Starting phenix.real_space_refine on Sat Sep 28 23:15:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqw_21359/09_2024/6vqw_21359.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqw_21359/09_2024/6vqw_21359.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqw_21359/09_2024/6vqw_21359.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqw_21359/09_2024/6vqw_21359.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqw_21359/09_2024/6vqw_21359.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqw_21359/09_2024/6vqw_21359.cif" } resolution = 3.42 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.016 sd= 0.098 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 39 5.49 5 S 17 5.16 5 C 12609 2.51 5 N 3779 2.21 5 O 4035 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 20479 Number of models: 1 Model: "" Number of chains: 11 Chain: "C" Number of atoms: 2309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2309 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 22, 'TRANS': 274} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 2272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2272 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 10, 'TRANS': 282} Chain breaks: 2 Chain: "E" Number of atoms: 2575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2575 Classifications: {'peptide': 333} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 320} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 2587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2587 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 12, 'TRANS': 321} Chain: "G" Number of atoms: 2559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2559 Classifications: {'peptide': 331} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 318} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 2516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2516 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 312} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 2523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2523 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 313} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "J" Number of atoms: 350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 350 Classifications: {'peptide': 87} Incomplete info: {'backbone_only': 80} Link IDs: {'PTRANS': 6, 'TRANS': 80} Chain breaks: 1 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 353 Unresolved non-hydrogen angles: 506 Unresolved non-hydrogen dihedrals: 225 Unresolved non-hydrogen chiralities: 101 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 7, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 176 Chain: "A" Number of atoms: 552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 552 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 1, 'TRANS': 78} Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 58 Chain: "B" Number of atoms: 1391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1391 Classifications: {'peptide': 242} Incomplete info: {'backbone_only': 133} Link IDs: {'PTRANS': 16, 'TRANS': 225} Chain breaks: 2 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 616 Unresolved non-hydrogen angles: 885 Unresolved non-hydrogen dihedrals: 410 Unresolved non-hydrogen chiralities: 163 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 5, 'ASP:plan': 7, 'PHE:plan': 5, 'GLU:plan': 13, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 347 Chain: "K" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 845 Classifications: {'RNA': 40} Modifications used: {'5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 10, 'rna3p_pur': 11, 'rna3p_pyr': 10} Link IDs: {'rna2p': 18, 'rna3p': 21} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 12.31, per 1000 atoms: 0.60 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: 4.53 Conformation dependent library (CDL) restraints added in 2.9 seconds 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4504 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 38 sheets defined 26.2% alpha, 14.2% beta 0 base pairs and 10 stacking pairs defined. Time for finding SS restraints: 6.88 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: 5.73 Time building geometry restraints manager: 5.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4849 1.33 - 1.45: 4762 1.45 - 1.57: 11221 1.57 - 1.70: 78 1.70 - 1.82: 25 Bond restraints: 20935 Sorted by residual: bond pdb=" C SER C 33 " pdb=" N PRO C 34 " ideal model delta sigma weight residual 1.334 1.307 0.026 8.40e-03 1.42e+04 9.75e+00 bond pdb=" C THR G 96 " pdb=" N VAL G 97 " ideal model delta sigma weight residual 1.330 1.283 0.047 1.97e-02 2.58e+03 5.73e+00 bond pdb=" CG GLN H 241 " pdb=" CD GLN H 241 " ideal model delta sigma weight residual 1.516 1.463 0.053 2.50e-02 1.60e+03 4.56e+00 bond pdb=" N LYS E 256 " pdb=" CA LYS E 256 " ideal model delta sigma weight residual 1.457 1.485 -0.027 1.29e-02 6.01e+03 4.51e+00 bond pdb=" CB GLN G 276 " pdb=" CG GLN G 276 " ideal model delta sigma weight residual 1.520 1.459 0.061 3.00e-02 1.11e+03 4.07e+00 ... (remaining 20930 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 27607 2.37 - 4.75: 815 4.75 - 7.12: 67 7.12 - 9.49: 13 9.49 - 11.86: 7 Bond angle restraints: 28509 Sorted by residual: angle pdb=" C LYS H 76 " pdb=" N THR H 77 " pdb=" CA THR H 77 " ideal model delta sigma weight residual 121.54 129.86 -8.32 1.91e+00 2.74e-01 1.90e+01 angle pdb=" C ILE G 278 " pdb=" N GLY G 279 " pdb=" CA GLY G 279 " ideal model delta sigma weight residual 122.97 115.15 7.82 1.84e+00 2.95e-01 1.81e+01 angle pdb=" C ARG B 224 " pdb=" N GLN B 225 " pdb=" CA GLN B 225 " ideal model delta sigma weight residual 122.46 128.16 -5.70 1.41e+00 5.03e-01 1.64e+01 angle pdb=" C SER B 227 " pdb=" N TRP B 228 " pdb=" CA TRP B 228 " ideal model delta sigma weight residual 120.09 125.14 -5.05 1.25e+00 6.40e-01 1.63e+01 angle pdb=" N GLN H 185 " pdb=" CA GLN H 185 " pdb=" C GLN H 185 " ideal model delta sigma weight residual 110.80 102.38 8.42 2.13e+00 2.20e-01 1.56e+01 ... (remaining 28504 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.14: 11741 30.14 - 60.28: 481 60.28 - 90.42: 83 90.42 - 120.55: 1 120.55 - 150.69: 1 Dihedral angle restraints: 12307 sinusoidal: 5111 harmonic: 7196 Sorted by residual: dihedral pdb=" O4' U K 21 " pdb=" C1' U K 21 " pdb=" N1 U K 21 " pdb=" C2 U K 21 " ideal model delta sinusoidal sigma weight residual 200.00 49.31 150.69 1 1.50e+01 4.44e-03 7.99e+01 dihedral pdb=" O4' U K 35 " pdb=" C1' U K 35 " pdb=" N1 U K 35 " pdb=" C2 U K 35 " ideal model delta sinusoidal sigma weight residual -160.00 -87.71 -72.29 1 1.50e+01 4.44e-03 2.97e+01 dihedral pdb=" CA ASN G 159 " pdb=" C ASN G 159 " pdb=" N LEU G 160 " pdb=" CA LEU G 160 " ideal model delta harmonic sigma weight residual 180.00 153.98 26.02 0 5.00e+00 4.00e-02 2.71e+01 ... (remaining 12304 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2145 0.056 - 0.112: 798 0.112 - 0.168: 122 0.168 - 0.225: 27 0.225 - 0.281: 2 Chirality restraints: 3094 Sorted by residual: chirality pdb=" CB VAL A 44 " pdb=" CA VAL A 44 " pdb=" CG1 VAL A 44 " pdb=" CG2 VAL A 44 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CB VAL C 59 " pdb=" CA VAL C 59 " pdb=" CG1 VAL C 59 " pdb=" CG2 VAL C 59 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CB THR H 96 " pdb=" CA THR H 96 " pdb=" OG1 THR H 96 " pdb=" CG2 THR H 96 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 3091 not shown) Planarity restraints: 3683 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 154 " -0.054 5.00e-02 4.00e+02 8.09e-02 1.05e+01 pdb=" N PRO C 155 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO C 155 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO C 155 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 33 " -0.045 5.00e-02 4.00e+02 6.81e-02 7.43e+00 pdb=" N PRO C 34 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO C 34 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 34 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR E 289 " 0.045 5.00e-02 4.00e+02 6.77e-02 7.33e+00 pdb=" N PRO E 290 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO E 290 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO E 290 " 0.037 5.00e-02 4.00e+02 ... (remaining 3680 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 5133 2.78 - 3.31: 18181 3.31 - 3.84: 33556 3.84 - 4.37: 37718 4.37 - 4.90: 63621 Nonbonded interactions: 158209 Sorted by model distance: nonbonded pdb=" OG SER F 54 " pdb=" OE1 GLN F 55 " model vdw 2.245 3.040 nonbonded pdb=" O GLY E 46 " pdb=" OG1 THR E 108 " model vdw 2.273 3.040 nonbonded pdb=" OD2 ASP G 40 " pdb=" OH TYR G 265 " model vdw 2.275 3.040 nonbonded pdb=" OH TYR H 289 " pdb=" O GLY H 296 " model vdw 2.283 3.040 nonbonded pdb=" O GLY I 46 " pdb=" OG1 THR I 108 " model vdw 2.296 3.040 ... (remaining 158204 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'D' and resid 26 through 355) selection = (chain 'E' and (resid 26 through 66 or resid 95 through 249 or resid 262 through \ 355)) selection = (chain 'F' and (resid 26 through 66 or resid 95 through 249 or resid 262 through \ 355)) selection = (chain 'G' and (resid 26 through 66 or resid 95 through 249 or resid 262 through \ 355)) selection = (chain 'H' and (resid 26 through 66 or resid 95 through 249 or resid 262 through \ 355)) selection = (chain 'I' and (resid 26 through 66 or resid 95 through 249 or resid 262 through \ 355)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.800 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: 0.020 Extract box with map and model: 0.730 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 49.010 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.080 20935 Z= 0.640 Angle : 0.940 11.865 28509 Z= 0.512 Chirality : 0.057 0.281 3094 Planarity : 0.006 0.081 3683 Dihedral : 16.438 150.693 7803 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.10 % Favored : 86.90 % Rotamer: Outliers : 0.57 % Allowed : 14.92 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.04 (0.12), residues: 2610 helix: -3.67 (0.11), residues: 727 sheet: -2.07 (0.24), residues: 419 loop : -3.70 (0.12), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP D 329 HIS 0.011 0.002 HIS C 64 PHE 0.027 0.003 PHE G 165 TYR 0.029 0.003 TYR D 303 ARG 0.022 0.001 ARG F 190 *********************** 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 fitting. rotamer outliers: 11 poor density : 217 time to evaluate : 2.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 151 ARG cc_start: 0.8804 (pmt170) cc_final: 0.8354 (pmt170) REVERT: C 171 LYS cc_start: 0.9377 (tptt) cc_final: 0.8953 (tppt) REVERT: C 262 TYR cc_start: 0.9056 (m-10) cc_final: 0.8705 (m-10) REVERT: E 68 ARG cc_start: 0.8138 (ttt-90) cc_final: 0.7680 (ttp-170) REVERT: E 132 TYR cc_start: 0.8841 (t80) cc_final: 0.8557 (t80) REVERT: F 37 ASP cc_start: 0.8414 (t70) cc_final: 0.8099 (t70) REVERT: F 301 GLU cc_start: 0.8306 (mm-30) cc_final: 0.7986 (mm-30) REVERT: G 93 ASN cc_start: 0.8590 (p0) cc_final: 0.8315 (p0) REVERT: G 134 ASP cc_start: 0.9154 (t0) cc_final: 0.8926 (t0) REVERT: G 252 ASP cc_start: 0.7084 (t0) cc_final: 0.6487 (p0) REVERT: H 78 LYS cc_start: 0.8761 (tptp) cc_final: 0.8301 (tptp) REVERT: H 264 LEU cc_start: 0.8514 (mt) cc_final: 0.8116 (mt) REVERT: H 301 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8472 (mm-30) REVERT: I 50 GLN cc_start: 0.8996 (tt0) cc_final: 0.8529 (tm-30) REVERT: I 298 ILE cc_start: 0.8882 (mp) cc_final: 0.8560 (mp) REVERT: I 301 GLU cc_start: 0.8632 (tp30) cc_final: 0.8407 (tp30) REVERT: A 46 GLU cc_start: 0.8661 (mm-30) cc_final: 0.7743 (tp30) REVERT: A 51 ASN cc_start: 0.8839 (m110) cc_final: 0.8504 (m110) REVERT: A 85 ASN cc_start: 0.7693 (t0) cc_final: 0.7160 (t0) REVERT: B 219 ARG cc_start: 0.8356 (tpm170) cc_final: 0.7409 (ptm-80) REVERT: B 235 TYR cc_start: 0.5804 (p90) cc_final: 0.5525 (p90) outliers start: 11 outliers final: 5 residues processed: 226 average time/residue: 0.3646 time to fit residues: 121.7926 Evaluate side-chains 167 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 162 time to evaluate : 2.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain G residue 333 ASP Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain I residue 353 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 223 optimal weight: 50.0000 chunk 200 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 135 optimal weight: 7.9990 chunk 107 optimal weight: 0.6980 chunk 207 optimal weight: 7.9990 chunk 80 optimal weight: 0.8980 chunk 126 optimal weight: 0.9980 chunk 154 optimal weight: 3.9990 chunk 240 optimal weight: 8.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 19 ASN C 69 GLN C 104 HIS D 50 GLN D 226 HIS D 315 GLN D 318 GLN D 340 GLN D 341 GLN E 55 GLN E 101 ASN E 169 ASN E 342 HIS F 93 ASN F 147 GLN F 181 ASN F 182 HIS F 309 GLN F 341 GLN F 347 ASN G 73 ASN G 226 HIS G 318 GLN H 73 ASN H 181 ASN H 341 GLN H 347 ASN I 90 GLN I 101 ASN I 182 HIS I 241 GLN I 274 HIS I 309 GLN I 347 ASN B 188 HIS B 230 HIS Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 20935 Z= 0.155 Angle : 0.530 7.902 28509 Z= 0.280 Chirality : 0.040 0.167 3094 Planarity : 0.004 0.061 3683 Dihedral : 13.244 147.493 3501 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 2.03 % Allowed : 16.33 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.89 (0.14), residues: 2610 helix: -2.05 (0.16), residues: 726 sheet: -1.53 (0.26), residues: 399 loop : -3.31 (0.13), residues: 1485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 329 HIS 0.005 0.001 HIS H 158 PHE 0.013 0.001 PHE D 165 TYR 0.018 0.001 TYR D 132 ARG 0.006 0.000 ARG E 63 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5220 Ramachandran restraints generated. 2610 Oldfield, 0 Emsley, 2610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 225 time to evaluate : 2.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 89 ASN cc_start: 0.8362 (t0) cc_final: 0.7912 (t0) REVERT: C 106 GLU cc_start: 0.6409 (tt0) cc_final: 0.5956 (mt-10) REVERT: C 147 TRP cc_start: 0.6810 (OUTLIER) cc_final: 0.6293 (t60) REVERT: C 151 ARG cc_start: 0.8564 (pmt170) cc_final: 0.8218 (pmt170) REVERT: C 156 ASN cc_start: 0.8782 (p0) cc_final: 0.8393 (p0) REVERT: C 171 LYS cc_start: 0.9356 (tptt) cc_final: 0.8966 (tppt) REVERT: C 262 TYR cc_start: 0.9022 (m-10) cc_final: 0.8699 (m-10) REVERT: D 110 LYS cc_start: 0.8050 (tttt) cc_final: 0.6972 (mttp) REVERT: D 328 ASN cc_start: 0.8569 (p0) cc_final: 0.8241 (p0) REVERT: D 347 ASN cc_start: 0.9248 (t0) cc_final: 0.8874 (t0) REVERT: F 37 ASP cc_start: 0.8150 (t70) cc_final: 0.7570 (p0) REVERT: G 286 ASP cc_start: 0.9050 (t0) cc_final: 0.8723 (t0) REVERT: H 321 ASP cc_start: 0.8496 (p0) cc_final: 0.8245 (p0) REVERT: I 274 HIS cc_start: 0.7725 (OUTLIER) cc_final: 0.6949 (m90) REVERT: I 298 ILE cc_start: 0.8325 (OUTLIER) cc_final: 0.8034 (mp) REVERT: A 45 LYS cc_start: 0.7555 (mtmm) cc_final: 0.6683 (pttp) REVERT: A 46 GLU cc_start: 0.8573 (mm-30) cc_final: 0.7827 (tp30) REVERT: A 51 ASN cc_start: 0.9021 (m110) cc_final: 0.8757 (m110) REVERT: A 85 ASN cc_start: 0.7794 (t0) cc_final: 0.7582 (t0) REVERT: B 219 ARG cc_start: 0.8115 (tpm170) cc_final: 0.7411 (ptm-80) REVERT: B 235 TYR cc_start: 0.5571 (p90) cc_final: 0.5022 (p90) outliers start: 39 outliers final: 18 residues processed: 251 average time/residue: 0.3190 time to fit residues: 123.8610 Evaluate side-chains 203 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 182 time to evaluate : 2.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 147 TRP Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain I residue 274 HIS Chi-restraints excluded: chain I residue 298 ILE Chi-restraints excluded: chain I residue 349 ILE Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 211 PHE Chi-restraints excluded: chain B residue 230 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 133 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 chunk 200 optimal weight: 8.9990 chunk 163 optimal weight: 0.0020 chunk 66 optimal weight: 0.9990 chunk 241 optimal weight: 8.9990 chunk 260 optimal weight: 8.9990 chunk 214 optimal weight: 10.0000 chunk 239 optimal weight: 8.9990 chunk 82 optimal weight: 8.9990 chunk 193 optimal weight: 6.9990 overall best weight: 4.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 72 GLN D 309 GLN E 147 GLN E 347 ASN H 347 ASN I 274 HIS B 188 HIS B 230 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 20935 Z= 0.352 Angle : 0.608 7.601 28509 Z= 0.316 Chirality : 0.042 0.183 3094 Planarity : 0.004 0.056 3683 Dihedral : 13.193 150.492 3497 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.15 % Favored : 89.85 % Rotamer: Outliers : 3.34 % Allowed : 17.74 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.45 (0.15), residues: 2610 helix: -1.27 (0.18), residues: 722 sheet: -1.66 (0.26), residues: 395 loop : -3.15 (0.13), residues: 1493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 329 HIS 0.013 0.002 HIS I 274 PHE 0.019 0.002 PHE G 165 TYR 0.023 0.002 TYR B 179 ARG 0.005 0.000 ARG D 268 *********************** 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 238 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 174 time to evaluate : 2.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 67 GLU cc_start: 0.6349 (pm20) cc_final: 0.5771 (pm20) REVERT: C 106 GLU cc_start: 0.6451 (tt0) cc_final: 0.5961 (mt-10) REVERT: C 147 TRP cc_start: 0.7046 (OUTLIER) cc_final: 0.6331 (t60) REVERT: C 151 ARG cc_start: 0.8580 (pmt170) cc_final: 0.8251 (pmt170) REVERT: C 171 LYS cc_start: 0.9381 (tptt) cc_final: 0.8988 (tppt) REVERT: C 262 TYR cc_start: 0.9017 (m-10) cc_final: 0.8721 (m-10) REVERT: D 110 LYS cc_start: 0.8105 (tttt) cc_final: 0.6882 (mttp) REVERT: D 317 LYS cc_start: 0.8552 (mmtm) cc_final: 0.8243 (mmtm) REVERT: D 328 ASN cc_start: 0.8614 (p0) cc_final: 0.8252 (p0) REVERT: D 347 ASN cc_start: 0.9289 (t0) cc_final: 0.8833 (t0) REVERT: E 68 ARG cc_start: 0.8260 (ttp80) cc_final: 0.7731 (ttp80) REVERT: F 37 ASP cc_start: 0.8269 (t70) cc_final: 0.7587 (t0) REVERT: F 268 ARG cc_start: 0.8724 (mtp-110) cc_final: 0.8522 (ptp-110) REVERT: G 93 ASN cc_start: 0.8472 (p0) cc_final: 0.8214 (p0) REVERT: H 248 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7415 (mp0) REVERT: I 298 ILE cc_start: 0.8375 (OUTLIER) cc_final: 0.8144 (mp) REVERT: A 46 GLU cc_start: 0.8590 (mm-30) cc_final: 0.7889 (tp30) REVERT: A 51 ASN cc_start: 0.8910 (m110) cc_final: 0.8649 (m110) REVERT: A 85 ASN cc_start: 0.7760 (t0) cc_final: 0.7544 (t0) outliers start: 64 outliers final: 45 residues processed: 230 average time/residue: 0.3280 time to fit residues: 115.4203 Evaluate side-chains 207 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 159 time to evaluate : 2.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 147 TRP Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 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 306 VAL Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 248 GLU Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain H residue 347 ASN Chi-restraints excluded: chain 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 94 LEU Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain I residue 274 HIS Chi-restraints excluded: chain I residue 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 238 optimal weight: 10.0000 chunk 181 optimal weight: 4.9990 chunk 125 optimal weight: 0.3980 chunk 26 optimal weight: 8.9990 chunk 115 optimal weight: 0.7980 chunk 161 optimal weight: 1.9990 chunk 241 optimal weight: 0.9980 chunk 256 optimal weight: 5.9990 chunk 126 optimal weight: 0.9990 chunk 229 optimal weight: 30.0000 chunk 69 optimal weight: 7.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 347 ASN H 347 ASN I 274 HIS B 188 HIS B 200 HIS B 230 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 20935 Z= 0.149 Angle : 0.504 7.076 28509 Z= 0.264 Chirality : 0.040 0.140 3094 Planarity : 0.004 0.053 3683 Dihedral : 13.007 149.854 3497 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 2.92 % Allowed : 18.62 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.15), residues: 2610 helix: -0.72 (0.19), residues: 728 sheet: -1.22 (0.27), residues: 400 loop : -2.95 (0.14), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 329 HIS 0.015 0.001 HIS I 274 PHE 0.014 0.001 PHE B 232 TYR 0.017 0.001 TYR D 265 ARG 0.006 0.000 ARG D 268 *********************** 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 244 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 188 time to evaluate : 2.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 67 GLU cc_start: 0.6372 (pm20) cc_final: 0.5833 (pm20) REVERT: C 106 GLU cc_start: 0.6500 (tt0) cc_final: 0.6122 (mt-10) REVERT: C 147 TRP cc_start: 0.6441 (OUTLIER) cc_final: 0.6123 (t60) REVERT: C 156 ASN cc_start: 0.8790 (p0) cc_final: 0.8428 (p0) REVERT: C 171 LYS cc_start: 0.9368 (tptt) cc_final: 0.8992 (tppt) REVERT: C 262 TYR cc_start: 0.8989 (m-10) cc_final: 0.8687 (m-10) REVERT: D 33 GLU cc_start: 0.8324 (tt0) cc_final: 0.7913 (pm20) REVERT: D 110 LYS cc_start: 0.8073 (tttt) cc_final: 0.6955 (mttp) REVERT: D 317 LYS cc_start: 0.8505 (mmtm) cc_final: 0.8165 (mmtm) REVERT: D 328 ASN cc_start: 0.8594 (p0) cc_final: 0.8287 (p0) REVERT: D 347 ASN cc_start: 0.9268 (t0) cc_final: 0.8844 (t0) REVERT: E 68 ARG cc_start: 0.8334 (ttp80) cc_final: 0.7892 (ttp80) REVERT: F 37 ASP cc_start: 0.8299 (t70) cc_final: 0.7520 (p0) REVERT: F 43 MET cc_start: 0.8300 (mtt) cc_final: 0.8040 (mtt) REVERT: F 268 ARG cc_start: 0.8693 (mtp-110) cc_final: 0.8475 (ptp-110) REVERT: G 40 ASP cc_start: 0.8543 (OUTLIER) cc_final: 0.8235 (t0) REVERT: G 93 ASN cc_start: 0.8580 (p0) cc_final: 0.8322 (p0) REVERT: G 158 HIS cc_start: 0.6038 (OUTLIER) cc_final: 0.5711 (m170) REVERT: H 248 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7374 (mp0) REVERT: H 321 ASP cc_start: 0.8501 (p0) cc_final: 0.8288 (p0) REVERT: I 274 HIS cc_start: 0.7876 (OUTLIER) cc_final: 0.7046 (m90) REVERT: I 298 ILE cc_start: 0.8322 (OUTLIER) cc_final: 0.8097 (mp) REVERT: I 323 TYR cc_start: 0.7893 (t80) cc_final: 0.7551 (t80) REVERT: A 46 GLU cc_start: 0.8544 (mm-30) cc_final: 0.7852 (tp30) REVERT: A 51 ASN cc_start: 0.8946 (m110) cc_final: 0.8685 (m110) REVERT: A 85 ASN cc_start: 0.7661 (t0) cc_final: 0.7457 (t0) outliers start: 56 outliers final: 31 residues processed: 232 average time/residue: 0.3095 time to fit residues: 112.3632 Evaluate side-chains 210 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 173 time to evaluate : 2.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 25 SER 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 262 LYS Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 158 HIS Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain G residue 40 ASP Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 158 HIS Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 248 GLU Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain H residue 347 ASN Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain I residue 274 HIS Chi-restraints excluded: chain I residue 298 ILE Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 211 PHE Chi-restraints excluded: chain B residue 230 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 213 optimal weight: 0.6980 chunk 145 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 190 optimal weight: 6.9990 chunk 105 optimal weight: 5.9990 chunk 218 optimal weight: 10.0000 chunk 177 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 130 optimal weight: 6.9990 chunk 229 optimal weight: 20.0000 chunk 64 optimal weight: 0.8980 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 82 ASN H 159 ASN H 347 ASN I 274 HIS B 230 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 20935 Z= 0.315 Angle : 0.571 8.472 28509 Z= 0.294 Chirality : 0.041 0.153 3094 Planarity : 0.004 0.051 3683 Dihedral : 13.032 151.658 3497 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.46 % Favored : 90.54 % Rotamer: Outliers : 3.86 % Allowed : 18.88 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.16), residues: 2610 helix: -0.54 (0.20), residues: 723 sheet: -1.21 (0.26), residues: 412 loop : -2.92 (0.14), residues: 1475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 329 HIS 0.007 0.001 HIS E 158 PHE 0.018 0.002 PHE G 165 TYR 0.020 0.001 TYR B 179 ARG 0.007 0.000 ARG H 133 *********************** 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 244 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 170 time to evaluate : 2.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 67 GLU cc_start: 0.6448 (pm20) cc_final: 0.5848 (pm20) REVERT: C 106 GLU cc_start: 0.6542 (tt0) cc_final: 0.6135 (mt-10) REVERT: C 147 TRP cc_start: 0.6709 (OUTLIER) cc_final: 0.6205 (t60) REVERT: C 171 LYS cc_start: 0.9385 (tptt) cc_final: 0.8997 (tppt) REVERT: C 262 TYR cc_start: 0.9026 (m-10) cc_final: 0.8740 (m-10) REVERT: D 110 LYS cc_start: 0.8067 (tttt) cc_final: 0.6878 (mttp) REVERT: D 317 LYS cc_start: 0.8461 (mmtm) cc_final: 0.8173 (mmtm) REVERT: D 328 ASN cc_start: 0.8678 (p0) cc_final: 0.8417 (p0) REVERT: D 347 ASN cc_start: 0.9304 (t0) cc_final: 0.8817 (t0) REVERT: E 68 ARG cc_start: 0.8265 (ttp80) cc_final: 0.7643 (ttp80) REVERT: E 132 TYR cc_start: 0.8849 (t80) cc_final: 0.8584 (t80) REVERT: E 192 TRP cc_start: 0.8859 (OUTLIER) cc_final: 0.6800 (m-90) REVERT: F 37 ASP cc_start: 0.8365 (t70) cc_final: 0.7689 (t70) REVERT: F 43 MET cc_start: 0.8362 (mtt) cc_final: 0.8129 (mtt) REVERT: F 268 ARG cc_start: 0.8708 (mtp-110) cc_final: 0.8480 (ptp-110) REVERT: G 40 ASP cc_start: 0.8601 (OUTLIER) cc_final: 0.8265 (t0) REVERT: G 93 ASN cc_start: 0.8593 (p0) cc_final: 0.8293 (p0) REVERT: H 248 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7469 (mp0) REVERT: H 321 ASP cc_start: 0.8655 (p0) cc_final: 0.8405 (p0) REVERT: I 298 ILE cc_start: 0.8424 (OUTLIER) cc_final: 0.8220 (mp) REVERT: I 323 TYR cc_start: 0.7960 (t80) cc_final: 0.7638 (t80) REVERT: A 46 GLU cc_start: 0.8527 (mm-30) cc_final: 0.7864 (tp30) REVERT: A 51 ASN cc_start: 0.8794 (m110) cc_final: 0.8533 (m110) REVERT: A 85 ASN cc_start: 0.7707 (t0) cc_final: 0.7483 (t0) REVERT: B 242 LYS cc_start: 0.8030 (tppt) cc_final: 0.7820 (tppt) outliers start: 74 outliers final: 48 residues processed: 230 average time/residue: 0.3449 time to fit residues: 124.6735 Evaluate side-chains 215 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 162 time to evaluate : 2.380 ------------------------------------------------------------------------------- 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 327 ASP Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 158 HIS Chi-restraints excluded: chain E residue 192 TRP Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 99 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 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 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 353 VAL Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain I residue 274 HIS Chi-restraints excluded: chain I residue 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 200 HIS Chi-restraints excluded: chain B residue 230 HIS Chi-restraints excluded: chain B residue 240 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 86 optimal weight: 10.0000 chunk 230 optimal weight: 20.0000 chunk 50 optimal weight: 6.9990 chunk 150 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 256 optimal weight: 6.9990 chunk 212 optimal weight: 2.9990 chunk 118 optimal weight: 0.6980 chunk 21 optimal weight: 10.0000 chunk 84 optimal weight: 0.9990 chunk 134 optimal weight: 10.0000 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 159 ASN I 274 HIS B 188 HIS B 225 GLN B 230 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 20935 Z= 0.286 Angle : 0.561 7.890 28509 Z= 0.289 Chirality : 0.041 0.150 3094 Planarity : 0.004 0.050 3683 Dihedral : 13.033 151.464 3497 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.16), residues: 2610 helix: -0.39 (0.20), residues: 721 sheet: -1.16 (0.26), residues: 412 loop : -2.86 (0.14), residues: 1477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 329 HIS 0.011 0.001 HIS I 274 PHE 0.016 0.002 PHE G 165 TYR 0.020 0.001 TYR D 132 ARG 0.006 0.000 ARG H 133 *********************** 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 248 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 170 time to evaluate : 2.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 67 GLU cc_start: 0.6416 (pm20) cc_final: 0.5821 (pm20) REVERT: C 106 GLU cc_start: 0.6539 (tt0) cc_final: 0.6131 (mt-10) REVERT: C 147 TRP cc_start: 0.6638 (OUTLIER) cc_final: 0.6190 (t60) REVERT: C 171 LYS cc_start: 0.9382 (tptt) cc_final: 0.8997 (tppt) REVERT: C 262 TYR cc_start: 0.9025 (m-10) cc_final: 0.8741 (m-10) REVERT: D 110 LYS cc_start: 0.8072 (tttt) cc_final: 0.6882 (mttp) REVERT: D 317 LYS cc_start: 0.8429 (mmtm) cc_final: 0.8210 (mmtm) REVERT: D 328 ASN cc_start: 0.8637 (p0) cc_final: 0.8392 (p0) REVERT: D 347 ASN cc_start: 0.9291 (t0) cc_final: 0.8794 (t0) REVERT: E 68 ARG cc_start: 0.8272 (ttp80) cc_final: 0.7617 (ttp80) REVERT: E 132 TYR cc_start: 0.8848 (t80) cc_final: 0.8583 (t80) REVERT: E 192 TRP cc_start: 0.8840 (OUTLIER) cc_final: 0.6758 (m-90) REVERT: F 37 ASP cc_start: 0.8226 (t70) cc_final: 0.7346 (t0) REVERT: F 43 MET cc_start: 0.8351 (mtt) cc_final: 0.8140 (mtt) REVERT: F 51 ARG cc_start: 0.7859 (mmt180) cc_final: 0.7659 (mmt180) REVERT: F 268 ARG cc_start: 0.8740 (mtp-110) cc_final: 0.8500 (ptp-110) REVERT: G 40 ASP cc_start: 0.8546 (OUTLIER) cc_final: 0.8178 (t0) REVERT: G 93 ASN cc_start: 0.8602 (p0) cc_final: 0.8307 (p0) REVERT: H 248 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7525 (mp0) REVERT: H 321 ASP cc_start: 0.8640 (p0) cc_final: 0.8402 (p0) REVERT: I 298 ILE cc_start: 0.8425 (OUTLIER) cc_final: 0.8156 (mp) REVERT: I 323 TYR cc_start: 0.7991 (t80) cc_final: 0.7696 (t80) REVERT: A 46 GLU cc_start: 0.8501 (mm-30) cc_final: 0.7903 (tp30) REVERT: A 51 ASN cc_start: 0.8710 (m110) cc_final: 0.8440 (m110) REVERT: A 58 ASN cc_start: 0.7746 (OUTLIER) cc_final: 0.7092 (m110) REVERT: A 85 ASN cc_start: 0.7764 (t0) cc_final: 0.7516 (t0) outliers start: 78 outliers final: 58 residues processed: 232 average time/residue: 0.3072 time to fit residues: 111.5542 Evaluate side-chains 227 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 163 time to evaluate : 2.227 ------------------------------------------------------------------------------- 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 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 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 146 ASP Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain G residue 40 ASP Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 210 LEU Chi-restraints excluded: chain G residue 246 SER Chi-restraints excluded: chain G residue 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 306 VAL Chi-restraints excluded: chain H residue 347 ASN Chi-restraints excluded: chain H residue 353 VAL Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain I residue 274 HIS Chi-restraints excluded: chain I residue 298 ILE Chi-restraints excluded: chain I residue 303 TYR Chi-restraints excluded: chain I residue 349 ILE Chi-restraints excluded: chain I residue 353 VAL Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 200 HIS Chi-restraints excluded: chain B residue 240 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 247 optimal weight: 0.4980 chunk 28 optimal weight: 1.9990 chunk 146 optimal weight: 5.9990 chunk 187 optimal weight: 8.9990 chunk 145 optimal weight: 6.9990 chunk 215 optimal weight: 3.9990 chunk 143 optimal weight: 6.9990 chunk 255 optimal weight: 3.9990 chunk 159 optimal weight: 2.9990 chunk 155 optimal weight: 0.9990 chunk 117 optimal weight: 5.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 342 HIS I 274 HIS B 188 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20935 Z= 0.204 Angle : 0.523 7.709 28509 Z= 0.270 Chirality : 0.040 0.142 3094 Planarity : 0.004 0.049 3683 Dihedral : 12.970 151.010 3497 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 3.50 % Allowed : 20.45 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.16), residues: 2610 helix: -0.25 (0.20), residues: 719 sheet: -1.15 (0.26), residues: 432 loop : -2.77 (0.15), residues: 1459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 329 HIS 0.014 0.001 HIS I 274 PHE 0.013 0.001 PHE G 165 TYR 0.020 0.001 TYR D 132 ARG 0.005 0.000 ARG H 133 *********************** 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 244 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 177 time to evaluate : 2.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 67 GLU cc_start: 0.6393 (pm20) cc_final: 0.5758 (pm20) REVERT: C 106 GLU cc_start: 0.6524 (tt0) cc_final: 0.6130 (mt-10) REVERT: C 147 TRP cc_start: 0.6551 (OUTLIER) cc_final: 0.6227 (t60) REVERT: C 156 ASN cc_start: 0.8797 (p0) cc_final: 0.8485 (p0) REVERT: C 171 LYS cc_start: 0.9371 (tptt) cc_final: 0.8987 (tppt) REVERT: C 262 TYR cc_start: 0.8992 (m-10) cc_final: 0.8693 (m-10) REVERT: D 33 GLU cc_start: 0.8252 (tt0) cc_final: 0.8031 (pm20) REVERT: D 98 ASP cc_start: 0.6421 (m-30) cc_final: 0.6206 (m-30) REVERT: D 110 LYS cc_start: 0.8065 (tttt) cc_final: 0.6874 (mttp) REVERT: D 328 ASN cc_start: 0.8620 (p0) cc_final: 0.8367 (p0) REVERT: D 347 ASN cc_start: 0.9271 (t0) cc_final: 0.8783 (t0) REVERT: E 68 ARG cc_start: 0.8323 (ttp80) cc_final: 0.7692 (ttp80) REVERT: E 132 TYR cc_start: 0.8866 (t80) cc_final: 0.8610 (t80) REVERT: E 192 TRP cc_start: 0.8835 (OUTLIER) cc_final: 0.6912 (m-90) REVERT: F 37 ASP cc_start: 0.8094 (t70) cc_final: 0.7212 (t0) REVERT: F 268 ARG cc_start: 0.8725 (mtp-110) cc_final: 0.8472 (ptp-110) REVERT: G 40 ASP cc_start: 0.8547 (OUTLIER) cc_final: 0.8209 (t0) REVERT: G 93 ASN cc_start: 0.8574 (p0) cc_final: 0.8277 (p0) REVERT: H 230 GLU cc_start: 0.7886 (tt0) cc_final: 0.7511 (tt0) REVERT: H 321 ASP cc_start: 0.8576 (p0) cc_final: 0.8367 (p0) REVERT: I 289 TYR cc_start: 0.5840 (m-10) cc_final: 0.5482 (m-10) REVERT: I 298 ILE cc_start: 0.8373 (OUTLIER) cc_final: 0.8120 (mp) REVERT: A 46 GLU cc_start: 0.8490 (mm-30) cc_final: 0.7904 (tp30) REVERT: A 51 ASN cc_start: 0.8760 (m110) cc_final: 0.8499 (m110) REVERT: A 85 ASN cc_start: 0.7766 (t0) cc_final: 0.7539 (t0) outliers start: 67 outliers final: 54 residues processed: 231 average time/residue: 0.3207 time to fit residues: 114.7338 Evaluate side-chains 226 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 168 time to evaluate : 2.439 ------------------------------------------------------------------------------- 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 275 THR Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 262 LYS Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 158 HIS Chi-restraints excluded: chain E residue 192 TRP Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 109 LEU Chi-restraints excluded: chain F residue 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 282 LEU Chi-restraints excluded: chain G residue 306 VAL 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 94 LEU Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 97 VAL Chi-restraints excluded: chain H residue 303 TYR Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain H residue 350 ARG Chi-restraints excluded: chain H residue 353 VAL Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain I residue 274 HIS Chi-restraints excluded: chain I residue 298 ILE Chi-restraints excluded: chain I residue 353 VAL Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 200 HIS Chi-restraints excluded: chain B residue 211 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 158 optimal weight: 8.9990 chunk 101 optimal weight: 7.9990 chunk 152 optimal weight: 5.9990 chunk 76 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 49 optimal weight: 20.0000 chunk 162 optimal weight: 0.0870 chunk 174 optimal weight: 0.0870 chunk 126 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 200 optimal weight: 6.9990 overall best weight: 1.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 274 HIS B 188 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20935 Z= 0.188 Angle : 0.518 8.926 28509 Z= 0.267 Chirality : 0.040 0.132 3094 Planarity : 0.004 0.047 3683 Dihedral : 12.915 151.093 3497 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 3.76 % Allowed : 20.29 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.16), residues: 2610 helix: -0.12 (0.20), residues: 718 sheet: -1.01 (0.26), residues: 419 loop : -2.72 (0.15), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 329 HIS 0.011 0.001 HIS I 274 PHE 0.012 0.001 PHE G 165 TYR 0.020 0.001 TYR D 132 ARG 0.009 0.000 ARG H 133 *********************** 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 255 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 183 time to evaluate : 2.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 67 GLU cc_start: 0.6391 (pm20) cc_final: 0.5816 (pm20) REVERT: C 106 GLU cc_start: 0.6534 (tt0) cc_final: 0.6131 (mt-10) REVERT: C 147 TRP cc_start: 0.6468 (OUTLIER) cc_final: 0.6206 (t60) REVERT: C 156 ASN cc_start: 0.8803 (p0) cc_final: 0.8477 (p0) REVERT: C 171 LYS cc_start: 0.9367 (tptt) cc_final: 0.8983 (tppt) REVERT: D 33 GLU cc_start: 0.8342 (tt0) cc_final: 0.7993 (pm20) REVERT: D 98 ASP cc_start: 0.6400 (m-30) cc_final: 0.6200 (m-30) REVERT: D 110 LYS cc_start: 0.8055 (tttt) cc_final: 0.6877 (mttp) REVERT: D 328 ASN cc_start: 0.8597 (p0) cc_final: 0.8347 (p0) REVERT: D 347 ASN cc_start: 0.9269 (t0) cc_final: 0.8777 (t0) REVERT: E 68 ARG cc_start: 0.8316 (ttp80) cc_final: 0.7682 (ttp80) REVERT: E 132 TYR cc_start: 0.8863 (t80) cc_final: 0.8648 (t80) REVERT: E 192 TRP cc_start: 0.8785 (OUTLIER) cc_final: 0.6789 (m-90) REVERT: F 37 ASP cc_start: 0.8088 (t70) cc_final: 0.7173 (t0) REVERT: F 268 ARG cc_start: 0.8693 (mtp-110) cc_final: 0.8446 (ptp-110) REVERT: G 40 ASP cc_start: 0.8563 (OUTLIER) cc_final: 0.8257 (t0) REVERT: G 93 ASN cc_start: 0.8581 (p0) cc_final: 0.8272 (p0) REVERT: G 158 HIS cc_start: 0.6192 (OUTLIER) cc_final: 0.5927 (m170) REVERT: H 230 GLU cc_start: 0.7925 (tt0) cc_final: 0.7552 (tt0) REVERT: I 298 ILE cc_start: 0.8320 (OUTLIER) cc_final: 0.8061 (mp) REVERT: A 46 GLU cc_start: 0.8475 (mm-30) cc_final: 0.7899 (tp30) REVERT: A 51 ASN cc_start: 0.8814 (m110) cc_final: 0.8535 (m110) REVERT: A 58 ASN cc_start: 0.7857 (OUTLIER) cc_final: 0.7185 (m110) REVERT: A 85 ASN cc_start: 0.7921 (t0) cc_final: 0.7667 (t0) outliers start: 72 outliers final: 58 residues processed: 244 average time/residue: 0.3086 time to fit residues: 116.9239 Evaluate side-chains 237 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 173 time to evaluate : 2.424 ------------------------------------------------------------------------------- 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 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 99 VAL 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 158 HIS 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 282 LEU Chi-restraints excluded: chain G residue 306 VAL 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 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 42 LEU Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain I residue 274 HIS Chi-restraints excluded: chain I residue 298 ILE Chi-restraints excluded: chain I residue 353 VAL Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 200 HIS Chi-restraints excluded: chain B residue 211 PHE 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 232 optimal weight: 0.9990 chunk 244 optimal weight: 9.9990 chunk 223 optimal weight: 10.0000 chunk 238 optimal weight: 9.9990 chunk 143 optimal weight: 7.9990 chunk 103 optimal weight: 8.9990 chunk 186 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 215 optimal weight: 2.9990 chunk 225 optimal weight: 0.0020 chunk 237 optimal weight: 5.9990 overall best weight: 3.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 133 GLN H 95 GLN I 159 ASN I 274 HIS B 188 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 20935 Z= 0.305 Angle : 0.575 9.466 28509 Z= 0.294 Chirality : 0.041 0.148 3094 Planarity : 0.004 0.045 3683 Dihedral : 12.970 151.933 3497 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.50 % Favored : 90.50 % Rotamer: Outliers : 4.02 % Allowed : 20.61 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.16), residues: 2610 helix: -0.18 (0.20), residues: 723 sheet: -1.16 (0.25), residues: 442 loop : -2.72 (0.15), residues: 1445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 329 HIS 0.013 0.001 HIS I 274 PHE 0.017 0.002 PHE G 165 TYR 0.022 0.001 TYR D 132 ARG 0.009 0.000 ARG H 133 *********************** 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 245 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 168 time to evaluate : 2.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 67 GLU cc_start: 0.6452 (pm20) cc_final: 0.5652 (pm20) REVERT: C 106 GLU cc_start: 0.6565 (tt0) cc_final: 0.6146 (mt-10) REVERT: C 147 TRP cc_start: 0.6652 (OUTLIER) cc_final: 0.6189 (t60) REVERT: C 171 LYS cc_start: 0.9378 (tptt) cc_final: 0.8992 (tppt) REVERT: D 98 ASP cc_start: 0.6379 (m-30) cc_final: 0.6175 (m-30) REVERT: D 110 LYS cc_start: 0.7977 (tttt) cc_final: 0.6780 (mttp) REVERT: D 280 ASN cc_start: 0.9082 (m-40) cc_final: 0.8874 (m-40) REVERT: D 317 LYS cc_start: 0.8549 (mmtm) cc_final: 0.8254 (mmtm) REVERT: D 328 ASN cc_start: 0.8584 (p0) cc_final: 0.8317 (p0) REVERT: D 347 ASN cc_start: 0.9292 (t0) cc_final: 0.8779 (t0) REVERT: E 68 ARG cc_start: 0.8246 (ttp80) cc_final: 0.7723 (ttp80) REVERT: E 132 TYR cc_start: 0.8850 (t80) cc_final: 0.8632 (t80) REVERT: E 192 TRP cc_start: 0.8841 (OUTLIER) cc_final: 0.6742 (m-90) REVERT: F 37 ASP cc_start: 0.8115 (t70) cc_final: 0.7222 (t0) REVERT: F 268 ARG cc_start: 0.8748 (mtp-110) cc_final: 0.8501 (ptp-110) REVERT: G 40 ASP cc_start: 0.8590 (OUTLIER) cc_final: 0.8248 (t0) REVERT: G 93 ASN cc_start: 0.8601 (p0) cc_final: 0.8283 (p0) REVERT: G 273 ILE cc_start: 0.7779 (OUTLIER) cc_final: 0.7510 (mt) REVERT: I 289 TYR cc_start: 0.5773 (m-10) cc_final: 0.5382 (m-10) REVERT: I 298 ILE cc_start: 0.8366 (OUTLIER) cc_final: 0.8143 (mp) REVERT: A 46 GLU cc_start: 0.8509 (mm-30) cc_final: 0.7913 (tp30) REVERT: A 51 ASN cc_start: 0.8760 (m110) cc_final: 0.8488 (m110) REVERT: A 58 ASN cc_start: 0.7873 (OUTLIER) cc_final: 0.7242 (m110) REVERT: A 85 ASN cc_start: 0.7820 (t0) cc_final: 0.7562 (t0) outliers start: 77 outliers final: 65 residues processed: 231 average time/residue: 0.3065 time to fit residues: 110.8151 Evaluate side-chains 237 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 166 time to evaluate : 2.407 ------------------------------------------------------------------------------- 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 275 THR Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 262 LYS Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 158 HIS Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 192 TRP Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 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 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 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 197 LEU Chi-restraints excluded: chain H residue 303 TYR Chi-restraints excluded: chain H residue 306 VAL Chi-restraints excluded: chain H residue 347 ASN Chi-restraints excluded: chain H residue 350 ARG Chi-restraints excluded: chain H residue 353 VAL Chi-restraints excluded: chain I residue 30 LEU Chi-restraints excluded: chain I residue 42 LEU Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 188 VAL Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain I residue 274 HIS Chi-restraints excluded: chain I residue 298 ILE Chi-restraints excluded: chain I residue 353 VAL Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 200 HIS Chi-restraints excluded: chain B residue 240 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 156 optimal weight: 0.0980 chunk 251 optimal weight: 50.0000 chunk 153 optimal weight: 5.9990 chunk 119 optimal weight: 9.9990 chunk 174 optimal weight: 3.9990 chunk 264 optimal weight: 10.0000 chunk 242 optimal weight: 20.0000 chunk 210 optimal weight: 0.5980 chunk 21 optimal weight: 8.9990 chunk 162 optimal weight: 7.9990 chunk 128 optimal weight: 2.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 274 HIS B 188 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20935 Z= 0.247 Angle : 0.552 8.989 28509 Z= 0.283 Chirality : 0.041 0.146 3094 Planarity : 0.004 0.045 3683 Dihedral : 12.954 151.398 3497 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 3.81 % Allowed : 20.97 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.16), residues: 2610 helix: -0.10 (0.20), residues: 722 sheet: -1.12 (0.26), residues: 442 loop : -2.67 (0.15), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 329 HIS 0.009 0.001 HIS I 274 PHE 0.015 0.001 PHE G 165 TYR 0.022 0.001 TYR D 132 ARG 0.009 0.000 ARG H 133 ********************** 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 246 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 173 time to evaluate : 2.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 67 GLU cc_start: 0.6403 (pm20) cc_final: 0.5628 (pm20) REVERT: C 106 GLU cc_start: 0.6556 (tt0) cc_final: 0.6143 (mt-10) REVERT: C 147 TRP cc_start: 0.6549 (OUTLIER) cc_final: 0.6157 (t60) REVERT: C 156 ASN cc_start: 0.8811 (p0) cc_final: 0.8497 (p0) REVERT: C 171 LYS cc_start: 0.9375 (tptt) cc_final: 0.8990 (tppt) REVERT: D 110 LYS cc_start: 0.7980 (tttt) cc_final: 0.6876 (mttp) REVERT: D 317 LYS cc_start: 0.8568 (mmtm) cc_final: 0.8299 (mmtm) REVERT: D 328 ASN cc_start: 0.8558 (p0) cc_final: 0.8296 (p0) REVERT: D 347 ASN cc_start: 0.9273 (t0) cc_final: 0.8777 (t0) REVERT: E 68 ARG cc_start: 0.8277 (ttp80) cc_final: 0.7603 (ttp80) REVERT: E 80 ARG cc_start: 0.8819 (mmp-170) cc_final: 0.8310 (mmp-170) REVERT: E 132 TYR cc_start: 0.8871 (t80) cc_final: 0.8651 (t80) REVERT: E 192 TRP cc_start: 0.8828 (OUTLIER) cc_final: 0.6763 (m-90) REVERT: F 37 ASP cc_start: 0.8087 (t70) cc_final: 0.7190 (t0) REVERT: F 268 ARG cc_start: 0.8736 (mtp-110) cc_final: 0.8480 (ptp-110) REVERT: G 40 ASP cc_start: 0.8549 (OUTLIER) cc_final: 0.8211 (t0) REVERT: G 93 ASN cc_start: 0.8601 (p0) cc_final: 0.8284 (p0) REVERT: G 273 ILE cc_start: 0.7764 (OUTLIER) cc_final: 0.7500 (mt) REVERT: H 230 GLU cc_start: 0.7846 (tt0) cc_final: 0.7488 (tt0) REVERT: I 289 TYR cc_start: 0.5823 (m-10) cc_final: 0.5467 (m-10) REVERT: I 298 ILE cc_start: 0.8361 (OUTLIER) cc_final: 0.8151 (mp) REVERT: A 46 GLU cc_start: 0.8497 (mm-30) cc_final: 0.7903 (tp30) REVERT: A 51 ASN cc_start: 0.8739 (m110) cc_final: 0.8455 (m110) REVERT: A 58 ASN cc_start: 0.7912 (OUTLIER) cc_final: 0.7275 (m110) REVERT: A 85 ASN cc_start: 0.7875 (t0) cc_final: 0.7599 (t0) outliers start: 73 outliers final: 64 residues processed: 233 average time/residue: 0.3104 time to fit residues: 111.9818 Evaluate side-chains 238 residues out of total 2133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 168 time to evaluate : 2.415 ------------------------------------------------------------------------------- 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 275 THR Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 262 LYS Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 307 THR Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 158 HIS Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 192 TRP Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain F residue 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 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 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 197 LEU 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 42 LEU Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 75 LEU Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 263 THR Chi-restraints excluded: chain I residue 274 HIS Chi-restraints excluded: chain I residue 298 ILE Chi-restraints excluded: chain I residue 353 VAL Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 22 SER Chi-restraints excluded: chain A residue 58 ASN Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 188 HIS Chi-restraints excluded: chain B residue 200 HIS Chi-restraints excluded: chain B residue 240 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 166 optimal weight: 4.9990 chunk 223 optimal weight: 50.0000 chunk 64 optimal weight: 0.7980 chunk 193 optimal weight: 7.9990 chunk 31 optimal weight: 20.0000 chunk 58 optimal weight: 6.9990 chunk 210 optimal weight: 5.9990 chunk 88 optimal weight: 7.9990 chunk 216 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 38 optimal weight: 0.3980 overall best weight: 3.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 274 HIS B 188 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.106262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.075993 restraints weight = 45915.493| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 4.47 r_work: 0.2988 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 20935 Z= 0.323 Angle : 0.588 9.181 28509 Z= 0.301 Chirality : 0.042 0.143 3094 Planarity : 0.004 0.045 3683 Dihedral : 12.992 151.926 3497 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.81 % Favored : 90.19 % Rotamer: Outliers : 4.02 % Allowed : 20.92 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.16), residues: 2610 helix: -0.12 (0.20), residues: 721 sheet: -1.19 (0.25), residues: 441 loop : -2.69 (0.15), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 147 HIS 0.011 0.001 HIS I 274 PHE 0.017 0.002 PHE G 165 TYR 0.023 0.002 TYR D 265 ARG 0.010 0.000 ARG H 133 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4088.94 seconds wall clock time: 73 minutes 44.09 seconds (4424.09 seconds total)