Starting phenix.real_space_refine on Thu Sep 26 21:44:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rk5_19260/09_2024/8rk5_19260.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rk5_19260/09_2024/8rk5_19260.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rk5_19260/09_2024/8rk5_19260.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rk5_19260/09_2024/8rk5_19260.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rk5_19260/09_2024/8rk5_19260.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rk5_19260/09_2024/8rk5_19260.cif" } resolution = 4.54 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 48 5.16 5 C 9177 2.51 5 N 2496 2.21 5 O 2703 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 14424 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2470 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 295} Chain: "B" Number of atoms: 2338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2338 Classifications: {'peptide': 305} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 285} Restraints were copied for chains: E, F, C, D Time building chain proxies: 7.99, per 1000 atoms: 0.55 Number of scatterers: 14424 At special positions: 0 Unit cell: (118.371, 114.203, 145.046, 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 48 16.00 O 2703 8.00 N 2496 7.00 C 9177 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 142 " - pdb=" SG CYS B 174 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.34 Conformation dependent library (CDL) restraints added in 1.8 seconds 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3336 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 21 sheets defined 11.1% alpha, 29.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.81 Creating SS restraints... Processing helix chain 'A' and resid 10 through 25 Processing helix chain 'A' and resid 25 through 31 Processing helix chain 'A' and resid 94 through 98 removed outlier: 3.534A pdb=" N ILE A 98 " --> pdb=" O PRO A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 223 removed outlier: 3.618A pdb=" N TYR A 222 " --> pdb=" O GLU A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 235 Processing helix chain 'A' and resid 308 through 310 No H-bonds generated for 'chain 'A' and resid 308 through 310' Processing helix chain 'B' and resid 10 through 25 removed outlier: 3.533A pdb=" N LEU B 14 " --> pdb=" O ASN B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 184 Processing helix chain 'B' and resid 217 through 223 removed outlier: 3.560A pdb=" N ILE B 221 " --> pdb=" O ASP B 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 25 Processing helix chain 'C' and resid 25 through 31 Processing helix chain 'C' and resid 94 through 98 removed outlier: 3.533A pdb=" N ILE C 98 " --> pdb=" O PRO C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 223 removed outlier: 3.618A pdb=" N TYR C 222 " --> pdb=" O GLU C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 235 Processing helix chain 'C' and resid 308 through 310 No H-bonds generated for 'chain 'C' and resid 308 through 310' Processing helix chain 'E' and resid 10 through 25 removed outlier: 3.533A pdb=" N LEU E 14 " --> pdb=" O ASN E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 184 Processing helix chain 'E' and resid 217 through 223 removed outlier: 3.560A pdb=" N ILE E 221 " --> pdb=" O ASP E 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 25 Processing helix chain 'D' and resid 25 through 31 Processing helix chain 'D' and resid 94 through 98 removed outlier: 3.534A pdb=" N ILE D 98 " --> pdb=" O PRO D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 223 removed outlier: 3.618A pdb=" N TYR D 222 " --> pdb=" O GLU D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 235 Processing helix chain 'D' and resid 308 through 310 No H-bonds generated for 'chain 'D' and resid 308 through 310' Processing helix chain 'F' and resid 10 through 25 removed outlier: 3.533A pdb=" N LEU F 14 " --> pdb=" O ASN F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 184 Processing helix chain 'F' and resid 217 through 223 removed outlier: 3.561A pdb=" N ILE F 221 " --> pdb=" O ASP F 217 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 8 removed outlier: 4.882A pdb=" N LEU A 166 " --> pdb=" O ARG A 201 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 41 removed outlier: 6.466A pdb=" N THR A 56 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASP A 40 " --> pdb=" O GLN A 54 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLN A 54 " --> pdb=" O ASP A 40 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN A 116 " --> pdb=" O TYR A 172 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N TYR A 172 " --> pdb=" O GLN A 116 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 225 through 227 removed outlier: 9.889A pdb=" N LYS A 256 " --> pdb=" O GLY A 276 " (cutoff:3.500A) removed outlier: 8.856A pdb=" N GLY A 276 " --> pdb=" O LYS A 256 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N LEU A 258 " --> pdb=" O PHE A 274 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLY A 272 " --> pdb=" O PHE A 260 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N THR A 262 " --> pdb=" O TYR A 270 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N TYR A 270 " --> pdb=" O THR A 262 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLY A 276 " --> pdb=" O ARG A 316 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 246 through 247 removed outlier: 4.585A pdb=" N TYR B 250 " --> pdb=" O ARG A 247 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N TYR B 250 " --> pdb=" O ALA B 241 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ALA B 241 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLY B 252 " --> pdb=" O ILE B 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 3 through 8 removed outlier: 5.719A pdb=" N ALA B 8 " --> pdb=" O THR B 98 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N THR B 98 " --> pdb=" O ALA B 8 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N PHE B 97 " --> pdb=" O ALA B 116 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ALA B 116 " --> pdb=" O PHE B 97 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N HIS B 110 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ILE B 125 " --> pdb=" O HIS B 110 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N HIS B 112 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N VAL B 123 " --> pdb=" O HIS B 112 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N GLU B 114 " --> pdb=" O ARG B 121 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ARG B 121 " --> pdb=" O GLU B 114 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLN B 139 " --> pdb=" O ARG B 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 28 through 32 removed outlier: 5.031A pdb=" N THR B 29 " --> pdb=" O HIS B 40 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N HIS B 40 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR B 45 " --> pdb=" O ASN B 60 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 257 through 261 removed outlier: 4.310A pdb=" N THR B 277 " --> pdb=" O VAL B 305 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 3 through 8 removed outlier: 4.882A pdb=" N LEU C 166 " --> pdb=" O ARG C 201 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 36 through 41 removed outlier: 6.465A pdb=" N THR C 56 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASP C 40 " --> pdb=" O GLN C 54 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLN C 54 " --> pdb=" O ASP C 40 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN C 116 " --> pdb=" O TYR C 172 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N TYR C 172 " --> pdb=" O GLN C 116 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 225 through 227 removed outlier: 9.889A pdb=" N LYS C 256 " --> pdb=" O GLY C 276 " (cutoff:3.500A) removed outlier: 8.856A pdb=" N GLY C 276 " --> pdb=" O LYS C 256 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N LEU C 258 " --> pdb=" O PHE C 274 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLY C 272 " --> pdb=" O PHE C 260 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N THR C 262 " --> pdb=" O TYR C 270 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N TYR C 270 " --> pdb=" O THR C 262 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLY C 276 " --> pdb=" O ARG C 316 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 246 through 247 removed outlier: 4.584A pdb=" N TYR E 250 " --> pdb=" O ARG C 247 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N TYR E 250 " --> pdb=" O ALA E 241 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ALA E 241 " --> pdb=" O TYR E 250 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLY E 252 " --> pdb=" O ILE E 239 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 3 through 8 removed outlier: 5.719A pdb=" N ALA E 8 " --> pdb=" O THR E 98 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N THR E 98 " --> pdb=" O ALA E 8 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N PHE E 97 " --> pdb=" O ALA E 116 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA E 116 " --> pdb=" O PHE E 97 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N HIS E 110 " --> pdb=" O ILE E 125 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ILE E 125 " --> pdb=" O HIS E 110 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N HIS E 112 " --> pdb=" O VAL E 123 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N VAL E 123 " --> pdb=" O HIS E 112 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N GLU E 114 " --> pdb=" O ARG E 121 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ARG E 121 " --> pdb=" O GLU E 114 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLN E 139 " --> pdb=" O ARG E 177 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 28 through 32 removed outlier: 5.031A pdb=" N THR E 29 " --> pdb=" O HIS E 40 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N HIS E 40 " --> pdb=" O THR E 29 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR E 45 " --> pdb=" O ASN E 60 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 257 through 261 removed outlier: 4.310A pdb=" N THR E 277 " --> pdb=" O VAL E 305 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 3 through 8 removed outlier: 4.882A pdb=" N LEU D 166 " --> pdb=" O ARG D 201 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 36 through 41 removed outlier: 6.466A pdb=" N THR D 56 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASP D 40 " --> pdb=" O GLN D 54 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLN D 54 " --> pdb=" O ASP D 40 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN D 116 " --> pdb=" O TYR D 172 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N TYR D 172 " --> pdb=" O GLN D 116 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 225 through 227 removed outlier: 9.890A pdb=" N LYS D 256 " --> pdb=" O GLY D 276 " (cutoff:3.500A) removed outlier: 8.856A pdb=" N GLY D 276 " --> pdb=" O LYS D 256 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N LEU D 258 " --> pdb=" O PHE D 274 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLY D 272 " --> pdb=" O PHE D 260 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N THR D 262 " --> pdb=" O TYR D 270 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N TYR D 270 " --> pdb=" O THR D 262 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLY D 276 " --> pdb=" O ARG D 316 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 246 through 247 removed outlier: 4.585A pdb=" N TYR F 250 " --> pdb=" O ARG D 247 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N TYR F 250 " --> pdb=" O ALA F 241 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ALA F 241 " --> pdb=" O TYR F 250 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLY F 252 " --> pdb=" O ILE F 239 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 3 through 8 removed outlier: 5.719A pdb=" N ALA F 8 " --> pdb=" O THR F 98 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N THR F 98 " --> pdb=" O ALA F 8 " (cutoff:3.500A) removed outlier: 8.502A pdb=" N PHE F 97 " --> pdb=" O ALA F 116 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ALA F 116 " --> pdb=" O PHE F 97 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N HIS F 110 " --> pdb=" O ILE F 125 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ILE F 125 " --> pdb=" O HIS F 110 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N HIS F 112 " --> pdb=" O VAL F 123 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N VAL F 123 " --> pdb=" O HIS F 112 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N GLU F 114 " --> pdb=" O ARG F 121 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ARG F 121 " --> pdb=" O GLU F 114 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLN F 139 " --> pdb=" O ARG F 177 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 28 through 32 removed outlier: 5.031A pdb=" N THR F 29 " --> pdb=" O HIS F 40 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N HIS F 40 " --> pdb=" O THR F 29 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TYR F 45 " --> pdb=" O ASN F 60 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 257 through 261 removed outlier: 4.309A pdb=" N THR F 277 " --> pdb=" O VAL F 305 " (cutoff:3.500A) 459 hydrogen bonds defined for protein. 1224 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: 4.22 Time building geometry restraints manager: 3.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4731 1.34 - 1.46: 2990 1.46 - 1.57: 7078 1.57 - 1.69: 0 1.69 - 1.81: 69 Bond restraints: 14868 Sorted by residual: bond pdb=" C ILE D 43 " pdb=" N PRO D 44 " ideal model delta sigma weight residual 1.329 1.346 -0.017 1.20e-02 6.94e+03 1.99e+00 bond pdb=" C ILE C 43 " pdb=" N PRO C 44 " ideal model delta sigma weight residual 1.329 1.345 -0.017 1.20e-02 6.94e+03 1.89e+00 bond pdb=" C ILE A 43 " pdb=" N PRO A 44 " ideal model delta sigma weight residual 1.329 1.345 -0.016 1.20e-02 6.94e+03 1.87e+00 bond pdb=" N GLU D 288 " pdb=" CA GLU D 288 " ideal model delta sigma weight residual 1.458 1.475 -0.017 1.37e-02 5.33e+03 1.53e+00 bond pdb=" CB TRP F 37 " pdb=" CG TRP F 37 " ideal model delta sigma weight residual 1.498 1.460 0.038 3.10e-02 1.04e+03 1.48e+00 ... (remaining 14863 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 19329 1.40 - 2.80: 822 2.80 - 4.20: 137 4.20 - 5.60: 25 5.60 - 7.00: 9 Bond angle restraints: 20322 Sorted by residual: angle pdb=" C ALA D 287 " pdb=" N GLU D 288 " pdb=" CA GLU D 288 " ideal model delta sigma weight residual 125.02 131.23 -6.21 1.76e+00 3.23e-01 1.25e+01 angle pdb=" C ALA C 287 " pdb=" N GLU C 288 " pdb=" CA GLU C 288 " ideal model delta sigma weight residual 125.02 131.21 -6.19 1.76e+00 3.23e-01 1.24e+01 angle pdb=" C ALA A 287 " pdb=" N GLU A 288 " pdb=" CA GLU A 288 " ideal model delta sigma weight residual 125.02 131.20 -6.18 1.76e+00 3.23e-01 1.23e+01 angle pdb=" CA GLU D 288 " pdb=" CB GLU D 288 " pdb=" CG GLU D 288 " ideal model delta sigma weight residual 114.10 120.17 -6.07 2.00e+00 2.50e-01 9.23e+00 angle pdb=" CA GLU C 288 " pdb=" CB GLU C 288 " pdb=" CG GLU C 288 " ideal model delta sigma weight residual 114.10 120.15 -6.05 2.00e+00 2.50e-01 9.16e+00 ... (remaining 20317 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 7901 17.96 - 35.92: 497 35.92 - 53.88: 86 53.88 - 71.84: 6 71.84 - 89.80: 9 Dihedral angle restraints: 8499 sinusoidal: 3195 harmonic: 5304 Sorted by residual: dihedral pdb=" CA TRP F 37 " pdb=" C TRP F 37 " pdb=" N LEU F 38 " pdb=" CA LEU F 38 " ideal model delta harmonic sigma weight residual 180.00 162.92 17.08 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA TRP E 37 " pdb=" C TRP E 37 " pdb=" N LEU E 38 " pdb=" CA LEU E 38 " ideal model delta harmonic sigma weight residual 180.00 162.94 17.06 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA TRP B 37 " pdb=" C TRP B 37 " pdb=" N LEU B 38 " pdb=" CA LEU B 38 " ideal model delta harmonic sigma weight residual 180.00 162.96 17.04 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 8496 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1098 0.027 - 0.054: 654 0.054 - 0.082: 181 0.082 - 0.109: 117 0.109 - 0.136: 62 Chirality restraints: 2112 Sorted by residual: chirality pdb=" CA ILE D 144 " pdb=" N ILE D 144 " pdb=" C ILE D 144 " pdb=" CB ILE D 144 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.62e-01 chirality pdb=" CA ILE A 144 " pdb=" N ILE A 144 " pdb=" C ILE A 144 " pdb=" CB ILE A 144 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.33e-01 chirality pdb=" CA ILE F 125 " pdb=" N ILE F 125 " pdb=" C ILE F 125 " pdb=" CB ILE F 125 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.25e-01 ... (remaining 2109 not shown) Planarity restraints: 2694 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 204 " -0.039 5.00e-02 4.00e+02 5.98e-02 5.73e+00 pdb=" N PRO B 205 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO B 205 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 205 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY F 204 " 0.039 5.00e-02 4.00e+02 5.98e-02 5.73e+00 pdb=" N PRO F 205 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO F 205 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO F 205 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E 204 " 0.039 5.00e-02 4.00e+02 5.98e-02 5.72e+00 pdb=" N PRO E 205 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO E 205 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 205 " 0.033 5.00e-02 4.00e+02 ... (remaining 2691 not shown) Histogram of nonbonded interaction distances: 0.40 - 1.30: 58 1.30 - 2.20: 231 2.20 - 3.10: 11453 3.10 - 4.00: 37011 4.00 - 4.90: 69963 Warning: very small nonbonded interaction distances. Nonbonded interactions: 118716 Sorted by model distance: nonbonded pdb=" NH2 ARG A 206 " pdb=" CB GLU D 264 " model vdw 0.400 3.520 nonbonded pdb=" CB GLU A 264 " pdb=" NH2 ARG D 206 " model vdw 0.449 3.520 nonbonded pdb=" OE1 GLN B 245 " pdb=" CA ALA C 79 " model vdw 0.555 3.470 nonbonded pdb=" CD ARG A 306 " pdb=" CB VAL C 183 " model vdw 0.573 3.870 nonbonded pdb=" CA ALA A 79 " pdb=" CD GLN E 245 " model vdw 0.605 3.700 ... (remaining 118711 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 'C' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' } Set up NCS constraints Number of NCS constrained groups: 2 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' } pdb_interpretation.ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' } 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: 1.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.640 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 32.550 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.020 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4375 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 : 0.003 0.038 14868 Z= 0.189 Angle : 0.674 7.003 20322 Z= 0.391 Chirality : 0.044 0.136 2112 Planarity : 0.006 0.060 2694 Dihedral : 12.152 89.798 5160 Min Nonbonded Distance : 0.400 Molprobity Statistics. All-atom Clashscore : 21.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -1.01 (0.18), residues: 1854 helix: 0.02 (0.38), residues: 153 sheet: 0.08 (0.20), residues: 597 loop : -1.23 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 189 HIS 0.003 0.001 HIS A 298 PHE 0.018 0.001 PHE A 128 TYR 0.019 0.002 TYR E 82 ARG 0.011 0.001 ARG A 179 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3708 Ramachandran restraints generated. 1854 Oldfield, 0 Emsley, 1854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 TRP cc_start: 0.6618 (m100) cc_final: 0.6279 (m100) REVERT: A 200 LEU cc_start: 0.8144 (tp) cc_final: 0.7925 (tp) REVERT: A 260 PHE cc_start: 0.7328 (m-80) cc_final: 0.6391 (m-80) REVERT: A 269 ARG cc_start: 0.6735 (ptp90) cc_final: 0.6003 (ttm170) REVERT: A 288 GLU cc_start: 0.4162 (pp20) cc_final: 0.3907 (pp20) REVERT: A 318 ASP cc_start: 0.7451 (t70) cc_final: 0.7221 (t0) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.1517 time to fit residues: 11.7803 Evaluate side-chains 46 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.271 Evaluate side-chains 62 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 70 ASN cc_start: 0.7275 (p0) cc_final: 0.7062 (t0) REVERT: B 286 ARG cc_start: 0.3551 (ttt-90) cc_final: 0.3028 (tpt170) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.1224 time to fit residues: 9.1744 Evaluate side-chains 40 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 154 optimal weight: 4.9990 chunk 138 optimal weight: 3.9990 chunk 76 optimal weight: 0.0980 chunk 47 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 74 optimal weight: 0.0040 chunk 143 optimal weight: 9.9990 chunk 55 optimal weight: 7.9990 chunk 87 optimal weight: 0.9980 chunk 106 optimal weight: 8.9990 chunk 166 optimal weight: 9.9990 overall best weight: 2.0196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN A 309 ASN Total number of N/Q/H flips: 2 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4565 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14868 Z= 0.227 Angle : 0.727 15.978 20322 Z= 0.375 Chirality : 0.048 0.212 2112 Planarity : 0.006 0.065 2694 Dihedral : 4.883 23.575 2079 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -1.11 (0.18), residues: 1854 helix: 0.04 (0.37), residues: 138 sheet: -0.09 (0.20), residues: 570 loop : -1.20 (0.18), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 127 HIS 0.003 0.001 HIS E 110 PHE 0.024 0.002 PHE E 55 TYR 0.021 0.002 TYR C 126 ARG 0.009 0.001 ARG A 268 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3706 Ramachandran restraints generated. 1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3706 Ramachandran restraints generated. 1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.247 Fit side-chains revert: symmetry clash REVERT: A 136 TRP cc_start: 0.6459 (m100) cc_final: 0.6111 (m100) REVERT: A 169 VAL cc_start: 0.5776 (p) cc_final: 0.5315 (p) REVERT: A 269 ARG cc_start: 0.6148 (ptp90) cc_final: 0.5690 (mmt90) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.1623 time to fit residues: 9.2566 Evaluate side-chains 39 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.260 Evaluate side-chains 49 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.254 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.1199 time to fit residues: 7.2396 Evaluate side-chains 33 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 92 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 138 optimal weight: 4.9990 chunk 113 optimal weight: 0.0000 chunk 45 optimal weight: 5.9990 chunk 166 optimal weight: 6.9990 chunk 179 optimal weight: 0.9980 chunk 148 optimal weight: 0.9990 chunk 165 optimal weight: 8.9990 chunk 56 optimal weight: 0.4980 chunk 133 optimal weight: 1.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 GLN ** B 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4546 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 14868 Z= 0.280 Angle : 0.859 21.082 20322 Z= 0.449 Chirality : 0.051 0.279 2112 Planarity : 0.011 0.126 2694 Dihedral : 5.240 21.271 2079 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 0.20 % Allowed : 3.43 % Favored : 96.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -1.61 (0.17), residues: 1854 helix: -0.94 (0.36), residues: 135 sheet: -0.06 (0.21), residues: 510 loop : -1.62 (0.16), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.004 TRP C 127 HIS 0.012 0.002 HIS D 298 PHE 0.039 0.004 PHE A 129 TYR 0.042 0.003 TYR C 35 ARG 0.046 0.003 ARG C 53 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3706 Ramachandran restraints generated. 1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3706 Ramachandran restraints generated. 1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 43 time to evaluate : 0.237 Fit side-chains revert: symmetry clash REVERT: A 120 TRP cc_start: 0.6985 (p90) cc_final: 0.5410 (p90) REVERT: A 136 TRP cc_start: 0.6345 (m100) cc_final: 0.6112 (m100) REVERT: A 169 VAL cc_start: 0.5675 (p) cc_final: 0.5251 (p) REVERT: A 269 ARG cc_start: 0.6231 (ptp90) cc_final: 0.5674 (mmt90) outliers start: 1 outliers final: 0 residues processed: 44 average time/residue: 0.1569 time to fit residues: 8.2204 Evaluate side-chains 37 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.254 Evaluate side-chains 41 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.0840 time to fit residues: 4.6790 Evaluate side-chains 38 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 164 optimal weight: 1.9990 chunk 125 optimal weight: 0.0670 chunk 86 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 79 optimal weight: 8.9990 chunk 111 optimal weight: 0.0570 chunk 167 optimal weight: 5.9990 chunk 176 optimal weight: 1.9990 chunk 87 optimal weight: 9.9990 chunk 158 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 overall best weight: 1.0242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4527 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 14868 Z= 0.283 Angle : 0.860 21.082 20322 Z= 0.449 Chirality : 0.051 0.279 2112 Planarity : 0.011 0.126 2694 Dihedral : 5.240 21.271 2079 Min Nonbonded Distance : 1.157 Molprobity Statistics. All-atom Clashscore : 22.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -1.61 (0.17), residues: 1854 helix: -0.94 (0.36), residues: 135 sheet: -0.06 (0.21), residues: 510 loop : -1.62 (0.16), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.004 TRP C 127 HIS 0.012 0.002 HIS A 298 PHE 0.039 0.004 PHE C 129 TYR 0.042 0.003 TYR C 35 ARG 0.046 0.003 ARG C 53 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3706 Ramachandran restraints generated. 1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3706 Ramachandran restraints generated. 1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.285 Fit side-chains revert: symmetry clash REVERT: A 120 TRP cc_start: 0.7027 (p90) cc_final: 0.5417 (p90) REVERT: A 169 VAL cc_start: 0.5676 (p) cc_final: 0.5261 (p) REVERT: A 269 ARG cc_start: 0.6143 (ptp90) cc_final: 0.5651 (mmt90) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.1497 time to fit residues: 7.6578 Evaluate side-chains 35 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.238 Evaluate side-chains 40 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 264 PHE cc_start: 0.5184 (m-80) cc_final: 0.4969 (m-10) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.0849 time to fit residues: 4.6344 Evaluate side-chains 36 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 147 optimal weight: 0.0980 chunk 100 optimal weight: 0.0980 chunk 2 optimal weight: 7.9990 chunk 131 optimal weight: 0.4980 chunk 72 optimal weight: 4.9990 chunk 150 optimal weight: 0.0970 chunk 122 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 90 optimal weight: 0.5980 chunk 158 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.2778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 94 ASN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4539 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14868 Z= 0.244 Angle : 0.827 21.099 20322 Z= 0.421 Chirality : 0.052 0.324 2112 Planarity : 0.011 0.190 2694 Dihedral : 5.222 27.129 2079 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.18 % Favored : 94.66 % Rotamer: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -1.72 (0.17), residues: 1854 helix: -1.09 (0.34), residues: 135 sheet: -0.17 (0.20), residues: 558 loop : -1.72 (0.16), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.004 TRP C 120 HIS 0.017 0.002 HIS C 298 PHE 0.057 0.004 PHE C 129 TYR 0.046 0.003 TYR D 35 ARG 0.044 0.003 ARG D 53 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3706 Ramachandran restraints generated. 1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3706 Ramachandran restraints generated. 1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.270 Fit side-chains revert: symmetry clash REVERT: A 120 TRP cc_start: 0.7160 (p90) cc_final: 0.5573 (p90) REVERT: A 169 VAL cc_start: 0.5839 (p) cc_final: 0.5561 (p) REVERT: A 200 LEU cc_start: 0.7978 (tp) cc_final: 0.7720 (tp) REVERT: A 260 PHE cc_start: 0.7181 (m-80) cc_final: 0.6674 (m-80) REVERT: A 269 ARG cc_start: 0.6095 (ptp90) cc_final: 0.5431 (mmt90) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.1465 time to fit residues: 8.0547 Evaluate side-chains 35 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.235 Evaluate side-chains 40 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 218 VAL cc_start: 0.7281 (t) cc_final: 0.6565 (t) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.0783 time to fit residues: 4.2734 Evaluate side-chains 31 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 59 optimal weight: 8.9990 chunk 159 optimal weight: 0.0170 chunk 34 optimal weight: 0.9990 chunk 103 optimal weight: 9.9990 chunk 43 optimal weight: 0.0050 chunk 177 optimal weight: 0.9980 chunk 146 optimal weight: 9.9990 chunk 81 optimal weight: 0.0970 chunk 14 optimal weight: 6.9990 chunk 58 optimal weight: 7.9990 chunk 92 optimal weight: 1.9990 overall best weight: 0.4232 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4521 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.236 14868 Z= 0.268 Angle : 0.831 21.099 20322 Z= 0.423 Chirality : 0.052 0.324 2112 Planarity : 0.011 0.190 2694 Dihedral : 5.222 27.129 2079 Min Nonbonded Distance : 1.546 Molprobity Statistics. All-atom Clashscore : 24.44 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.18 % Favored : 94.66 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -1.72 (0.17), residues: 1854 helix: -1.09 (0.34), residues: 135 sheet: -0.17 (0.20), residues: 558 loop : -1.72 (0.16), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.004 TRP C 120 HIS 0.017 0.002 HIS C 298 PHE 0.057 0.004 PHE D 129 TYR 0.046 0.003 TYR D 35 ARG 0.044 0.003 ARG C 53 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3706 Ramachandran restraints generated. 1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3706 Ramachandran restraints generated. 1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.532 Fit side-chains revert: symmetry clash REVERT: A 120 TRP cc_start: 0.7132 (p90) cc_final: 0.5576 (p90) REVERT: A 169 VAL cc_start: 0.5874 (p) cc_final: 0.5558 (p) REVERT: A 200 LEU cc_start: 0.7932 (tp) cc_final: 0.7714 (tp) REVERT: A 260 PHE cc_start: 0.6919 (m-80) cc_final: 0.6541 (m-80) REVERT: A 269 ARG cc_start: 0.6058 (ptp90) cc_final: 0.5434 (mmt90) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.1721 time to fit residues: 8.0706 Evaluate side-chains 34 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.253 Evaluate side-chains 39 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 218 VAL cc_start: 0.7286 (t) cc_final: 0.6538 (t) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.0852 time to fit residues: 4.5722 Evaluate side-chains 31 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 170 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 100 optimal weight: 0.0020 chunk 129 optimal weight: 9.9990 chunk 149 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 107 optimal weight: 0.0060 chunk 81 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 overall best weight: 0.5608 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4523 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.234 14868 Z= 0.267 Angle : 0.830 21.098 20322 Z= 0.423 Chirality : 0.052 0.324 2112 Planarity : 0.011 0.190 2694 Dihedral : 5.222 27.126 2079 Min Nonbonded Distance : 1.548 Molprobity Statistics. All-atom Clashscore : 23.33 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.18 % Favored : 94.66 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: -1.72 (0.17), residues: 1854 helix: -1.09 (0.34), residues: 135 sheet: -0.17 (0.20), residues: 558 loop : -1.72 (0.16), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.004 TRP C 120 HIS 0.017 0.002 HIS C 298 PHE 0.057 0.004 PHE D 129 TYR 0.046 0.003 TYR D 35 ARG 0.044 0.003 ARG C 53 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3706 Ramachandran restraints generated. 1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3706 Ramachandran restraints generated. 1853 Oldfield, 0 Emsley, 1853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.243 Fit side-chains revert: symmetry clash REVERT: A 120 TRP cc_start: 0.7132 (p90) cc_final: 0.5576 (p90) REVERT: A 169 VAL cc_start: 0.5874 (p) cc_final: 0.5558 (p) REVERT: A 200 LEU cc_start: 0.7932 (tp) cc_final: 0.7714 (tp) REVERT: A 260 PHE cc_start: 0.6919 (m-80) cc_final: 0.6541 (m-80) REVERT: A 269 ARG cc_start: 0.6058 (ptp90) cc_final: 0.5434 (mmt90) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.1543 time to fit residues: 7.0391 Evaluate side-chains 34 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.242 Evaluate side-chains 38 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 218 VAL cc_start: 0.7281 (t) cc_final: 0.6538 (t) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.0816 time to fit residues: 4.2410 Evaluate side-chains 31 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- 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 704, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 800, in minimization_ncs ncs_groups = ncs_groups) 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 400, 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 133, in refine refine_sites = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-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/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-5461/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-5461/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-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: 72.5014 > 50: distance: 0 - 1: 57.092 distance: 1 - 2: 55.065 distance: 1 - 4: 16.960 distance: 2 - 3: 57.674 distance: 2 - 9: 40.461 distance: 4 - 5: 16.580 distance: 5 - 6: 39.459 distance: 6 - 8: 18.826 distance: 9 - 10: 69.200 distance: 10 - 11: 57.020 distance: 10 - 13: 70.422 distance: 11 - 12: 68.298 distance: 11 - 21: 69.934 distance: 13 - 14: 57.568 distance: 14 - 15: 55.348 distance: 15 - 17: 57.517 distance: 17 - 19: 40.852 distance: 18 - 19: 38.689 distance: 19 - 20: 56.347 distance: 21 - 22: 70.110 distance: 21 - 27: 40.161 distance: 22 - 23: 57.286 distance: 22 - 25: 56.593 distance: 23 - 24: 56.767 distance: 23 - 28: 39.504 distance: 25 - 26: 40.078 distance: 26 - 27: 41.254 distance: 28 - 29: 57.875 distance: 29 - 30: 68.401 distance: 29 - 32: 56.450 distance: 30 - 31: 57.721 distance: 30 - 40: 40.698 distance: 32 - 33: 40.267 distance: 33 - 34: 38.796 distance: 33 - 35: 40.759 distance: 34 - 36: 56.803 distance: 35 - 37: 40.498 distance: 36 - 38: 40.645 distance: 37 - 38: 55.913 distance: 40 - 41: 56.334 distance: 40 - 46: 40.673 distance: 41 - 42: 55.192 distance: 41 - 44: 70.502 distance: 42 - 43: 70.082 distance: 42 - 47: 56.833 distance: 44 - 45: 39.031 distance: 45 - 46: 41.062 distance: 47 - 48: 56.089 distance: 48 - 49: 55.169 distance: 48 - 51: 56.492 distance: 49 - 50: 39.987 distance: 49 - 55: 39.526 distance: 51 - 52: 42.675 distance: 55 - 56: 55.426 distance: 56 - 57: 57.730 distance: 56 - 59: 41.392 distance: 57 - 58: 39.547 distance: 57 - 60: 38.801 distance: 61 - 62: 39.601 distance: 61 - 64: 68.905 distance: 62 - 67: 40.635 distance: 64 - 65: 41.120 distance: 64 - 66: 38.880 distance: 67 - 68: 55.447 distance: 68 - 69: 57.718 distance: 69 - 70: 68.106 distance: 69 - 74: 41.038 distance: 71 - 73: 41.535 distance: 75 - 76: 40.501 distance: 76 - 77: 55.675