Starting phenix.real_space_refine on Wed Jan 15 04:15:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8id9_35360/01_2025/8id9_35360.cif Found real_map, /net/cci-nas-00/data/ceres_data/8id9_35360/01_2025/8id9_35360.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8id9_35360/01_2025/8id9_35360.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8id9_35360/01_2025/8id9_35360.map" model { file = "/net/cci-nas-00/data/ceres_data/8id9_35360/01_2025/8id9_35360.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8id9_35360/01_2025/8id9_35360.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.007 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 46 5.16 5 C 5148 2.51 5 N 1364 2.21 5 O 1438 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 7996 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2448 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 5, 'TRANS': 328} Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 5, 'ARG:plan': 4, 'ASN:plan1': 3, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 91 Chain: "Y" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 372 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "S" Number of atoms: 1661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1661 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 216} Chain breaks: 1 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 6, 'ARG:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 64 Chain: "A" Number of atoms: 1429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1429 Classifications: {'peptide': 197} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'TRANS': 196} Chain breaks: 5 Unresolved non-hydrogen bonds: 165 Unresolved non-hydrogen angles: 197 Unresolved non-hydrogen dihedrals: 133 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 10, 'ARG:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 11} Unresolved non-hydrogen planarities: 98 Chain: "R" Number of atoms: 2064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2064 Classifications: {'peptide': 282} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 11, 'TRANS': 270} Chain breaks: 5 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 185 Unresolved non-hydrogen angles: 240 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 2, 'GLU:plan': 3, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 88 Chain: "R" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'EPA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.87, per 1000 atoms: 0.61 Number of scatterers: 7996 At special positions: 0 Unit cell: (103.428, 126.75, 111.54, 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 46 16.00 O 1438 8.00 N 1364 7.00 C 5148 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS S 160 " - pdb=" SG CYS S 230 " distance=2.04 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: 2.07 Conformation dependent library (CDL) restraints added in 1.1 seconds 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2052 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 12 sheets defined 35.9% alpha, 21.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'B' and resid 8 through 24 removed outlier: 3.501A pdb=" N ARG B 19 " --> pdb=" O LYS B 15 " (cutoff:3.500A) Processing helix chain 'Y' and resid 9 through 24 Processing helix chain 'Y' and resid 29 through 44 removed outlier: 3.565A pdb=" N CYS Y 41 " --> pdb=" O LEU Y 37 " (cutoff:3.500A) Processing helix chain 'Y' and resid 55 through 59 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.979A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 31 removed outlier: 3.718A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 removed outlier: 4.108A pdb=" N GLN A 52 " --> pdb=" O THR A 48 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N MET A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 216 Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 271 through 276 removed outlier: 4.087A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 309 Processing helix chain 'A' and resid 329 through 351 removed outlier: 3.650A pdb=" N GLN A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'R' and resid 35 through 71 removed outlier: 3.585A pdb=" N GLU R 43 " --> pdb=" O LEU R 39 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU R 64 " --> pdb=" O CYS R 60 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL R 65 " --> pdb=" O ALA R 61 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG R 67 " --> pdb=" O VAL R 63 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ARG R 68 " --> pdb=" O LEU R 64 " (cutoff:3.500A) Processing helix chain 'R' and resid 78 through 90 removed outlier: 3.920A pdb=" N LEU R 86 " --> pdb=" O PHE R 82 " (cutoff:3.500A) Processing helix chain 'R' and resid 91 through 100 removed outlier: 3.695A pdb=" N TRP R 100 " --> pdb=" O LEU R 96 " (cutoff:3.500A) Processing helix chain 'R' and resid 107 through 140 removed outlier: 3.626A pdb=" N CYS R 111 " --> pdb=" O GLY R 107 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU R 113 " --> pdb=" O VAL R 109 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N PHE R 115 " --> pdb=" O CYS R 111 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N TYR R 116 " --> pdb=" O HIS R 112 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET R 118 " --> pdb=" O LEU R 114 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER R 123 " --> pdb=" O THR R 119 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE R 140 " --> pdb=" O ARG R 136 " (cutoff:3.500A) Processing helix chain 'R' and resid 152 through 170 removed outlier: 3.579A pdb=" N VAL R 168 " --> pdb=" O GLY R 164 " (cutoff:3.500A) Processing helix chain 'R' and resid 170 through 176 removed outlier: 3.957A pdb=" N CYS R 174 " --> pdb=" O ALA R 170 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N PHE R 176 " --> pdb=" O PRO R 172 " (cutoff:3.500A) Processing helix chain 'R' and resid 200 through 243 removed outlier: 3.513A pdb=" N TRP R 207 " --> pdb=" O GLY R 203 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASP R 208 " --> pdb=" O GLU R 204 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU R 214 " --> pdb=" O SER R 210 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASN R 215 " --> pdb=" O PHE R 211 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N VAL R 218 " --> pdb=" O LEU R 214 " (cutoff:3.500A) Proline residue: R 219 - end of helix Processing helix chain 'R' and resid 249 through 251 No H-bonds generated for 'chain 'R' and resid 249 through 251' Processing helix chain 'R' and resid 252 through 276 removed outlier: 3.529A pdb=" N GLN R 257 " --> pdb=" O ILE R 253 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU R 262 " --> pdb=" O GLN R 258 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N PHE R 273 " --> pdb=" O LEU R 269 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N PHE R 274 " --> pdb=" O MET R 270 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N MET R 276 " --> pdb=" O SER R 272 " (cutoff:3.500A) Processing helix chain 'R' and resid 277 through 293 removed outlier: 3.871A pdb=" N ILE R 281 " --> pdb=" O TRP R 277 " (cutoff:3.500A) Processing helix chain 'R' and resid 301 through 312 Processing helix chain 'R' and resid 312 through 322 Proline residue: R 318 - end of helix Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.561A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.173A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.887A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.501A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.768A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.680A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 277 removed outlier: 3.540A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'S' and resid 10 through 11 removed outlier: 6.327A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 141 through 142 removed outlier: 3.686A pdb=" N ALA S 212 " --> pdb=" O SER S 209 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 195 through 196 removed outlier: 5.685A pdb=" N LEU S 188 " --> pdb=" O LEU S 179 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU S 179 " --> pdb=" O LEU S 188 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE S 190 " --> pdb=" O TRP S 177 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.765A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) 402 hydrogen bonds defined for protein. 1125 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: 2.24 Time building geometry restraints manager: 2.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1254 1.29 - 1.42: 2211 1.42 - 1.55: 4623 1.55 - 1.68: 5 1.68 - 1.81: 66 Bond restraints: 8159 Sorted by residual: bond pdb=" CA ASN R 322 " pdb=" C ASN R 322 " ideal model delta sigma weight residual 1.523 1.426 0.097 1.34e-02 5.57e+03 5.21e+01 bond pdb=" CA ARG R 70 " pdb=" CB ARG R 70 " ideal model delta sigma weight residual 1.531 1.434 0.097 1.56e-02 4.11e+03 3.86e+01 bond pdb=" C ARG R 238 " pdb=" O ARG R 238 " ideal model delta sigma weight residual 1.236 1.159 0.077 1.29e-02 6.01e+03 3.59e+01 bond pdb=" C ARG R 70 " pdb=" O ARG R 70 " ideal model delta sigma weight residual 1.237 1.163 0.074 1.31e-02 5.83e+03 3.19e+01 bond pdb=" N ASN R 322 " pdb=" CA ASN R 322 " ideal model delta sigma weight residual 1.457 1.388 0.070 1.29e-02 6.01e+03 2.90e+01 ... (remaining 8154 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 10860 2.00 - 4.01: 198 4.01 - 6.01: 34 6.01 - 8.01: 15 8.01 - 10.01: 7 Bond angle restraints: 11114 Sorted by residual: angle pdb=" N LEU R 316 " pdb=" CA LEU R 316 " pdb=" C LEU R 316 " ideal model delta sigma weight residual 111.36 120.65 -9.29 1.09e+00 8.42e-01 7.26e+01 angle pdb=" N VAL R 175 " pdb=" CA VAL R 175 " pdb=" C VAL R 175 " ideal model delta sigma weight residual 110.62 118.42 -7.80 1.02e+00 9.61e-01 5.85e+01 angle pdb=" N VAL R 141 " pdb=" CA VAL R 141 " pdb=" C VAL R 141 " ideal model delta sigma weight residual 113.53 106.06 7.47 9.80e-01 1.04e+00 5.80e+01 angle pdb=" N VAL R 65 " pdb=" CA VAL R 65 " pdb=" C VAL R 65 " ideal model delta sigma weight residual 113.53 107.27 6.26 9.80e-01 1.04e+00 4.08e+01 angle pdb=" C LEU R 171 " pdb=" N PRO R 172 " pdb=" CA PRO R 172 " ideal model delta sigma weight residual 119.84 114.13 5.71 1.25e+00 6.40e-01 2.09e+01 ... (remaining 11109 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 4300 18.00 - 36.00: 343 36.00 - 54.00: 72 54.00 - 72.00: 7 72.00 - 89.99: 6 Dihedral angle restraints: 4728 sinusoidal: 1566 harmonic: 3162 Sorted by residual: dihedral pdb=" CD ARG R 238 " pdb=" NE ARG R 238 " pdb=" CZ ARG R 238 " pdb=" NH1 ARG R 238 " ideal model delta sinusoidal sigma weight residual 0.00 68.48 -68.48 1 1.00e+01 1.00e-02 6.08e+01 dihedral pdb=" CD ARG R 254 " pdb=" NE ARG R 254 " pdb=" CZ ARG R 254 " pdb=" NH1 ARG R 254 " ideal model delta sinusoidal sigma weight residual 0.00 -53.39 53.39 1 1.00e+01 1.00e-02 3.87e+01 dihedral pdb=" CB CYS S 160 " pdb=" SG CYS S 160 " pdb=" SG CYS S 230 " pdb=" CB CYS S 230 " ideal model delta sinusoidal sigma weight residual 93.00 130.52 -37.52 1 1.00e+01 1.00e-02 1.99e+01 ... (remaining 4725 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1192 0.076 - 0.152: 128 0.152 - 0.228: 8 0.228 - 0.304: 2 0.304 - 0.380: 1 Chirality restraints: 1331 Sorted by residual: chirality pdb=" CA LEU R 171 " pdb=" N LEU R 171 " pdb=" C LEU R 171 " pdb=" CB LEU R 171 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.62e+00 chirality pdb=" CA LEU R 316 " pdb=" N LEU R 316 " pdb=" C LEU R 316 " pdb=" CB LEU R 316 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CA ARG R 238 " pdb=" N ARG R 238 " pdb=" C ARG R 238 " pdb=" CB ARG R 238 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 1328 not shown) Planarity restraints: 1393 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG R 238 " 1.011 9.50e-02 1.11e+02 4.53e-01 1.24e+02 pdb=" NE ARG R 238 " -0.061 2.00e-02 2.50e+03 pdb=" CZ ARG R 238 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG R 238 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG R 238 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG R 254 " 0.865 9.50e-02 1.11e+02 3.88e-01 9.13e+01 pdb=" NE ARG R 254 " -0.053 2.00e-02 2.50e+03 pdb=" CZ ARG R 254 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG R 254 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG R 254 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP S 74 " -0.074 5.00e-02 4.00e+02 1.10e-01 1.92e+01 pdb=" N PRO S 75 " 0.189 5.00e-02 4.00e+02 pdb=" CA PRO S 75 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO S 75 " -0.059 5.00e-02 4.00e+02 ... (remaining 1390 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 412 2.73 - 3.27: 7745 3.27 - 3.81: 12969 3.81 - 4.36: 15217 4.36 - 4.90: 27164 Nonbonded interactions: 63507 Sorted by model distance: nonbonded pdb=" OG1 THR B 86 " pdb=" OD1 ASN B 88 " model vdw 2.182 3.040 nonbonded pdb=" O LEU R 87 " pdb=" OG SER R 90 " model vdw 2.213 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.228 3.040 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.230 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.234 3.040 ... (remaining 63502 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.340 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 21.190 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 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 : 0.005 0.097 8159 Z= 0.313 Angle : 0.732 10.014 11114 Z= 0.424 Chirality : 0.047 0.380 1331 Planarity : 0.017 0.453 1393 Dihedral : 13.948 89.995 2673 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.13 % Allowed : 6.12 % Favored : 93.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.21 (0.26), residues: 1063 helix: 0.70 (0.28), residues: 356 sheet: 0.30 (0.32), residues: 282 loop : -1.10 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 104 HIS 0.002 0.001 HIS B 91 PHE 0.019 0.001 PHE R 263 TYR 0.008 0.001 TYR S 191 ARG 0.005 0.001 ARG S 18 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 132 time to evaluate : 0.919 Fit side-chains REVERT: A 53 MET cc_start: 0.5715 (mmm) cc_final: 0.5334 (mmm) REVERT: R 290 GLN cc_start: 0.8340 (pp30) cc_final: 0.8099 (pp30) outliers start: 1 outliers final: 0 residues processed: 133 average time/residue: 1.1610 time to fit residues: 164.4488 Evaluate side-chains 115 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 45 optimal weight: 0.0030 chunk 27 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 83 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 8.9990 chunk 62 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN A 255 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.101164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.078796 restraints weight = 15335.080| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.60 r_work: 0.3023 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8159 Z= 0.166 Angle : 0.557 7.440 11114 Z= 0.293 Chirality : 0.042 0.136 1331 Planarity : 0.005 0.070 1393 Dihedral : 5.118 51.774 1169 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.56 % Allowed : 12.24 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.15 (0.26), residues: 1063 helix: 1.26 (0.28), residues: 358 sheet: 0.36 (0.31), residues: 276 loop : -1.04 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 104 HIS 0.003 0.001 HIS B 142 PHE 0.015 0.001 PHE R 176 TYR 0.013 0.001 TYR S 191 ARG 0.006 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 125 time to evaluate : 0.863 Fit side-chains REVERT: B 228 ASP cc_start: 0.8466 (p0) cc_final: 0.7945 (p0) REVERT: Y 62 ARG cc_start: 0.7990 (mtm180) cc_final: 0.7708 (mtt90) REVERT: A 53 MET cc_start: 0.5479 (mmm) cc_final: 0.5170 (mmm) REVERT: A 243 MET cc_start: 0.8651 (tpp) cc_final: 0.8066 (mpp) REVERT: R 25 PHE cc_start: 0.8622 (t80) cc_final: 0.8420 (t80) REVERT: R 238 ARG cc_start: 0.8367 (mmm-85) cc_final: 0.8065 (tpt170) REVERT: R 290 GLN cc_start: 0.8752 (pp30) cc_final: 0.8355 (pp30) outliers start: 12 outliers final: 4 residues processed: 131 average time/residue: 1.3786 time to fit residues: 190.3589 Evaluate side-chains 121 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 117 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain R residue 135 GLU Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 271 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 73 optimal weight: 0.0010 chunk 30 optimal weight: 7.9990 chunk 90 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 80 optimal weight: 20.0000 chunk 74 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 34 optimal weight: 20.0000 overall best weight: 1.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN A 255 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.099163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.076603 restraints weight = 15499.053| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.47 r_work: 0.2942 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8159 Z= 0.285 Angle : 0.569 7.812 11114 Z= 0.301 Chirality : 0.043 0.151 1331 Planarity : 0.005 0.064 1393 Dihedral : 5.129 49.318 1169 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.43 % Allowed : 14.84 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.21 (0.26), residues: 1063 helix: 1.38 (0.28), residues: 358 sheet: 0.32 (0.31), residues: 278 loop : -1.03 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 104 HIS 0.003 0.001 HIS S 35 PHE 0.012 0.002 PHE B 151 TYR 0.012 0.001 TYR S 191 ARG 0.003 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 117 time to evaluate : 1.078 Fit side-chains REVERT: B 59 TYR cc_start: 0.8575 (m-80) cc_final: 0.8138 (m-80) REVERT: B 226 GLU cc_start: 0.7956 (pm20) cc_final: 0.7732 (pm20) REVERT: B 280 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8294 (ttpp) REVERT: A 53 MET cc_start: 0.5789 (mmm) cc_final: 0.5312 (mmm) REVERT: A 242 ARG cc_start: 0.7999 (mpt180) cc_final: 0.7494 (mpp-170) REVERT: R 25 PHE cc_start: 0.8542 (t80) cc_final: 0.8298 (t80) REVERT: R 238 ARG cc_start: 0.8258 (mmm-85) cc_final: 0.7917 (tpt170) REVERT: R 290 GLN cc_start: 0.8746 (pp30) cc_final: 0.8312 (pp30) outliers start: 11 outliers final: 4 residues processed: 125 average time/residue: 1.3519 time to fit residues: 178.6209 Evaluate side-chains 118 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 113 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain R residue 135 GLU Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 271 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 44 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 12 optimal weight: 0.0670 chunk 94 optimal weight: 0.0030 chunk 78 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 34 optimal weight: 0.2980 chunk 63 optimal weight: 0.8980 overall best weight: 0.4530 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN B 220 GLN S 77 ASN A 255 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.101852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.079405 restraints weight = 15421.682| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.49 r_work: 0.3009 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8159 Z= 0.136 Angle : 0.499 8.339 11114 Z= 0.261 Chirality : 0.040 0.130 1331 Planarity : 0.005 0.054 1393 Dihedral : 4.794 48.529 1169 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.82 % Allowed : 15.36 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.54 (0.26), residues: 1063 helix: 1.78 (0.28), residues: 358 sheet: 0.42 (0.31), residues: 283 loop : -0.92 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 104 HIS 0.002 0.000 HIS A 244 PHE 0.010 0.001 PHE A 189 TYR 0.012 0.001 TYR S 191 ARG 0.010 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 0.893 Fit side-chains REVERT: B 228 ASP cc_start: 0.8394 (p0) cc_final: 0.7946 (p0) REVERT: B 280 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8189 (ttpp) REVERT: Y 47 GLU cc_start: 0.8181 (mp0) cc_final: 0.7923 (mp0) REVERT: S 82 GLN cc_start: 0.8425 (tp40) cc_final: 0.8223 (mm-40) REVERT: A 242 ARG cc_start: 0.8218 (mpt180) cc_final: 0.7662 (mpp-170) REVERT: A 304 GLN cc_start: 0.9189 (tm-30) cc_final: 0.8706 (tm-30) REVERT: R 25 PHE cc_start: 0.8483 (t80) cc_final: 0.8222 (t80) REVERT: R 238 ARG cc_start: 0.8292 (mmm-85) cc_final: 0.7961 (tpt170) REVERT: R 290 GLN cc_start: 0.8728 (pp30) cc_final: 0.8282 (pp30) outliers start: 14 outliers final: 5 residues processed: 129 average time/residue: 1.3278 time to fit residues: 180.8166 Evaluate side-chains 119 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 113 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain R residue 135 GLU Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 256 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 82 optimal weight: 0.9980 chunk 102 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 96 optimal weight: 0.5980 chunk 38 optimal weight: 6.9990 chunk 100 optimal weight: 1.9990 chunk 86 optimal weight: 10.0000 chunk 37 optimal weight: 0.5980 chunk 105 optimal weight: 0.8980 chunk 60 optimal weight: 7.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN B 220 GLN R 291 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.101271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.078701 restraints weight = 15267.582| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.50 r_work: 0.2990 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8159 Z= 0.162 Angle : 0.510 8.968 11114 Z= 0.265 Chirality : 0.041 0.178 1331 Planarity : 0.005 0.054 1393 Dihedral : 4.669 46.701 1169 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.95 % Allowed : 15.62 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.61 (0.26), residues: 1063 helix: 1.90 (0.28), residues: 358 sheet: 0.37 (0.30), residues: 279 loop : -0.85 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 104 HIS 0.002 0.001 HIS A 244 PHE 0.011 0.001 PHE A 189 TYR 0.012 0.001 TYR S 191 ARG 0.010 0.000 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.902 Fit side-chains REVERT: B 226 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7725 (pm20) REVERT: B 228 ASP cc_start: 0.8422 (p0) cc_final: 0.8174 (p0) REVERT: B 280 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8212 (ttpp) REVERT: Y 47 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7910 (mp0) REVERT: A 243 MET cc_start: 0.8633 (tpp) cc_final: 0.8142 (mpp) REVERT: A 304 GLN cc_start: 0.9168 (tm-30) cc_final: 0.8680 (tm-30) REVERT: R 25 PHE cc_start: 0.8522 (t80) cc_final: 0.8231 (t80) REVERT: R 290 GLN cc_start: 0.8808 (pp30) cc_final: 0.8360 (pp30) outliers start: 15 outliers final: 7 residues processed: 127 average time/residue: 1.3502 time to fit residues: 181.2483 Evaluate side-chains 123 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 113 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain Y residue 47 GLU Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain R residue 135 GLU Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 256 SER Chi-restraints excluded: chain R residue 319 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 24 optimal weight: 0.0060 chunk 46 optimal weight: 10.0000 chunk 79 optimal weight: 0.8980 chunk 68 optimal weight: 5.9990 chunk 94 optimal weight: 0.8980 chunk 55 optimal weight: 0.4980 chunk 95 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN B 220 GLN A 255 ASN R 291 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.101796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.079167 restraints weight = 15318.191| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.54 r_work: 0.2997 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8159 Z= 0.148 Angle : 0.513 8.329 11114 Z= 0.265 Chirality : 0.040 0.149 1331 Planarity : 0.004 0.054 1393 Dihedral : 4.597 46.253 1169 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.34 % Allowed : 17.19 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.69 (0.26), residues: 1063 helix: 2.03 (0.28), residues: 354 sheet: 0.49 (0.30), residues: 274 loop : -0.88 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 104 HIS 0.002 0.000 HIS S 35 PHE 0.014 0.001 PHE R 177 TYR 0.011 0.001 TYR S 191 ARG 0.011 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 1.143 Fit side-chains REVERT: B 228 ASP cc_start: 0.8422 (p0) cc_final: 0.8167 (p0) REVERT: Y 47 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7868 (mp0) REVERT: S 187 GLN cc_start: 0.9019 (tt0) cc_final: 0.8819 (pt0) REVERT: A 241 ASN cc_start: 0.7114 (p0) cc_final: 0.6711 (t0) REVERT: A 242 ARG cc_start: 0.8007 (mpt180) cc_final: 0.7793 (mpp-170) REVERT: A 243 MET cc_start: 0.8682 (tpp) cc_final: 0.8020 (mpp) REVERT: A 304 GLN cc_start: 0.9124 (tm-30) cc_final: 0.8658 (tm-30) REVERT: R 25 PHE cc_start: 0.8520 (t80) cc_final: 0.8215 (t80) REVERT: R 238 ARG cc_start: 0.8372 (mmm-85) cc_final: 0.7869 (tpt170) REVERT: R 290 GLN cc_start: 0.8812 (pp30) cc_final: 0.8345 (pp30) REVERT: R 291 ASN cc_start: 0.8767 (t0) cc_final: 0.8561 (t160) outliers start: 18 outliers final: 9 residues processed: 134 average time/residue: 1.3550 time to fit residues: 191.9529 Evaluate side-chains 126 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain Y residue 42 GLU Chi-restraints excluded: chain Y residue 47 GLU Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain R residue 135 GLU Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 256 SER Chi-restraints excluded: chain R residue 324 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 77 optimal weight: 0.5980 chunk 66 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 13 optimal weight: 8.9990 chunk 31 optimal weight: 0.7980 chunk 15 optimal weight: 5.9990 chunk 105 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 GLN B 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.101601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.078963 restraints weight = 15337.925| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.53 r_work: 0.2994 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8159 Z= 0.164 Angle : 0.522 8.502 11114 Z= 0.269 Chirality : 0.041 0.133 1331 Planarity : 0.004 0.057 1393 Dihedral : 4.559 45.718 1169 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.60 % Allowed : 17.32 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.75 (0.26), residues: 1063 helix: 2.11 (0.28), residues: 355 sheet: 0.50 (0.30), residues: 281 loop : -0.89 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 104 HIS 0.002 0.000 HIS S 35 PHE 0.010 0.001 PHE A 189 TYR 0.011 0.001 TYR S 191 ARG 0.011 0.001 ARG A 208 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2126 Ramachandran restraints generated. 1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.939 Fit side-chains REVERT: B 226 GLU cc_start: 0.8110 (pm20) cc_final: 0.7849 (pm20) REVERT: B 228 ASP cc_start: 0.8421 (p0) cc_final: 0.8156 (p0) REVERT: Y 47 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7858 (mp0) REVERT: S 18 ARG cc_start: 0.9102 (tpp80) cc_final: 0.8842 (tpp80) REVERT: A 186 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7871 (mm-30) REVERT: A 242 ARG cc_start: 0.7952 (mpt180) cc_final: 0.7613 (mpp-170) REVERT: A 304 GLN cc_start: 0.9109 (tm-30) cc_final: 0.8654 (tm-30) REVERT: R 25 PHE cc_start: 0.8509 (t80) cc_final: 0.8202 (t80) REVERT: R 290 GLN cc_start: 0.8839 (pp30) cc_final: 0.8374 (pp30) REVERT: R 291 ASN cc_start: 0.8739 (t0) cc_final: 0.8530 (t160) outliers start: 20 outliers final: 10 residues processed: 130 average time/residue: 1.2777 time to fit residues: 176.0257 Evaluate side-chains 125 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain Y residue 42 GLU Chi-restraints excluded: chain Y residue 47 GLU Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain R residue 135 GLU Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 256 SER Chi-restraints excluded: chain R residue 319 ILE Chi-restraints excluded: chain R residue 324 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.5362 > 50: distance: 6 - 11: 28.193 distance: 11 - 12: 17.099 distance: 11 - 17: 46.341 distance: 12 - 13: 57.092 distance: 13 - 14: 56.679 distance: 13 - 18: 33.476 distance: 15 - 16: 56.323 distance: 19 - 20: 57.740 distance: 20 - 21: 39.320 distance: 20 - 25: 19.644 distance: 22 - 24: 40.550 distance: 25 - 26: 44.154 distance: 26 - 27: 59.101 distance: 26 - 29: 38.588 distance: 27 - 28: 20.295 distance: 27 - 32: 60.870 distance: 29 - 30: 44.884 distance: 29 - 31: 39.163 distance: 32 - 33: 46.822 distance: 32 - 38: 40.092 distance: 33 - 34: 32.785 distance: 33 - 36: 42.911 distance: 34 - 35: 44.070 distance: 34 - 39: 20.336 distance: 36 - 37: 56.333 distance: 39 - 40: 37.012 distance: 40 - 41: 54.103 distance: 41 - 42: 68.025 distance: 43 - 44: 54.778 distance: 44 - 45: 38.913 distance: 44 - 47: 35.621 distance: 45 - 46: 33.026 distance: 45 - 48: 43.325 distance: 48 - 49: 4.034 distance: 49 - 50: 11.943 distance: 49 - 52: 10.547 distance: 50 - 51: 36.774 distance: 50 - 54: 40.514 distance: 52 - 53: 67.933 distance: 54 - 55: 31.386 distance: 54 - 107: 35.088 distance: 55 - 56: 51.876 distance: 55 - 58: 40.420 distance: 56 - 57: 40.568 distance: 56 - 61: 37.702 distance: 57 - 104: 28.600 distance: 58 - 59: 53.849 distance: 61 - 62: 27.957 distance: 62 - 63: 39.681 distance: 62 - 65: 22.084 distance: 63 - 64: 45.183 distance: 63 - 67: 40.814 distance: 65 - 66: 32.252 distance: 67 - 68: 55.689 distance: 67 - 95: 35.077 distance: 68 - 69: 27.521 distance: 68 - 71: 8.059 distance: 69 - 70: 31.672 distance: 69 - 75: 29.811 distance: 70 - 92: 36.030 distance: 71 - 72: 42.112 distance: 71 - 73: 41.688 distance: 72 - 74: 12.134