8113 (mt-10) REVERT: O 96 TYR cc_start: 0.7483 (t80) cc_final: 0.6732 (t80) REVERT: O 108 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8832 (mp) REVERT: O 127 TYR cc_start: 0.5723 (OUTLIER) cc_final: 0.4853 (t80) REVERT: P 61 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.7206 (mm-30) REVERT: P 143 GLU cc_start: 0.8406 (mt-10) cc_final: 0.8205 (mt-10) REVERT: R 127 TYR cc_start: 0.5845 (OUTLIER) cc_final: 0.4904 (t80) REVERT: S 60 MET cc_start: 0.8647 (mtp) cc_final: 0.8444 (mtp) REVERT: S 90 ASP cc_start: 0.5677 (t0) cc_final: 0.5460 (t0) REVERT: S 94 THR cc_start: 0.6893 (t) cc_final: 0.6642 (m) REVERT: S 133 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7488 (mp0) REVERT: T 116 ILE cc_start: 0.8735 (mt) cc_final: 0.8446 (tt) outliers start: 173 outliers final: 77 residues processed: 616 average time/residue: 1.2301 time to fit residues: 861.8303 Evaluate side-chains 630 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 535 time to evaluate : 2.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 127 TYR Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 127 TYR Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 127 TYR Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 127 TYR Chi-restraints excluded: chain E residue 145 ASP Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 127 TYR Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 127 TYR Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 59 ASN Chi-restraints excluded: chain I residue 103 THR Chi-restraints excluded: chain I residue 127 TYR Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 144 GLU Chi-restraints excluded: chain I residue 145 ASP Chi-restraints excluded: chain J residue 45 ASP Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 127 TYR Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 26 ILE Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 127 TYR Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 155 ASP Chi-restraints excluded: chain L residue 45 ASP Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 127 TYR Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 127 TYR Chi-restraints excluded: chain M residue 133 GLU Chi-restraints excluded: chain N residue 45 ASP Chi-restraints excluded: chain N residue 50 VAL Chi-restraints excluded: chain N residue 61 GLU Chi-restraints excluded: chain N residue 127 TYR Chi-restraints excluded: chain N residue 133 GLU Chi-restraints excluded: chain N residue 144 GLU Chi-restraints excluded: chain O residue 50 VAL Chi-restraints excluded: chain O residue 108 LEU Chi-restraints excluded: chain O residue 127 TYR Chi-restraints excluded: chain P residue 50 VAL Chi-restraints excluded: chain P residue 61 GLU Chi-restraints excluded: chain P residue 108 LEU Chi-restraints excluded: chain P residue 127 TYR Chi-restraints excluded: chain P residue 154 VAL Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 89 ILE Chi-restraints excluded: chain Q residue 127 TYR Chi-restraints excluded: chain Q residue 153 SER Chi-restraints excluded: chain Q residue 154 VAL Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain R residue 61 GLU Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain R residue 127 TYR Chi-restraints excluded: chain S residue 45 ASP Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 127 TYR Chi-restraints excluded: chain S residue 133 GLU Chi-restraints excluded: chain S residue 144 GLU Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain T residue 50 VAL Chi-restraints excluded: chain T residue 90 ASP Chi-restraints excluded: chain T residue 103 THR Chi-restraints excluded: chain T residue 127 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/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-5461/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-5461/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-5461/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-5461/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-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/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-5461/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-dev-5461/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-dev-5461/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: 72.4672 > 50: distance: 18 - 20: 24.696 distance: 20 - 21: 51.781 distance: 21 - 22: 7.815 distance: 21 - 24: 30.999 distance: 22 - 23: 42.749 distance: 22 - 26: 65.594 distance: 24 - 25: 39.738 distance: 26 - 27: 40.782 distance: 27 - 28: 54.478 distance: 27 - 30: 30.533 distance: 28 - 29: 48.335 distance: 28 - 34: 40.963 distance: 30 - 31: 15.086 distance: 30 - 32: 46.367 distance: 31 - 33: 53.291 distance: 34 - 35: 65.207 distance: 35 - 36: 54.356 distance: 35 - 38: 23.473 distance: 36 - 37: 39.390 distance: 36 - 42: 57.541 distance: 38 - 39: 8.965 distance: 39 - 40: 23.348 distance: 39 - 41: 21.188 distance: 42 - 43: 40.199 distance: 43 - 46: 39.772 distance: 44 - 45: 39.395 distance: 46 - 47: 3.628 distance: 48 - 49: 32.792 distance: 49 - 50: 44.249 distance: 49 - 52: 53.267 distance: 50 - 51: 44.387 distance: 50 - 56: 38.430 distance: 52 - 53: 43.036 distance: 53 - 54: 39.887 distance: 53 - 55: 55.538 distance: 56 - 57: 27.720 distance: 57 - 58: 33.568 distance: 57 - 60: 39.129 distance: 58 - 59: 4.411 distance: 58 - 65: 35.853 distance: 60 - 61: 28.205 distance: 61 - 62: 19.100 distance: 62 - 63: 31.284 distance: 62 - 64: 32.118 distance: 65 - 66: 11.319 distance: 66 - 67: 47.835 distance: 66 - 69: 3.167 distance: 67 - 68: 51.112 distance: 67 - 72: 55.825 distance: 69 - 70: 53.327 distance: 69 - 71: 19.282 distance: 72 - 73: 4.265 distance: 72 - 78: 34.322 distance: 73 - 74: 35.170 distance: 73 - 76: 66.023 distance: 74 - 79: 47.144 distance: 76 - 77: 17.924 distance: 77 - 78: 45.515 distance: 79 - 80: 42.718 distance: 80 - 81: 22.852 distance: 81 - 82: 36.570 distance: 83 - 84: 21.709 distance: 84 - 85: 41.620 distance: 84 - 86: 28.003 distance: 85 - 87: 19.980 distance: 86 - 88: 27.074 distance: 87 - 89: 28.314 distance: 88 - 89: 8.979 distance: 89 - 90: 24.744 distance: 91 - 92: 14.183 distance: 92 - 93: 41.474 distance: 92 - 95: 57.205 distance: 93 - 94: 48.880 distance: 93 - 100: 30.438 distance: 95 - 96: 38.882 distance: 96 - 97: 4.417 distance: 97 - 98: 48.086 distance: 97 - 99: 53.918