Starting phenix.real_space_refine on Wed Jun 18 03:37:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vqw_21359/06_2025/6vqw_21359.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vqw_21359/06_2025/6vqw_21359.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vqw_21359/06_2025/6vqw_21359.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vqw_21359/06_2025/6vqw_21359.map" model { file = "/net/cci-nas-00/data/ceres_data/6vqw_21359/06_2025/6vqw_21359.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vqw_21359/06_2025/6vqw_21359.cif" } resolution = 3.42 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= 0.016 sd= 0.098 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: 5 Type Number sf(0) Gaussians P 39 5.49 5 S 17 5.16 5 C 12609 2.51 5 N 3779 2.21 5 O 4035 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 20479 Number of models: 1 Model: "" Number of chains: 11 Chain: "C" Number of atoms: 2309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2309 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 22, 'TRANS': 274} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 2272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2272 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 10, 'TRANS': 282} Chain breaks: 2 Chain: "E" Number of atoms: 2575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2575 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 320} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 2587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2587 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 12, 'TRANS': 321} Chain: "G" Number of atoms: 2559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2559 Classifications: {'peptide': 331} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 318} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 2516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2516 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 2523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2523 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 313} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "J" Number of atoms: 350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 350 Classifications: {'peptide': 87} Incomplete info: {'backbone_only': 80} Link IDs: {'PTRANS': 6, 'TRANS': 80} Chain breaks: 1 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 353 Unresolved non-hydrogen angles: 506 Unresolved non-hydrogen dihedrals: 225 Unresolved non-hydrogen chiralities: 101 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 7, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 176 Chain: "A" Number of atoms: 552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 552 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 1, 'TRANS': 78} Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 58 Chain: "B" Number of atoms: 1391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1391 Classifications: {'peptide': 242} Incomplete info: {'backbone_only': 133} Link IDs: {'PTRANS': 16, 'TRANS': 225} Chain breaks: 2 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 616 Unresolved non-hydrogen angles: 885 Unresolved non-hydrogen dihedrals: 410 Unresolved non-hydrogen chiralities: 163 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 5, 'ASP:plan': 7, 'PHE:plan': 5, 'GLU:plan': 13, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 347 Chain: "K" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 845 Classifications: {'RNA': 40} Modifications used: {'5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 10, 'rna3p_pur': 11, 'rna3p_pyr': 10} Link IDs: {'rna2p': 18, 'rna3p': 21} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 17.79, per 1000 atoms: 0.87 Number of scatterers: 20479 At special positions: 0 Unit cell: (106, 138.86, 151.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 17 16.00 P 39 15.00 O 4035 8.00 N 3779 7.00 C 12609 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.81 Conformation dependent library (CDL) restraints added in 3.6 seconds 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4504 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 38 sheets defined 26.2% alpha, 14.2% beta 0 base pairs and 10 stacking pairs defined. Time for finding SS restraints: 6.80 Creating SS restraints... Processing helix chain 'C' and resid 33 through 48 removed outlier: 3.949A pdb=" N PHE C 37 " --> pdb=" O SER C 33 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL C 41 " --> pdb=" O PHE C 37 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N HIS C 42 " --> pdb=" O THR C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 134 removed outlier: 3.690A pdb=" N VAL C 130 " --> pdb=" O ILE C 126 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN C 131 " --> pdb=" O ALA C 127 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLU C 132 " --> pdb=" O ARG C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 178 removed outlier: 3.752A pdb=" N ARG C 174 " --> pdb=" O ARG C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 200 removed outlier: 4.400A pdb=" N LEU C 193 " --> pdb=" O ARG C 189 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLN C 194 " --> pdb=" O GLU C 190 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN C 195 " --> pdb=" O ALA C 191 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N GLU C 198 " --> pdb=" O GLN C 194 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR C 199 " --> pdb=" O GLN C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 213 Processing helix chain 'D' and resid 50 through 54 removed outlier: 3.770A pdb=" N SER D 54 " --> pdb=" O ARG D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 147 removed outlier: 4.083A pdb=" N LYS D 135 " --> pdb=" O ALA D 131 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP D 146 " --> pdb=" O THR D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 162 removed outlier: 3.640A pdb=" N ASN D 159 " --> pdb=" O ARG D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 223 removed outlier: 3.597A pdb=" N LEU D 216 " --> pdb=" O ALA D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 282 removed outlier: 3.608A pdb=" N ILE D 278 " --> pdb=" O HIS D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 331 Processing helix chain 'D' and resid 337 through 351 removed outlier: 4.057A pdb=" N TYR D 343 " --> pdb=" O GLU D 339 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG D 350 " --> pdb=" O ALA D 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 145 removed outlier: 4.161A pdb=" N LYS E 135 " --> pdb=" O ALA E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 162 Processing helix chain 'E' and resid 208 through 222 removed outlier: 3.854A pdb=" N ALA E 212 " --> pdb=" O ALA E 208 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU E 213 " --> pdb=" O GLU E 209 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU E 216 " --> pdb=" O ALA E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 283 removed outlier: 3.684A pdb=" N ARG E 283 " --> pdb=" O GLY E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 322 through 331 Processing helix chain 'E' and resid 337 through 351 removed outlier: 3.664A pdb=" N HIS E 342 " --> pdb=" O VAL E 338 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR E 343 " --> pdb=" O GLU E 339 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 91 Processing helix chain 'F' and resid 129 through 147 removed outlier: 3.791A pdb=" N ALA F 141 " --> pdb=" O LEU F 137 " (cutoff:3.500A) Processing helix chain 'F' and resid 151 through 162 removed outlier: 3.683A pdb=" N ASN F 159 " --> pdb=" O ARG F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 222 removed outlier: 3.841A pdb=" N GLU F 215 " --> pdb=" O ASP F 211 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU F 216 " --> pdb=" O ALA F 212 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N SER F 219 " --> pdb=" O GLU F 215 " (cutoff:3.500A) Processing helix chain 'F' and resid 276 through 283 removed outlier: 3.760A pdb=" N ALA F 281 " --> pdb=" O LYS F 277 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG F 283 " --> pdb=" O GLY F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 331 removed outlier: 3.734A pdb=" N ASP F 327 " --> pdb=" O TYR F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 351 removed outlier: 4.546A pdb=" N TYR F 343 " --> pdb=" O GLU F 339 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL F 344 " --> pdb=" O GLN F 340 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE F 345 " --> pdb=" O GLN F 341 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 51 Processing helix chain 'G' and resid 81 through 91 removed outlier: 3.615A pdb=" N LEU G 85 " --> pdb=" O ASP G 81 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASP G 86 " --> pdb=" O PRO G 82 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA G 87 " --> pdb=" O ALA G 83 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER G 91 " --> pdb=" O ALA G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 129 through 147 removed outlier: 3.686A pdb=" N GLN G 147 " --> pdb=" O TYR G 143 " (cutoff:3.500A) Processing helix chain 'G' and resid 155 through 162 Processing helix chain 'G' and resid 211 through 223 removed outlier: 3.637A pdb=" N LEU G 216 " --> pdb=" O ALA G 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 322 through 327 Processing helix chain 'G' and resid 337 through 350 removed outlier: 4.937A pdb=" N TYR G 343 " --> pdb=" O GLU G 339 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE G 345 " --> pdb=" O GLN G 341 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA G 346 " --> pdb=" O HIS G 342 " (cutoff:3.500A) Processing helix chain 'H' and resid 81 through 90 removed outlier: 4.062A pdb=" N ASP H 86 " --> pdb=" O PRO H 82 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ALA H 87 " --> pdb=" O ALA H 83 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN H 90 " --> pdb=" O ASP H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 129 through 147 removed outlier: 3.773A pdb=" N LYS H 135 " --> pdb=" O ALA H 131 " (cutoff:3.500A) Processing helix chain 'H' and resid 149 through 162 removed outlier: 3.610A pdb=" N ARG H 155 " --> pdb=" O GLU H 151 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N HIS H 158 " --> pdb=" O ARG H 154 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASN H 159 " --> pdb=" O ARG H 155 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LEU H 160 " --> pdb=" O TYR H 156 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN H 162 " --> pdb=" O HIS H 158 " (cutoff:3.500A) Processing helix chain 'H' and resid 209 through 222 removed outlier: 3.628A pdb=" N LEU H 213 " --> pdb=" O GLU H 209 " (cutoff:3.500A) Processing helix chain 'H' and resid 274 through 283 removed outlier: 3.646A pdb=" N ILE H 278 " --> pdb=" O HIS H 274 " (cutoff:3.500A) Processing helix chain 'H' and resid 292 through 296 removed outlier: 4.047A pdb=" N LEU H 295 " --> pdb=" O GLU H 292 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLY H 296 " --> pdb=" O ASP H 293 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 292 through 296' Processing helix chain 'H' and resid 322 through 327 removed outlier: 4.077A pdb=" N ASP H 327 " --> pdb=" O TYR H 323 " (cutoff:3.500A) Processing helix chain 'H' and resid 337 through 350 removed outlier: 3.922A pdb=" N HIS H 342 " --> pdb=" O VAL H 338 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR H 343 " --> pdb=" O GLU H 339 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU H 348 " --> pdb=" O VAL H 344 " (cutoff:3.500A) Processing helix chain 'I' and resid 50 through 54 removed outlier: 3.569A pdb=" N SER I 54 " --> pdb=" O ARG I 51 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 90 removed outlier: 4.007A pdb=" N ASP I 86 " --> pdb=" O PRO I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 131 through 145 removed outlier: 3.790A pdb=" N LYS I 135 " --> pdb=" O ALA I 131 " (cutoff:3.500A) Processing helix chain 'I' and resid 151 through 157 Processing helix chain 'I' and resid 157 through 162 Processing helix chain 'I' and resid 209 through 223 Processing helix chain 'I' and resid 274 through 283 removed outlier: 3.925A pdb=" N ALA I 281 " --> pdb=" O LYS I 277 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG I 283 " --> pdb=" O GLY I 279 " (cutoff:3.500A) Processing helix chain 'I' and resid 321 through 331 removed outlier: 3.713A pdb=" N ASP I 327 " --> pdb=" O TYR I 323 " (cutoff:3.500A) Processing helix chain 'I' and resid 337 through 351 Processing helix chain 'J' and resid 16 through 24 removed outlier: 4.468A pdb=" N MET J 21 " --> pdb=" O PRO J 17 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER J 22 " --> pdb=" O ALA J 18 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 69 Processing helix chain 'J' and resid 73 through 77 removed outlier: 3.912A pdb=" N LEU J 76 " --> pdb=" O ARG J 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 73 Processing helix chain 'B' and resid 199 through 211 removed outlier: 4.644A pdb=" N ALA B 209 " --> pdb=" O LEU B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 217 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 304 through 306 No H-bonds generated for 'chain 'B' and resid 304 through 306' Processing helix chain 'B' and resid 319 through 339 removed outlier: 3.841A pdb=" N ALA B 333 " --> pdb=" O ILE B 329 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LEU B 334 " --> pdb=" O CYS B 330 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN B 335 " --> pdb=" O ASP B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 395 removed outlier: 4.185A pdb=" N ALA B 392 " --> pdb=" O GLY B 388 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASN B 393 " --> pdb=" O ASN B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 433 removed outlier: 3.644A pdb=" N GLU B 432 " --> pdb=" O ILE B 428 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG B 433 " --> pdb=" O LEU B 429 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 8 through 11 removed outlier: 3.596A pdb=" N LEU C 159 " --> pdb=" O LEU C 9 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU C 11 " --> pdb=" O ALA C 157 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA C 157 " --> pdb=" O LEU C 11 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 65 through 68 removed outlier: 3.975A pdb=" N LEU C 105 " --> pdb=" O ILE C 17 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 70 through 71 Processing sheet with id=AA4, first strand: chain 'C' and resid 186 through 188 removed outlier: 7.495A pdb=" N PHE C 279 " --> pdb=" O ALA C 257 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ALA C 257 " --> pdb=" O PHE C 279 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N GLU C 281 " --> pdb=" O TYR C 255 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N TYR C 255 " --> pdb=" O GLU C 281 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N LEU C 283 " --> pdb=" O ALA C 253 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N VAL C 249 " --> pdb=" O GLY C 287 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 186 through 188 Processing sheet with id=AA6, first strand: chain 'D' and resid 30 through 32 Processing sheet with id=AA7, first strand: chain 'D' and resid 42 through 44 removed outlier: 3.735A pdb=" N LYS D 110 " --> pdb=" O SER D 44 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL D 117 " --> pdb=" O VAL D 227 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N VAL D 227 " --> pdb=" O VAL D 117 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU D 228 " --> pdb=" O ILE D 183 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASN D 181 " --> pdb=" O GLU D 230 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 62 through 64 Processing sheet with id=AA9, first strand: chain 'D' and resid 247 through 248 Processing sheet with id=AB1, first strand: chain 'E' and resid 30 through 31 removed outlier: 4.070A pdb=" N ALA E 126 " --> pdb=" O ALA E 31 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 42 through 46 removed outlier: 3.752A pdb=" N VAL E 117 " --> pdb=" O VAL E 227 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N VAL E 227 " --> pdb=" O VAL E 117 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA E 175 " --> pdb=" O ARG E 236 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 62 through 68 Processing sheet with id=AB4, first strand: chain 'F' and resid 126 through 127 removed outlier: 3.736A pdb=" N ALA F 126 " --> pdb=" O ALA F 31 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 37 through 38 removed outlier: 3.594A pdb=" N VAL F 117 " --> pdb=" O VAL F 227 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N VAL F 227 " --> pdb=" O VAL F 117 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU F 228 " --> pdb=" O ILE F 183 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 37 through 38 Processing sheet with id=AB7, first strand: chain 'F' and resid 63 through 64 Processing sheet with id=AB8, first strand: chain 'F' and resid 67 through 68 Processing sheet with id=AB9, first strand: chain 'F' and resid 284 through 286 Processing sheet with id=AC1, first strand: chain 'G' and resid 31 through 32 Processing sheet with id=AC2, first strand: chain 'G' and resid 37 through 38 Processing sheet with id=AC3, first strand: chain 'G' and resid 37 through 38 removed outlier: 4.289A pdb=" N VAL G 227 " --> pdb=" O VAL G 117 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 63 through 64 Processing sheet with id=AC5, first strand: chain 'G' and resid 284 through 286 Processing sheet with id=AC6, first strand: chain 'H' and resid 30 through 32 removed outlier: 3.638A pdb=" N LEU H 30 " --> pdb=" O PHE H 354 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 37 through 38 removed outlier: 3.975A pdb=" N VAL H 227 " --> pdb=" O VAL H 117 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LEU H 228 " --> pdb=" O ILE H 183 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG H 190 " --> pdb=" O HIS H 182 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 37 through 38 removed outlier: 3.671A pdb=" N ALA H 41 " --> pdb=" O ILE H 273 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 63 through 64 removed outlier: 4.356A pdb=" N ALA H 100 " --> pdb=" O VAL H 243 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 284 through 286 Processing sheet with id=AD2, first strand: chain 'H' and resid 304 through 305 Processing sheet with id=AD3, first strand: chain 'I' and resid 30 through 32 Processing sheet with id=AD4, first strand: chain 'I' and resid 41 through 46 removed outlier: 3.970A pdb=" N LEU I 228 " --> pdb=" O ILE I 183 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE I 183 " --> pdb=" O LEU I 228 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL I 178 " --> pdb=" O ARG I 193 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ARG I 193 " --> pdb=" O VAL I 178 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE I 180 " --> pdb=" O ALA I 191 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ALA I 191 " --> pdb=" O ILE I 180 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N HIS I 182 " --> pdb=" O ALA I 189 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 63 through 64 Processing sheet with id=AD6, first strand: chain 'I' and resid 67 through 69 Processing sheet with id=AD7, first strand: chain 'I' and resid 247 through 248 removed outlier: 4.534A pdb=" N THR I 263 " --> pdb=" O GLU I 248 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 284 through 286 Processing sheet with id=AD9, first strand: chain 'J' and resid 42 through 43 Processing sheet with id=AE1, first strand: chain 'A' and resid 23 through 24 Processing sheet with id=AE2, first strand: chain 'B' and resid 239 through 241 removed outlier: 3.877A pdb=" N GLN B 241 " --> pdb=" O ASN B 262 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ASN B 262 " --> pdb=" O GLN B 241 " (cutoff:3.500A) 621 hydrogen bonds defined for protein. 1713 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 10 stacking parallelities Total time for adding SS restraints: 6.38 Time building geometry restraints manager: 7.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4849 1.33 - 1.45: 4762 1.45 - 1.57: 11221 1.57 - 1.70: 78 1.70 - 1.82: 25 Bond restraints: 20935 Sorted by residual: bond pdb=" C SER C 33 " pdb=" N PRO C 34 " ideal model delta sigma weight residual 1.334 1.307 0.026 8.40e-03 1.42e+04 9.75e+00 bond pdb=" C THR G 96 " pdb=" N VAL G 97 " ideal model delta sigma weight residual 1.330 1.283 0.047 1.97e-02 2.58e+03 5.73e+00 bond pdb=" CG GLN H 241 " pdb=" CD GLN H 241 " ideal model delta sigma weight residual 1.516 1.463 0.053 2.50e-02 1.60e+03 4.56e+00 bond pdb=" N LYS E 256 " pdb=" CA LYS E 256 " ideal model delta sigma weight residual 1.457 1.485 -0.027 1.29e-02 6.01e+03 4.51e+00 bond pdb=" CB GLN G 276 " pdb=" CG GLN G 276 " ideal model delta sigma weight residual 1.520 1.459 0.061 3.00e-02 1.11e+03 4.07e+00 ... (remaining 20930 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 27607 2.37 - 4.75: 815 4.75 - 7.12: 67 7.12 - 9.49: 13 9.49 - 11.86: 7 Bond angle restraints: 28509 Sorted by residual: angle pdb=" C LYS H 76 " pdb=" N THR H 77 " pdb=" CA THR H 77 " ideal model delta sigma weight residual 121.54 129.86 -8.32 1.91e+00 2.74e-01 1.90e+01 angle pdb=" C ILE G 278 " pdb=" N GLY G 279 " pdb=" CA GLY G 279 " ideal model delta sigma weight residual 122.97 115.15 7.82 1.84e+00 2.95e-01 1.81e+01 angle pdb=" C ARG B 224 " pdb=" N GLN B 225 " pdb=" CA GLN B 225 " ideal model delta sigma weight residual 122.46 128.16 -5.70 1.41e+00 5.03e-01 1.64e+01 angle pdb=" C SER B 227 " pdb=" N TRP B 228 " pdb=" CA TRP B 228 " ideal model delta sigma weight residual 120.09 125.14 -5.05 1.25e+00 6.40e-01 1.63e+01 angle pdb=" N GLN H 185 " pdb=" CA GLN H 185 " pdb=" C GLN H 185 " ideal model delta sigma weight residual 110.80 102.38 8.42 2.13e+00 2.20e-01 1.56e+01 ... (remaining 28504 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.14: 11741 30.14 - 60.28: 481 60.28 - 90.42: 83 90.42 - 120.55: 1 120.55 - 150.69: 1 Dihedral angle restraints: 12307 sinusoidal: 5111 harmonic: 7196 Sorted by residual: dihedral pdb=" O4' U K 21 " pdb=" C1' U K 21 " pdb=" N1 U K 21 " pdb=" C2 U K 21 " ideal model delta sinusoidal sigma weight residual 200.00 49.31 150.69 1 1.50e+01 4.44e-03 7.99e+01 dihedral pdb=" O4' U K 35 " pdb=" C1' U K 35 " pdb=" N1 U K 35 " pdb=" C2 U K 35 " ideal model delta sinusoidal sigma weight residual -160.00 -87.71 -72.29 1 1.50e+01 4.44e-03 2.97e+01 dihedral pdb=" CA ASN G 159 " pdb=" C ASN G 159 " pdb=" N LEU G 160 " pdb=" CA LEU G 160 " ideal model delta harmonic sigma weight residual 180.00 153.98 26.02 0 5.00e+00 4.00e-02 2.71e+01 ... (remaining 12304 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2145 0.056 - 0.112: 798 0.112 - 0.168: 122 0.168 - 0.225: 27 0.225 - 0.281: 2 Chirality restraints: 3094 Sorted by residual: chirality pdb=" CB VAL A 44 " pdb=" CA VAL A 44 " pdb=" CG1 VAL A 44 " pdb=" CG2 VAL A 44 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CB VAL C 59 " pdb=" CA VAL C 59 " pdb=" CG1 VAL C 59 " pdb=" CG2 VAL C 59 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CB THR H 96 " pdb=" CA THR H 96 " pdb=" OG1 THR H 96 " pdb=" CG2 THR H 96 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 3091 not shown) Planarity restraints: 3683 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 154 " -0.054 5.00e-02 4.00e+02 8.09e-02 1.05e+01 pdb=" N PRO C 155 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO C 155 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO C 155 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 33 " -0.045 5.00e-02 4.00e+02 6.81e-02 7.43e+00 pdb=" N PRO C 34 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO C 34 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 34 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR E 289 " 0.045 5.00e-02 4.00e+02 6.77e-02 7.33e+00 pdb=" N PRO E 290 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO E 290 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO E 290 " 0.037 5.00e-02 4.00e+02 ... (remaining 3680 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 5133 2.78 - 3.31: 18181 3.31 - 3.84: 33556 3.84 - 4.37: 37718 4.37 - 4.90: 63621 Nonbonded interactions: 158209 Sorted by model distance: nonbonded pdb=" OG SER F 54 " pdb=" OE1 GLN F 55 " model vdw 2.245 3.040 nonbonded pdb=" O GLY E 46 " pdb=" OG1 THR E 108 " model vdw 2.273 3.040 nonbonded pdb=" OD2 ASP G 40 " pdb=" OH TYR G 265 " model vdw 2.275 3.040 nonbonded pdb=" OH TYR H 289 " pdb=" O GLY H 296 " model vdw 2.283 3.040 nonbonded pdb=" O GLY I 46 " pdb=" OG1 THR I 108 " model vdw 2.296 3.040 ... (remaining 158204 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'D' and resid 26 through 355) selection = (chain 'E' and (resid 26 through 66 or resid 95 through 249 or resid 262 through \ 355)) selection = (chain 'F' and (resid 26 through 66 or resid 95 through 249 or resid 262 through \ 355)) selection = (chain 'G' and (resid 26 through 66 or resid 95 through 249 or resid 262 through \ 355)) selection = (chain 'H' and (resid 26 through 66 or resid 95 through 249 or resid 262 through \ 355)) selection = (chain 'I' and (resid 26 through 66 or resid 95 through 249 or resid 262 through \ 355)) } 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: 0.660 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: 0.040 Extract box with map and model: 0.800 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 60.190 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.110 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: 0.010 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 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 : 0.010 0.080 20935 Z= 0.441 Angle : 0.940 11.865 28509 Z= 0.512 Chirality : 0.057 0.281 3094 Planarity : 0.006 0.081 3683 Dihedral : 16.438 150.693 7803 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.10 % Favored : 86.90 % Rotamer: Outliers : 0.57 % Allowed : 14.92 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.04 (0.12), residues: 2610 helix: -3.67 (0.11), residues: 727 sheet: -2.07 (0.24), residues: 419 loop : -3.70 (0.12), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP D 329 HIS 0.011 0.002 HIS C 64 PHE 0.027 0.003 PHE G 165 TYR 0.029 0.003 TYR D 303 ARG 0.022 0.001 ARG F 190 Details of bonding type rmsd hydrogen bonds : bond 0.16953 ( 613) hydrogen bonds : angle 7.40985 ( 1713) covalent geometry : bond 0.00971 (20935) covalent geometry : angle 0.93997 (28509) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 217 time to evaluate : 2.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 151 ARG cc_start: 0.8804 (pmt170) cc_final: 0.8354 (pmt170) REVERT: C 171 LYS cc_start: 0.9377 (tptt) cc_final: 0.8953 (tppt) REVERT: C 262 TYR cc_start: 0.9056 (m-10) cc_final: 0.8705 (m-10) REVERT: E 68 ARG cc_start: 0.8138 (ttt-90) cc_final: 0.7680 (ttp-170) REVERT: E 132 TYR cc_start: 0.8841 (t80) cc_final: 0.8557 (t80) REVERT: F 37 ASP cc_start: 0.8414 (t70) cc_final: 0.8099 (t70) REVERT: F 301 GLU cc_start: 0.8306 (mm-30) cc_final: 0.7986 (mm-30) REVERT: G 93 ASN cc_start: 0.8590 (p0) cc_final: 0.8315 (p0) REVERT: G 134 ASP cc_start: 0.9154 (t0) cc_final: 0.8926 (t0) REVERT: G 252 ASP cc_start: 0.7084 (t0) cc_final: 0.6487 (p0) REVERT: H 78 LYS cc_start: 0.8761 (tptp) cc_final: 0.8301 (tptp) REVERT: H 264 LEU cc_start: 0.8514 (mt) cc_final: 0.8116 (mt) REVERT: H 301 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8472 (mm-30) REVERT: I 50 GLN cc_start: 0.8996 (tt0) cc_final: 0.8529 (tm-30) REVERT: I 298 ILE cc_start: 0.8882 (mp) cc_final: 0.8560 (mp) REVERT: I 301 GLU cc_start: 0.8632 (tp30) cc_final: 0.8407 (tp30) REVERT: A 46 GLU cc_start: 0.8661 (mm-30) cc_final: 0.7743 (tp30) REVERT: A 51 ASN cc_start: 0.8839 (m110) cc_final: 0.8504 (m110) REVERT: A 85 ASN cc_start: 0.7693 (t0) cc_final: 0.7160 (t0) REVERT: B 219 ARG cc_start: 0.8356 (tpm170) cc_final: 0.7409 (ptm-80) REVERT: B 235 TYR cc_start: 0.5804 (p90) cc_final: 0.5525 (p90) outliers start: 11 outliers final: 5 residues processed: 226 average time/residue: 0.3610 time to fit residues: 121.0416 Evaluate side-chains 167 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 162 time to evaluate : 2.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain G residue 333 ASP Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain I residue 353 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 223 optimal weight: 50.0000 chunk 200 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 135 optimal weight: 7.9990 chunk 107 optimal weight: 0.6980 chunk 207 optimal weight: 7.9990 chunk 80 optimal weight: 0.8980 chunk 126 optimal weight: 0.9980 chunk 154 optimal weight: 3.9990 chunk 240 optimal weight: 8.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 19 ASN C 69 GLN C 104 HIS D 50 GLN D 226 HIS D 315 GLN D 318 GLN D 340 GLN D 341 GLN E 55 GLN E 101 ASN E 169 ASN E 342 HIS F 93 ASN F 147 GLN F 181 ASN F 182 HIS F 309 GLN F 341 GLN F 347 ASN G 73 ASN G 226 HIS G 318 GLN H 73 ASN H 181 ASN H 341 GLN H 347 ASN I 90 GLN I 101 ASN I 182 HIS I 241 GLN I 274 HIS I 309 GLN I 347 ASN B 188 HIS B 230 HIS Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.109824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.079654 restraints weight = 44796.093| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 4.50 r_work: 0.3024 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 20935 Z= 0.108 Angle : 0.530 7.902 28509 Z= 0.280 Chirality : 0.040 0.167 3094 Planarity : 0.004 0.061 3683 Dihedral : 13.244 147.494 3501 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 2.03 % Allowed : 16.33 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.89 (0.14), residues: 2610 helix: -2.05 (0.16), residues: 726 sheet: -1.53 (0.26), residues: 399 loop : -3.31 (0.13), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 329 HIS 0.005 0.001 HIS H 158 PHE 0.013 0.001 PHE D 165 TYR 0.018 0.001 TYR D 132 ARG 0.006 0.000 ARG E 63 Details of bonding type rmsd hydrogen bonds : bond 0.03092 ( 613) hydrogen bonds : angle 5.16303 ( 1713) covalent geometry : bond 0.00235 (20935) covalent geometry : angle 0.53021 (28509) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 225 time to evaluate : 2.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 89 ASN cc_start: 0.8110 (t0) cc_final: 0.7716 (t0) REVERT: C 106 GLU cc_start: 0.6443 (tt0) cc_final: 0.5964 (mt-10) REVERT: C 147 TRP cc_start: 0.6797 (OUTLIER) cc_final: 0.6140 (t60) REVERT: C 149 ASN cc_start: 0.8490 (m-40) cc_final: 0.8274 (m-40) REVERT: C 151 ARG cc_start: 0.8716 (pmt170) cc_final: 0.8330 (pmt170) REVERT: C 156 ASN cc_start: 0.8712 (p0) cc_final: 0.8319 (p0) REVERT: C 171 LYS cc_start: 0.9284 (tptt) cc_final: 0.8922 (tppt) REVERT: C 262 TYR cc_start: 0.8994 (m-10) cc_final: 0.8658 (m-10) REVERT: D 110 LYS cc_start: 0.7970 (tttt) cc_final: 0.6849 (mttp) REVERT: D 265 TYR cc_start: 0.8728 (t80) cc_final: 0.8488 (t80) REVERT: D 328 ASN cc_start: 0.8952 (p0) cc_final: 0.8608 (p0) REVERT: D 347 ASN cc_start: 0.9330 (t0) cc_final: 0.9006 (t0) REVERT: F 37 ASP cc_start: 0.8530 (t70) cc_final: 0.7671 (p0) REVERT: F 286 ASP cc_start: 0.8182 (t0) cc_final: 0.7949 (t0) REVERT: G 286 ASP cc_start: 0.9104 (t0) cc_final: 0.8751 (t0) REVERT: H 321 ASP cc_start: 0.8542 (p0) cc_final: 0.8228 (p0) REVERT: I 274 HIS cc_start: 0.7434 (OUTLIER) cc_final: 0.6711 (m90) REVERT: I 298 ILE cc_start: 0.8080 (OUTLIER) cc_final: 0.7809 (mp) REVERT: A 45 LYS cc_start: 0.7250 (mtmm) cc_final: 0.6421 (pttp) REVERT: A 46 GLU cc_start: 0.8468 (mm-30) cc_final: 0.7676 (tp30) REVERT: A 51 ASN cc_start: 0.8839 (m110) cc_final: 0.8580 (m110) REVERT: B 219 ARG cc_start: 0.8205 (tpm170) cc_final: 0.7450 (ptm-80) REVERT: B 235 TYR cc_start: 0.6051 (p90) cc_final: 0.5459 (p90) outliers start: 39 outliers final: 18 residues processed: 251 average time/residue: 0.4185 time to fit residues: 167.0750 Evaluate side-chains 204 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 183 time to evaluate : 2.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 147 TRP Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain I residue 274 HIS Chi-restraints excluded: chain I residue 298 ILE Chi-restraints excluded: chain I residue 349 ILE Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 211 PHE Chi-restraints excluded: chain B residue 230 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 167 optimal weight: 5.9990 chunk 32 optimal weight: 0.0770 chunk 197 optimal weight: 0.9990 chunk 64 optimal weight: 6.9990 chunk 227 optimal weight: 50.0000 chunk 118 optimal weight: 7.9990 chunk 98 optimal weight: 3.9990 chunk 238 optimal weight: 10.0000 chunk 184 optimal weight: 2.9990 chunk 114 optimal weight: 6.9990 chunk 130 optimal weight: 9.9990 overall best weight: 2.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 72 GLN D 309 GLN E 147 GLN E 347 ASN H 347 ASN I 274 HIS B 188 HIS B 230 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.107873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.077815 restraints weight = 45336.308| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 4.47 r_work: 0.2988 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20935 Z= 0.173 Angle : 0.555 7.648 28509 Z= 0.290 Chirality : 0.041 0.180 3094 Planarity : 0.004 0.056 3683 Dihedral : 13.117 150.138 3497 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 3.03 % Allowed : 17.48 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.37 (0.15), residues: 2610 helix: -1.19 (0.18), residues: 720 sheet: -1.54 (0.26), residues: 388 loop : -3.12 (0.13), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 329 HIS 0.013 0.001 HIS I 274 PHE 0.016 0.002 PHE G 165 TYR 0.018 0.001 TYR B 179 ARG 0.005 0.000 ARG D 268 Details of bonding type rmsd hydrogen bonds : bond 0.03043 ( 613) hydrogen bonds : angle 4.96500 ( 1713) covalent geometry : bond 0.00385 (20935) covalent geometry : angle 0.55458 (28509) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 179 time to evaluate : 2.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 67 GLU cc_start: 0.6280 (pm20) cc_final: 0.5734 (pm20) REVERT: C 106 GLU cc_start: 0.6524 (tt0) cc_final: 0.6044 (mt-10) REVERT: C 147 TRP cc_start: 0.6916 (OUTLIER) cc_final: 0.6188 (t60) REVERT: C 151 ARG cc_start: 0.8684 (pmt170) cc_final: 0.8354 (pmt170) REVERT: C 171 LYS cc_start: 0.9289 (tptt) cc_final: 0.8929 (tppt) REVERT: C 262 TYR cc_start: 0.8998 (m-10) cc_final: 0.8678 (m-10) REVERT: D 110 LYS cc_start: 0.7974 (tttt) cc_final: 0.6785 (mttt) REVERT: D 248 GLU cc_start: 0.8213 (tp30) cc_final: 0.7982 (tp30) REVERT: D 280 ASN cc_start: 0.8849 (t0) cc_final: 0.8598 (t0) REVERT: D 317 LYS cc_start: 0.8648 (mmtm) cc_final: 0.8361 (mmtm) REVERT: D 328 ASN cc_start: 0.8950 (p0) cc_final: 0.8651 (p0) REVERT: D 347 ASN cc_start: 0.9347 (t0) cc_final: 0.8960 (t0) REVERT: E 68 ARG cc_start: 0.8286 (ttp80) cc_final: 0.7837 (ttp80) REVERT: F 37 ASP cc_start: 0.8571 (t70) cc_final: 0.7666 (p0) REVERT: F 43 MET cc_start: 0.8368 (mtt) cc_final: 0.8145 (mtt) REVERT: F 286 ASP cc_start: 0.8338 (t0) cc_final: 0.8071 (t0) REVERT: G 93 ASN cc_start: 0.8539 (p0) cc_final: 0.8291 (p0) REVERT: G 286 ASP cc_start: 0.9199 (t0) cc_final: 0.8889 (t0) REVERT: H 248 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7546 (mp0) REVERT: H 321 ASP cc_start: 0.8625 (p0) cc_final: 0.8316 (p0) REVERT: I 228 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7799 (tt) REVERT: I 274 HIS cc_start: 0.7589 (OUTLIER) cc_final: 0.6738 (m90) REVERT: I 298 ILE cc_start: 0.8095 (OUTLIER) cc_final: 0.7892 (mp) REVERT: A 46 GLU cc_start: 0.8512 (mm-30) cc_final: 0.7763 (tp30) REVERT: A 51 ASN cc_start: 0.8745 (m110) cc_final: 0.8486 (m110) outliers start: 58 outliers final: 39 residues processed: 228 average time/residue: 0.3216 time to fit residues: 114.7592 Evaluate side-chains 211 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 167 time to evaluate : 2.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 147 TRP Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 158 HIS Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 248 GLU Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain H residue 347 ASN Chi-restraints excluded: chain H residue 353 VAL Chi-restraints excluded: chain I residue 30 LEU Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 228 LEU Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain I residue 274 HIS Chi-restraints excluded: chain I residue 298 ILE Chi-restraints excluded: chain I residue 349 ILE Chi-restraints excluded: chain I residue 353 VAL Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 200 HIS Chi-restraints excluded: chain B residue 230 HIS Chi-restraints excluded: chain B residue 240 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 162 optimal weight: 0.2980 chunk 212 optimal weight: 8.9990 chunk 87 optimal weight: 8.9990 chunk 52 optimal weight: 0.0770 chunk 179 optimal weight: 1.9990 chunk 151 optimal weight: 0.9990 chunk 222 optimal weight: 50.0000 chunk 169 optimal weight: 7.9990 chunk 246 optimal weight: 7.9990 chunk 161 optimal weight: 2.9990 chunk 120 optimal weight: 0.8980 overall best weight: 0.8542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 159 ASN H 347 ASN I 274 HIS B 188 HIS B 230 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.111067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.081056 restraints weight = 45085.692| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 4.52 r_work: 0.3048 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 20935 Z= 0.093 Angle : 0.494 7.489 28509 Z= 0.259 Chirality : 0.039 0.135 3094 Planarity : 0.004 0.054 3683 Dihedral : 12.956 149.941 3497 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 2.76 % Allowed : 18.26 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.15), residues: 2610 helix: -0.70 (0.19), residues: 728 sheet: -1.27 (0.27), residues: 389 loop : -2.90 (0.14), residues: 1493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 329 HIS 0.015 0.001 HIS I 274 PHE 0.011 0.001 PHE D 165 TYR 0.017 0.001 TYR D 132 ARG 0.006 0.000 ARG D 268 Details of bonding type rmsd hydrogen bonds : bond 0.02641 ( 613) hydrogen bonds : angle 4.58298 ( 1713) covalent geometry : bond 0.00207 (20935) covalent geometry : angle 0.49377 (28509) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 194 time to evaluate : 2.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 67 GLU cc_start: 0.6242 (pm20) cc_final: 0.5705 (pm20) REVERT: C 106 GLU cc_start: 0.6501 (tt0) cc_final: 0.6106 (mt-10) REVERT: C 147 TRP cc_start: 0.6469 (OUTLIER) cc_final: 0.6026 (t60) REVERT: C 156 ASN cc_start: 0.8730 (p0) cc_final: 0.8345 (p0) REVERT: C 171 LYS cc_start: 0.9291 (tptt) cc_final: 0.8941 (tppt) REVERT: C 262 TYR cc_start: 0.8945 (m-10) cc_final: 0.8638 (m-10) REVERT: D 110 LYS cc_start: 0.7957 (tttt) cc_final: 0.6756 (mttp) REVERT: D 317 LYS cc_start: 0.8620 (mmtm) cc_final: 0.8295 (mmtm) REVERT: D 328 ASN cc_start: 0.8973 (p0) cc_final: 0.8646 (p0) REVERT: D 347 ASN cc_start: 0.9336 (t0) cc_final: 0.8980 (t0) REVERT: E 68 ARG cc_start: 0.8303 (ttp80) cc_final: 0.7873 (ttp80) REVERT: E 132 TYR cc_start: 0.8803 (t80) cc_final: 0.8592 (t80) REVERT: F 37 ASP cc_start: 0.8502 (t70) cc_final: 0.7561 (p0) REVERT: F 43 MET cc_start: 0.8303 (mtt) cc_final: 0.8060 (mtt) REVERT: F 268 ARG cc_start: 0.9089 (mtp-110) cc_final: 0.8833 (ptp-110) REVERT: F 286 ASP cc_start: 0.8287 (t0) cc_final: 0.8000 (t0) REVERT: G 40 ASP cc_start: 0.8667 (OUTLIER) cc_final: 0.8397 (t0) REVERT: G 93 ASN cc_start: 0.8604 (p0) cc_final: 0.8338 (p0) REVERT: G 286 ASP cc_start: 0.9168 (t0) cc_final: 0.8846 (t0) REVERT: H 230 GLU cc_start: 0.8355 (tt0) cc_final: 0.8035 (tt0) REVERT: H 248 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7492 (mp0) REVERT: H 321 ASP cc_start: 0.8462 (p0) cc_final: 0.8189 (p0) REVERT: I 282 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8727 (mm) REVERT: I 298 ILE cc_start: 0.8006 (OUTLIER) cc_final: 0.7803 (mp) REVERT: I 323 TYR cc_start: 0.7997 (t80) cc_final: 0.7733 (t80) REVERT: A 46 GLU cc_start: 0.8411 (mm-30) cc_final: 0.7697 (tp30) REVERT: A 51 ASN cc_start: 0.8732 (m110) cc_final: 0.8476 (m110) outliers start: 53 outliers final: 31 residues processed: 238 average time/residue: 0.3116 time to fit residues: 117.5491 Evaluate side-chains 213 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 177 time to evaluate : 2.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 147 TRP Chi-restraints excluded: chain D residue 262 LYS Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 158 HIS Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain G residue 40 ASP Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 158 HIS Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 248 GLU Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain H residue 347 ASN Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain I residue 274 HIS Chi-restraints excluded: chain I residue 282 LEU Chi-restraints excluded: chain I residue 298 ILE Chi-restraints excluded: chain I residue 353 VAL Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 230 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 195 optimal weight: 9.9990 chunk 86 optimal weight: 10.0000 chunk 219 optimal weight: 5.9990 chunk 18 optimal weight: 8.9990 chunk 166 optimal weight: 9.9990 chunk 97 optimal weight: 5.9990 chunk 204 optimal weight: 10.0000 chunk 117 optimal weight: 7.9990 chunk 208 optimal weight: 7.9990 chunk 233 optimal weight: 40.0000 chunk 2 optimal weight: 5.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 82 ASN ** C 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 GLN D 241 GLN E 226 HIS H 95 GLN H 159 ASN H 347 ASN I 159 ASN I 274 HIS B 188 HIS B 225 GLN B 230 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.103984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.073836 restraints weight = 46899.195| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 4.45 r_work: 0.2943 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.116 20935 Z= 0.372 Angle : 0.716 7.341 28509 Z= 0.368 Chirality : 0.045 0.167 3094 Planarity : 0.004 0.053 3683 Dihedral : 13.229 151.263 3496 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.88 % Favored : 88.08 % Rotamer: Outliers : 4.75 % Allowed : 18.26 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.09 (0.15), residues: 2610 helix: -0.84 (0.19), residues: 725 sheet: -1.35 (0.26), residues: 410 loop : -3.04 (0.14), residues: 1475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 329 HIS 0.015 0.002 HIS I 274 PHE 0.021 0.002 PHE G 165 TYR 0.033 0.002 TYR B 179 ARG 0.006 0.001 ARG H 133 Details of bonding type rmsd hydrogen bonds : bond 0.03509 ( 613) hydrogen bonds : angle 5.30833 ( 1713) covalent geometry : bond 0.00831 (20935) covalent geometry : angle 0.71646 (28509) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 157 time to evaluate : 2.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 67 GLU cc_start: 0.6626 (pm20) cc_final: 0.5998 (pm20) REVERT: C 106 GLU cc_start: 0.6568 (tt0) cc_final: 0.5962 (mt-10) REVERT: C 147 TRP cc_start: 0.6930 (OUTLIER) cc_final: 0.6256 (t60) REVERT: C 151 ARG cc_start: 0.8732 (pmt170) cc_final: 0.8418 (ptt-90) REVERT: C 171 LYS cc_start: 0.9283 (tptt) cc_final: 0.8912 (tppt) REVERT: C 262 TYR cc_start: 0.9035 (m-10) cc_final: 0.8746 (m-10) REVERT: D 317 LYS cc_start: 0.8626 (mmtm) cc_final: 0.8351 (mmtm) REVERT: D 328 ASN cc_start: 0.8970 (p0) cc_final: 0.8683 (p0) REVERT: D 347 ASN cc_start: 0.9421 (t0) cc_final: 0.8921 (t0) REVERT: E 68 ARG cc_start: 0.8200 (ttp80) cc_final: 0.7879 (ttp80) REVERT: E 132 TYR cc_start: 0.8852 (t80) cc_final: 0.8595 (t80) REVERT: E 192 TRP cc_start: 0.8960 (OUTLIER) cc_final: 0.6984 (m-90) REVERT: F 37 ASP cc_start: 0.8698 (t70) cc_final: 0.8130 (t0) REVERT: F 190 ARG cc_start: 0.7331 (OUTLIER) cc_final: 0.6059 (tmm160) REVERT: F 268 ARG cc_start: 0.9178 (mtp-110) cc_final: 0.8917 (ptp-110) REVERT: G 40 ASP cc_start: 0.8813 (OUTLIER) cc_final: 0.8538 (t0) REVERT: G 93 ASN cc_start: 0.8671 (p0) cc_final: 0.8339 (p0) REVERT: H 248 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7664 (mp0) REVERT: I 228 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8107 (tt) REVERT: I 298 ILE cc_start: 0.8305 (OUTLIER) cc_final: 0.8061 (mp) REVERT: A 46 GLU cc_start: 0.8512 (mm-30) cc_final: 0.7841 (tp30) REVERT: A 51 ASN cc_start: 0.8377 (m110) cc_final: 0.8118 (m110) REVERT: A 58 ASN cc_start: 0.7425 (OUTLIER) cc_final: 0.6811 (m110) REVERT: B 219 ARG cc_start: 0.8557 (tpm170) cc_final: 0.7804 (ptt90) outliers start: 91 outliers final: 60 residues processed: 231 average time/residue: 0.3277 time to fit residues: 116.4682 Evaluate side-chains 217 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 149 time to evaluate : 2.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 137 MET Chi-restraints excluded: chain C residue 147 TRP Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 262 LYS Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 158 HIS Chi-restraints excluded: chain E residue 192 TRP Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 71 ILE Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 190 ARG Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain G residue 33 GLU Chi-restraints excluded: chain G residue 40 ASP Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain G residue 330 VAL Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 248 GLU Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain H residue 347 ASN Chi-restraints excluded: chain H residue 350 ARG Chi-restraints excluded: chain H residue 353 VAL Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain I residue 228 LEU Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain I residue 269 ASP Chi-restraints excluded: chain I residue 274 HIS Chi-restraints excluded: chain I residue 298 ILE Chi-restraints excluded: chain I residue 303 TYR Chi-restraints excluded: chain I residue 349 ILE Chi-restraints excluded: chain I residue 353 VAL Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 200 HIS Chi-restraints excluded: chain B residue 230 HIS Chi-restraints excluded: chain B residue 240 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 190 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 chunk 242 optimal weight: 1.9990 chunk 216 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 43 optimal weight: 0.4980 chunk 222 optimal weight: 30.0000 chunk 113 optimal weight: 6.9990 chunk 100 optimal weight: 0.9990 chunk 76 optimal weight: 9.9990 chunk 135 optimal weight: 8.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 159 ASN H 347 ASN I 274 HIS B 230 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.107635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.077545 restraints weight = 45773.641| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 4.49 r_work: 0.3011 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20935 Z= 0.147 Angle : 0.539 7.532 28509 Z= 0.280 Chirality : 0.041 0.141 3094 Planarity : 0.004 0.050 3683 Dihedral : 13.085 150.450 3496 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 3.60 % Allowed : 19.77 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.16), residues: 2610 helix: -0.45 (0.20), residues: 722 sheet: -1.28 (0.26), residues: 423 loop : -2.85 (0.14), residues: 1465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 329 HIS 0.010 0.001 HIS I 274 PHE 0.014 0.001 PHE G 165 TYR 0.019 0.001 TYR D 132 ARG 0.006 0.000 ARG H 133 Details of bonding type rmsd hydrogen bonds : bond 0.02865 ( 613) hydrogen bonds : angle 4.77187 ( 1713) covalent geometry : bond 0.00329 (20935) covalent geometry : angle 0.53877 (28509) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 171 time to evaluate : 2.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 67 GLU cc_start: 0.6256 (pm20) cc_final: 0.5595 (pm20) REVERT: C 106 GLU cc_start: 0.6588 (tt0) cc_final: 0.6140 (mt-10) REVERT: C 147 TRP cc_start: 0.6587 (OUTLIER) cc_final: 0.5935 (t60) REVERT: C 152 PHE cc_start: 0.7429 (OUTLIER) cc_final: 0.6929 (t80) REVERT: C 171 LYS cc_start: 0.9295 (tptt) cc_final: 0.8935 (tppt) REVERT: C 262 TYR cc_start: 0.8993 (m-10) cc_final: 0.8673 (m-10) REVERT: D 110 LYS cc_start: 0.7992 (tttt) cc_final: 0.6779 (mttp) REVERT: D 265 TYR cc_start: 0.8740 (t80) cc_final: 0.8403 (t80) REVERT: D 317 LYS cc_start: 0.8548 (mmtm) cc_final: 0.8339 (mmtm) REVERT: D 328 ASN cc_start: 0.8973 (p0) cc_final: 0.8680 (p0) REVERT: D 347 ASN cc_start: 0.9374 (t0) cc_final: 0.8923 (t0) REVERT: E 68 ARG cc_start: 0.8294 (ttp80) cc_final: 0.7727 (ttp80) REVERT: E 132 TYR cc_start: 0.8821 (t80) cc_final: 0.8574 (t80) REVERT: E 192 TRP cc_start: 0.8876 (OUTLIER) cc_final: 0.6882 (m-90) REVERT: F 37 ASP cc_start: 0.8625 (t70) cc_final: 0.7672 (p0) REVERT: F 268 ARG cc_start: 0.9144 (mtp-110) cc_final: 0.8869 (ptp-110) REVERT: G 40 ASP cc_start: 0.8719 (OUTLIER) cc_final: 0.8404 (t0) REVERT: G 93 ASN cc_start: 0.8664 (p0) cc_final: 0.8371 (p0) REVERT: H 248 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7659 (mp0) REVERT: H 321 ASP cc_start: 0.8641 (p0) cc_final: 0.8358 (p0) REVERT: I 289 TYR cc_start: 0.5670 (m-10) cc_final: 0.5331 (m-10) REVERT: A 46 GLU cc_start: 0.8426 (mm-30) cc_final: 0.7790 (tp30) REVERT: A 51 ASN cc_start: 0.8537 (m110) cc_final: 0.8276 (m110) outliers start: 69 outliers final: 52 residues processed: 222 average time/residue: 0.3052 time to fit residues: 106.8456 Evaluate side-chains 218 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 161 time to evaluate : 2.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 137 MET Chi-restraints excluded: chain C residue 147 TRP Chi-restraints excluded: chain C residue 152 PHE Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 262 LYS Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 158 HIS Chi-restraints excluded: chain E residue 192 TRP Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 146 ASP Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain G residue 33 GLU Chi-restraints excluded: chain G residue 40 ASP Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain G residue 307 THR Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 248 GLU Chi-restraints excluded: chain H residue 303 TYR Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain H residue 347 ASN Chi-restraints excluded: chain H residue 350 ARG Chi-restraints excluded: chain H residue 353 VAL Chi-restraints excluded: chain I residue 30 LEU Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain I residue 274 HIS Chi-restraints excluded: chain I residue 303 TYR Chi-restraints excluded: chain I residue 353 VAL Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain B residue 200 HIS Chi-restraints excluded: chain B residue 230 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 211 optimal weight: 10.0000 chunk 136 optimal weight: 0.0040 chunk 0 optimal weight: 10.0000 chunk 31 optimal weight: 7.9990 chunk 71 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 132 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 chunk 231 optimal weight: 0.0670 chunk 180 optimal weight: 3.9990 overall best weight: 3.6136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 159 ASN H 347 ASN I 274 HIS B 188 HIS B 225 GLN B 230 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.106672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.076337 restraints weight = 46038.063| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 4.47 r_work: 0.2958 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 20935 Z= 0.211 Angle : 0.575 7.220 28509 Z= 0.296 Chirality : 0.042 0.161 3094 Planarity : 0.004 0.055 3683 Dihedral : 13.076 151.497 3496 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.11 % Favored : 89.89 % Rotamer: Outliers : 4.23 % Allowed : 19.87 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.16), residues: 2610 helix: -0.39 (0.20), residues: 722 sheet: -1.27 (0.26), residues: 440 loop : -2.83 (0.15), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 329 HIS 0.010 0.001 HIS I 274 PHE 0.017 0.002 PHE G 165 TYR 0.021 0.002 TYR D 132 ARG 0.005 0.000 ARG H 133 Details of bonding type rmsd hydrogen bonds : bond 0.02966 ( 613) hydrogen bonds : angle 4.84110 ( 1713) covalent geometry : bond 0.00472 (20935) covalent geometry : angle 0.57544 (28509) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 164 time to evaluate : 2.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 67 GLU cc_start: 0.6413 (pm20) cc_final: 0.5624 (pm20) REVERT: C 106 GLU cc_start: 0.6566 (tt0) cc_final: 0.6100 (mt-10) REVERT: C 147 TRP cc_start: 0.6633 (OUTLIER) cc_final: 0.6087 (t60) REVERT: C 171 LYS cc_start: 0.9283 (tptt) cc_final: 0.8921 (tppt) REVERT: D 110 LYS cc_start: 0.7976 (tttt) cc_final: 0.6757 (mttp) REVERT: D 265 TYR cc_start: 0.8727 (t80) cc_final: 0.8379 (t80) REVERT: D 317 LYS cc_start: 0.8568 (mmtm) cc_final: 0.8351 (mmtm) REVERT: D 328 ASN cc_start: 0.8966 (p0) cc_final: 0.8678 (p0) REVERT: D 347 ASN cc_start: 0.9391 (t0) cc_final: 0.8926 (t0) REVERT: E 68 ARG cc_start: 0.8240 (ttp80) cc_final: 0.7617 (ttp80) REVERT: E 132 TYR cc_start: 0.8815 (t80) cc_final: 0.8571 (t80) REVERT: E 192 TRP cc_start: 0.8858 (OUTLIER) cc_final: 0.6835 (m-90) REVERT: F 268 ARG cc_start: 0.9190 (mtp-110) cc_final: 0.8913 (ptp-110) REVERT: G 40 ASP cc_start: 0.8773 (OUTLIER) cc_final: 0.8460 (t0) REVERT: G 93 ASN cc_start: 0.8674 (p0) cc_final: 0.8375 (p0) REVERT: H 230 GLU cc_start: 0.8401 (tt0) cc_final: 0.8108 (tt0) REVERT: H 321 ASP cc_start: 0.8699 (p0) cc_final: 0.8408 (p0) REVERT: I 282 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8728 (mm) REVERT: A 46 GLU cc_start: 0.8481 (mm-30) cc_final: 0.7816 (tp30) REVERT: A 51 ASN cc_start: 0.8494 (m110) cc_final: 0.8235 (m110) REVERT: A 58 ASN cc_start: 0.7709 (OUTLIER) cc_final: 0.7002 (m110) outliers start: 81 outliers final: 62 residues processed: 225 average time/residue: 0.3246 time to fit residues: 114.2482 Evaluate side-chains 227 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 160 time to evaluate : 2.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 137 MET Chi-restraints excluded: chain C residue 147 TRP Chi-restraints excluded: chain C residue 152 PHE Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 262 LYS Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 158 HIS Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 192 TRP Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 146 ASP Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain G residue 33 GLU Chi-restraints excluded: chain G residue 40 ASP Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain G residue 307 THR Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 303 TYR Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain H residue 347 ASN Chi-restraints excluded: chain H residue 350 ARG Chi-restraints excluded: chain H residue 353 VAL Chi-restraints excluded: chain I residue 30 LEU Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain I residue 274 HIS Chi-restraints excluded: chain I residue 282 LEU Chi-restraints excluded: chain I residue 303 TYR Chi-restraints excluded: chain I residue 353 VAL Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 200 HIS Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain B residue 240 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 47 optimal weight: 10.0000 chunk 111 optimal weight: 8.9990 chunk 6 optimal weight: 7.9990 chunk 141 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 chunk 214 optimal weight: 10.0000 chunk 190 optimal weight: 7.9990 chunk 175 optimal weight: 0.0030 chunk 84 optimal weight: 5.9990 chunk 173 optimal weight: 7.9990 chunk 195 optimal weight: 4.9990 overall best weight: 4.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 342 HIS ** G 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 347 ASN I 274 HIS B 188 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.105628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.075355 restraints weight = 46422.781| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 4.46 r_work: 0.2967 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 20935 Z= 0.260 Angle : 0.619 11.448 28509 Z= 0.317 Chirality : 0.043 0.149 3094 Planarity : 0.004 0.056 3683 Dihedral : 13.120 151.929 3496 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.04 % Favored : 89.96 % Rotamer: Outliers : 4.33 % Allowed : 19.77 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.16), residues: 2610 helix: -0.44 (0.20), residues: 728 sheet: -1.36 (0.25), residues: 442 loop : -2.82 (0.15), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 329 HIS 0.008 0.001 HIS I 274 PHE 0.019 0.002 PHE G 165 TYR 0.024 0.002 TYR B 179 ARG 0.004 0.000 ARG H 133 Details of bonding type rmsd hydrogen bonds : bond 0.03114 ( 613) hydrogen bonds : angle 4.96082 ( 1713) covalent geometry : bond 0.00579 (20935) covalent geometry : angle 0.61930 (28509) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 163 time to evaluate : 2.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 67 GLU cc_start: 0.6468 (pm20) cc_final: 0.5681 (pm20) REVERT: C 106 GLU cc_start: 0.6579 (tt0) cc_final: 0.6095 (mt-10) REVERT: C 147 TRP cc_start: 0.6625 (OUTLIER) cc_final: 0.6062 (t60) REVERT: C 171 LYS cc_start: 0.9287 (tptt) cc_final: 0.8917 (tppt) REVERT: D 110 LYS cc_start: 0.7926 (tttt) cc_final: 0.6677 (mttp) REVERT: D 328 ASN cc_start: 0.8960 (p0) cc_final: 0.8674 (p0) REVERT: D 347 ASN cc_start: 0.9384 (t0) cc_final: 0.8924 (t0) REVERT: E 68 ARG cc_start: 0.8220 (ttp80) cc_final: 0.7771 (ttp80) REVERT: E 80 ARG cc_start: 0.8857 (mmp-170) cc_final: 0.8630 (mmp80) REVERT: E 132 TYR cc_start: 0.8835 (t80) cc_final: 0.8589 (t80) REVERT: E 192 TRP cc_start: 0.8917 (OUTLIER) cc_final: 0.6880 (m-90) REVERT: F 37 ASP cc_start: 0.8756 (t70) cc_final: 0.8269 (t0) REVERT: F 43 MET cc_start: 0.8365 (mtt) cc_final: 0.8073 (mtt) REVERT: G 40 ASP cc_start: 0.8816 (OUTLIER) cc_final: 0.8488 (t0) REVERT: G 93 ASN cc_start: 0.8678 (p0) cc_final: 0.8337 (p0) REVERT: G 273 ILE cc_start: 0.7974 (OUTLIER) cc_final: 0.7623 (mt) REVERT: H 321 ASP cc_start: 0.8736 (p0) cc_final: 0.8494 (p0) REVERT: I 282 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8755 (mm) REVERT: I 289 TYR cc_start: 0.3901 (m-80) cc_final: 0.3638 (m-10) REVERT: A 46 GLU cc_start: 0.8445 (mm-30) cc_final: 0.7802 (tp30) REVERT: A 51 ASN cc_start: 0.8462 (m110) cc_final: 0.8204 (m110) REVERT: A 58 ASN cc_start: 0.7736 (OUTLIER) cc_final: 0.7110 (m110) outliers start: 83 outliers final: 68 residues processed: 228 average time/residue: 0.3084 time to fit residues: 109.5695 Evaluate side-chains 234 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 160 time to evaluate : 2.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 137 MET Chi-restraints excluded: chain C residue 147 TRP Chi-restraints excluded: chain C residue 152 PHE Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 262 LYS Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 307 THR Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 158 HIS Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 192 TRP Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain F residue 146 ASP Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain G residue 33 GLU Chi-restraints excluded: chain G residue 40 ASP Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain G residue 273 ILE Chi-restraints excluded: chain G residue 307 THR Chi-restraints excluded: chain G residue 330 VAL Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 303 TYR Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain H residue 347 ASN Chi-restraints excluded: chain H residue 350 ARG Chi-restraints excluded: chain H residue 353 VAL Chi-restraints excluded: chain I residue 30 LEU Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain I residue 250 ILE Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain I residue 274 HIS Chi-restraints excluded: chain I residue 282 LEU Chi-restraints excluded: chain I residue 303 TYR Chi-restraints excluded: chain I residue 353 VAL Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 200 HIS Chi-restraints excluded: chain B residue 240 ILE Chi-restraints excluded: chain B residue 265 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 227 optimal weight: 50.0000 chunk 79 optimal weight: 3.9990 chunk 235 optimal weight: 20.0000 chunk 103 optimal weight: 9.9990 chunk 186 optimal weight: 3.9990 chunk 256 optimal weight: 0.6980 chunk 4 optimal weight: 9.9990 chunk 7 optimal weight: 0.9980 chunk 189 optimal weight: 8.9990 chunk 70 optimal weight: 2.9990 chunk 194 optimal weight: 8.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 347 ASN I 274 HIS B 188 HIS B 225 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.107308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.077293 restraints weight = 45634.078| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 4.48 r_work: 0.3003 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20935 Z= 0.161 Angle : 0.554 12.554 28509 Z= 0.285 Chirality : 0.041 0.137 3094 Planarity : 0.004 0.057 3683 Dihedral : 13.047 151.122 3496 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 4.12 % Allowed : 20.50 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.16), residues: 2610 helix: -0.21 (0.20), residues: 717 sheet: -1.15 (0.26), residues: 424 loop : -2.75 (0.15), residues: 1469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 329 HIS 0.011 0.001 HIS I 274 PHE 0.014 0.001 PHE G 165 TYR 0.022 0.002 TYR D 132 ARG 0.005 0.000 ARG H 133 Details of bonding type rmsd hydrogen bonds : bond 0.02858 ( 613) hydrogen bonds : angle 4.71099 ( 1713) covalent geometry : bond 0.00362 (20935) covalent geometry : angle 0.55447 (28509) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 172 time to evaluate : 2.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 67 GLU cc_start: 0.6241 (pm20) cc_final: 0.5463 (pm20) REVERT: C 106 GLU cc_start: 0.6592 (tt0) cc_final: 0.6138 (mt-10) REVERT: C 147 TRP cc_start: 0.6799 (OUTLIER) cc_final: 0.6193 (t60) REVERT: C 151 ARG cc_start: 0.8650 (pmt170) cc_final: 0.8276 (ptp90) REVERT: C 156 ASN cc_start: 0.8808 (p0) cc_final: 0.8458 (p0) REVERT: C 171 LYS cc_start: 0.9296 (tptt) cc_final: 0.8938 (tppt) REVERT: D 110 LYS cc_start: 0.7987 (tttt) cc_final: 0.6776 (mttp) REVERT: D 317 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.8343 (mmtm) REVERT: D 328 ASN cc_start: 0.8928 (p0) cc_final: 0.8646 (p0) REVERT: D 347 ASN cc_start: 0.9359 (t0) cc_final: 0.8907 (t0) REVERT: E 68 ARG cc_start: 0.8281 (ttp80) cc_final: 0.7667 (ttp80) REVERT: E 132 TYR cc_start: 0.8831 (t80) cc_final: 0.8586 (t80) REVERT: E 192 TRP cc_start: 0.8858 (OUTLIER) cc_final: 0.6832 (m-90) REVERT: F 37 ASP cc_start: 0.8724 (t70) cc_final: 0.7791 (p0) REVERT: F 43 MET cc_start: 0.8338 (mtt) cc_final: 0.8000 (mtt) REVERT: F 268 ARG cc_start: 0.9179 (mtm180) cc_final: 0.8959 (ptp-110) REVERT: G 40 ASP cc_start: 0.8729 (OUTLIER) cc_final: 0.8410 (t0) REVERT: G 93 ASN cc_start: 0.8684 (p0) cc_final: 0.8370 (p0) REVERT: G 273 ILE cc_start: 0.8052 (OUTLIER) cc_final: 0.7764 (mt) REVERT: H 230 GLU cc_start: 0.8351 (tt0) cc_final: 0.8074 (tt0) REVERT: H 321 ASP cc_start: 0.8661 (p0) cc_final: 0.8388 (p0) REVERT: I 282 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8706 (mm) REVERT: A 46 GLU cc_start: 0.8438 (mm-30) cc_final: 0.7794 (tp30) REVERT: A 51 ASN cc_start: 0.8525 (m110) cc_final: 0.8248 (m110) REVERT: A 58 ASN cc_start: 0.7825 (OUTLIER) cc_final: 0.7154 (m110) outliers start: 79 outliers final: 68 residues processed: 231 average time/residue: 0.3364 time to fit residues: 122.2061 Evaluate side-chains 239 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 164 time to evaluate : 2.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 137 MET Chi-restraints excluded: chain C residue 147 TRP Chi-restraints excluded: chain C residue 152 PHE Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 262 LYS Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 307 THR Chi-restraints excluded: chain D residue 317 LYS Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 158 HIS Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 192 TRP Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain F residue 146 ASP Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain G residue 33 GLU Chi-restraints excluded: chain G residue 40 ASP Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain G residue 273 ILE Chi-restraints excluded: chain G residue 307 THR Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 303 TYR Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain H residue 347 ASN Chi-restraints excluded: chain H residue 350 ARG Chi-restraints excluded: chain H residue 353 VAL Chi-restraints excluded: chain I residue 30 LEU Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 250 ILE Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain I residue 274 HIS Chi-restraints excluded: chain I residue 282 LEU Chi-restraints excluded: chain I residue 303 TYR Chi-restraints excluded: chain I residue 353 VAL Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 200 HIS Chi-restraints excluded: chain B residue 211 PHE Chi-restraints excluded: chain B residue 225 GLN Chi-restraints excluded: chain B residue 240 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 166 optimal weight: 0.9990 chunk 6 optimal weight: 8.9990 chunk 106 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 236 optimal weight: 2.9990 chunk 214 optimal weight: 0.9980 chunk 176 optimal weight: 6.9990 chunk 116 optimal weight: 2.9990 chunk 175 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 202 optimal weight: 0.7980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 341 GLN ** G 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 347 ASN I 159 ASN I 274 HIS B 188 HIS B 225 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.108242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.078248 restraints weight = 45244.140| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 4.47 r_work: 0.3029 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20935 Z= 0.126 Angle : 0.534 12.941 28509 Z= 0.274 Chirality : 0.040 0.132 3094 Planarity : 0.004 0.058 3683 Dihedral : 12.968 150.926 3496 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 3.91 % Allowed : 21.18 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.16), residues: 2610 helix: -0.06 (0.20), residues: 717 sheet: -1.07 (0.26), residues: 416 loop : -2.71 (0.15), residues: 1477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 329 HIS 0.010 0.001 HIS I 274 PHE 0.011 0.001 PHE G 165 TYR 0.022 0.001 TYR D 132 ARG 0.009 0.000 ARG H 133 Details of bonding type rmsd hydrogen bonds : bond 0.02723 ( 613) hydrogen bonds : angle 4.56206 ( 1713) covalent geometry : bond 0.00286 (20935) covalent geometry : angle 0.53401 (28509) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 183 time to evaluate : 2.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 19 ASN cc_start: 0.8594 (m-40) cc_final: 0.7956 (m-40) REVERT: C 67 GLU cc_start: 0.6282 (pm20) cc_final: 0.5632 (pm20) REVERT: C 89 ASN cc_start: 0.8145 (t0) cc_final: 0.7723 (t0) REVERT: C 106 GLU cc_start: 0.6573 (tt0) cc_final: 0.6124 (mt-10) REVERT: C 109 LEU cc_start: 0.8858 (mp) cc_final: 0.8646 (mt) REVERT: C 147 TRP cc_start: 0.6743 (OUTLIER) cc_final: 0.6229 (t60) REVERT: C 156 ASN cc_start: 0.8797 (p0) cc_final: 0.8446 (p0) REVERT: C 171 LYS cc_start: 0.9290 (tptt) cc_final: 0.8935 (tppt) REVERT: D 33 GLU cc_start: 0.8622 (tt0) cc_final: 0.8123 (pm20) REVERT: D 110 LYS cc_start: 0.8022 (tttt) cc_final: 0.6820 (mttp) REVERT: D 265 TYR cc_start: 0.8639 (t80) cc_final: 0.8254 (t80) REVERT: D 317 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8327 (mmtm) REVERT: D 328 ASN cc_start: 0.8936 (p0) cc_final: 0.8652 (p0) REVERT: D 347 ASN cc_start: 0.9347 (t0) cc_final: 0.8911 (t0) REVERT: E 68 ARG cc_start: 0.8288 (ttp80) cc_final: 0.7682 (ttp80) REVERT: E 132 TYR cc_start: 0.8848 (t80) cc_final: 0.8611 (t80) REVERT: E 192 TRP cc_start: 0.8829 (OUTLIER) cc_final: 0.6776 (m-90) REVERT: F 37 ASP cc_start: 0.8666 (t70) cc_final: 0.7711 (p0) REVERT: F 43 MET cc_start: 0.8299 (mtt) cc_final: 0.7931 (mtt) REVERT: F 268 ARG cc_start: 0.9167 (mtm180) cc_final: 0.8967 (ptp-110) REVERT: G 40 ASP cc_start: 0.8762 (OUTLIER) cc_final: 0.8498 (t0) REVERT: G 93 ASN cc_start: 0.8675 (p0) cc_final: 0.8359 (p0) REVERT: G 273 ILE cc_start: 0.8022 (OUTLIER) cc_final: 0.7754 (mt) REVERT: H 230 GLU cc_start: 0.8319 (tt0) cc_final: 0.8067 (tt0) REVERT: H 321 ASP cc_start: 0.8620 (p0) cc_final: 0.8360 (p0) REVERT: I 282 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8662 (mm) REVERT: A 46 GLU cc_start: 0.8419 (mm-30) cc_final: 0.7785 (tp30) REVERT: A 51 ASN cc_start: 0.8524 (m110) cc_final: 0.8242 (m110) REVERT: A 58 ASN cc_start: 0.7851 (OUTLIER) cc_final: 0.7194 (m110) outliers start: 75 outliers final: 62 residues processed: 240 average time/residue: 0.3223 time to fit residues: 120.6930 Evaluate side-chains 245 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 176 time to evaluate : 2.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 137 MET Chi-restraints excluded: chain C residue 147 TRP Chi-restraints excluded: chain C residue 152 PHE Chi-restraints excluded: chain C residue 188 SER Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 262 LYS Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 317 LYS Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 158 HIS Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 192 TRP Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain F residue 146 ASP Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain G residue 40 ASP Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain G residue 273 ILE Chi-restraints excluded: chain G residue 307 THR Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 303 TYR Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain H residue 347 ASN Chi-restraints excluded: chain H residue 350 ARG Chi-restraints excluded: chain H residue 353 VAL Chi-restraints excluded: chain I residue 30 LEU Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 250 ILE Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain I residue 274 HIS Chi-restraints excluded: chain I residue 282 LEU Chi-restraints excluded: chain I residue 298 ILE Chi-restraints excluded: chain I residue 353 VAL Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 200 HIS Chi-restraints excluded: chain B residue 211 PHE Chi-restraints excluded: chain B residue 225 GLN 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: 70.7197 > 50: distance: 19 - 73: 19.672 distance: 22 - 70: 37.035 distance: 64 - 66: 30.105 distance: 66 - 67: 12.434 distance: 68 - 69: 56.750 distance: 68 - 70: 55.715 distance: 71 - 72: 29.165 distance: 71 - 74: 57.314 distance: 72 - 73: 39.212 distance: 72 - 76: 10.930 distance: 74 - 75: 41.130 distance: 76 - 77: 67.857 distance: 77 - 78: 55.873 distance: 77 - 80: 56.436 distance: 78 - 79: 23.777 distance: 78 - 84: 55.776 distance: 80 - 81: 38.487 distance: 80 - 82: 40.474 distance: 81 - 83: 40.935 distance: 84 - 85: 41.649 distance: 85 - 86: 22.869 distance: 85 - 88: 64.446 distance: 86 - 87: 15.757 distance: 86 - 92: 31.082 distance: 88 - 89: 7.912 distance: 89 - 90: 7.628 distance: 89 - 91: 52.081 distance: 92 - 93: 56.542 distance: 92 - 98: 55.499 distance: 93 - 94: 68.907 distance: 93 - 96: 40.640 distance: 94 - 99: 28.162 distance: 97 - 98: 39.400 distance: 99 - 100: 47.075 distance: 100 - 101: 5.085 distance: 100 - 103: 37.842 distance: 101 - 102: 39.806 distance: 101 - 113: 39.121 distance: 103 - 104: 4.795 distance: 104 - 105: 11.553 distance: 105 - 107: 16.583 distance: 106 - 108: 18.945 distance: 106 - 109: 25.956 distance: 107 - 108: 20.843 distance: 108 - 110: 22.026 distance: 109 - 111: 12.786 distance: 114 - 115: 47.520 distance: 114 - 117: 52.601 distance: 115 - 116: 38.932 distance: 115 - 119: 46.730 distance: 117 - 118: 19.737 distance: 123 - 124: 16.739 distance: 124 - 125: 59.020 distance: 124 - 126: 48.531 distance: 127 - 128: 6.951 distance: 128 - 129: 33.551 distance: 128 - 131: 40.856 distance: 129 - 136: 56.922 distance: 132 - 133: 57.687 distance: 133 - 134: 55.567 distance: 133 - 135: 28.641 distance: 136 - 137: 56.761 distance: 137 - 138: 52.158 distance: 137 - 140: 55.840 distance: 138 - 139: 4.730 distance: 138 - 147: 31.489 distance: 140 - 141: 41.181 distance: 141 - 142: 40.866 distance: 142 - 143: 40.157 distance: 143 - 144: 50.776 distance: 144 - 145: 11.603 distance: 144 - 146: 26.613