Starting phenix.real_space_refine on Sat Dec 9 12:59:40 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7v_36050/12_2023/8j7v_36050.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7v_36050/12_2023/8j7v_36050.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7v_36050/12_2023/8j7v_36050.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7v_36050/12_2023/8j7v_36050.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7v_36050/12_2023/8j7v_36050.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j7v_36050/12_2023/8j7v_36050.pdb" } resolution = 2.79 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 ------------------------------------------------------------------------------- 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= 0.014 sd= 0.072 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 47 5.16 5 C 7093 2.51 5 N 1844 2.21 5 O 2099 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 11083 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2242 Classifications: {'peptide': 286} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 276} Chain breaks: 2 Chain: "C" Number of atoms: 1672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1672 Classifications: {'peptide': 215} Link IDs: {'PCIS': 4, 'PTRANS': 7, 'TRANS': 203} Chain: "E" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1642 Classifications: {'peptide': 218} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 203} Chain: "B" Number of atoms: 2213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2213 Classifications: {'peptide': 280} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 272} Chain breaks: 3 Chain: "F" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1642 Classifications: {'peptide': 218} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 203} Chain: "D" Number of atoms: 1672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1672 Classifications: {'peptide': 215} Link IDs: {'PCIS': 4, 'PTRANS': 7, 'TRANS': 203} Time building chain proxies: 6.14, per 1000 atoms: 0.55 Number of scatterers: 11083 At special positions: 0 Unit cell: (103.228, 95.348, 158.388, 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 47 16.00 O 2099 8.00 N 1844 7.00 C 7093 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 92 " distance=2.04 Simple disulfide: pdb=" SG CYS C 138 " - pdb=" SG CYS C 198 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.04 Simple disulfide: pdb=" SG CYS E 145 " - pdb=" SG CYS E 200 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 95 " distance=2.03 Simple disulfide: pdb=" SG CYS F 145 " - pdb=" SG CYS F 200 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 92 " distance=2.04 Simple disulfide: pdb=" SG CYS D 138 " - pdb=" SG CYS D 198 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.07 Conformation dependent library (CDL) restraints added in 2.2 seconds 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2682 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 26 sheets defined 32.8% alpha, 36.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'A' and resid 22 through 32 removed outlier: 3.508A pdb=" N PHE A 26 " --> pdb=" O ILE A 22 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG A 27 " --> pdb=" O SER A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 58 Processing helix chain 'A' and resid 63 through 89 removed outlier: 4.038A pdb=" N LYS A 89 " --> pdb=" O SER A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 129 removed outlier: 4.031A pdb=" N VAL A 105 " --> pdb=" O VAL A 101 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY A 112 " --> pdb=" O GLY A 108 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE A 117 " --> pdb=" O LEU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 159 removed outlier: 3.840A pdb=" N ILE A 146 " --> pdb=" O LEU A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 259 Processing helix chain 'A' and resid 265 through 294 removed outlier: 4.460A pdb=" N ILE A 269 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N CYS A 270 " --> pdb=" O ALA A 266 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER A 271 " --> pdb=" O ASP A 267 " (cutoff:3.500A) Proline residue: A 284 - end of helix Processing helix chain 'A' and resid 298 through 303 removed outlier: 4.272A pdb=" N ASN A 303 " --> pdb=" O PRO A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 314 Processing helix chain 'A' and resid 347 through 362 Processing helix chain 'C' and resid 83 through 87 removed outlier: 3.513A pdb=" N ALA C 87 " --> pdb=" O ALA C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 132 Processing helix chain 'C' and resid 187 through 192 Processing helix chain 'E' and resid 61 through 64 removed outlier: 3.631A pdb=" N ILE E 64 " --> pdb=" O ALA E 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 61 through 64' Processing helix chain 'E' and resid 86 through 90 removed outlier: 3.727A pdb=" N THR E 90 " --> pdb=" O ALA E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 163 No H-bonds generated for 'chain 'E' and resid 161 through 163' Processing helix chain 'B' and resid 23 through 32 removed outlier: 3.679A pdb=" N ILE B 29 " --> pdb=" O TRP B 25 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N LEU B 30 " --> pdb=" O PHE B 26 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER B 31 " --> pdb=" O ARG B 27 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP B 32 " --> pdb=" O SER B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 59 Processing helix chain 'B' and resid 61 through 89 Processing helix chain 'B' and resid 101 through 132 removed outlier: 4.152A pdb=" N VAL B 105 " --> pdb=" O VAL B 101 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR B 118 " --> pdb=" O PHE B 114 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA B 119 " --> pdb=" O LEU B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 159 removed outlier: 3.917A pdb=" N LEU B 147 " --> pdb=" O LEU B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 259 removed outlier: 4.170A pdb=" N LEU B 234 " --> pdb=" O SER B 230 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN B 235 " --> pdb=" O ARG B 231 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N GLY B 236 " --> pdb=" O GLN B 232 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL B 237 " --> pdb=" O ILE B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 294 removed outlier: 3.682A pdb=" N CYS B 270 " --> pdb=" O ALA B 266 " (cutoff:3.500A) Proline residue: B 284 - end of helix Processing helix chain 'B' and resid 298 through 303 removed outlier: 4.691A pdb=" N ASN B 303 " --> pdb=" O PRO B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 314 Processing helix chain 'B' and resid 347 through 362 removed outlier: 3.542A pdb=" N ALA B 362 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 64 removed outlier: 3.626A pdb=" N ILE F 64 " --> pdb=" O ALA F 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 61 through 64' Processing helix chain 'F' and resid 86 through 90 removed outlier: 4.059A pdb=" N THR F 90 " --> pdb=" O ALA F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 161 through 163 No H-bonds generated for 'chain 'F' and resid 161 through 163' Processing helix chain 'D' and resid 125 through 132 Processing helix chain 'D' and resid 187 through 192 Processing sheet with id=AA1, first strand: chain 'A' and resid 318 through 330 removed outlier: 5.781A pdb=" N LEU A 321 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ILE A 341 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N GLU A 323 " --> pdb=" O LYS A 339 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N LYS A 339 " --> pdb=" O GLU A 323 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N VAL A 333 " --> pdb=" O LEU A 329 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N TYR A 334 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AA3, first strand: chain 'C' and resid 10 through 14 removed outlier: 6.260A pdb=" N LEU C 11 " --> pdb=" O GLU C 109 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LYS C 111 " --> pdb=" O LEU C 11 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL C 13 " --> pdb=" O LYS C 111 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N MET C 37 " --> pdb=" O TYR C 53 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N TYR C 53 " --> pdb=" O MET C 37 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N TRP C 39 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 10 through 14 removed outlier: 6.260A pdb=" N LEU C 11 " --> pdb=" O GLU C 109 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LYS C 111 " --> pdb=" O LEU C 11 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N VAL C 13 " --> pdb=" O LYS C 111 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR C 101 " --> pdb=" O GLN C 94 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 30 through 31 Processing sheet with id=AA6, first strand: chain 'C' and resid 118 through 122 removed outlier: 5.968A pdb=" N TYR C 177 " --> pdb=" O ASN C 142 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 157 through 158 removed outlier: 6.053A pdb=" N HIS C 202 " --> pdb=" O SER C 207 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N SER C 207 " --> pdb=" O HIS C 202 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.132A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N SER E 40 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N LEU E 45 " --> pdb=" O SER E 40 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12 Processing sheet with id=AB2, first strand: chain 'E' and resid 125 through 129 removed outlier: 6.344A pdb=" N TYR E 180 " --> pdb=" O GLY E 149 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 125 through 129 removed outlier: 6.344A pdb=" N TYR E 180 " --> pdb=" O GLY E 149 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 156 through 159 Processing sheet with id=AB5, first strand: chain 'B' and resid 318 through 330 removed outlier: 5.732A pdb=" N LEU B 321 " --> pdb=" O ILE B 341 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE B 341 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N GLU B 323 " --> pdb=" O LYS B 339 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LYS B 339 " --> pdb=" O GLU B 323 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL B 333 " --> pdb=" O LEU B 329 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AB7, first strand: chain 'F' and resid 11 through 12 removed outlier: 6.462A pdb=" N VAL F 34 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL F 50 " --> pdb=" O VAL F 34 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N TRP F 36 " --> pdb=" O LEU F 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.679A pdb=" N TYR F 107 " --> pdb=" O ARG F 97 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 125 through 129 removed outlier: 6.122A pdb=" N TYR F 180 " --> pdb=" O GLY F 149 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 125 through 129 removed outlier: 6.122A pdb=" N TYR F 180 " --> pdb=" O GLY F 149 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 156 through 159 Processing sheet with id=AC3, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AC4, first strand: chain 'D' and resid 10 through 14 removed outlier: 6.317A pdb=" N LEU D 11 " --> pdb=" O GLU D 109 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N LYS D 111 " --> pdb=" O LEU D 11 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL D 13 " --> pdb=" O LYS D 111 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N MET D 37 " --> pdb=" O TYR D 53 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N TYR D 53 " --> pdb=" O MET D 37 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N TRP D 39 " --> pdb=" O LEU D 51 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 10 through 14 removed outlier: 6.317A pdb=" N LEU D 11 " --> pdb=" O GLU D 109 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N LYS D 111 " --> pdb=" O LEU D 11 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL D 13 " --> pdb=" O LYS D 111 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR D 101 " --> pdb=" O GLN D 94 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 30 through 31 Processing sheet with id=AC7, first strand: chain 'D' and resid 118 through 122 removed outlier: 5.838A pdb=" N TYR D 177 " --> pdb=" O ASN D 142 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 157 through 158 651 hydrogen bonds defined for protein. 1779 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: 3.74 Time building geometry restraints manager: 4.45 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: 3463 1.34 - 1.46: 2479 1.46 - 1.58: 5337 1.58 - 1.70: 0 1.70 - 1.82: 68 Bond restraints: 11347 Sorted by residual: bond pdb=" N LYS F 213 " pdb=" CA LYS F 213 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.22e-02 6.72e+03 8.40e+00 bond pdb=" N ILE B 274 " pdb=" CA ILE B 274 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.30e-02 5.92e+03 6.25e+00 bond pdb=" N CYS E 95 " pdb=" CA CYS E 95 " ideal model delta sigma weight residual 1.456 1.486 -0.030 1.23e-02 6.61e+03 5.84e+00 bond pdb=" N ASN F 138 " pdb=" CA ASN F 138 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.29e-02 6.01e+03 5.70e+00 bond pdb=" N MET E 140 " pdb=" CA MET E 140 " ideal model delta sigma weight residual 1.456 1.485 -0.029 1.21e-02 6.83e+03 5.62e+00 ... (remaining 11342 not shown) Histogram of bond angle deviations from ideal: 100.05 - 106.86: 339 106.86 - 113.66: 6290 113.66 - 120.46: 4159 120.46 - 127.26: 4516 127.26 - 134.07: 141 Bond angle restraints: 15445 Sorted by residual: angle pdb=" CB LYS C 187 " pdb=" CG LYS C 187 " pdb=" CD LYS C 187 " ideal model delta sigma weight residual 111.30 119.18 -7.88 2.30e+00 1.89e-01 1.17e+01 angle pdb=" CA LEU A 153 " pdb=" CB LEU A 153 " pdb=" CG LEU A 153 " ideal model delta sigma weight residual 116.30 128.20 -11.90 3.50e+00 8.16e-02 1.16e+01 angle pdb=" N MET B 257 " pdb=" CA MET B 257 " pdb=" C MET B 257 " ideal model delta sigma weight residual 112.23 108.02 4.21 1.26e+00 6.30e-01 1.12e+01 angle pdb=" N VAL D 29 " pdb=" CA VAL D 29 " pdb=" C VAL D 29 " ideal model delta sigma weight residual 111.77 108.40 3.37 1.04e+00 9.25e-01 1.05e+01 angle pdb=" CG ARG A 231 " pdb=" CD ARG A 231 " pdb=" NE ARG A 231 " ideal model delta sigma weight residual 112.00 119.08 -7.08 2.20e+00 2.07e-01 1.04e+01 ... (remaining 15440 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.15: 5786 17.15 - 34.30: 673 34.30 - 51.46: 189 51.46 - 68.61: 40 68.61 - 85.76: 20 Dihedral angle restraints: 6708 sinusoidal: 2553 harmonic: 4155 Sorted by residual: dihedral pdb=" CB CYS D 138 " pdb=" SG CYS D 138 " pdb=" SG CYS D 198 " pdb=" CB CYS D 198 " ideal model delta sinusoidal sigma weight residual 93.00 39.00 54.00 1 1.00e+01 1.00e-02 3.96e+01 dihedral pdb=" CB CYS C 138 " pdb=" SG CYS C 138 " pdb=" SG CYS C 198 " pdb=" CB CYS C 198 " ideal model delta sinusoidal sigma weight residual 93.00 42.51 50.49 1 1.00e+01 1.00e-02 3.49e+01 dihedral pdb=" CA TYR F 94 " pdb=" C TYR F 94 " pdb=" N CYS F 95 " pdb=" CA CYS F 95 " ideal model delta harmonic sigma weight residual 180.00 160.54 19.46 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 6705 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1585 0.078 - 0.156: 181 0.156 - 0.234: 7 0.234 - 0.312: 0 0.312 - 0.390: 1 Chirality restraints: 1774 Sorted by residual: chirality pdb=" CG LEU A 153 " pdb=" CB LEU A 153 " pdb=" CD1 LEU A 153 " pdb=" CD2 LEU A 153 " both_signs ideal model delta sigma weight residual False -2.59 -2.20 -0.39 2.00e-01 2.50e+01 3.80e+00 chirality pdb=" CA PHE B 72 " pdb=" N PHE B 72 " pdb=" C PHE B 72 " pdb=" CB PHE B 72 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA TYR D 144 " pdb=" N TYR D 144 " pdb=" C TYR D 144 " pdb=" CB TYR D 144 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.53e-01 ... (remaining 1771 not shown) Planarity restraints: 1952 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL F 188 " 0.036 5.00e-02 4.00e+02 5.41e-02 4.69e+00 pdb=" N PRO F 189 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO F 189 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO F 189 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL E 188 " 0.032 5.00e-02 4.00e+02 4.88e-02 3.82e+00 pdb=" N PRO E 189 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO E 189 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 189 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 107 " 0.010 2.00e-02 2.50e+03 1.91e-02 3.65e+00 pdb=" C ALA B 107 " -0.033 2.00e-02 2.50e+03 pdb=" O ALA B 107 " 0.012 2.00e-02 2.50e+03 pdb=" N GLY B 108 " 0.011 2.00e-02 2.50e+03 ... (remaining 1949 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 983 2.75 - 3.28: 10877 3.28 - 3.82: 19356 3.82 - 4.36: 23130 4.36 - 4.90: 38632 Nonbonded interactions: 92978 Sorted by model distance: nonbonded pdb=" OD2 ASP D 174 " pdb=" OG1 THR D 176 " model vdw 2.208 2.440 nonbonded pdb=" OG1 THR D 186 " pdb=" OD1 ASP D 188 " model vdw 2.223 2.440 nonbonded pdb=" OD1 ASP D 30 " pdb=" OG SER D 35 " model vdw 2.248 2.440 nonbonded pdb=" OD2 ASP C 174 " pdb=" OG1 THR C 176 " model vdw 2.271 2.440 nonbonded pdb=" NH2 ARG F 66 " pdb=" OD2 ASP F 89 " model vdw 2.293 2.520 ... (remaining 92973 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 22 through 132 or resid 141 through 161 or resid 229 throu \ gh 259 or resid 265 through 376)) selection = (chain 'B' and (resid 22 through 132 or resid 141 through 376)) } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 2.730 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 32.430 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.060 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:11.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11347 Z= 0.240 Angle : 0.725 11.901 15445 Z= 0.388 Chirality : 0.047 0.390 1774 Planarity : 0.005 0.054 1952 Dihedral : 16.710 85.760 4002 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.54 % Allowed : 25.79 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.22), residues: 1410 helix: 0.75 (0.26), residues: 413 sheet: 0.71 (0.23), residues: 460 loop : -0.43 (0.27), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 159 HIS 0.008 0.001 HIS B 70 PHE 0.017 0.002 PHE C 36 TYR 0.029 0.002 TYR E 150 ARG 0.011 0.001 ARG C 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1237 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 163 time to evaluate : 1.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 14 residues processed: 179 average time/residue: 1.4206 time to fit residues: 271.9313 Evaluate side-chains 162 residues out of total 1237 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 148 time to evaluate : 1.306 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 13 residues processed: 1 average time/residue: 0.2419 time to fit residues: 2.0025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 36 optimal weight: 9.9990 chunk 71 optimal weight: 7.9990 chunk 56 optimal weight: 1.9990 chunk 109 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 66 optimal weight: 30.0000 chunk 81 optimal weight: 0.0020 chunk 127 optimal weight: 7.9990 overall best weight: 3.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN A 310 GLN A 322 GLN A 325 HIS A 356 HIS C 57 ASN E 110 GLN E 204 HIS B 37 ASN B 45 ASN B 111 ASN ** B 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 356 HIS ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 ASN F 204 HIS D 142 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.0944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 11347 Z= 0.332 Angle : 0.614 7.775 15445 Z= 0.318 Chirality : 0.045 0.251 1774 Planarity : 0.005 0.049 1952 Dihedral : 4.609 29.520 1530 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 4.61 % Allowed : 23.61 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.23), residues: 1410 helix: 1.37 (0.26), residues: 413 sheet: 0.83 (0.24), residues: 476 loop : -0.22 (0.28), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 167 HIS 0.004 0.001 HIS A 356 PHE 0.022 0.002 PHE C 36 TYR 0.020 0.002 TYR C 144 ARG 0.005 0.001 ARG C 72 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1237 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 151 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 25 residues processed: 189 average time/residue: 1.3573 time to fit residues: 275.1080 Evaluate side-chains 172 residues out of total 1237 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 147 time to evaluate : 1.290 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 20 residues processed: 5 average time/residue: 0.4023 time to fit residues: 4.2315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 70.0000 chunk 39 optimal weight: 10.0000 chunk 105 optimal weight: 3.9990 chunk 86 optimal weight: 40.0000 chunk 35 optimal weight: 3.9990 chunk 127 optimal weight: 9.9990 chunk 137 optimal weight: 20.0000 chunk 113 optimal weight: 20.0000 chunk 126 optimal weight: 4.9990 chunk 43 optimal weight: 20.0000 chunk 102 optimal weight: 3.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN A 310 GLN A 361 GLN E 110 GLN B 45 ASN B 70 HIS ** B 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 325 HIS ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 11347 Z= 0.460 Angle : 0.677 9.230 15445 Z= 0.348 Chirality : 0.048 0.317 1774 Planarity : 0.005 0.046 1952 Dihedral : 4.832 35.931 1530 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.48 % Favored : 96.45 % Rotamer: Outliers : 5.42 % Allowed : 23.85 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.23), residues: 1410 helix: 1.47 (0.25), residues: 412 sheet: 0.78 (0.24), residues: 476 loop : -0.28 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 47 HIS 0.004 0.001 HIS B 325 PHE 0.025 0.002 PHE C 36 TYR 0.020 0.002 TYR C 32 ARG 0.006 0.001 ARG C 72 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1237 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 148 time to evaluate : 1.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 67 outliers final: 32 residues processed: 200 average time/residue: 1.2740 time to fit residues: 274.1326 Evaluate side-chains 177 residues out of total 1237 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 145 time to evaluate : 1.133 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 27 residues processed: 5 average time/residue: 0.5138 time to fit residues: 4.5528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 7.9990 chunk 95 optimal weight: 0.6980 chunk 66 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 60 optimal weight: 9.9990 chunk 85 optimal weight: 20.0000 chunk 127 optimal weight: 20.0000 chunk 135 optimal weight: 20.0000 chunk 121 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 chunk 112 optimal weight: 5.9990 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN A 310 GLN E 110 GLN ** B 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 161 HIS ** B 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 322 GLN ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 11347 Z= 0.452 Angle : 0.681 9.645 15445 Z= 0.347 Chirality : 0.048 0.238 1774 Planarity : 0.005 0.052 1952 Dihedral : 4.843 35.623 1530 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.19 % Favored : 96.74 % Rotamer: Outliers : 5.42 % Allowed : 25.14 % Favored : 69.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.23), residues: 1410 helix: 1.58 (0.26), residues: 410 sheet: 0.63 (0.23), residues: 480 loop : -0.27 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 167 HIS 0.005 0.001 HIS D 193 PHE 0.026 0.003 PHE B 41 TYR 0.021 0.002 TYR C 32 ARG 0.007 0.001 ARG C 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1237 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 153 time to evaluate : 1.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 67 outliers final: 39 residues processed: 204 average time/residue: 1.2744 time to fit residues: 280.6896 Evaluate side-chains 186 residues out of total 1237 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 147 time to evaluate : 1.390 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 32 residues processed: 7 average time/residue: 1.0177 time to fit residues: 9.8919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 100 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 115 optimal weight: 30.0000 chunk 93 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 69 optimal weight: 5.9990 chunk 121 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 45 optimal weight: 20.0000 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN A 310 GLN B 45 ASN ** B 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11347 Z= 0.223 Angle : 0.617 11.422 15445 Z= 0.307 Chirality : 0.044 0.365 1774 Planarity : 0.004 0.052 1952 Dihedral : 4.533 34.610 1530 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 4.77 % Allowed : 25.71 % Favored : 69.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.88 % 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: 1.08 (0.23), residues: 1410 helix: 1.87 (0.26), residues: 411 sheet: 0.81 (0.24), residues: 476 loop : -0.24 (0.28), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 167 HIS 0.003 0.001 HIS E 169 PHE 0.026 0.002 PHE A 117 TYR 0.030 0.002 TYR C 144 ARG 0.007 0.001 ARG A 231 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1237 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 153 time to evaluate : 1.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 37 residues processed: 200 average time/residue: 1.2843 time to fit residues: 276.4604 Evaluate side-chains 184 residues out of total 1237 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 147 time to evaluate : 1.208 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 32 residues processed: 5 average time/residue: 0.6258 time to fit residues: 5.2815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 79 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 135 optimal weight: 20.0000 chunk 112 optimal weight: 4.9990 chunk 62 optimal weight: 50.0000 chunk 11 optimal weight: 40.0000 chunk 44 optimal weight: 20.0000 chunk 71 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN A 310 GLN E 110 GLN B 232 GLN ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 142 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 11347 Z= 0.406 Angle : 0.673 10.268 15445 Z= 0.339 Chirality : 0.046 0.289 1774 Planarity : 0.005 0.050 1952 Dihedral : 4.734 36.023 1530 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.26 % Favored : 96.67 % Rotamer: Outliers : 5.01 % Allowed : 25.87 % Favored : 69.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.88 % 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: 1.00 (0.23), residues: 1410 helix: 1.75 (0.26), residues: 411 sheet: 0.69 (0.24), residues: 480 loop : -0.15 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 167 HIS 0.004 0.001 HIS A 356 PHE 0.025 0.002 PHE C 36 TYR 0.020 0.002 TYR C 32 ARG 0.008 0.001 ARG C 72 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1237 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 147 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 35 residues processed: 197 average time/residue: 1.2437 time to fit residues: 264.9119 Evaluate side-chains 181 residues out of total 1237 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 146 time to evaluate : 1.229 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 30 residues processed: 5 average time/residue: 0.3629 time to fit residues: 3.9633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 chunk 98 optimal weight: 8.9990 chunk 76 optimal weight: 5.9990 chunk 114 optimal weight: 0.0670 chunk 75 optimal weight: 6.9990 chunk 134 optimal weight: 4.9990 chunk 84 optimal weight: 8.9990 chunk 82 optimal weight: 9.9990 chunk 62 optimal weight: 20.0000 chunk 83 optimal weight: 7.9990 overall best weight: 3.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN A 310 GLN E 110 GLN ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 11347 Z= 0.348 Angle : 0.657 11.367 15445 Z= 0.331 Chirality : 0.045 0.273 1774 Planarity : 0.005 0.051 1952 Dihedral : 4.708 35.627 1530 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.12 % Favored : 96.81 % Rotamer: Outliers : 4.28 % Allowed : 26.92 % Favored : 68.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.23), residues: 1410 helix: 1.71 (0.25), residues: 410 sheet: 0.68 (0.24), residues: 480 loop : -0.17 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 167 HIS 0.003 0.001 HIS D 193 PHE 0.024 0.002 PHE C 36 TYR 0.024 0.002 TYR C 144 ARG 0.008 0.001 ARG C 72 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1237 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 149 time to evaluate : 1.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 36 residues processed: 194 average time/residue: 1.2308 time to fit residues: 257.9302 Evaluate side-chains 182 residues out of total 1237 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 146 time to evaluate : 1.283 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 31 residues processed: 5 average time/residue: 0.1909 time to fit residues: 3.1565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 2.9990 chunk 80 optimal weight: 7.9990 chunk 40 optimal weight: 40.0000 chunk 26 optimal weight: 0.7980 chunk 85 optimal weight: 50.0000 chunk 91 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 106 optimal weight: 9.9990 chunk 122 optimal weight: 3.9990 chunk 129 optimal weight: 5.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN A 310 GLN E 110 GLN ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 11347 Z= 0.270 Angle : 0.670 13.096 15445 Z= 0.331 Chirality : 0.045 0.372 1774 Planarity : 0.005 0.053 1952 Dihedral : 4.628 34.960 1530 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 4.12 % Allowed : 27.16 % Favored : 68.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.88 % 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: 1.00 (0.23), residues: 1410 helix: 1.67 (0.25), residues: 411 sheet: 0.73 (0.24), residues: 480 loop : -0.11 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C 167 HIS 0.003 0.001 HIS C 38 PHE 0.022 0.002 PHE A 117 TYR 0.025 0.002 TYR F 150 ARG 0.006 0.001 ARG C 72 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1237 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 151 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 37 residues processed: 190 average time/residue: 1.2412 time to fit residues: 254.2900 Evaluate side-chains 187 residues out of total 1237 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 150 time to evaluate : 1.127 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 32 residues processed: 5 average time/residue: 0.1734 time to fit residues: 2.8671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 7.9990 chunk 125 optimal weight: 0.0070 chunk 129 optimal weight: 5.9990 chunk 75 optimal weight: 9.9990 chunk 54 optimal weight: 1.9990 chunk 98 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 118 optimal weight: 20.0000 chunk 82 optimal weight: 7.9990 chunk 132 optimal weight: 7.9990 overall best weight: 4.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN A 310 GLN ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 11347 Z= 0.369 Angle : 0.705 12.877 15445 Z= 0.352 Chirality : 0.047 0.353 1774 Planarity : 0.005 0.062 1952 Dihedral : 4.784 39.138 1530 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 4.04 % Allowed : 27.89 % Favored : 68.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.23), residues: 1410 helix: 1.62 (0.25), residues: 410 sheet: 0.67 (0.24), residues: 480 loop : -0.16 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP C 167 HIS 0.003 0.001 HIS C 38 PHE 0.028 0.002 PHE B 48 TYR 0.024 0.002 TYR E 150 ARG 0.011 0.001 ARG A 231 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2820 Ramachandran restraints generated. 1410 Oldfield, 0 Emsley, 1410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1237 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 152 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 36 residues processed: 193 average time/residue: 1.2584 time to fit residues: 262.4568 Evaluate side-chains 186 residues out of total 1237 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 150 time to evaluate : 1.300 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 33 residues processed: 3 average time/residue: 0.1821 time to fit residues: 2.5336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 62.9905 > 50: distance: 66 - 204: 25.525 distance: 101 - 208: 18.325 distance: 104 - 205: 17.512 distance: 123 - 190: 25.182 distance: 126 - 187: 24.229 distance: 170 - 175: 8.480 distance: 175 - 176: 9.887 distance: 175 - 304: 7.200 distance: 176 - 177: 9.542 distance: 176 - 179: 12.611 distance: 177 - 178: 40.190 distance: 177 - 187: 12.798 distance: 178 - 301: 25.734 distance: 179 - 180: 8.995 distance: 180 - 181: 4.066 distance: 180 - 182: 17.629 distance: 181 - 183: 15.137 distance: 182 - 184: 12.780 distance: 183 - 185: 14.095 distance: 184 - 185: 5.073 distance: 185 - 186: 10.700 distance: 187 - 188: 12.003 distance: 188 - 189: 16.386 distance: 188 - 191: 18.386 distance: 189 - 190: 32.089 distance: 189 - 199: 19.218 distance: 191 - 192: 5.256 distance: 192 - 194: 3.786 distance: 193 - 195: 14.153 distance: 194 - 196: 9.217 distance: 195 - 197: 3.335 distance: 196 - 197: 9.039 distance: 197 - 198: 10.549 distance: 199 - 200: 8.515 distance: 200 - 201: 25.720 distance: 200 - 203: 14.541 distance: 201 - 202: 10.134 distance: 201 - 205: 17.105 distance: 203 - 204: 14.366 distance: 205 - 206: 10.861 distance: 206 - 207: 12.831 distance: 206 - 209: 19.988 distance: 207 - 208: 14.619 distance: 207 - 214: 19.860 distance: 209 - 210: 27.930 distance: 210 - 211: 20.647 distance: 211 - 212: 22.596 distance: 211 - 213: 21.542 distance: 214 - 215: 8.006 distance: 214 - 276: 18.793 distance: 215 - 216: 13.690 distance: 215 - 218: 18.045 distance: 216 - 217: 18.019 distance: 216 - 223: 22.550 distance: 218 - 219: 32.702 distance: 219 - 220: 5.985 distance: 220 - 221: 17.579 distance: 220 - 222: 29.935 distance: 223 - 224: 10.284 distance: 224 - 225: 40.403 distance: 224 - 227: 21.370 distance: 225 - 226: 18.590 distance: 225 - 229: 15.277 distance: 227 - 228: 14.422 distance: 229 - 230: 18.654 distance: 230 - 231: 15.014 distance: 230 - 233: 11.886 distance: 231 - 232: 15.898 distance: 231 - 237: 14.947 distance: 233 - 234: 11.431 distance: 234 - 235: 11.212 distance: 234 - 236: 11.378 distance: 237 - 238: 26.055 distance: 238 - 239: 22.708 distance: 238 - 241: 22.417 distance: 239 - 240: 31.966 distance: 239 - 246: 14.106 distance: 241 - 242: 13.955 distance: 242 - 243: 17.449 distance: 243 - 244: 25.749 distance: 243 - 245: 29.378 distance: 246 - 247: 21.844 distance: 247 - 248: 11.587 distance: 247 - 250: 29.671 distance: 248 - 249: 19.006 distance: 250 - 251: 11.430 distance: 251 - 252: 7.334 distance: 251 - 253: 40.343 distance: 254 - 255: 34.025 distance: 254 - 260: 32.660 distance: 255 - 256: 35.352 distance: 255 - 258: 30.264 distance: 256 - 257: 16.475 distance: 256 - 261: 9.918 distance: 258 - 259: 38.453 distance: 259 - 260: 40.570