Starting phenix.real_space_refine on Sat Jun 7 10:55:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zme_60244/06_2025/8zme_60244_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zme_60244/06_2025/8zme_60244.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zme_60244/06_2025/8zme_60244.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zme_60244/06_2025/8zme_60244.map" model { file = "/net/cci-nas-00/data/ceres_data/8zme_60244/06_2025/8zme_60244_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zme_60244/06_2025/8zme_60244_neut.cif" } resolution = 3.2 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= 0.001 sd= 0.022 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 55 5.16 5 C 5556 2.51 5 N 1452 2.21 5 O 1624 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 8687 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1692 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 3, 'TRANS': 209} Chain breaks: 1 Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 5, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "B" Number of atoms: 2515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2515 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 3, 'ARG:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 60 Chain: "E" Number of atoms: 1772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1772 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "G" Number of atoms: 369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 369 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 35 Chain: "R" Number of atoms: 2339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2339 Classifications: {'peptide': 303} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 11, 'TRANS': 291} Chain breaks: 2 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 72 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 2, 'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 37 Time building chain proxies: 5.42, per 1000 atoms: 0.62 Number of scatterers: 8687 At special positions: 0 Unit cell: (93.5, 116.6, 145.2, 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 55 16.00 O 1624 8.00 N 1452 7.00 C 5556 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS E 160 " - pdb=" SG CYS E 230 " distance=2.06 Simple disulfide: pdb=" SG CYS R 148 " - pdb=" SG CYS R 226 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.15 Conformation dependent library (CDL) restraints added in 1.0 seconds 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2148 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 14 sheets defined 37.4% alpha, 22.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 10 through 31 removed outlier: 4.097A pdb=" N GLU A 14 " --> pdb=" O LYS A 10 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR A 28 " --> pdb=" O SER A 24 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N TYR A 29 " --> pdb=" O ARG A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 52 Processing helix chain 'A' and resid 88 through 92 removed outlier: 3.808A pdb=" N SER A 91 " --> pdb=" O GLY A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 98 Processing helix chain 'A' and resid 117 through 130 removed outlier: 3.763A pdb=" N GLU A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR A 127 " --> pdb=" O ASN A 123 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASN A 130 " --> pdb=" O GLU A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 154 removed outlier: 4.130A pdb=" N GLN A 154 " --> pdb=" O GLU A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 161 removed outlier: 3.606A pdb=" N ASP A 160 " --> pdb=" O SER A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 185 Processing helix chain 'A' and resid 206 through 227 removed outlier: 3.808A pdb=" N LYS A 225 " --> pdb=" O HIS A 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.748A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 3.971A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.719A pdb=" N ASP E 90 " --> pdb=" O ARG E 87 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 87 through 91' Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.707A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.644A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'R' and resid 62 through 70 removed outlier: 3.606A pdb=" N THR R 70 " --> pdb=" O ALA R 66 " (cutoff:3.500A) Processing helix chain 'R' and resid 76 through 103 removed outlier: 4.219A pdb=" N ILE R 80 " --> pdb=" O VAL R 76 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL R 81 " --> pdb=" O PHE R 77 " (cutoff:3.500A) Proline residue: R 91 - end of helix Processing helix chain 'R' and resid 108 through 126 removed outlier: 3.641A pdb=" N ILE R 112 " --> pdb=" O HIS R 108 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE R 126 " --> pdb=" O LEU R 122 " (cutoff:3.500A) Processing helix chain 'R' and resid 127 through 138 removed outlier: 4.058A pdb=" N LYS R 131 " --> pdb=" O TRP R 127 " (cutoff:3.500A) Processing helix chain 'R' and resid 143 through 179 removed outlier: 4.351A pdb=" N LEU R 147 " --> pdb=" O TYR R 143 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N CYS R 148 " --> pdb=" O GLY R 144 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TYR R 156 " --> pdb=" O ILE R 152 " (cutoff:3.500A) Processing helix chain 'R' and resid 187 through 204 Processing helix chain 'R' and resid 205 through 210 Proline residue: R 208 - end of helix No H-bonds generated for 'chain 'R' and resid 205 through 210' Processing helix chain 'R' and resid 232 through 236 removed outlier: 3.693A pdb=" N VAL R 236 " --> pdb=" O GLU R 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 232 through 236' Processing helix chain 'R' and resid 237 through 250 removed outlier: 3.553A pdb=" N ASN R 241 " --> pdb=" O GLY R 237 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL R 250 " --> pdb=" O LEU R 246 " (cutoff:3.500A) Processing helix chain 'R' and resid 251 through 270 Processing helix chain 'R' and resid 275 through 277 No H-bonds generated for 'chain 'R' and resid 275 through 277' Processing helix chain 'R' and resid 278 through 315 removed outlier: 4.239A pdb=" N ARG R 284 " --> pdb=" O LYS R 280 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE R 289 " --> pdb=" O ALA R 285 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR R 291 " --> pdb=" O LYS R 287 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N VAL R 292 " --> pdb=" O LEU R 288 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N MET R 295 " --> pdb=" O THR R 291 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE R 298 " --> pdb=" O ALA R 294 " (cutoff:3.500A) Proline residue: R 302 - end of helix removed outlier: 4.036A pdb=" N LEU R 306 " --> pdb=" O PRO R 302 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU R 313 " --> pdb=" O VAL R 309 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE R 314 " --> pdb=" O HIS R 310 " (cutoff:3.500A) Processing helix chain 'R' and resid 322 through 335 removed outlier: 3.801A pdb=" N LEU R 335 " --> pdb=" O CYS R 331 " (cutoff:3.500A) Processing helix chain 'R' and resid 335 through 345 Proline residue: R 341 - end of helix Processing helix chain 'R' and resid 349 through 358 removed outlier: 3.749A pdb=" N ASP R 353 " --> pdb=" O HIS R 349 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 70 through 76 removed outlier: 6.317A pdb=" N VAL A 34 " --> pdb=" O LYS A 82 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N VAL A 84 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE A 36 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER A 105 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ILE A 106 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N PHE A 142 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N PHE A 108 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N ASN A 144 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N VAL A 110 " --> pdb=" O ASN A 144 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE A 139 " --> pdb=" O TYR A 196 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N HIS A 198 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU A 141 " --> pdb=" O HIS A 198 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N THR A 200 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LEU A 143 " --> pdb=" O THR A 200 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.872A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.864A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.849A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 7.048A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.612A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.997A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.547A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.330A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 141 through 143 Processing sheet with id=AB3, first strand: chain 'E' and resid 147 through 149 removed outlier: 3.614A pdb=" N GLU E 247 " --> pdb=" O VAL E 148 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR E 244 " --> pdb=" O TYR E 228 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LEU E 179 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N LEU E 188 " --> pdb=" O LEU E 179 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'R' and resid 38 through 40 removed outlier: 5.981A pdb=" N LEU R 38 " --> pdb=" O LEU R 230 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'R' and resid 215 through 218 393 hydrogen bonds defined for protein. 1116 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: 2.26 Time building geometry restraints manager: 2.53 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: 2794 1.34 - 1.47: 2263 1.47 - 1.59: 3733 1.59 - 1.72: 0 1.72 - 1.84: 80 Bond restraints: 8870 Sorted by residual: bond pdb=" C LYS A 145 " pdb=" O LYS A 145 " ideal model delta sigma weight residual 1.235 1.282 -0.046 1.26e-02 6.30e+03 1.36e+01 bond pdb=" N THR A 146 " pdb=" CA THR A 146 " ideal model delta sigma weight residual 1.457 1.505 -0.047 1.29e-02 6.01e+03 1.35e+01 bond pdb=" CA LYS A 145 " pdb=" C LYS A 145 " ideal model delta sigma weight residual 1.523 1.562 -0.039 1.34e-02 5.57e+03 8.38e+00 bond pdb=" C TYR R 210 " pdb=" N VAL R 211 " ideal model delta sigma weight residual 1.338 1.309 0.029 1.01e-02 9.80e+03 8.08e+00 bond pdb=" N LYS A 145 " pdb=" CA LYS A 145 " ideal model delta sigma weight residual 1.457 1.493 -0.035 1.29e-02 6.01e+03 7.47e+00 ... (remaining 8865 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 11816 2.49 - 4.99: 224 4.99 - 7.48: 22 7.48 - 9.97: 6 9.97 - 12.46: 1 Bond angle restraints: 12069 Sorted by residual: angle pdb=" N ILE R 126 " pdb=" CA ILE R 126 " pdb=" C ILE R 126 " ideal model delta sigma weight residual 110.53 116.21 -5.68 9.40e-01 1.13e+00 3.65e+01 angle pdb=" N ALA B 203 " pdb=" CA ALA B 203 " pdb=" C ALA B 203 " ideal model delta sigma weight residual 110.61 117.49 -6.88 1.25e+00 6.40e-01 3.03e+01 angle pdb=" C HIS R 227 " pdb=" CA HIS R 227 " pdb=" CB HIS R 227 " ideal model delta sigma weight residual 111.06 102.73 8.33 1.89e+00 2.80e-01 1.94e+01 angle pdb=" N GLN A 191 " pdb=" CA GLN A 191 " pdb=" C GLN A 191 " ideal model delta sigma weight residual 107.67 116.49 -8.82 2.09e+00 2.29e-01 1.78e+01 angle pdb=" N ASN A 144 " pdb=" CA ASN A 144 " pdb=" C ASN A 144 " ideal model delta sigma weight residual 109.95 116.59 -6.64 1.59e+00 3.96e-01 1.74e+01 ... (remaining 12064 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 4863 17.53 - 35.06: 289 35.06 - 52.58: 38 52.58 - 70.11: 14 70.11 - 87.64: 7 Dihedral angle restraints: 5211 sinusoidal: 1886 harmonic: 3325 Sorted by residual: dihedral pdb=" CB CYS E 160 " pdb=" SG CYS E 160 " pdb=" SG CYS E 230 " pdb=" CB CYS E 230 " ideal model delta sinusoidal sigma weight residual 93.00 142.72 -49.72 1 1.00e+01 1.00e-02 3.39e+01 dihedral pdb=" CA VAL R 125 " pdb=" C VAL R 125 " pdb=" N ILE R 126 " pdb=" CA ILE R 126 " ideal model delta harmonic sigma weight residual -180.00 -160.22 -19.78 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA GLY B 202 " pdb=" C GLY B 202 " pdb=" N ALA B 203 " pdb=" CA ALA B 203 " ideal model delta harmonic sigma weight residual 180.00 -160.36 -19.64 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 5208 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1067 0.057 - 0.114: 293 0.114 - 0.170: 49 0.170 - 0.227: 3 0.227 - 0.284: 1 Chirality restraints: 1413 Sorted by residual: chirality pdb=" CA ALA B 203 " pdb=" N ALA B 203 " pdb=" C ALA B 203 " pdb=" CB ALA B 203 " both_signs ideal model delta sigma weight residual False 2.48 2.20 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CA PHE B 292 " pdb=" N PHE B 292 " pdb=" C PHE B 292 " pdb=" CB PHE B 292 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA LYS A 145 " pdb=" N LYS A 145 " pdb=" C LYS A 145 " pdb=" CB LYS A 145 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.57e-01 ... (remaining 1410 not shown) Planarity restraints: 1526 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP R 127 " -0.018 2.00e-02 2.50e+03 1.73e-02 7.45e+00 pdb=" CG TRP R 127 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP R 127 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP R 127 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP R 127 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP R 127 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP R 127 " -0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 127 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 127 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP R 127 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 155 " 0.021 2.00e-02 2.50e+03 2.02e-02 7.13e+00 pdb=" CG PHE R 155 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE R 155 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE R 155 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE R 155 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE R 155 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE R 155 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE R 128 " -0.040 5.00e-02 4.00e+02 6.03e-02 5.82e+00 pdb=" N PRO R 129 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO R 129 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO R 129 " -0.034 5.00e-02 4.00e+02 ... (remaining 1523 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 46 2.58 - 3.16: 7016 3.16 - 3.74: 11924 3.74 - 4.32: 16170 4.32 - 4.90: 28204 Nonbonded interactions: 63360 Sorted by model distance: nonbonded pdb=" O LYS A 145 " pdb=" OG1 THR A 201 " model vdw 2.000 3.040 nonbonded pdb=" O ASN G 24 " pdb=" OD1 ASN G 24 " model vdw 2.158 3.040 nonbonded pdb=" OG SER E 17 " pdb=" O MET E 83 " model vdw 2.182 3.040 nonbonded pdb=" O ASP B 333 " pdb=" OG SER B 334 " model vdw 2.225 3.040 nonbonded pdb=" O GLY E 8 " pdb=" NH2 ARG E 18 " model vdw 2.290 3.120 ... (remaining 63355 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: 1.460 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: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 22.240 Find NCS groups from input model: 0.120 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.049 8872 Z= 0.342 Angle : 0.870 12.465 12073 Z= 0.511 Chirality : 0.052 0.284 1413 Planarity : 0.005 0.060 1526 Dihedral : 12.335 87.640 3057 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.71 (0.24), residues: 1125 helix: 0.52 (0.28), residues: 354 sheet: 0.18 (0.30), residues: 281 loop : -1.62 (0.25), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP R 127 HIS 0.007 0.002 HIS B 183 PHE 0.047 0.003 PHE R 155 TYR 0.025 0.003 TYR R 296 ARG 0.010 0.001 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.16351 ( 393) hydrogen bonds : angle 6.72936 ( 1116) SS BOND : bond 0.01849 ( 2) SS BOND : angle 1.79565 ( 4) covalent geometry : bond 0.00751 ( 8870) covalent geometry : angle 0.86942 (12069) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.902 Fit side-chains revert: symmetry clash REVERT: A 69 ILE cc_start: 0.8371 (mm) cc_final: 0.8136 (mt) REVERT: B 29 THR cc_start: 0.8219 (t) cc_final: 0.7818 (p) REVERT: B 271 CYS cc_start: 0.7314 (m) cc_final: 0.7108 (m) REVERT: E 90 ASP cc_start: 0.8657 (m-30) cc_final: 0.8158 (m-30) REVERT: R 73 LEU cc_start: 0.7448 (mt) cc_final: 0.7194 (mt) REVERT: R 277 ASN cc_start: 0.7777 (m-40) cc_final: 0.7493 (m110) REVERT: R 291 THR cc_start: 0.7824 (t) cc_final: 0.7596 (p) outliers start: 0 outliers final: 0 residues processed: 182 average time/residue: 0.2361 time to fit residues: 57.0824 Evaluate side-chains 164 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 47 optimal weight: 0.3980 chunk 28 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 184 GLN R 172 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.138538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.113690 restraints weight = 12840.834| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 2.87 r_work: 0.3337 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8872 Z= 0.173 Angle : 0.638 9.075 12073 Z= 0.345 Chirality : 0.045 0.138 1413 Planarity : 0.005 0.063 1526 Dihedral : 5.040 25.466 1221 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.56 % Favored : 96.36 % Rotamer: Outliers : 1.20 % Allowed : 6.43 % Favored : 92.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.19 (0.25), residues: 1125 helix: 1.34 (0.28), residues: 369 sheet: 0.34 (0.30), residues: 272 loop : -1.60 (0.26), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP R 127 HIS 0.004 0.001 HIS B 183 PHE 0.024 0.002 PHE R 155 TYR 0.032 0.002 TYR R 296 ARG 0.005 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.06814 ( 393) hydrogen bonds : angle 4.79606 ( 1116) SS BOND : bond 0.01309 ( 2) SS BOND : angle 1.18258 ( 4) covalent geometry : bond 0.00387 ( 8870) covalent geometry : angle 0.63775 (12069) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 170 time to evaluate : 1.059 Fit side-chains revert: symmetry clash REVERT: A 82 LYS cc_start: 0.8212 (ttmm) cc_final: 0.7773 (ttmm) REVERT: A 116 ASN cc_start: 0.8859 (m-40) cc_final: 0.8516 (m-40) REVERT: B 137 ARG cc_start: 0.7818 (tpt170) cc_final: 0.7586 (tpt170) REVERT: B 271 CYS cc_start: 0.7613 (m) cc_final: 0.7394 (m) REVERT: E 90 ASP cc_start: 0.8776 (m-30) cc_final: 0.8267 (m-30) REVERT: E 141 MET cc_start: 0.8781 (mmt) cc_final: 0.8449 (mmm) REVERT: E 178 PHE cc_start: 0.8228 (m-80) cc_final: 0.7987 (m-80) REVERT: E 231 MET cc_start: 0.7473 (ttm) cc_final: 0.7259 (ttm) REVERT: E 234 LEU cc_start: 0.8383 (tp) cc_final: 0.8136 (tp) REVERT: R 73 LEU cc_start: 0.7486 (mt) cc_final: 0.7241 (mt) outliers start: 11 outliers final: 8 residues processed: 172 average time/residue: 0.2341 time to fit residues: 53.6692 Evaluate side-chains 173 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 165 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 184 GLN Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain R residue 159 MET Chi-restraints excluded: chain R residue 216 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 90 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 110 optimal weight: 0.3980 chunk 36 optimal weight: 0.8980 chunk 26 optimal weight: 0.0870 chunk 28 optimal weight: 0.7980 chunk 53 optimal weight: 0.5980 chunk 95 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 GLN E 184 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.139450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.114049 restraints weight = 12847.641| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.98 r_work: 0.3338 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8872 Z= 0.141 Angle : 0.594 12.753 12073 Z= 0.317 Chirality : 0.044 0.148 1413 Planarity : 0.004 0.064 1526 Dihedral : 4.781 25.640 1221 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.18 % Favored : 95.73 % Rotamer: Outliers : 2.18 % Allowed : 9.26 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.12 (0.25), residues: 1125 helix: 1.75 (0.28), residues: 369 sheet: 0.46 (0.30), residues: 282 loop : -1.57 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 127 HIS 0.003 0.001 HIS B 183 PHE 0.018 0.002 PHE R 155 TYR 0.024 0.002 TYR R 296 ARG 0.006 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.06112 ( 393) hydrogen bonds : angle 4.45721 ( 1116) SS BOND : bond 0.01135 ( 2) SS BOND : angle 0.81644 ( 4) covalent geometry : bond 0.00304 ( 8870) covalent geometry : angle 0.59411 (12069) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 168 time to evaluate : 0.955 Fit side-chains revert: symmetry clash REVERT: A 46 LYS cc_start: 0.7331 (OUTLIER) cc_final: 0.6959 (tttp) REVERT: A 82 LYS cc_start: 0.8220 (ttmm) cc_final: 0.7796 (ttmm) REVERT: A 116 ASN cc_start: 0.8936 (m-40) cc_final: 0.8659 (m-40) REVERT: B 271 CYS cc_start: 0.7663 (m) cc_final: 0.7418 (m) REVERT: E 90 ASP cc_start: 0.8817 (m-30) cc_final: 0.8279 (m-30) REVERT: E 178 PHE cc_start: 0.8166 (m-80) cc_final: 0.7936 (m-80) REVERT: E 220 LEU cc_start: 0.7753 (mm) cc_final: 0.7504 (mp) REVERT: E 234 LEU cc_start: 0.8394 (tp) cc_final: 0.8151 (tp) REVERT: R 73 LEU cc_start: 0.7462 (mt) cc_final: 0.7201 (mt) REVERT: R 277 ASN cc_start: 0.7794 (m110) cc_final: 0.7473 (m110) outliers start: 20 outliers final: 14 residues processed: 174 average time/residue: 0.2882 time to fit residues: 66.5788 Evaluate side-chains 175 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 160 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain R residue 80 ILE Chi-restraints excluded: chain R residue 132 ILE Chi-restraints excluded: chain R residue 159 MET Chi-restraints excluded: chain R residue 170 SER Chi-restraints excluded: chain R residue 190 ILE Chi-restraints excluded: chain R residue 204 LEU Chi-restraints excluded: chain R residue 216 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 45 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 67 optimal weight: 7.9990 chunk 27 optimal weight: 0.5980 chunk 98 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 184 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.137109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.111854 restraints weight = 12918.640| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.97 r_work: 0.3265 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8872 Z= 0.186 Angle : 0.630 10.177 12073 Z= 0.336 Chirality : 0.045 0.143 1413 Planarity : 0.005 0.066 1526 Dihedral : 4.852 27.033 1221 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.18 % Favored : 95.73 % Rotamer: Outliers : 2.51 % Allowed : 11.00 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.06 (0.25), residues: 1125 helix: 1.75 (0.28), residues: 369 sheet: 0.36 (0.32), residues: 263 loop : -1.53 (0.26), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.004 0.001 HIS A 197 PHE 0.026 0.002 PHE R 155 TYR 0.031 0.002 TYR R 296 ARG 0.005 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.06733 ( 393) hydrogen bonds : angle 4.48850 ( 1116) SS BOND : bond 0.01362 ( 2) SS BOND : angle 0.90211 ( 4) covalent geometry : bond 0.00432 ( 8870) covalent geometry : angle 0.62964 (12069) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 167 time to evaluate : 1.338 Fit side-chains revert: symmetry clash REVERT: A 46 LYS cc_start: 0.7309 (OUTLIER) cc_final: 0.6956 (tttp) REVERT: A 82 LYS cc_start: 0.8220 (ttmm) cc_final: 0.7765 (ttmm) REVERT: A 116 ASN cc_start: 0.8975 (m-40) cc_final: 0.8724 (m-40) REVERT: B 179 THR cc_start: 0.8449 (p) cc_final: 0.8231 (t) REVERT: B 271 CYS cc_start: 0.7735 (m) cc_final: 0.7456 (m) REVERT: E 90 ASP cc_start: 0.8789 (m-30) cc_final: 0.8244 (m-30) REVERT: E 220 LEU cc_start: 0.7807 (mm) cc_final: 0.7583 (mp) REVERT: E 234 LEU cc_start: 0.8323 (tp) cc_final: 0.8057 (tp) REVERT: R 73 LEU cc_start: 0.7429 (mt) cc_final: 0.7171 (mt) REVERT: R 277 ASN cc_start: 0.7851 (m110) cc_final: 0.7448 (m110) outliers start: 23 outliers final: 17 residues processed: 174 average time/residue: 0.2804 time to fit residues: 64.6041 Evaluate side-chains 179 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 161 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 184 GLN Chi-restraints excluded: chain R residue 80 ILE Chi-restraints excluded: chain R residue 132 ILE Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain R residue 159 MET Chi-restraints excluded: chain R residue 190 ILE Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain R residue 274 MET Chi-restraints excluded: chain R residue 313 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 45 optimal weight: 0.0050 chunk 41 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 184 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.137346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.111907 restraints weight = 12757.083| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 3.01 r_work: 0.3316 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8872 Z= 0.160 Angle : 0.599 9.433 12073 Z= 0.321 Chirality : 0.044 0.137 1413 Planarity : 0.004 0.066 1526 Dihedral : 4.784 27.720 1221 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.09 % Favored : 95.82 % Rotamer: Outliers : 2.51 % Allowed : 12.42 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 (0.25), residues: 1125 helix: 1.90 (0.28), residues: 370 sheet: 0.41 (0.32), residues: 261 loop : -1.54 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 127 HIS 0.004 0.001 HIS A 197 PHE 0.019 0.002 PHE R 155 TYR 0.027 0.002 TYR R 296 ARG 0.002 0.000 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.06244 ( 393) hydrogen bonds : angle 4.36323 ( 1116) SS BOND : bond 0.01276 ( 2) SS BOND : angle 0.80102 ( 4) covalent geometry : bond 0.00365 ( 8870) covalent geometry : angle 0.59922 (12069) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 171 time to evaluate : 0.889 Fit side-chains revert: symmetry clash REVERT: A 46 LYS cc_start: 0.7406 (OUTLIER) cc_final: 0.7034 (tttp) REVERT: A 82 LYS cc_start: 0.8240 (ttmm) cc_final: 0.7804 (ttmm) REVERT: A 116 ASN cc_start: 0.8986 (m-40) cc_final: 0.8736 (m-40) REVERT: B 179 THR cc_start: 0.8460 (p) cc_final: 0.8256 (t) REVERT: B 271 CYS cc_start: 0.7743 (m) cc_final: 0.7482 (m) REVERT: E 90 ASP cc_start: 0.8772 (m-30) cc_final: 0.8237 (m-30) REVERT: E 220 LEU cc_start: 0.7808 (mm) cc_final: 0.7602 (mp) REVERT: E 234 LEU cc_start: 0.8425 (tp) cc_final: 0.8167 (tp) REVERT: R 73 LEU cc_start: 0.7435 (mt) cc_final: 0.7174 (mt) REVERT: R 268 MET cc_start: 0.7627 (tmm) cc_final: 0.7210 (tmm) REVERT: R 269 LEU cc_start: 0.7650 (mt) cc_final: 0.6836 (mp) REVERT: R 277 ASN cc_start: 0.7871 (m110) cc_final: 0.7479 (m110) outliers start: 23 outliers final: 17 residues processed: 179 average time/residue: 0.2360 time to fit residues: 58.2816 Evaluate side-chains 184 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 166 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 184 GLN Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain R residue 80 ILE Chi-restraints excluded: chain R residue 132 ILE Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain R residue 159 MET Chi-restraints excluded: chain R residue 190 ILE Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain R residue 274 MET Chi-restraints excluded: chain R residue 313 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 66 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 82 optimal weight: 0.0770 chunk 12 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 184 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.138731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.114095 restraints weight = 12636.120| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.85 r_work: 0.3303 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8872 Z= 0.145 Angle : 0.579 8.608 12073 Z= 0.311 Chirality : 0.043 0.137 1413 Planarity : 0.004 0.066 1526 Dihedral : 4.711 27.415 1221 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.27 % Favored : 95.64 % Rotamer: Outliers : 2.18 % Allowed : 13.51 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.25 (0.25), residues: 1125 helix: 2.03 (0.28), residues: 371 sheet: 0.45 (0.32), residues: 260 loop : -1.52 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 127 HIS 0.003 0.001 HIS A 197 PHE 0.018 0.002 PHE B 199 TYR 0.025 0.002 TYR R 296 ARG 0.004 0.000 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.05915 ( 393) hydrogen bonds : angle 4.27142 ( 1116) SS BOND : bond 0.01209 ( 2) SS BOND : angle 0.76386 ( 4) covalent geometry : bond 0.00326 ( 8870) covalent geometry : angle 0.57901 (12069) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 168 time to evaluate : 1.395 Fit side-chains revert: symmetry clash REVERT: A 46 LYS cc_start: 0.7221 (OUTLIER) cc_final: 0.6865 (tttp) REVERT: A 82 LYS cc_start: 0.8205 (ttmm) cc_final: 0.7735 (ttmm) REVERT: A 116 ASN cc_start: 0.8962 (m-40) cc_final: 0.8732 (m-40) REVERT: A 216 LYS cc_start: 0.7139 (ttpt) cc_final: 0.6864 (mtpt) REVERT: B 271 CYS cc_start: 0.7703 (m) cc_final: 0.7352 (m) REVERT: E 90 ASP cc_start: 0.8774 (m-30) cc_final: 0.8164 (m-30) REVERT: E 220 LEU cc_start: 0.7740 (mm) cc_final: 0.7538 (mp) REVERT: E 231 MET cc_start: 0.7487 (ttm) cc_final: 0.7212 (ttm) REVERT: E 234 LEU cc_start: 0.8358 (tp) cc_final: 0.8095 (tp) REVERT: R 73 LEU cc_start: 0.7380 (mt) cc_final: 0.7155 (mt) REVERT: R 269 LEU cc_start: 0.7382 (mt) cc_final: 0.7145 (mp) REVERT: R 277 ASN cc_start: 0.7823 (m110) cc_final: 0.7370 (m110) outliers start: 20 outliers final: 16 residues processed: 175 average time/residue: 0.2988 time to fit residues: 73.8169 Evaluate side-chains 182 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 165 time to evaluate : 1.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain R residue 80 ILE Chi-restraints excluded: chain R residue 132 ILE Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain R residue 159 MET Chi-restraints excluded: chain R residue 190 ILE Chi-restraints excluded: chain R residue 216 ILE Chi-restraints excluded: chain R residue 274 MET Chi-restraints excluded: chain R residue 313 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 58 optimal weight: 0.3980 chunk 24 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 43 optimal weight: 0.2980 chunk 89 optimal weight: 0.2980 chunk 9 optimal weight: 0.0570 chunk 26 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 111 optimal weight: 0.7980 overall best weight: 0.3298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 184 GLN R 116 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.141493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.116798 restraints weight = 12857.491| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.88 r_work: 0.3390 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8872 Z= 0.111 Angle : 0.533 7.535 12073 Z= 0.285 Chirality : 0.042 0.139 1413 Planarity : 0.004 0.065 1526 Dihedral : 4.418 25.690 1221 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.85 % Allowed : 13.62 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.56 (0.25), residues: 1125 helix: 2.33 (0.28), residues: 370 sheet: 0.54 (0.30), residues: 292 loop : -1.44 (0.27), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 127 HIS 0.003 0.001 HIS E 35 PHE 0.020 0.001 PHE R 77 TYR 0.017 0.001 TYR R 296 ARG 0.002 0.000 ARG B 137 Details of bonding type rmsd hydrogen bonds : bond 0.04795 ( 393) hydrogen bonds : angle 4.04415 ( 1116) SS BOND : bond 0.00898 ( 2) SS BOND : angle 0.72040 ( 4) covalent geometry : bond 0.00230 ( 8870) covalent geometry : angle 0.53248 (12069) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 167 time to evaluate : 0.914 Fit side-chains revert: symmetry clash REVERT: A 46 LYS cc_start: 0.7393 (ttmm) cc_final: 0.7054 (tttp) REVERT: A 82 LYS cc_start: 0.8223 (ttmm) cc_final: 0.7799 (ttmm) REVERT: A 216 LYS cc_start: 0.7156 (ttpt) cc_final: 0.6861 (mtpt) REVERT: B 200 VAL cc_start: 0.8179 (m) cc_final: 0.7851 (p) REVERT: B 271 CYS cc_start: 0.7683 (m) cc_final: 0.7390 (m) REVERT: E 90 ASP cc_start: 0.8720 (m-30) cc_final: 0.8132 (m-30) REVERT: E 220 LEU cc_start: 0.7733 (mm) cc_final: 0.7524 (mp) REVERT: E 234 LEU cc_start: 0.8420 (tp) cc_final: 0.8210 (tp) REVERT: R 73 LEU cc_start: 0.7354 (mt) cc_final: 0.7121 (mt) REVERT: R 176 VAL cc_start: 0.7057 (t) cc_final: 0.6665 (t) REVERT: R 277 ASN cc_start: 0.7817 (m110) cc_final: 0.7369 (m110) outliers start: 17 outliers final: 14 residues processed: 174 average time/residue: 0.2050 time to fit residues: 48.9320 Evaluate side-chains 179 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 165 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain R residue 80 ILE Chi-restraints excluded: chain R residue 132 ILE Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain R residue 190 ILE Chi-restraints excluded: chain R residue 274 MET Chi-restraints excluded: chain R residue 313 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 84 optimal weight: 0.2980 chunk 23 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 82 optimal weight: 0.0470 chunk 0 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 4 optimal weight: 0.4980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 220 GLN E 184 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.141215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.116279 restraints weight = 12917.929| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.90 r_work: 0.3380 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8872 Z= 0.128 Angle : 0.554 8.250 12073 Z= 0.295 Chirality : 0.043 0.137 1413 Planarity : 0.004 0.065 1526 Dihedral : 4.430 25.582 1221 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.00 % Favored : 95.91 % Rotamer: Outliers : 1.74 % Allowed : 14.60 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.63 (0.26), residues: 1125 helix: 2.38 (0.28), residues: 370 sheet: 0.61 (0.31), residues: 277 loop : -1.35 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 127 HIS 0.003 0.001 HIS A 197 PHE 0.018 0.002 PHE R 77 TYR 0.022 0.002 TYR R 296 ARG 0.004 0.000 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.05243 ( 393) hydrogen bonds : angle 4.07378 ( 1116) SS BOND : bond 0.01051 ( 2) SS BOND : angle 0.71919 ( 4) covalent geometry : bond 0.00283 ( 8870) covalent geometry : angle 0.55354 (12069) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 163 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.7408 (ttmm) cc_final: 0.7059 (tttp) REVERT: A 82 LYS cc_start: 0.8231 (ttmm) cc_final: 0.7793 (ttmm) REVERT: A 216 LYS cc_start: 0.7164 (ttpt) cc_final: 0.6881 (mtpt) REVERT: B 200 VAL cc_start: 0.8160 (m) cc_final: 0.7820 (p) REVERT: B 271 CYS cc_start: 0.7694 (m) cc_final: 0.7418 (m) REVERT: E 90 ASP cc_start: 0.8746 (m-30) cc_final: 0.8159 (m-30) REVERT: E 220 LEU cc_start: 0.7708 (mm) cc_final: 0.7481 (mp) REVERT: E 234 LEU cc_start: 0.8426 (tp) cc_final: 0.8193 (tp) REVERT: R 73 LEU cc_start: 0.7360 (mt) cc_final: 0.7123 (mt) REVERT: R 155 PHE cc_start: 0.6143 (OUTLIER) cc_final: 0.5592 (t80) REVERT: R 176 VAL cc_start: 0.7149 (t) cc_final: 0.6782 (t) REVERT: R 269 LEU cc_start: 0.7597 (mt) cc_final: 0.7348 (mp) REVERT: R 277 ASN cc_start: 0.7925 (m110) cc_final: 0.7464 (m110) outliers start: 16 outliers final: 14 residues processed: 170 average time/residue: 0.2065 time to fit residues: 48.3257 Evaluate side-chains 176 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 161 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 184 GLN Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain R residue 80 ILE Chi-restraints excluded: chain R residue 132 ILE Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain R residue 155 PHE Chi-restraints excluded: chain R residue 190 ILE Chi-restraints excluded: chain R residue 274 MET Chi-restraints excluded: chain R residue 313 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 102 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 21 optimal weight: 0.0040 chunk 14 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 184 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.139134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.114499 restraints weight = 12892.409| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.89 r_work: 0.3361 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8872 Z= 0.153 Angle : 0.573 7.413 12073 Z= 0.307 Chirality : 0.043 0.133 1413 Planarity : 0.004 0.065 1526 Dihedral : 4.525 25.939 1221 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.18 % Allowed : 13.94 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 0.56 (0.25), residues: 1125 helix: 2.29 (0.28), residues: 370 sheet: 0.49 (0.31), residues: 278 loop : -1.31 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 127 HIS 0.004 0.001 HIS A 197 PHE 0.020 0.002 PHE E 68 TYR 0.027 0.002 TYR R 296 ARG 0.004 0.000 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.05754 ( 393) hydrogen bonds : angle 4.15317 ( 1116) SS BOND : bond 0.01136 ( 2) SS BOND : angle 0.71504 ( 4) covalent geometry : bond 0.00352 ( 8870) covalent geometry : angle 0.57326 (12069) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2250 Ramachandran restraints generated. 1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 166 time to evaluate : 0.979 Fit side-chains revert: symmetry clash REVERT: A 46 LYS cc_start: 0.7471 (ttmm) cc_final: 0.7116 (tttp) REVERT: A 82 LYS cc_start: 0.8217 (ttmm) cc_final: 0.7762 (ttmm) REVERT: A 216 LYS cc_start: 0.7258 (ttpt) cc_final: 0.6981 (mtpt) REVERT: B 200 VAL cc_start: 0.8166 (m) cc_final: 0.7811 (p) REVERT: B 271 CYS cc_start: 0.7724 (m) cc_final: 0.7441 (m) REVERT: E 90 ASP cc_start: 0.8773 (m-30) cc_final: 0.8206 (m-30) REVERT: E 220 LEU cc_start: 0.7711 (mm) cc_final: 0.7467 (mp) REVERT: E 234 LEU cc_start: 0.8425 (tp) cc_final: 0.8190 (tp) REVERT: R 73 LEU cc_start: 0.7359 (mt) cc_final: 0.7129 (mt) REVERT: R 155 PHE cc_start: 0.6174 (OUTLIER) cc_final: 0.5679 (t80) REVERT: R 269 LEU cc_start: 0.7611 (mt) cc_final: 0.7119 (mp) REVERT: R 277 ASN cc_start: 0.8065 (m110) cc_final: 0.7576 (m110) outliers start: 20 outliers final: 17 residues processed: 175 average time/residue: 0.2039 time to fit residues: 49.0802 Evaluate side-chains 184 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 166 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 207 SER Chi-restraints excluded: chain R residue 80 ILE Chi-restraints excluded: chain R residue 132 ILE Chi-restraints excluded: chain R residue 142 ILE Chi-restraints excluded: chain R residue 155 PHE Chi-restraints excluded: chain R residue 190 ILE Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 274 MET Chi-restraints excluded: chain R residue 313 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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: 50.7969 > 50: distance: 17 - 22: 7.197 distance: 22 - 23: 16.846 distance: 23 - 24: 8.558 distance: 23 - 26: 6.273 distance: 24 - 25: 7.871 distance: 24 - 30: 11.835 distance: 25 - 52: 10.807 distance: 26 - 27: 23.054 distance: 27 - 28: 9.720 distance: 27 - 29: 16.584 distance: 30 - 31: 18.191 distance: 31 - 32: 10.566 distance: 31 - 34: 19.589 distance: 32 - 33: 32.441 distance: 32 - 35: 13.218 distance: 33 - 61: 8.634 distance: 35 - 36: 8.600 distance: 36 - 37: 21.339 distance: 36 - 39: 17.414 distance: 37 - 38: 9.695 distance: 37 - 43: 29.313 distance: 38 - 66: 25.278 distance: 39 - 40: 30.712 distance: 40 - 41: 12.065 distance: 40 - 42: 40.169 distance: 43 - 44: 6.567 distance: 44 - 45: 11.049 distance: 44 - 47: 13.432 distance: 45 - 46: 19.028 distance: 45 - 52: 15.176 distance: 48 - 49: 12.020 distance: 49 - 50: 12.305 distance: 49 - 51: 7.907 distance: 52 - 53: 10.769 distance: 53 - 54: 25.369 distance: 53 - 56: 23.927 distance: 54 - 55: 31.601 distance: 54 - 61: 30.754 distance: 56 - 57: 16.440 distance: 57 - 58: 14.351 distance: 58 - 59: 14.542 distance: 58 - 60: 32.650 distance: 61 - 62: 21.898 distance: 62 - 63: 6.804 distance: 62 - 65: 25.666 distance: 63 - 64: 4.491 distance: 63 - 66: 6.805 distance: 66 - 67: 11.477 distance: 67 - 68: 17.618 distance: 67 - 70: 5.783 distance: 68 - 69: 10.464 distance: 68 - 73: 8.101 distance: 70 - 71: 25.418 distance: 70 - 72: 25.630 distance: 73 - 74: 10.281 distance: 74 - 75: 7.678 distance: 74 - 77: 11.431 distance: 75 - 76: 24.831 distance: 75 - 78: 12.055 distance: 78 - 79: 14.926 distance: 79 - 80: 4.787 distance: 79 - 82: 14.363 distance: 80 - 81: 22.239 distance: 80 - 86: 11.387 distance: 82 - 83: 20.452 distance: 82 - 84: 8.931 distance: 83 - 85: 23.672 distance: 86 - 87: 9.579 distance: 87 - 88: 7.675 distance: 87 - 90: 7.233 distance: 88 - 89: 5.306 distance: 88 - 93: 11.913 distance: 90 - 91: 8.626 distance: 90 - 92: 17.741