Starting phenix.real_space_refine on Sun Sep 13 04:10:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6vqw_21359/09_2026/6vqw_21359.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vqw_21359/09_2026/6vqw_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6vqw_21359/09_2026/6vqw_21359.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6vqw_21359/09_2026/6vqw_21359.cif" model { file = "/net/cci-nas-00/data/ceres_data/6vqw_21359/09_2026/6vqw_21359.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vqw_21359/09_2026/6vqw_21359.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vqw_21359/09_2026/6vqw_21359.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vqw_21359/09_2026/6vqw_21359.map" } resolution = 3.42 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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: {'ARG:plan': 1, 'GLU: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: {'ARG:plan': 11, 'ASP:plan': 7, 'GLU:plan': 4, 'PHE:plan': 3, 'GLN:plan1': 6, 'HIS:plan': 3, 'TRP:plan': 1, 'ASN:plan1': 1} 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: {'PHE:plan': 2, 'ASN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 4, 'ASP:plan': 1, 'TRP:plan': 1} 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: {'ARG:plan': 18, 'GLN:plan1': 10, 'HIS:plan': 4, 'PHE:plan': 5, 'GLU:plan': 13, 'ASP:plan': 7, 'ASN:plan1': 5, 'TYR:plan': 1, 'TRP:plan': 5} Unresolved non-hydrogen planarities: 347 Chain: "K" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 845 Classifications: {'RNAv2': 40} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 10, 'rna3p_pur': 11, 'rna3p_pyr': 10} Link IDs: {'rna2p': 18, 'rna3p': 21} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.65, per 1000 atoms: 0.23 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: 1.61 Conformation dependent library (CDL) restraints added in 807.9 milliseconds 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: 2.20 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: 3.70 Time building geometry restraints manager: 2.25 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: 27488 2.37 - 4.75: 905 4.75 - 7.12: 96 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 - 17.05: 10482 17.05 - 34.11: 1282 34.11 - 51.16: 250 51.16 - 68.22: 105 68.22 - 85.27: 40 Dihedral angle restraints: 12159 sinusoidal: 4963 harmonic: 7196 Sorted by residual: dihedral pdb=" C4' A K 3 " pdb=" C3' A K 3 " pdb=" C2' A K 3 " pdb=" C1' A K 3 " ideal model delta sinusoidal sigma weight residual 36.34 -39.04 75.38 1 3.10e+00 1.04e-01 7.47e+02 dihedral pdb=" C4' C K 31 " pdb=" C3' C K 31 " pdb=" C2' C K 31 " pdb=" C1' C K 31 " ideal model delta sinusoidal sigma weight residual 36.35 -38.87 75.21 1 3.10e+00 1.04e-01 7.44e+02 dihedral pdb=" C4' A K 7 " pdb=" C3' A K 7 " pdb=" C2' A K 7 " pdb=" C1' A K 7 " ideal model delta sinusoidal sigma weight residual 36.34 -37.88 74.22 1 3.10e+00 1.04e-01 7.27e+02 ... (remaining 12156 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 2326 0.066 - 0.132: 622 0.132 - 0.198: 84 0.198 - 0.264: 41 0.264 - 0.330: 21 Chirality restraints: 3094 Sorted by residual: chirality pdb=" C2' C K 31 " pdb=" C3' C K 31 " pdb=" O2' C K 31 " pdb=" C1' C K 31 " both_signs ideal model delta sigma weight residual False -2.79 -2.46 -0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" C2' C K 29 " pdb=" C3' C K 29 " pdb=" O2' C K 29 " pdb=" C1' C K 29 " both_signs ideal model delta sigma weight residual False -2.79 -2.47 -0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" C2' G K 26 " pdb=" C3' G K 26 " pdb=" O2' G K 26 " pdb=" C1' G K 26 " both_signs ideal model delta sigma weight residual False -2.79 -2.47 -0.32 2.00e-01 2.50e+01 2.54e+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: 0.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 20.540 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 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= 0.440 Angle : 0.977 11.865 28509 Z= 0.519 Chirality : 0.067 0.330 3094 Planarity : 0.006 0.081 3683 Dihedral : 16.365 85.272 7655 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.022 0.001 ARG F 190 TYR 0.029 0.003 TYR D 303 PHE 0.027 0.003 PHE G 165 TRP 0.020 0.003 TRP D 329 HIS 0.011 0.002 HIS C 64 Details of bonding type rmsd/Z covalent geometry : bond 0.00974 / 0.44 (20935) covalent geometry : angle 0.97748 / 0.52 (28509) hydrogen bonds : bond 0.16953 / 11.38 ( 613) hydrogen bonds : angle 7.40985 / 5.10 ( 1713) *********************** 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 : 0.636 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: 0.8415 (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: 0.1634 time to fit residues: 55.0952 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 : 0.576 ------------------------------------------------------------------------------- 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 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.0470 chunk 20 optimal weight: 40.0000 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 40.0000 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 0.9980 overall best weight: 1.1680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 19 ASN C 69 GLN C 104 HIS D 50 GLN D 226 HIS D 309 GLN 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: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.110517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.080235 restraints weight = 45054.551| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 4.52 r_work: 0.3045 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20935 Z= 0.127 Angle : 0.725 14.865 28509 Z= 0.335 Chirality : 0.064 1.190 3094 Planarity : 0.004 0.062 3683 Dihedral : 10.234 162.807 3353 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 2.09 % Allowed : 16.17 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.92 (0.14), residues: 2610 helix: -2.10 (0.16), residues: 726 sheet: -1.56 (0.26), residues: 400 loop : -3.31 (0.13), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 133 TYR 0.017 0.001 TYR D 132 PHE 0.014 0.001 PHE D 165 TRP 0.017 0.001 TRP D 329 HIS 0.004 0.001 HIS H 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (20935) covalent geometry : angle 0.72468 / 0.34 (28509) hydrogen bonds : bond 0.03227 / 2.21 ( 613) hydrogen bonds : angle 5.20259 / 3.60 ( 1713) *********************** 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 260 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 220 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 89 ASN cc_start: 0.8098 (t0) cc_final: 0.7715 (t0) REVERT: C 106 GLU cc_start: 0.6409 (tt0) cc_final: 0.5912 (mt-10) REVERT: C 147 TRP cc_start: 0.6794 (OUTLIER) cc_final: 0.6126 (t60) REVERT: C 149 ASN cc_start: 0.8487 (m-40) cc_final: 0.8266 (m-40) REVERT: C 151 ARG cc_start: 0.8726 (pmt170) cc_final: 0.8339 (pmt170) REVERT: C 156 ASN cc_start: 0.8715 (p0) cc_final: 0.8315 (p0) REVERT: C 171 LYS cc_start: 0.9282 (tptt) cc_final: 0.8917 (tppt) REVERT: C 262 TYR cc_start: 0.8988 (m-10) cc_final: 0.8656 (m-10) REVERT: D 110 LYS cc_start: 0.7952 (tttt) cc_final: 0.6833 (mttp) REVERT: D 265 TYR cc_start: 0.8721 (t80) cc_final: 0.8478 (t80) REVERT: D 280 ASN cc_start: 0.8660 (t0) cc_final: 0.8084 (t0) REVERT: D 317 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8371 (mmtm) REVERT: D 328 ASN cc_start: 0.8965 (p0) cc_final: 0.8626 (p0) REVERT: D 347 ASN cc_start: 0.9340 (t0) cc_final: 0.9013 (t0) REVERT: F 37 ASP cc_start: 0.8531 (t70) cc_final: 0.7584 (p0) REVERT: F 286 ASP cc_start: 0.8156 (t0) cc_final: 0.7938 (t0) REVERT: G 286 ASP cc_start: 0.9095 (t0) cc_final: 0.8758 (t0) REVERT: H 321 ASP cc_start: 0.8510 (p0) cc_final: 0.8199 (p0) REVERT: I 298 ILE cc_start: 0.8041 (OUTLIER) cc_final: 0.7772 (mp) REVERT: A 46 GLU cc_start: 0.8463 (mm-30) cc_final: 0.7741 (tp30) REVERT: A 51 ASN cc_start: 0.8828 (m110) cc_final: 0.8568 (m110) REVERT: B 219 ARG cc_start: 0.8226 (tpm170) cc_final: 0.7457 (ptm-80) REVERT: B 235 TYR cc_start: 0.6036 (p90) cc_final: 0.5416 (p90) outliers start: 40 outliers final: 20 residues processed: 248 average time/residue: 0.1392 time to fit residues: 53.9968 Evaluate side-chains 205 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 182 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 SER 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 317 LYS 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 96 THR Chi-restraints excluded: chain I residue 263 THR 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 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 254 optimal weight: 50.0000 chunk 154 optimal weight: 0.0020 chunk 206 optimal weight: 10.0000 chunk 193 optimal weight: 5.9990 chunk 229 optimal weight: 10.0000 chunk 46 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 133 optimal weight: 5.9990 chunk 4 optimal weight: 9.9990 chunk 230 optimal weight: 20.0000 chunk 123 optimal weight: 4.9990 overall best weight: 4.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 72 GLN D 241 GLN E 147 GLN E 347 ASN H 347 ASN B 188 HIS B 230 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.105663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.075436 restraints weight = 46657.589| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 4.45 r_work: 0.2940 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 20935 Z= 0.289 Angle : 0.759 10.773 28509 Z= 0.366 Chirality : 0.058 0.849 3094 Planarity : 0.004 0.056 3683 Dihedral : 10.317 162.636 3351 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.96 % Favored : 89.04 % Rotamer: Outliers : 3.70 % Allowed : 18.15 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.52 (0.15), residues: 2610 helix: -1.35 (0.18), residues: 719 sheet: -1.72 (0.26), residues: 396 loop : -3.17 (0.14), residues: 1495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 268 TYR 0.026 0.002 TYR B 179 PHE 0.020 0.002 PHE G 165 TRP 0.017 0.002 TRP D 329 HIS 0.010 0.002 HIS B 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00645 / 0.29 (20935) covalent geometry : angle 0.75922 / 0.37 (28509) hydrogen bonds : bond 0.03408 / 2.32 ( 613) hydrogen bonds : angle 5.27952 / 3.68 ( 1713) *********************** 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 235 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 164 time to evaluate : 0.578 Fit side-chains revert: symmetry clash REVERT: C 67 GLU cc_start: 0.6346 (pm20) cc_final: 0.5748 (pm20) REVERT: C 106 GLU cc_start: 0.6512 (tt0) cc_final: 0.5980 (mt-10) REVERT: C 147 TRP cc_start: 0.7038 (OUTLIER) cc_final: 0.6214 (t60) REVERT: C 151 ARG cc_start: 0.8702 (pmt170) cc_final: 0.8354 (pmt170) REVERT: C 171 LYS cc_start: 0.9298 (tptt) cc_final: 0.8933 (tppt) REVERT: C 262 TYR cc_start: 0.8989 (m-10) cc_final: 0.8702 (m-10) REVERT: D 110 LYS cc_start: 0.7998 (tttt) cc_final: 0.6761 (mttt) REVERT: D 280 ASN cc_start: 0.8809 (t0) cc_final: 0.8254 (t0) REVERT: D 317 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8246 (mmtm) REVERT: D 328 ASN cc_start: 0.9006 (p0) cc_final: 0.8656 (p0) REVERT: D 347 ASN cc_start: 0.9380 (t0) cc_final: 0.9026 (t0) REVERT: E 68 ARG cc_start: 0.8087 (ttp80) cc_final: 0.7809 (ttp80) REVERT: F 37 ASP cc_start: 0.8747 (t70) cc_final: 0.7860 (t0) REVERT: F 268 ARG cc_start: 0.9201 (mtp-110) cc_final: 0.8970 (ptp-110) REVERT: F 286 ASP cc_start: 0.8418 (t0) cc_final: 0.8217 (t0) REVERT: G 93 ASN cc_start: 0.8421 (p0) cc_final: 0.8170 (p0) REVERT: H 248 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7590 (mp0) REVERT: I 228 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.7982 (tt) REVERT: I 298 ILE cc_start: 0.8226 (OUTLIER) cc_final: 0.8013 (mp) REVERT: A 46 GLU cc_start: 0.8516 (mm-30) cc_final: 0.7769 (tp30) REVERT: A 51 ASN cc_start: 0.8640 (m110) cc_final: 0.8387 (m110) REVERT: B 219 ARG cc_start: 0.8470 (tpm170) cc_final: 0.7758 (ptt90) outliers start: 71 outliers final: 42 residues processed: 223 average time/residue: 0.1399 time to fit residues: 48.9936 Evaluate side-chains 201 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 154 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 158 HIS 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 140 VAL Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 307 THR 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 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 353 VAL Chi-restraints excluded: chain I residue 30 LEU 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 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 213 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 189 optimal weight: 1.9990 chunk 151 optimal weight: 4.9990 chunk 261 optimal weight: 7.9990 chunk 14 optimal weight: 20.0000 chunk 27 optimal weight: 9.9990 chunk 136 optimal weight: 6.9990 chunk 246 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 347 ASN H 347 ASN B 188 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 = 0.3727 r_free = 0.3727 target = 0.108064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.077997 restraints weight = 46053.386| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 4.49 r_work: 0.3010 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20935 Z= 0.166 Angle : 0.643 8.637 28509 Z= 0.311 Chirality : 0.052 0.609 3094 Planarity : 0.004 0.054 3683 Dihedral : 10.182 164.575 3350 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 3.65 % Allowed : 19.04 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.13 (0.15), residues: 2610 helix: -0.89 (0.19), residues: 730 sheet: -1.59 (0.26), residues: 402 loop : -2.98 (0.14), residues: 1478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 268 TYR 0.018 0.001 TYR D 132 PHE 0.014 0.001 PHE G 165 TRP 0.016 0.001 TRP D 329 HIS 0.009 0.001 HIS E 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.17 (20935) covalent geometry : angle 0.64336 / 0.31 (28509) hydrogen bonds : bond 0.02966 / 2.02 ( 613) hydrogen bonds : angle 4.90045 / 3.41 ( 1713) *********************** 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 245 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 175 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 67 GLU cc_start: 0.6670 (pm20) cc_final: 0.6058 (pm20) REVERT: C 106 GLU cc_start: 0.6775 (tt0) cc_final: 0.6291 (mt-10) REVERT: C 147 TRP cc_start: 0.6769 (OUTLIER) cc_final: 0.6177 (t60) REVERT: C 151 ARG cc_start: 0.8677 (pmt170) cc_final: 0.8319 (ptt-90) REVERT: C 171 LYS cc_start: 0.9325 (tptt) cc_final: 0.8947 (tppt) REVERT: C 262 TYR cc_start: 0.9026 (m-10) cc_final: 0.8737 (m-10) REVERT: D 110 LYS cc_start: 0.8089 (tttt) cc_final: 0.6840 (mttp) REVERT: D 265 TYR cc_start: 0.8804 (t80) cc_final: 0.8546 (t80) REVERT: D 280 ASN cc_start: 0.8930 (t0) cc_final: 0.8476 (t0) REVERT: D 317 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8239 (mmtm) REVERT: D 328 ASN cc_start: 0.8897 (p0) cc_final: 0.8555 (p0) REVERT: D 347 ASN cc_start: 0.9378 (t0) cc_final: 0.8983 (t0) REVERT: E 68 ARG cc_start: 0.8205 (ttp80) cc_final: 0.7989 (ttp80) REVERT: F 37 ASP cc_start: 0.8638 (t70) cc_final: 0.7758 (t0) REVERT: F 43 MET cc_start: 0.8379 (mtt) cc_final: 0.8159 (mtt) REVERT: F 96 THR cc_start: 0.8858 (m) cc_final: 0.8553 (t) REVERT: F 268 ARG cc_start: 0.9125 (mtp-110) cc_final: 0.8895 (ptp-110) REVERT: F 286 ASP cc_start: 0.8426 (t0) cc_final: 0.8190 (t0) REVERT: G 40 ASP cc_start: 0.8757 (OUTLIER) cc_final: 0.8450 (t0) REVERT: G 93 ASN cc_start: 0.8654 (p0) cc_final: 0.8392 (p0) REVERT: H 248 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7748 (mp0) REVERT: H 321 ASP cc_start: 0.8698 (p0) cc_final: 0.8392 (p0) REVERT: I 282 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8919 (mm) REVERT: A 46 GLU cc_start: 0.8523 (mm-30) cc_final: 0.7850 (tp30) REVERT: A 51 ASN cc_start: 0.8755 (m110) cc_final: 0.8493 (m110) outliers start: 70 outliers final: 44 residues processed: 229 average time/residue: 0.1421 time to fit residues: 51.0681 Evaluate side-chains 213 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 164 time to evaluate : 0.768 ------------------------------------------------------------------------------- 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 147 TRP Chi-restraints excluded: chain C residue 188 SER 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 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 158 HIS 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 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 178 VAL Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain G residue 246 SER 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 30 LEU 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 282 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 160 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 30 optimal weight: 9.9990 chunk 147 optimal weight: 4.9990 chunk 250 optimal weight: 0.0270 chunk 192 optimal weight: 0.2980 chunk 222 optimal weight: 50.0000 chunk 104 optimal weight: 7.9990 chunk 176 optimal weight: 1.9990 chunk 112 optimal weight: 6.9990 chunk 162 optimal weight: 10.0000 overall best weight: 2.0644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 342 HIS H 347 ASN I 159 ASN I 274 HIS B 188 HIS B 230 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.109048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.078939 restraints weight = 45432.425| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 4.49 r_work: 0.3015 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2184 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= 0.141 Angle : 0.604 7.811 28509 Z= 0.293 Chirality : 0.049 0.407 3094 Planarity : 0.004 0.051 3683 Dihedral : 10.064 166.432 3350 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 4.07 % Allowed : 19.09 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.83 (0.15), residues: 2610 helix: -0.52 (0.20), residues: 721 sheet: -1.42 (0.26), residues: 408 loop : -2.85 (0.14), residues: 1481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 80 TYR 0.018 0.001 TYR D 132 PHE 0.013 0.001 PHE G 165 TRP 0.015 0.001 TRP D 329 HIS 0.008 0.001 HIS E 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (20935) covalent geometry : angle 0.60352 / 0.29 (28509) hydrogen bonds : bond 0.02778 / 1.89 ( 613) hydrogen bonds : angle 4.69758 / 3.28 ( 1713) *********************** 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 260 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 182 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 67 GLU cc_start: 0.6329 (pm20) cc_final: 0.5714 (pm20) REVERT: C 106 GLU cc_start: 0.6623 (tt0) cc_final: 0.6175 (mt-10) REVERT: C 147 TRP cc_start: 0.6616 (OUTLIER) cc_final: 0.6094 (t60) REVERT: C 171 LYS cc_start: 0.9295 (tptt) cc_final: 0.8934 (tppt) REVERT: C 262 TYR cc_start: 0.8988 (m-10) cc_final: 0.8705 (m-10) REVERT: D 110 LYS cc_start: 0.7992 (tttt) cc_final: 0.6777 (mttp) REVERT: D 280 ASN cc_start: 0.8860 (t0) cc_final: 0.8425 (t0) REVERT: D 317 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.8095 (mmtm) REVERT: D 328 ASN cc_start: 0.8977 (p0) cc_final: 0.8692 (p0) REVERT: D 347 ASN cc_start: 0.9365 (t0) cc_final: 0.8965 (t0) REVERT: E 68 ARG cc_start: 0.8108 (ttp80) cc_final: 0.7881 (ttp80) REVERT: E 132 TYR cc_start: 0.8824 (t80) cc_final: 0.8572 (t80) REVERT: E 192 TRP cc_start: 0.8876 (OUTLIER) cc_final: 0.7002 (m-90) REVERT: F 37 ASP cc_start: 0.8612 (t70) cc_final: 0.7678 (t0) REVERT: F 43 MET cc_start: 0.8318 (mtt) cc_final: 0.8091 (mtt) REVERT: F 96 THR cc_start: 0.8791 (m) cc_final: 0.8476 (t) REVERT: F 268 ARG cc_start: 0.9124 (mtp-110) cc_final: 0.8870 (ptp-110) REVERT: F 286 ASP cc_start: 0.8432 (t0) cc_final: 0.8182 (t0) REVERT: G 40 ASP cc_start: 0.8734 (OUTLIER) cc_final: 0.8422 (t0) REVERT: G 93 ASN cc_start: 0.8606 (p0) cc_final: 0.8320 (p0) REVERT: H 230 GLU cc_start: 0.8394 (tt0) cc_final: 0.8113 (tt0) REVERT: H 248 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7716 (mp0) REVERT: H 321 ASP cc_start: 0.8623 (p0) cc_final: 0.8329 (p0) REVERT: I 228 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.8026 (tt) REVERT: I 282 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8867 (mm) REVERT: I 323 TYR cc_start: 0.8051 (t80) cc_final: 0.7792 (t80) REVERT: A 46 GLU cc_start: 0.8495 (mm-30) cc_final: 0.7749 (tp30) REVERT: A 51 ASN cc_start: 0.8704 (m110) cc_final: 0.8448 (m110) outliers start: 78 outliers final: 55 residues processed: 245 average time/residue: 0.1443 time to fit residues: 55.4981 Evaluate side-chains 229 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 167 time to evaluate : 0.743 ------------------------------------------------------------------------------- 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 188 SER 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 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 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 99 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 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 306 VAL 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 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 123 THR Chi-restraints excluded: chain I residue 228 LEU Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain I residue 282 LEU Chi-restraints excluded: chain I residue 306 VAL 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 211 PHE 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 212 optimal weight: 9.9990 chunk 106 optimal weight: 9.9990 chunk 162 optimal weight: 8.9990 chunk 36 optimal weight: 9.9990 chunk 64 optimal weight: 6.9990 chunk 119 optimal weight: 7.9990 chunk 154 optimal weight: 7.9990 chunk 171 optimal weight: 0.9990 chunk 26 optimal weight: 9.9990 chunk 149 optimal weight: 1.9990 chunk 260 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 133 GLN C 282 ASN G 274 HIS H 347 ASN I 274 HIS B 188 HIS B 230 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.105537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.075260 restraints weight = 46577.828| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 4.45 r_work: 0.2944 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 20935 Z= 0.295 Angle : 0.735 9.461 28509 Z= 0.354 Chirality : 0.054 0.546 3094 Planarity : 0.004 0.051 3683 Dihedral : 10.386 171.090 3350 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.03 % Favored : 88.97 % Rotamer: Outliers : 4.96 % Allowed : 19.46 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.92 (0.16), residues: 2610 helix: -0.62 (0.20), residues: 719 sheet: -1.48 (0.25), residues: 432 loop : -2.90 (0.15), residues: 1459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 80 TYR 0.026 0.002 TYR B 179 PHE 0.019 0.002 PHE G 165 TRP 0.015 0.002 TRP D 329 HIS 0.009 0.001 HIS B 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00657 / 0.29 (20935) covalent geometry : angle 0.73460 / 0.35 (28509) hydrogen bonds : bond 0.03238 / 2.22 ( 613) hydrogen bonds : angle 5.07709 / 3.55 ( 1713) *********************** 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 254 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 159 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 67 GLU cc_start: 0.6520 (pm20) cc_final: 0.5731 (pm20) REVERT: C 106 GLU cc_start: 0.6539 (tt0) cc_final: 0.5991 (mt-10) REVERT: C 147 TRP cc_start: 0.6717 (OUTLIER) cc_final: 0.6079 (t60) REVERT: C 171 LYS cc_start: 0.9271 (tptt) cc_final: 0.8904 (tppt) REVERT: C 262 TYR cc_start: 0.9016 (m-10) cc_final: 0.8724 (m-10) REVERT: D 110 LYS cc_start: 0.7929 (tttt) cc_final: 0.6669 (mttp) REVERT: D 280 ASN cc_start: 0.8892 (t0) cc_final: 0.8415 (t0) REVERT: D 317 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.8115 (mmtm) REVERT: D 328 ASN cc_start: 0.8977 (p0) cc_final: 0.8680 (p0) REVERT: D 347 ASN cc_start: 0.9388 (t0) cc_final: 0.8965 (t0) REVERT: E 68 ARG cc_start: 0.8103 (ttp80) cc_final: 0.7835 (ttp80) REVERT: E 132 TYR cc_start: 0.8832 (t80) cc_final: 0.8574 (t80) REVERT: E 192 TRP cc_start: 0.8878 (OUTLIER) cc_final: 0.6853 (m-90) REVERT: F 37 ASP cc_start: 0.8597 (t70) cc_final: 0.7776 (t70) REVERT: F 43 MET cc_start: 0.8366 (mtt) cc_final: 0.8130 (mtt) REVERT: F 190 ARG cc_start: 0.7200 (OUTLIER) cc_final: 0.5683 (tmm160) REVERT: F 268 ARG cc_start: 0.9184 (mtp-110) cc_final: 0.8921 (ptp-110) REVERT: G 40 ASP cc_start: 0.8784 (OUTLIER) cc_final: 0.8428 (t0) REVERT: G 93 ASN cc_start: 0.8671 (p0) cc_final: 0.8359 (p0) REVERT: G 273 ILE cc_start: 0.7863 (OUTLIER) cc_final: 0.7511 (mt) REVERT: H 248 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7744 (mp0) REVERT: I 228 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8146 (tt) REVERT: A 46 GLU cc_start: 0.8495 (mm-30) cc_final: 0.7820 (tp30) REVERT: A 51 ASN cc_start: 0.8410 (m110) cc_final: 0.8141 (m110) REVERT: A 58 ASN cc_start: 0.7484 (OUTLIER) cc_final: 0.6843 (m110) REVERT: B 219 ARG cc_start: 0.8563 (tpm170) cc_final: 0.7776 (ptt90) outliers start: 95 outliers final: 63 residues processed: 239 average time/residue: 0.1381 time to fit residues: 52.2648 Evaluate side-chains 227 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 155 time to evaluate : 0.778 ------------------------------------------------------------------------------- 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 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 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 190 ARG 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 249 LEU 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 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 75 LEU Chi-restraints excluded: chain I residue 94 LEU 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 228 LEU Chi-restraints excluded: chain I residue 250 ILE Chi-restraints excluded: chain I residue 263 THR 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 200 HIS Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 230 HIS Chi-restraints excluded: chain B residue 240 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 156 optimal weight: 3.9990 chunk 252 optimal weight: 5.9990 chunk 236 optimal weight: 8.9990 chunk 188 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 17 optimal weight: 7.9990 chunk 28 optimal weight: 9.9990 chunk 210 optimal weight: 5.9990 chunk 179 optimal weight: 1.9990 chunk 61 optimal weight: 8.9990 chunk 117 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 347 ASN I 274 HIS B 225 GLN B 230 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.107322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.077412 restraints weight = 45771.699| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 4.45 r_work: 0.2986 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 20935 Z= 0.183 Angle : 0.643 8.260 28509 Z= 0.311 Chirality : 0.050 0.417 3094 Planarity : 0.004 0.051 3683 Dihedral : 10.233 172.416 3350 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 4.54 % Allowed : 20.34 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.75 (0.16), residues: 2610 helix: -0.39 (0.20), residues: 716 sheet: -1.54 (0.26), residues: 411 loop : -2.77 (0.15), residues: 1483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 80 TYR 0.020 0.001 TYR D 132 PHE 0.015 0.001 PHE G 165 TRP 0.015 0.001 TRP D 329 HIS 0.007 0.001 HIS E 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.18 (20935) covalent geometry : angle 0.64303 / 0.31 (28509) hydrogen bonds : bond 0.02919 / 1.99 ( 613) hydrogen bonds : angle 4.82045 / 3.36 ( 1713) *********************** 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 254 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 167 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 67 GLU cc_start: 0.6363 (pm20) cc_final: 0.5546 (pm20) REVERT: C 106 GLU cc_start: 0.6606 (tt0) cc_final: 0.6115 (mt-10) REVERT: C 147 TRP cc_start: 0.6557 (OUTLIER) cc_final: 0.6039 (t60) REVERT: C 171 LYS cc_start: 0.9293 (tptt) cc_final: 0.8930 (tppt) REVERT: D 110 LYS cc_start: 0.8006 (tttt) cc_final: 0.6784 (mttp) REVERT: D 280 ASN cc_start: 0.8987 (t0) cc_final: 0.8518 (t0) REVERT: D 317 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.8107 (mmtm) REVERT: D 328 ASN cc_start: 0.8930 (p0) cc_final: 0.8642 (p0) REVERT: D 347 ASN cc_start: 0.9381 (t0) cc_final: 0.8960 (t0) REVERT: E 68 ARG cc_start: 0.8099 (ttp80) cc_final: 0.7863 (ttp80) REVERT: E 132 TYR cc_start: 0.8829 (t80) cc_final: 0.8575 (t80) REVERT: E 192 TRP cc_start: 0.8852 (OUTLIER) cc_final: 0.6827 (m-90) REVERT: F 37 ASP cc_start: 0.8543 (t70) cc_final: 0.7623 (t0) REVERT: F 268 ARG cc_start: 0.9171 (mtp-110) cc_final: 0.8907 (ptp-110) REVERT: G 40 ASP cc_start: 0.8738 (OUTLIER) cc_final: 0.8406 (t0) REVERT: G 93 ASN cc_start: 0.8654 (p0) cc_final: 0.8353 (p0) REVERT: G 273 ILE cc_start: 0.7993 (OUTLIER) cc_final: 0.7708 (mt) REVERT: H 230 GLU cc_start: 0.8393 (tt0) cc_final: 0.8105 (tt0) REVERT: H 248 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7848 (mp0) REVERT: H 321 ASP cc_start: 0.8652 (p0) cc_final: 0.8398 (p0) REVERT: I 276 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.8177 (mt0) REVERT: I 282 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8650 (mm) REVERT: A 46 GLU cc_start: 0.8477 (mm-30) cc_final: 0.7821 (tp30) REVERT: A 51 ASN cc_start: 0.8530 (m110) cc_final: 0.8271 (m110) REVERT: A 58 ASN cc_start: 0.7677 (OUTLIER) cc_final: 0.7046 (m110) outliers start: 87 outliers final: 63 residues processed: 238 average time/residue: 0.1379 time to fit residues: 51.7671 Evaluate side-chains 237 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 165 time to evaluate : 0.627 ------------------------------------------------------------------------------- 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 188 SER 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 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 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 36 LEU 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 248 GLU Chi-restraints excluded: chain H residue 303 TYR Chi-restraints excluded: chain H residue 306 VAL 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 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 263 THR Chi-restraints excluded: chain I residue 276 GLN Chi-restraints excluded: chain I residue 282 LEU Chi-restraints excluded: chain I residue 303 TYR Chi-restraints excluded: chain I residue 306 VAL 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 A residue 58 ASN Chi-restraints excluded: chain B residue 178 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 230 HIS 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 37 optimal weight: 10.0000 chunk 98 optimal weight: 8.9990 chunk 257 optimal weight: 50.0000 chunk 41 optimal weight: 9.9990 chunk 17 optimal weight: 7.9990 chunk 30 optimal weight: 10.0000 chunk 69 optimal weight: 8.9990 chunk 223 optimal weight: 50.0000 chunk 58 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 7 optimal weight: 0.1980 overall best weight: 4.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 274 HIS B 188 HIS B 230 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.106754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.076474 restraints weight = 46397.695| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 4.46 r_work: 0.2961 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 20935 Z= 0.244 Angle : 0.689 8.394 28509 Z= 0.332 Chirality : 0.051 0.436 3094 Planarity : 0.004 0.051 3683 Dihedral : 10.300 173.974 3350 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.65 % Favored : 89.35 % Rotamer: Outliers : 4.85 % Allowed : 20.19 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.73 (0.16), residues: 2610 helix: -0.39 (0.20), residues: 716 sheet: -1.42 (0.25), residues: 436 loop : -2.80 (0.15), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 268 TYR 0.025 0.002 TYR D 265 PHE 0.017 0.002 PHE G 165 TRP 0.028 0.001 TRP C 316 HIS 0.006 0.001 HIS E 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.24 (20935) covalent geometry : angle 0.68915 / 0.33 (28509) hydrogen bonds : bond 0.03061 / 2.09 ( 613) hydrogen bonds : angle 4.91341 / 3.43 ( 1713) *********************** 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 258 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 165 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 67 GLU cc_start: 0.6422 (pm20) cc_final: 0.5596 (pm20) REVERT: C 106 GLU cc_start: 0.6594 (tt0) cc_final: 0.6104 (mt-10) REVERT: C 147 TRP cc_start: 0.6565 (OUTLIER) cc_final: 0.6011 (t60) REVERT: C 171 LYS cc_start: 0.9274 (tptt) cc_final: 0.8910 (tppt) REVERT: D 110 LYS cc_start: 0.7944 (tttt) cc_final: 0.6743 (mttp) REVERT: D 280 ASN cc_start: 0.8991 (t0) cc_final: 0.8543 (t0) REVERT: D 317 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.8105 (mmtm) REVERT: D 328 ASN cc_start: 0.8947 (p0) cc_final: 0.8666 (p0) REVERT: D 347 ASN cc_start: 0.9383 (t0) cc_final: 0.8945 (t0) REVERT: E 68 ARG cc_start: 0.8059 (ttp80) cc_final: 0.7639 (ttp80) REVERT: E 132 TYR cc_start: 0.8827 (t80) cc_final: 0.8572 (t80) REVERT: E 192 TRP cc_start: 0.8854 (OUTLIER) cc_final: 0.6804 (m-90) REVERT: F 37 ASP cc_start: 0.8565 (t70) cc_final: 0.7712 (t70) REVERT: F 268 ARG cc_start: 0.9185 (mtp-110) cc_final: 0.8925 (ptp-110) REVERT: G 40 ASP cc_start: 0.8766 (OUTLIER) cc_final: 0.8433 (t0) REVERT: G 93 ASN cc_start: 0.8681 (p0) cc_final: 0.8383 (p0) REVERT: G 273 ILE cc_start: 0.7986 (OUTLIER) cc_final: 0.7690 (mt) REVERT: H 133 ARG cc_start: 0.9318 (ttp80) cc_final: 0.8775 (ttp80) REVERT: H 248 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7878 (mp0) REVERT: I 276 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.8210 (mt0) REVERT: I 282 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8678 (mm) REVERT: I 289 TYR cc_start: 0.5096 (m-80) cc_final: 0.4822 (m-10) REVERT: A 46 GLU cc_start: 0.8478 (mm-30) cc_final: 0.7814 (tp30) REVERT: A 51 ASN cc_start: 0.8463 (m110) cc_final: 0.8200 (m110) REVERT: A 58 ASN cc_start: 0.7702 (OUTLIER) cc_final: 0.7072 (m110) REVERT: B 219 ARG cc_start: 0.8568 (tpm170) cc_final: 0.7805 (ptt90) outliers start: 93 outliers final: 70 residues processed: 239 average time/residue: 0.1318 time to fit residues: 50.0461 Evaluate side-chains 240 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 161 time to evaluate : 0.693 ------------------------------------------------------------------------------- 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 61 ILE 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 188 SER 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 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 169 ASN 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 40 ASP Chi-restraints excluded: chain G residue 44 SER 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 248 GLU Chi-restraints excluded: chain H residue 303 TYR Chi-restraints excluded: chain H residue 306 VAL 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 75 LEU Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 114 THR 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 276 GLN Chi-restraints excluded: chain I residue 282 LEU Chi-restraints excluded: chain I residue 303 TYR Chi-restraints excluded: chain I residue 306 VAL 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 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 240 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 163 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 11 optimal weight: 30.0000 chunk 195 optimal weight: 5.9990 chunk 180 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 219 optimal weight: 9.9990 chunk 139 optimal weight: 0.8980 chunk 226 optimal weight: 50.0000 chunk 45 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 114 HIS F 341 GLN G 274 HIS 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 = 0.3765 r_free = 0.3765 target = 0.110413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.080312 restraints weight = 45233.276| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 4.49 r_work: 0.3033 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.2544 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= 0.121 Angle : 0.606 14.047 28509 Z= 0.292 Chirality : 0.047 0.304 3094 Planarity : 0.004 0.050 3683 Dihedral : 10.049 174.699 3350 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 3.55 % Allowed : 21.70 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.47 (0.16), residues: 2610 helix: -0.09 (0.20), residues: 717 sheet: -1.28 (0.26), residues: 404 loop : -2.66 (0.15), residues: 1489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 268 TYR 0.022 0.001 TYR D 132 PHE 0.012 0.001 PHE G 165 TRP 0.016 0.001 TRP C 316 HIS 0.008 0.001 HIS E 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (20935) covalent geometry : angle 0.60588 / 0.29 (28509) hydrogen bonds : bond 0.02692 / 1.83 ( 613) hydrogen bonds : angle 4.54069 / 3.17 ( 1713) *********************** 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 262 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 194 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 67 GLU cc_start: 0.6294 (pm20) cc_final: 0.5662 (pm20) REVERT: C 106 GLU cc_start: 0.6570 (tt0) cc_final: 0.6128 (mt-10) REVERT: C 147 TRP cc_start: 0.6590 (OUTLIER) cc_final: 0.6144 (t60) REVERT: C 156 ASN cc_start: 0.8673 (p0) cc_final: 0.8314 (p0) REVERT: C 171 LYS cc_start: 0.9277 (tptt) cc_final: 0.8930 (tppt) REVERT: D 110 LYS cc_start: 0.7987 (tttt) cc_final: 0.6805 (mttt) REVERT: D 280 ASN cc_start: 0.8961 (t0) cc_final: 0.8498 (t0) REVERT: D 328 ASN cc_start: 0.8931 (p0) cc_final: 0.8655 (p0) REVERT: D 347 ASN cc_start: 0.9323 (t0) cc_final: 0.8956 (t0) REVERT: E 68 ARG cc_start: 0.8014 (ttp80) cc_final: 0.7643 (ttp80) REVERT: E 132 TYR cc_start: 0.8823 (t80) cc_final: 0.8585 (t80) REVERT: E 192 TRP cc_start: 0.8810 (OUTLIER) cc_final: 0.6786 (m-90) REVERT: F 37 ASP cc_start: 0.8449 (t70) cc_final: 0.7431 (t0) REVERT: F 43 MET cc_start: 0.8346 (mtt) cc_final: 0.7977 (mtt) REVERT: F 96 THR cc_start: 0.8732 (m) cc_final: 0.8421 (t) REVERT: G 40 ASP cc_start: 0.8734 (OUTLIER) cc_final: 0.8466 (t0) REVERT: G 93 ASN cc_start: 0.8636 (p0) cc_final: 0.8354 (p0) REVERT: H 133 ARG cc_start: 0.9302 (ttp80) cc_final: 0.8782 (ttp80) REVERT: H 230 GLU cc_start: 0.8297 (tt0) cc_final: 0.8009 (tt0) REVERT: H 248 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7721 (mp0) REVERT: H 321 ASP cc_start: 0.8556 (p0) cc_final: 0.8334 (p0) REVERT: A 46 GLU cc_start: 0.8441 (mm-30) cc_final: 0.7785 (tp30) REVERT: A 51 ASN cc_start: 0.8571 (m110) cc_final: 0.8290 (m110) REVERT: A 83 GLU cc_start: 0.6680 (tp30) cc_final: 0.6366 (tp30) outliers start: 68 outliers final: 50 residues processed: 246 average time/residue: 0.1345 time to fit residues: 52.7593 Evaluate side-chains 226 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 172 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 61 ILE 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 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 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 137 LEU 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 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 248 GLU Chi-restraints excluded: chain H residue 303 TYR Chi-restraints excluded: chain H residue 306 VAL 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 75 LEU Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 114 THR Chi-restraints excluded: chain I residue 263 THR 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 178 LEU Chi-restraints excluded: chain B residue 200 HIS Chi-restraints excluded: chain B residue 225 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 238 optimal weight: 3.9990 chunk 235 optimal weight: 0.8980 chunk 180 optimal weight: 0.0670 chunk 57 optimal weight: 3.9990 chunk 261 optimal weight: 9.9990 chunk 151 optimal weight: 5.9990 chunk 247 optimal weight: 0.3980 chunk 67 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 167 optimal weight: 10.0000 chunk 78 optimal weight: 0.3980 overall best weight: 1.1520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 247 GLN I 274 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.111032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.081069 restraints weight = 45109.245| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 4.50 r_work: 0.3057 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 20935 Z= 0.109 Angle : 0.596 14.039 28509 Z= 0.288 Chirality : 0.046 0.268 3094 Planarity : 0.004 0.048 3683 Dihedral : 9.921 173.890 3350 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 2.97 % Allowed : 22.90 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.28 (0.16), residues: 2610 helix: 0.10 (0.21), residues: 713 sheet: -0.90 (0.28), residues: 377 loop : -2.62 (0.15), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 224 TYR 0.022 0.001 TYR D 132 PHE 0.010 0.001 PHE D 165 TRP 0.015 0.001 TRP D 329 HIS 0.007 0.001 HIS E 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (20935) covalent geometry : angle 0.59607 / 0.29 (28509) hydrogen bonds : bond 0.02579 / 1.76 ( 613) hydrogen bonds : angle 4.42882 / 3.08 ( 1713) ********************** 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 252 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 195 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 67 GLU cc_start: 0.6320 (pm20) cc_final: 0.5792 (pm20) REVERT: C 79 LYS cc_start: 0.7872 (mttm) cc_final: 0.7661 (ttmm) REVERT: C 106 GLU cc_start: 0.6597 (tt0) cc_final: 0.6129 (mt-10) REVERT: C 147 TRP cc_start: 0.6556 (OUTLIER) cc_final: 0.6167 (t60) REVERT: C 156 ASN cc_start: 0.8695 (p0) cc_final: 0.8328 (p0) REVERT: C 171 LYS cc_start: 0.9280 (tptt) cc_final: 0.8933 (tppt) REVERT: D 33 GLU cc_start: 0.8468 (tt0) cc_final: 0.7737 (mm-30) REVERT: D 110 LYS cc_start: 0.8006 (tttt) cc_final: 0.6806 (mttp) REVERT: D 280 ASN cc_start: 0.8983 (t0) cc_final: 0.8493 (t0) REVERT: D 311 LYS cc_start: 0.8385 (mtmm) cc_final: 0.7977 (mtmm) REVERT: D 317 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8163 (mmtm) REVERT: D 328 ASN cc_start: 0.8926 (p0) cc_final: 0.8667 (p0) REVERT: D 347 ASN cc_start: 0.9337 (t0) cc_final: 0.8974 (t0) REVERT: E 68 ARG cc_start: 0.8040 (ttp80) cc_final: 0.7674 (ttp80) REVERT: E 80 ARG cc_start: 0.8799 (mmp-170) cc_final: 0.8435 (mmp-170) REVERT: E 192 TRP cc_start: 0.8752 (OUTLIER) cc_final: 0.6842 (m-90) REVERT: F 37 ASP cc_start: 0.8416 (t70) cc_final: 0.7413 (t0) REVERT: F 43 MET cc_start: 0.8340 (mtt) cc_final: 0.7996 (mtt) REVERT: F 51 ARG cc_start: 0.7839 (mmt180) cc_final: 0.7569 (mmt-90) REVERT: F 96 THR cc_start: 0.8747 (m) cc_final: 0.8438 (t) REVERT: G 40 ASP cc_start: 0.8730 (OUTLIER) cc_final: 0.8510 (t0) REVERT: G 93 ASN cc_start: 0.8761 (p0) cc_final: 0.8480 (p0) REVERT: G 158 HIS cc_start: 0.6048 (OUTLIER) cc_final: 0.5787 (m170) REVERT: H 133 ARG cc_start: 0.9273 (ttp80) cc_final: 0.8729 (ttp80) REVERT: H 168 ARG cc_start: 0.8674 (ttt180) cc_final: 0.8371 (ttt180) REVERT: H 230 GLU cc_start: 0.8309 (tt0) cc_final: 0.8056 (tt0) REVERT: H 248 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.7750 (mp0) REVERT: H 321 ASP cc_start: 0.8582 (p0) cc_final: 0.8294 (p0) REVERT: A 46 GLU cc_start: 0.8410 (mm-30) cc_final: 0.7779 (tp30) REVERT: A 51 ASN cc_start: 0.8524 (m110) cc_final: 0.8245 (m110) REVERT: A 58 ASN cc_start: 0.7759 (OUTLIER) cc_final: 0.7126 (m110) REVERT: A 83 GLU cc_start: 0.6545 (tp30) cc_final: 0.6260 (tp30) outliers start: 57 outliers final: 39 residues processed: 237 average time/residue: 0.1409 time to fit residues: 52.0044 Evaluate side-chains 227 residues out of total 2133 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 181 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 137 MET Chi-restraints excluded: chain C residue 147 TRP Chi-restraints excluded: chain C residue 313 LEU 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 42 LEU Chi-restraints excluded: chain F residue 137 LEU Chi-restraints excluded: chain F residue 140 VAL Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 306 VAL 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 330 VAL 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 I residue 30 LEU Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 200 HIS Chi-restraints excluded: chain B residue 235 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 29 optimal weight: 5.9990 chunk 165 optimal weight: 7.9990 chunk 171 optimal weight: 5.9990 chunk 176 optimal weight: 6.9990 chunk 229 optimal weight: 30.0000 chunk 121 optimal weight: 8.9990 chunk 224 optimal weight: 3.9990 chunk 203 optimal weight: 0.0970 chunk 59 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 146 optimal weight: 3.9990 overall best weight: 1.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.110174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.080207 restraints weight = 45259.879| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 4.48 r_work: 0.3040 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2776 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= 0.138 Angle : 0.608 13.379 28509 Z= 0.294 Chirality : 0.046 0.294 3094 Planarity : 0.004 0.046 3683 Dihedral : 9.915 173.017 3348 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 2.82 % Allowed : 23.16 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.23 (0.16), residues: 2610 helix: 0.13 (0.20), residues: 713 sheet: -0.89 (0.27), residues: 392 loop : -2.60 (0.15), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 190 TYR 0.022 0.001 TYR D 132 PHE 0.014 0.001 PHE I 194 TRP 0.015 0.001 TRP C 316 HIS 0.007 0.001 HIS E 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (20935) covalent geometry : angle 0.60822 / 0.29 (28509) hydrogen bonds : bond 0.02621 / 1.78 ( 613) hydrogen bonds : angle 4.40506 / 3.05 ( 1713) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4826.53 seconds wall clock time: 83 minutes 23.33 seconds (5003.33 seconds total)