Starting phenix.real_space_refine on Sun Jun 15 16:31:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yjk_33873/06_2025/7yjk_33873.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yjk_33873/06_2025/7yjk_33873.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yjk_33873/06_2025/7yjk_33873.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yjk_33873/06_2025/7yjk_33873.map" model { file = "/net/cci-nas-00/data/ceres_data/7yjk_33873/06_2025/7yjk_33873.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yjk_33873/06_2025/7yjk_33873.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 2 5.49 5 S 100 5.16 5 C 11390 2.51 5 N 2978 2.21 5 O 3188 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 174 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 17658 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3424 Classifications: {'peptide': 445} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 424} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 3665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3665 Classifications: {'peptide': 470} Link IDs: {'PTRANS': 21, 'TRANS': 448} Chain breaks: 1 Chain: "D" Number of atoms: 1277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1277 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 9, 'TRANS': 146} Chain: "C" Number of atoms: 402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 402 Classifications: {'peptide': 47} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'TRANS': 46} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 2, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "E" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3424 Classifications: {'peptide': 445} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 20, 'TRANS': 424} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 14 Chain: "F" Number of atoms: 3665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3665 Classifications: {'peptide': 470} Link IDs: {'PTRANS': 21, 'TRANS': 448} Chain breaks: 1 Chain: "H" Number of atoms: 1277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1277 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 9, 'TRANS': 146} Chain: "G" Number of atoms: 402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 402 Classifications: {'peptide': 47} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'TRANS': 46} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 2, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'PLP': 1, 'Z1T': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'PLP': 1, 'Z1T': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 10.18, per 1000 atoms: 0.58 Number of scatterers: 17658 At special positions: 0 Unit cell: (126.36, 145.8, 118.8, 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 100 16.00 P 2 15.00 O 3188 8.00 N 2978 7.00 C 11390 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.52 Conformation dependent library (CDL) restraints added in 2.4 seconds 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4140 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 18 sheets defined 49.6% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.14 Creating SS restraints... Processing helix chain 'A' and resid 37 through 52 removed outlier: 4.134A pdb=" N GLU A 41 " --> pdb=" O HIS A 37 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLY A 45 " --> pdb=" O GLU A 41 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL A 46 " --> pdb=" O GLY A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 76 removed outlier: 3.662A pdb=" N GLU A 71 " --> pdb=" O GLN A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 137 removed outlier: 3.687A pdb=" N SER A 131 " --> pdb=" O LYS A 127 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR A 133 " --> pdb=" O LEU A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 168 removed outlier: 3.910A pdb=" N LEU A 157 " --> pdb=" O ILE A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 182 removed outlier: 4.021A pdb=" N MET A 182 " --> pdb=" O LEU A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 190 removed outlier: 3.653A pdb=" N PHE A 189 " --> pdb=" O THR A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 213 removed outlier: 3.528A pdb=" N GLY A 209 " --> pdb=" O GLY A 205 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLN A 211 " --> pdb=" O GLN A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 239 removed outlier: 3.534A pdb=" N LYS A 238 " --> pdb=" O LYS A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 275 removed outlier: 3.713A pdb=" N GLU A 272 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS A 273 " --> pdb=" O LYS A 269 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR A 274 " --> pdb=" O LEU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 301 Processing helix chain 'A' and resid 303 through 307 Processing helix chain 'A' and resid 328 through 335 Processing helix chain 'A' and resid 349 through 366 removed outlier: 3.716A pdb=" N ALA A 355 " --> pdb=" O TYR A 351 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA A 356 " --> pdb=" O LEU A 352 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ILE A 357 " --> pdb=" O ALA A 353 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N THR A 358 " --> pdb=" O SER A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 382 removed outlier: 4.119A pdb=" N VAL A 371 " --> pdb=" O PRO A 367 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU A 373 " --> pdb=" O MET A 369 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN A 376 " --> pdb=" O LYS A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 429 removed outlier: 3.763A pdb=" N LEU A 417 " --> pdb=" O LYS A 413 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU A 427 " --> pdb=" O ALA A 423 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU A 429 " --> pdb=" O ARG A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 477 removed outlier: 3.722A pdb=" N LEU A 464 " --> pdb=" O SER A 460 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU A 465 " --> pdb=" O GLU A 461 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER A 468 " --> pdb=" O LEU A 464 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 29 removed outlier: 3.649A pdb=" N SER B 11 " --> pdb=" O LEU B 7 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N TYR B 13 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE B 29 " --> pdb=" O LEU B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 58 Processing helix chain 'B' and resid 60 through 67 removed outlier: 3.834A pdb=" N GLN B 64 " --> pdb=" O HIS B 61 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N ASP B 65 " --> pdb=" O ARG B 62 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE B 67 " --> pdb=" O GLN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 129 Processing helix chain 'B' and resid 145 through 160 removed outlier: 3.738A pdb=" N GLU B 152 " --> pdb=" O HIS B 148 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU B 153 " --> pdb=" O ALA B 149 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR B 156 " --> pdb=" O GLU B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 176 removed outlier: 3.688A pdb=" N SER B 175 " --> pdb=" O TYR B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 182 Processing helix chain 'B' and resid 195 through 205 removed outlier: 3.555A pdb=" N VAL B 199 " --> pdb=" O HIS B 195 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER B 205 " --> pdb=" O GLY B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 231 removed outlier: 3.551A pdb=" N LEU B 220 " --> pdb=" O THR B 216 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG B 222 " --> pdb=" O SER B 218 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU B 226 " --> pdb=" O ARG B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 269 removed outlier: 4.016A pdb=" N ILE B 265 " --> pdb=" O GLU B 261 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS B 268 " --> pdb=" O ALA B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 295 Processing helix chain 'B' and resid 298 through 302 removed outlier: 3.913A pdb=" N VAL B 302 " --> pdb=" O THR B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 334 removed outlier: 3.569A pdb=" N HIS B 332 " --> pdb=" O GLN B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 339 Processing helix chain 'B' and resid 345 through 359 removed outlier: 3.619A pdb=" N GLN B 350 " --> pdb=" O PRO B 346 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ILE B 351 " --> pdb=" O SER B 347 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA B 354 " --> pdb=" O GLN B 350 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL B 357 " --> pdb=" O SER B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 388 removed outlier: 3.959A pdb=" N GLN B 369 " --> pdb=" O ASN B 365 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS B 370 " --> pdb=" O ARG B 366 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU B 371 " --> pdb=" O GLY B 367 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ARG B 375 " --> pdb=" O LEU B 371 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER B 378 " --> pdb=" O ILE B 374 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N PHE B 380 " --> pdb=" O GLU B 376 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N MET B 388 " --> pdb=" O GLU B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 421 removed outlier: 3.796A pdb=" N ALA B 413 " --> pdb=" O ALA B 409 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER B 415 " --> pdb=" O ILE B 411 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU B 417 " --> pdb=" O ALA B 413 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N CYS B 418 " --> pdb=" O PHE B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 468 removed outlier: 3.599A pdb=" N LYS B 458 " --> pdb=" O ILE B 454 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP B 465 " --> pdb=" O SER B 461 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU B 466 " --> pdb=" O LYS B 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 23 removed outlier: 3.952A pdb=" N GLU D 19 " --> pdb=" O ARG D 16 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N TRP D 20 " --> pdb=" O ASN D 17 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N PHE D 21 " --> pdb=" O THR D 18 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET D 22 " --> pdb=" O GLU D 19 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N TYR D 23 " --> pdb=" O TRP D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 45 removed outlier: 3.511A pdb=" N LEU D 34 " --> pdb=" O TYR D 30 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU D 42 " --> pdb=" O TRP D 38 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER D 43 " --> pdb=" O LEU D 39 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER D 45 " --> pdb=" O VAL D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 69 removed outlier: 3.664A pdb=" N VAL D 62 " --> pdb=" O LEU D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 80 removed outlier: 4.188A pdb=" N ASP D 79 " --> pdb=" O PHE D 76 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN D 80 " --> pdb=" O ALA D 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 76 through 80' Processing helix chain 'D' and resid 87 through 92 removed outlier: 3.505A pdb=" N MET D 92 " --> pdb=" O TRP D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 96 Processing helix chain 'D' and resid 99 through 119 Proline residue: D 109 - end of helix Processing helix chain 'D' and resid 126 through 141 Processing helix chain 'C' and resid 2 through 15 removed outlier: 3.557A pdb=" N THR C 14 " --> pdb=" O LEU C 10 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE C 15 " --> pdb=" O TYR C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 46 removed outlier: 3.563A pdb=" N LEU C 27 " --> pdb=" O TRP C 23 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE C 28 " --> pdb=" O GLU C 24 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER C 30 " --> pdb=" O TYR C 26 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU C 31 " --> pdb=" O LEU C 27 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU C 35 " --> pdb=" O LEU C 31 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG C 45 " --> pdb=" O TYR C 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 52 removed outlier: 4.135A pdb=" N GLU E 41 " --> pdb=" O HIS E 37 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLY E 45 " --> pdb=" O GLU E 41 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL E 46 " --> pdb=" O GLY E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 76 removed outlier: 3.662A pdb=" N GLU E 71 " --> pdb=" O GLN E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 137 removed outlier: 3.689A pdb=" N SER E 131 " --> pdb=" O LYS E 127 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR E 133 " --> pdb=" O LEU E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 168 removed outlier: 3.909A pdb=" N LEU E 157 " --> pdb=" O ILE E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 182 removed outlier: 4.021A pdb=" N MET E 182 " --> pdb=" O LEU E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 190 removed outlier: 3.653A pdb=" N PHE E 189 " --> pdb=" O THR E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 213 removed outlier: 3.527A pdb=" N GLY E 209 " --> pdb=" O GLY E 205 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLN E 211 " --> pdb=" O GLN E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 239 removed outlier: 3.534A pdb=" N LYS E 238 " --> pdb=" O LYS E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 275 removed outlier: 3.713A pdb=" N GLU E 272 " --> pdb=" O VAL E 268 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS E 273 " --> pdb=" O LYS E 269 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR E 274 " --> pdb=" O LEU E 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 301 Processing helix chain 'E' and resid 303 through 307 Processing helix chain 'E' and resid 328 through 335 Processing helix chain 'E' and resid 349 through 366 removed outlier: 3.716A pdb=" N ALA E 355 " --> pdb=" O TYR E 351 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA E 356 " --> pdb=" O LEU E 352 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ILE E 357 " --> pdb=" O ALA E 353 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N THR E 358 " --> pdb=" O SER E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 382 removed outlier: 4.119A pdb=" N VAL E 371 " --> pdb=" O PRO E 367 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU E 373 " --> pdb=" O MET E 369 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN E 376 " --> pdb=" O LYS E 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 411 through 429 removed outlier: 3.763A pdb=" N LEU E 417 " --> pdb=" O LYS E 413 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU E 427 " --> pdb=" O ALA E 423 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU E 429 " --> pdb=" O ARG E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 460 through 477 removed outlier: 3.723A pdb=" N LEU E 464 " --> pdb=" O SER E 460 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU E 465 " --> pdb=" O GLU E 461 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER E 468 " --> pdb=" O LEU E 464 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU E 471 " --> pdb=" O ALA E 467 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 29 removed outlier: 3.649A pdb=" N SER F 11 " --> pdb=" O LEU F 7 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N TYR F 13 " --> pdb=" O ALA F 9 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE F 29 " --> pdb=" O LEU F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 58 Processing helix chain 'F' and resid 60 through 67 removed outlier: 3.835A pdb=" N GLN F 64 " --> pdb=" O HIS F 61 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N ASP F 65 " --> pdb=" O ARG F 62 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE F 67 " --> pdb=" O GLN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 129 Processing helix chain 'F' and resid 145 through 160 removed outlier: 3.738A pdb=" N GLU F 152 " --> pdb=" O HIS F 148 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU F 153 " --> pdb=" O ALA F 149 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR F 156 " --> pdb=" O GLU F 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 171 through 176 removed outlier: 3.687A pdb=" N SER F 175 " --> pdb=" O TYR F 171 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 182 Processing helix chain 'F' and resid 195 through 205 removed outlier: 3.555A pdb=" N VAL F 199 " --> pdb=" O HIS F 195 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER F 205 " --> pdb=" O GLY F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 216 through 231 removed outlier: 3.550A pdb=" N LEU F 220 " --> pdb=" O THR F 216 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARG F 222 " --> pdb=" O SER F 218 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU F 226 " --> pdb=" O ARG F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 269 removed outlier: 4.015A pdb=" N ILE F 265 " --> pdb=" O GLU F 261 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS F 268 " --> pdb=" O ALA F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 290 through 295 Processing helix chain 'F' and resid 298 through 302 removed outlier: 3.913A pdb=" N VAL F 302 " --> pdb=" O THR F 299 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 334 removed outlier: 3.568A pdb=" N HIS F 332 " --> pdb=" O GLN F 328 " (cutoff:3.500A) Processing helix chain 'F' and resid 334 through 339 Processing helix chain 'F' and resid 345 through 359 removed outlier: 3.620A pdb=" N GLN F 350 " --> pdb=" O PRO F 346 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ILE F 351 " --> pdb=" O SER F 347 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA F 354 " --> pdb=" O GLN F 350 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL F 357 " --> pdb=" O SER F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 388 removed outlier: 3.960A pdb=" N GLN F 369 " --> pdb=" O ASN F 365 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS F 370 " --> pdb=" O ARG F 366 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU F 371 " --> pdb=" O GLY F 367 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ARG F 375 " --> pdb=" O LEU F 371 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER F 378 " --> pdb=" O ILE F 374 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N PHE F 380 " --> pdb=" O GLU F 376 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N MET F 388 " --> pdb=" O GLU F 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 409 through 421 removed outlier: 3.796A pdb=" N ALA F 413 " --> pdb=" O ALA F 409 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER F 415 " --> pdb=" O ILE F 411 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU F 417 " --> pdb=" O ALA F 413 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N CYS F 418 " --> pdb=" O PHE F 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 449 through 468 removed outlier: 3.600A pdb=" N LYS F 458 " --> pdb=" O ILE F 454 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP F 465 " --> pdb=" O SER F 461 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU F 466 " --> pdb=" O LYS F 462 " (cutoff:3.500A) Processing helix chain 'H' and resid 15 through 23 removed outlier: 3.952A pdb=" N GLU H 19 " --> pdb=" O ARG H 16 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N TRP H 20 " --> pdb=" O ASN H 17 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N PHE H 21 " --> pdb=" O THR H 18 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N MET H 22 " --> pdb=" O GLU H 19 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N TYR H 23 " --> pdb=" O TRP H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 25 through 45 removed outlier: 3.511A pdb=" N LEU H 34 " --> pdb=" O TYR H 30 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU H 42 " --> pdb=" O TRP H 38 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER H 43 " --> pdb=" O LEU H 39 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER H 45 " --> pdb=" O VAL H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 69 removed outlier: 3.664A pdb=" N VAL H 62 " --> pdb=" O LEU H 58 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 80 removed outlier: 4.188A pdb=" N ASP H 79 " --> pdb=" O PHE H 76 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN H 80 " --> pdb=" O ALA H 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 76 through 80' Processing helix chain 'H' and resid 87 through 92 removed outlier: 3.506A pdb=" N MET H 92 " --> pdb=" O TRP H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 96 Processing helix chain 'H' and resid 99 through 119 Proline residue: H 109 - end of helix Processing helix chain 'H' and resid 126 through 141 Processing helix chain 'G' and resid 2 through 15 removed outlier: 3.557A pdb=" N THR G 14 " --> pdb=" O LEU G 10 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE G 15 " --> pdb=" O TYR G 11 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 46 removed outlier: 3.563A pdb=" N LEU G 27 " --> pdb=" O TRP G 23 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE G 28 " --> pdb=" O GLU G 24 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER G 30 " --> pdb=" O TYR G 26 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU G 31 " --> pdb=" O LEU G 27 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU G 35 " --> pdb=" O LEU G 31 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG G 45 " --> pdb=" O TYR G 41 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 97 removed outlier: 3.727A pdb=" N THR A 105 " --> pdb=" O GLU A 97 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR A 104 " --> pdb=" O VAL A 111 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL A 111 " --> pdb=" O THR A 104 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 171 through 175 removed outlier: 3.643A pdb=" N ASP A 171 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY A 327 " --> pdb=" O ASP A 171 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL A 278 " --> pdb=" O VAL A 309 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N THR A 311 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU A 280 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N ALA A 313 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP A 281 " --> pdb=" O ALA A 251 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 390 through 391 Processing sheet with id=AA4, first strand: chain 'A' and resid 435 through 436 removed outlier: 3.663A pdb=" N VAL A 435 " --> pdb=" O LYS A 452 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 2 through 5 removed outlier: 3.732A pdb=" N ILE B 2 " --> pdb=" O ALA D 8 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 78 through 79 removed outlier: 3.504A pdb=" N PHE B 79 " --> pdb=" O CYS B 102 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LEU B 103 " --> pdb=" O ALA B 424 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 82 through 85 removed outlier: 5.569A pdb=" N GLU B 83 " --> pdb=" O THR B 96 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 163 through 167 removed outlier: 3.829A pdb=" N GLY B 318 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N TYR B 319 " --> pdb=" O GLY B 307 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N THR B 308 " --> pdb=" O GLU B 277 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL B 244 " --> pdb=" O TYR B 274 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N ASP B 276 " --> pdb=" O VAL B 244 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 400 through 404 removed outlier: 3.680A pdb=" N ILE B 442 " --> pdb=" O MET B 401 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG B 439 " --> pdb=" O VAL B 428 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL B 426 " --> pdb=" O ARG B 441 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 96 through 97 removed outlier: 3.727A pdb=" N THR E 105 " --> pdb=" O GLU E 97 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR E 104 " --> pdb=" O VAL E 111 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL E 111 " --> pdb=" O THR E 104 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 171 through 175 removed outlier: 3.643A pdb=" N ASP E 171 " --> pdb=" O GLY E 327 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY E 327 " --> pdb=" O ASP E 171 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL E 278 " --> pdb=" O VAL E 309 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N THR E 311 " --> pdb=" O VAL E 278 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU E 280 " --> pdb=" O THR E 311 " (cutoff:3.500A) removed outlier: 8.408A pdb=" N ALA E 313 " --> pdb=" O LEU E 280 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASP E 281 " --> pdb=" O ALA E 251 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 390 through 391 Processing sheet with id=AB4, first strand: chain 'E' and resid 435 through 436 removed outlier: 3.662A pdb=" N VAL E 435 " --> pdb=" O LYS E 452 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 2 through 5 removed outlier: 3.750A pdb=" N ILE F 2 " --> pdb=" O ALA H 8 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 78 through 79 removed outlier: 3.504A pdb=" N PHE F 79 " --> pdb=" O CYS F 102 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LEU F 103 " --> pdb=" O ALA F 424 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 82 through 85 removed outlier: 5.569A pdb=" N GLU F 83 " --> pdb=" O THR F 96 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 163 through 167 removed outlier: 3.829A pdb=" N GLY F 318 " --> pdb=" O PHE F 167 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N TYR F 319 " --> pdb=" O GLY F 307 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N THR F 308 " --> pdb=" O GLU F 277 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL F 244 " --> pdb=" O TYR F 274 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N ASP F 276 " --> pdb=" O VAL F 244 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 400 through 404 removed outlier: 3.679A pdb=" N ILE F 442 " --> pdb=" O MET F 401 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG F 439 " --> pdb=" O VAL F 428 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL F 426 " --> pdb=" O ARG F 441 " (cutoff:3.500A) 700 hydrogen bonds defined for protein. 1992 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.84 Time building geometry restraints manager: 5.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5575 1.34 - 1.46: 3163 1.46 - 1.57: 9172 1.57 - 1.69: 4 1.69 - 1.81: 156 Bond restraints: 18070 Sorted by residual: bond pdb=" C ARG E 62 " pdb=" N PRO E 63 " ideal model delta sigma weight residual 1.332 1.589 -0.258 1.26e-02 6.30e+03 4.18e+02 bond pdb=" C ARG A 62 " pdb=" N PRO A 63 " ideal model delta sigma weight residual 1.332 1.589 -0.258 1.26e-02 6.30e+03 4.18e+02 bond pdb=" C14 Z1T F 502 " pdb=" C15 Z1T F 502 " ideal model delta sigma weight residual 1.329 1.525 -0.196 2.00e-02 2.50e+03 9.65e+01 bond pdb=" C14 Z1T B 502 " pdb=" C15 Z1T B 502 " ideal model delta sigma weight residual 1.329 1.525 -0.196 2.00e-02 2.50e+03 9.64e+01 bond pdb=" C13 Z1T B 502 " pdb=" C14 Z1T B 502 " ideal model delta sigma weight residual 1.494 1.525 -0.031 2.00e-02 2.50e+03 2.33e+00 ... (remaining 18065 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 23659 2.12 - 4.24: 700 4.24 - 6.36: 103 6.36 - 8.48: 4 8.48 - 10.60: 8 Bond angle restraints: 24474 Sorted by residual: angle pdb=" N ARG B 30 " pdb=" CA ARG B 30 " pdb=" C ARG B 30 " ideal model delta sigma weight residual 113.55 106.70 6.85 1.26e+00 6.30e-01 2.95e+01 angle pdb=" N ARG F 30 " pdb=" CA ARG F 30 " pdb=" C ARG F 30 " ideal model delta sigma weight residual 113.55 106.71 6.84 1.26e+00 6.30e-01 2.95e+01 angle pdb=" N GLU F 253 " pdb=" CA GLU F 253 " pdb=" C GLU F 253 " ideal model delta sigma weight residual 114.75 108.80 5.95 1.26e+00 6.30e-01 2.23e+01 angle pdb=" N GLU B 253 " pdb=" CA GLU B 253 " pdb=" C GLU B 253 " ideal model delta sigma weight residual 114.75 108.85 5.90 1.26e+00 6.30e-01 2.19e+01 angle pdb=" C SER F 398 " pdb=" N PRO F 399 " pdb=" CA PRO F 399 " ideal model delta sigma weight residual 119.56 123.65 -4.09 1.01e+00 9.80e-01 1.64e+01 ... (remaining 24469 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 9619 17.41 - 34.81: 906 34.81 - 52.22: 188 52.22 - 69.63: 32 69.63 - 87.04: 17 Dihedral angle restraints: 10762 sinusoidal: 4304 harmonic: 6458 Sorted by residual: dihedral pdb=" CA VAL E 288 " pdb=" C VAL E 288 " pdb=" N LEU E 289 " pdb=" CA LEU E 289 " ideal model delta harmonic sigma weight residual 180.00 -155.28 -24.72 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA VAL A 288 " pdb=" C VAL A 288 " pdb=" N LEU A 289 " pdb=" CA LEU A 289 " ideal model delta harmonic sigma weight residual -180.00 -155.36 -24.64 0 5.00e+00 4.00e-02 2.43e+01 dihedral pdb=" CA GLY F 50 " pdb=" C GLY F 50 " pdb=" N HIS F 51 " pdb=" CA HIS F 51 " ideal model delta harmonic sigma weight residual -180.00 -159.92 -20.08 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 10759 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1841 0.050 - 0.100: 737 0.100 - 0.150: 154 0.150 - 0.200: 6 0.200 - 0.251: 2 Chirality restraints: 2740 Sorted by residual: chirality pdb=" CA TYR D 122 " pdb=" N TYR D 122 " pdb=" C TYR D 122 " pdb=" CB TYR D 122 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CA TYR H 122 " pdb=" N TYR H 122 " pdb=" C TYR H 122 " pdb=" CB TYR H 122 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CA GLU A 477 " pdb=" N GLU A 477 " pdb=" C GLU A 477 " pdb=" CB GLU A 477 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.18e-01 ... (remaining 2737 not shown) Planarity restraints: 3074 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR F 433 " 0.053 5.00e-02 4.00e+02 7.89e-02 9.96e+00 pdb=" N PRO F 434 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO F 434 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO F 434 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 433 " -0.052 5.00e-02 4.00e+02 7.88e-02 9.93e+00 pdb=" N PRO B 434 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO B 434 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 434 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 59 " -0.046 5.00e-02 4.00e+02 6.94e-02 7.72e+00 pdb=" N PRO A 60 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO A 60 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 60 " -0.038 5.00e-02 4.00e+02 ... (remaining 3071 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3140 2.76 - 3.29: 16059 3.29 - 3.83: 26498 3.83 - 4.36: 32340 4.36 - 4.90: 58063 Nonbonded interactions: 136100 Sorted by model distance: nonbonded pdb=" O LEU A 43 " pdb=" CG2 VAL A 46 " model vdw 2.223 3.460 nonbonded pdb=" O LEU E 43 " pdb=" CG2 VAL E 46 " model vdw 2.223 3.460 nonbonded pdb=" ND1 HIS D 118 " pdb=" OE2 GLU E 41 " model vdw 2.234 3.120 nonbonded pdb=" OE2 GLU A 41 " pdb=" ND1 HIS H 118 " model vdw 2.239 3.120 nonbonded pdb=" OD2 ASP F 27 " pdb=" NH2 ARG F 57 " model vdw 2.245 3.120 ... (remaining 136095 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'B' selection = chain 'F' } 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: 0.830 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: 0.700 Check model and map are aligned: 0.130 Set scattering table: 0.190 Process input model: 40.890 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.258 18072 Z= 0.400 Angle : 0.892 10.604 24474 Z= 0.535 Chirality : 0.053 0.251 2740 Planarity : 0.006 0.079 3074 Dihedral : 14.225 87.037 6622 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.72 % Allowed : 7.13 % Favored : 92.15 % Rotamer: Outliers : 0.21 % Allowed : 1.05 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.10 (0.17), residues: 2216 helix: -1.76 (0.15), residues: 1046 sheet: -1.60 (0.33), residues: 238 loop : -2.40 (0.19), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 23 HIS 0.008 0.001 HIS F 337 PHE 0.024 0.002 PHE E 220 TYR 0.033 0.002 TYR E 177 ARG 0.005 0.001 ARG B 455 Details of bonding type rmsd hydrogen bonds : bond 0.26275 ( 700) hydrogen bonds : angle 7.49189 ( 1992) covalent geometry : bond 0.00806 (18070) covalent geometry : angle 0.89207 (24474) Misc. bond : bond 0.00622 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 207 time to evaluate : 2.100 Fit side-chains REVERT: A 52 LEU cc_start: 0.8478 (tt) cc_final: 0.8136 (mp) REVERT: A 246 ARG cc_start: 0.8204 (mtm180) cc_final: 0.7897 (mtt180) REVERT: B 28 PHE cc_start: 0.7619 (t80) cc_final: 0.7349 (t80) REVERT: B 30 ARG cc_start: 0.7817 (tpt170) cc_final: 0.7299 (mpt180) REVERT: D 1 MET cc_start: 0.4792 (ttm) cc_final: 0.4160 (ptm) REVERT: E 52 LEU cc_start: 0.8461 (tt) cc_final: 0.8116 (mp) REVERT: E 246 ARG cc_start: 0.8200 (mtm180) cc_final: 0.7892 (mtt180) REVERT: F 28 PHE cc_start: 0.7590 (t80) cc_final: 0.7232 (t80) REVERT: F 30 ARG cc_start: 0.7797 (tpt170) cc_final: 0.7250 (mpt180) REVERT: H 1 MET cc_start: 0.4822 (ttm) cc_final: 0.4140 (ptm) outliers start: 4 outliers final: 4 residues processed: 211 average time/residue: 0.3179 time to fit residues: 100.2793 Evaluate side-chains 183 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 179 time to evaluate : 2.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 428 LYS Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 428 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 0.9990 chunk 166 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 112 optimal weight: 8.9990 chunk 89 optimal weight: 0.9990 chunk 172 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 104 optimal weight: 0.9980 chunk 128 optimal weight: 1.9990 chunk 199 optimal weight: 0.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 GLN A 223 ASN B 194 ASN B 214 HIS B 379 ASN D 80 GLN D 96 GLN E 207 GLN E 223 ASN F 194 ASN F 214 HIS F 379 ASN H 80 GLN H 96 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.122964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.094845 restraints weight = 24493.016| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 2.10 r_work: 0.2916 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18072 Z= 0.135 Angle : 0.588 8.057 24474 Z= 0.308 Chirality : 0.044 0.170 2740 Planarity : 0.005 0.079 3074 Dihedral : 6.904 59.421 2536 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.96 % Favored : 94.77 % Rotamer: Outliers : 0.63 % Allowed : 6.93 % Favored : 92.44 % 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: -1.96 (0.18), residues: 2216 helix: -0.72 (0.16), residues: 1056 sheet: -0.82 (0.34), residues: 250 loop : -2.05 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 23 HIS 0.006 0.001 HIS E 37 PHE 0.022 0.001 PHE F 79 TYR 0.013 0.001 TYR E 177 ARG 0.004 0.000 ARG B 373 Details of bonding type rmsd hydrogen bonds : bond 0.05884 ( 700) hydrogen bonds : angle 4.47729 ( 1992) covalent geometry : bond 0.00302 (18070) covalent geometry : angle 0.58779 (24474) Misc. bond : bond 0.00050 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 182 time to evaluate : 1.927 Fit side-chains REVERT: B 30 ARG cc_start: 0.8289 (tpt170) cc_final: 0.7205 (mpt180) REVERT: B 171 TYR cc_start: 0.7903 (t80) cc_final: 0.7563 (t80) REVERT: C 24 GLU cc_start: 0.8971 (mt-10) cc_final: 0.8750 (mt-10) REVERT: C 32 VAL cc_start: 0.8444 (OUTLIER) cc_final: 0.8213 (p) REVERT: F 30 ARG cc_start: 0.8319 (tpt170) cc_final: 0.7221 (mpt180) REVERT: F 171 TYR cc_start: 0.7987 (t80) cc_final: 0.7575 (t80) outliers start: 12 outliers final: 2 residues processed: 190 average time/residue: 0.4054 time to fit residues: 117.1354 Evaluate side-chains 174 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 171 time to evaluate : 2.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain E residue 288 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 194 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 181 optimal weight: 3.9990 chunk 211 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 152 optimal weight: 3.9990 chunk 163 optimal weight: 0.9990 chunk 191 optimal weight: 1.9990 chunk 143 optimal weight: 0.1980 chunk 139 optimal weight: 0.9980 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 96 GLN H 96 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.129347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.102544 restraints weight = 23912.689| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 1.99 r_work: 0.2949 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 18072 Z= 0.108 Angle : 0.523 8.404 24474 Z= 0.271 Chirality : 0.042 0.151 2740 Planarity : 0.005 0.071 3074 Dihedral : 6.063 58.518 2524 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.29 % Favored : 95.44 % Rotamer: Outliers : 1.00 % Allowed : 8.30 % Favored : 90.70 % 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: -1.44 (0.18), residues: 2216 helix: -0.19 (0.17), residues: 1040 sheet: -0.84 (0.35), residues: 240 loop : -1.81 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 23 HIS 0.002 0.001 HIS E 37 PHE 0.020 0.001 PHE F 79 TYR 0.010 0.001 TYR F 85 ARG 0.002 0.000 ARG E 147 Details of bonding type rmsd hydrogen bonds : bond 0.04161 ( 700) hydrogen bonds : angle 3.96346 ( 1992) covalent geometry : bond 0.00247 (18070) covalent geometry : angle 0.52332 (24474) Misc. bond : bond 0.00028 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 180 time to evaluate : 2.226 Fit side-chains REVERT: A 96 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8342 (pp) REVERT: B 30 ARG cc_start: 0.8279 (tpt170) cc_final: 0.7170 (mpt180) REVERT: B 171 TYR cc_start: 0.7775 (t80) cc_final: 0.7431 (t80) REVERT: C 24 GLU cc_start: 0.8967 (mt-10) cc_final: 0.8660 (mt-10) REVERT: E 96 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8332 (pp) REVERT: F 30 ARG cc_start: 0.8316 (tpt170) cc_final: 0.7187 (mpt180) REVERT: F 171 TYR cc_start: 0.7856 (t80) cc_final: 0.7436 (t80) outliers start: 19 outliers final: 9 residues processed: 192 average time/residue: 0.2930 time to fit residues: 86.8733 Evaluate side-chains 178 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 167 time to evaluate : 2.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain F residue 287 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 65 optimal weight: 9.9990 chunk 42 optimal weight: 0.0070 chunk 199 optimal weight: 1.9990 chunk 209 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 57 optimal weight: 10.0000 chunk 131 optimal weight: 7.9990 chunk 123 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 56 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 overall best weight: 2.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 96 GLN H 96 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.126299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.099203 restraints weight = 24140.846| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.00 r_work: 0.2899 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18072 Z= 0.180 Angle : 0.577 8.192 24474 Z= 0.298 Chirality : 0.046 0.163 2740 Planarity : 0.005 0.069 3074 Dihedral : 6.026 59.209 2524 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.23 % Favored : 94.49 % Rotamer: Outliers : 1.37 % Allowed : 10.24 % Favored : 88.39 % 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: -1.45 (0.18), residues: 2216 helix: -0.19 (0.17), residues: 1050 sheet: -0.86 (0.33), residues: 262 loop : -1.87 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 23 HIS 0.005 0.001 HIS E 203 PHE 0.027 0.002 PHE F 79 TYR 0.012 0.002 TYR F 108 ARG 0.003 0.000 ARG A 147 Details of bonding type rmsd hydrogen bonds : bond 0.04846 ( 700) hydrogen bonds : angle 3.98767 ( 1992) covalent geometry : bond 0.00443 (18070) covalent geometry : angle 0.57728 (24474) Misc. bond : bond 0.00052 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 176 time to evaluate : 2.016 Fit side-chains REVERT: A 421 LYS cc_start: 0.8663 (ptmt) cc_final: 0.8242 (ptmm) REVERT: B 30 ARG cc_start: 0.8421 (tpt170) cc_final: 0.7315 (mpt180) REVERT: B 171 TYR cc_start: 0.7950 (t80) cc_final: 0.7484 (t80) REVERT: B 306 MET cc_start: 0.8843 (tmm) cc_final: 0.8558 (ttp) REVERT: E 421 LYS cc_start: 0.8712 (ptmt) cc_final: 0.8195 (ptmm) REVERT: F 30 ARG cc_start: 0.8423 (tpt170) cc_final: 0.7306 (mpt180) REVERT: F 171 TYR cc_start: 0.7949 (t80) cc_final: 0.7479 (t80) outliers start: 26 outliers final: 14 residues processed: 190 average time/residue: 0.2950 time to fit residues: 86.0584 Evaluate side-chains 186 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 172 time to evaluate : 2.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 94 LYS Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 331 ILE Chi-restraints excluded: chain E residue 386 ASP Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain F residue 79 PHE Chi-restraints excluded: chain F residue 287 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 168 optimal weight: 0.9990 chunk 201 optimal weight: 0.0470 chunk 195 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 170 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 67 optimal weight: 0.0870 chunk 217 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 91 optimal weight: 8.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 GLN ** E 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 96 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.126250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.098042 restraints weight = 24674.615| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.12 r_work: 0.2962 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 18072 Z= 0.087 Angle : 0.487 8.795 24474 Z= 0.248 Chirality : 0.041 0.142 2740 Planarity : 0.004 0.063 3074 Dihedral : 5.601 59.343 2524 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.75 % Favored : 96.07 % Rotamer: Outliers : 0.63 % Allowed : 11.97 % Favored : 87.39 % 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: -0.92 (0.18), residues: 2216 helix: 0.29 (0.17), residues: 1028 sheet: -0.79 (0.35), residues: 240 loop : -1.53 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 23 HIS 0.002 0.000 HIS B 236 PHE 0.016 0.001 PHE F 79 TYR 0.009 0.001 TYR B 85 ARG 0.002 0.000 ARG D 123 Details of bonding type rmsd hydrogen bonds : bond 0.03308 ( 700) hydrogen bonds : angle 3.67476 ( 1992) covalent geometry : bond 0.00191 (18070) covalent geometry : angle 0.48659 (24474) Misc. bond : bond 0.00017 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 190 time to evaluate : 2.187 Fit side-chains REVERT: A 96 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8275 (pp) REVERT: A 421 LYS cc_start: 0.8728 (ptmt) cc_final: 0.8238 (ptmm) REVERT: B 30 ARG cc_start: 0.8461 (tpt170) cc_final: 0.7323 (mpt180) REVERT: B 171 TYR cc_start: 0.7926 (t80) cc_final: 0.7465 (t80) REVERT: B 306 MET cc_start: 0.8828 (tmm) cc_final: 0.8439 (ttp) REVERT: C 24 GLU cc_start: 0.8883 (mt-10) cc_final: 0.8653 (mt-10) REVERT: E 96 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8278 (pp) REVERT: E 421 LYS cc_start: 0.8728 (ptmt) cc_final: 0.8246 (ptmm) REVERT: F 30 ARG cc_start: 0.8401 (tpt170) cc_final: 0.7280 (mpt180) REVERT: F 171 TYR cc_start: 0.7938 (t80) cc_final: 0.7479 (t80) outliers start: 12 outliers final: 4 residues processed: 201 average time/residue: 0.4140 time to fit residues: 127.9121 Evaluate side-chains 183 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 177 time to evaluate : 3.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain F residue 79 PHE Chi-restraints excluded: chain F residue 287 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 138 optimal weight: 8.9990 chunk 171 optimal weight: 0.9980 chunk 29 optimal weight: 0.3980 chunk 144 optimal weight: 8.9990 chunk 15 optimal weight: 1.9990 chunk 173 optimal weight: 0.9990 chunk 197 optimal weight: 6.9990 chunk 133 optimal weight: 0.5980 chunk 187 optimal weight: 4.9990 chunk 147 optimal weight: 8.9990 chunk 67 optimal weight: 5.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 GLN ** E 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 96 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.124925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.096553 restraints weight = 24550.820| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 2.13 r_work: 0.2934 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 18072 Z= 0.100 Angle : 0.498 7.304 24474 Z= 0.252 Chirality : 0.042 0.147 2740 Planarity : 0.004 0.062 3074 Dihedral : 5.472 59.552 2524 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.02 % Favored : 95.80 % Rotamer: Outliers : 0.95 % Allowed : 12.55 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.18), residues: 2216 helix: 0.38 (0.17), residues: 1030 sheet: -0.75 (0.35), residues: 238 loop : -1.44 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 23 HIS 0.003 0.001 HIS A 203 PHE 0.019 0.001 PHE F 79 TYR 0.010 0.001 TYR B 85 ARG 0.001 0.000 ARG H 102 Details of bonding type rmsd hydrogen bonds : bond 0.03476 ( 700) hydrogen bonds : angle 3.65412 ( 1992) covalent geometry : bond 0.00234 (18070) covalent geometry : angle 0.49810 (24474) Misc. bond : bond 0.00015 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 188 time to evaluate : 1.991 Fit side-chains REVERT: A 96 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8324 (pp) REVERT: A 421 LYS cc_start: 0.8671 (ptmt) cc_final: 0.8210 (ptmm) REVERT: B 30 ARG cc_start: 0.8400 (tpt170) cc_final: 0.7228 (mpt180) REVERT: B 171 TYR cc_start: 0.7921 (t80) cc_final: 0.7433 (t80) REVERT: B 306 MET cc_start: 0.8840 (tmm) cc_final: 0.8489 (ttp) REVERT: C 24 GLU cc_start: 0.8897 (mt-10) cc_final: 0.8633 (mt-10) REVERT: E 96 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8295 (pp) REVERT: E 421 LYS cc_start: 0.8668 (ptmt) cc_final: 0.8214 (ptmm) REVERT: F 30 ARG cc_start: 0.8370 (tpt170) cc_final: 0.7231 (mpt180) REVERT: F 171 TYR cc_start: 0.7930 (t80) cc_final: 0.7456 (t80) outliers start: 18 outliers final: 10 residues processed: 201 average time/residue: 0.3262 time to fit residues: 99.1260 Evaluate side-chains 194 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 182 time to evaluate : 1.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain C residue 42 ASN Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 331 ILE Chi-restraints excluded: chain F residue 79 PHE Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain G residue 31 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 172 optimal weight: 1.9990 chunk 140 optimal weight: 0.8980 chunk 218 optimal weight: 1.9990 chunk 189 optimal weight: 0.6980 chunk 66 optimal weight: 4.9990 chunk 146 optimal weight: 7.9990 chunk 157 optimal weight: 10.0000 chunk 123 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 182 optimal weight: 0.7980 chunk 216 optimal weight: 0.3980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 GLN ** E 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 96 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.126506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.098633 restraints weight = 24414.001| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.08 r_work: 0.2946 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 18072 Z= 0.097 Angle : 0.490 7.321 24474 Z= 0.249 Chirality : 0.042 0.146 2740 Planarity : 0.004 0.060 3074 Dihedral : 5.377 58.044 2524 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.15 % Favored : 95.67 % Rotamer: Outliers : 1.00 % Allowed : 13.03 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.18), residues: 2216 helix: 0.49 (0.17), residues: 1032 sheet: -0.71 (0.35), residues: 238 loop : -1.33 (0.20), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 23 HIS 0.003 0.001 HIS E 203 PHE 0.019 0.001 PHE F 79 TYR 0.010 0.001 TYR F 85 ARG 0.002 0.000 ARG F 373 Details of bonding type rmsd hydrogen bonds : bond 0.03405 ( 700) hydrogen bonds : angle 3.61687 ( 1992) covalent geometry : bond 0.00225 (18070) covalent geometry : angle 0.49014 (24474) Misc. bond : bond 0.00018 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 181 time to evaluate : 1.985 Fit side-chains REVERT: A 96 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8296 (pp) REVERT: A 421 LYS cc_start: 0.8665 (ptmt) cc_final: 0.8207 (ptmm) REVERT: B 30 ARG cc_start: 0.8338 (tpt170) cc_final: 0.7151 (mpt180) REVERT: B 171 TYR cc_start: 0.7919 (t80) cc_final: 0.7431 (t80) REVERT: B 306 MET cc_start: 0.8828 (tmm) cc_final: 0.8485 (ttp) REVERT: C 24 GLU cc_start: 0.8917 (mt-10) cc_final: 0.8651 (mt-10) REVERT: E 96 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8290 (pp) REVERT: E 421 LYS cc_start: 0.8680 (ptmt) cc_final: 0.8220 (ptmm) REVERT: F 30 ARG cc_start: 0.8404 (tpt170) cc_final: 0.7242 (mpt180) REVERT: F 171 TYR cc_start: 0.7922 (t80) cc_final: 0.7369 (t80) outliers start: 19 outliers final: 10 residues processed: 194 average time/residue: 0.3133 time to fit residues: 91.8675 Evaluate side-chains 190 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 178 time to evaluate : 1.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain C residue 42 ASN Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 331 ILE Chi-restraints excluded: chain F residue 79 PHE Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain G residue 31 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 10 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 93 optimal weight: 0.6980 chunk 146 optimal weight: 7.9990 chunk 125 optimal weight: 2.9990 chunk 152 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 chunk 215 optimal weight: 0.6980 chunk 39 optimal weight: 7.9990 chunk 103 optimal weight: 7.9990 chunk 167 optimal weight: 8.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 GLN ** E 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 96 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.125668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.098503 restraints weight = 24131.741| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 2.01 r_work: 0.2896 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18072 Z= 0.181 Angle : 0.573 9.767 24474 Z= 0.290 Chirality : 0.045 0.159 2740 Planarity : 0.005 0.063 3074 Dihedral : 5.612 53.472 2524 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.14 % Favored : 94.68 % Rotamer: Outliers : 1.68 % Allowed : 12.71 % Favored : 85.61 % 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: -0.91 (0.18), residues: 2216 helix: 0.21 (0.17), residues: 1056 sheet: -0.90 (0.33), residues: 268 loop : -1.42 (0.20), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 22 HIS 0.005 0.001 HIS A 203 PHE 0.027 0.002 PHE F 79 TYR 0.012 0.002 TYR F 85 ARG 0.002 0.000 ARG B 373 Details of bonding type rmsd hydrogen bonds : bond 0.04518 ( 700) hydrogen bonds : angle 3.81557 ( 1992) covalent geometry : bond 0.00448 (18070) covalent geometry : angle 0.57276 (24474) Misc. bond : bond 0.00050 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 173 time to evaluate : 1.985 Fit side-chains REVERT: A 38 PHE cc_start: 0.6009 (m-80) cc_final: 0.5513 (m-80) REVERT: A 96 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8322 (pp) REVERT: A 421 LYS cc_start: 0.8665 (ptmt) cc_final: 0.8185 (ptmm) REVERT: B 30 ARG cc_start: 0.8399 (tpt170) cc_final: 0.7191 (mpt180) REVERT: B 171 TYR cc_start: 0.7941 (t80) cc_final: 0.7484 (t80) REVERT: B 256 ILE cc_start: 0.9150 (OUTLIER) cc_final: 0.8796 (mt) REVERT: B 306 MET cc_start: 0.8832 (tmm) cc_final: 0.8562 (ttp) REVERT: C 24 GLU cc_start: 0.8902 (mt-10) cc_final: 0.8625 (mt-10) REVERT: E 38 PHE cc_start: 0.5976 (m-80) cc_final: 0.5470 (m-80) REVERT: E 96 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8319 (pp) REVERT: E 421 LYS cc_start: 0.8668 (ptmt) cc_final: 0.8193 (ptmm) REVERT: F 30 ARG cc_start: 0.8395 (tpt170) cc_final: 0.7233 (mpt180) REVERT: F 171 TYR cc_start: 0.7972 (t80) cc_final: 0.7522 (t80) REVERT: F 256 ILE cc_start: 0.9145 (OUTLIER) cc_final: 0.8787 (mt) REVERT: F 306 MET cc_start: 0.8867 (tmm) cc_final: 0.8613 (ttp) outliers start: 32 outliers final: 18 residues processed: 193 average time/residue: 0.3044 time to fit residues: 91.4078 Evaluate side-chains 190 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 168 time to evaluate : 1.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 388 MET Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain C residue 42 ASN Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 331 ILE Chi-restraints excluded: chain E residue 386 ASP Chi-restraints excluded: chain E residue 433 LEU Chi-restraints excluded: chain F residue 79 PHE Chi-restraints excluded: chain F residue 256 ILE Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain F residue 466 LEU Chi-restraints excluded: chain G residue 31 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 164 optimal weight: 4.9990 chunk 207 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 172 optimal weight: 0.6980 chunk 25 optimal weight: 6.9990 chunk 121 optimal weight: 0.9990 chunk 52 optimal weight: 10.0000 chunk 200 optimal weight: 4.9990 chunk 185 optimal weight: 3.9990 chunk 198 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 GLN ** E 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 96 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.124468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.096258 restraints weight = 24579.732| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 2.10 r_work: 0.2937 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18072 Z= 0.113 Angle : 0.510 8.401 24474 Z= 0.260 Chirality : 0.043 0.151 2740 Planarity : 0.004 0.063 3074 Dihedral : 5.478 53.236 2524 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.11 % Favored : 95.71 % Rotamer: Outliers : 1.00 % Allowed : 13.13 % Favored : 85.87 % 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: -0.67 (0.18), residues: 2216 helix: 0.47 (0.17), residues: 1032 sheet: -0.77 (0.33), residues: 260 loop : -1.34 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 23 HIS 0.003 0.001 HIS A 203 PHE 0.022 0.001 PHE F 79 TYR 0.010 0.001 TYR F 85 ARG 0.002 0.000 ARG B 373 Details of bonding type rmsd hydrogen bonds : bond 0.03753 ( 700) hydrogen bonds : angle 3.69377 ( 1992) covalent geometry : bond 0.00271 (18070) covalent geometry : angle 0.51033 (24474) Misc. bond : bond 0.00027 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 170 time to evaluate : 1.962 Fit side-chains REVERT: A 38 PHE cc_start: 0.6066 (m-80) cc_final: 0.5559 (m-80) REVERT: A 96 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8313 (pp) REVERT: A 421 LYS cc_start: 0.8720 (ptmt) cc_final: 0.8244 (ptmm) REVERT: B 30 ARG cc_start: 0.8448 (tpt170) cc_final: 0.7276 (mpt180) REVERT: B 171 TYR cc_start: 0.8026 (t80) cc_final: 0.7546 (t80) REVERT: B 306 MET cc_start: 0.8819 (tmm) cc_final: 0.8436 (ttp) REVERT: C 24 GLU cc_start: 0.8914 (mt-10) cc_final: 0.8630 (mt-10) REVERT: E 96 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8305 (pp) REVERT: E 421 LYS cc_start: 0.8714 (ptmt) cc_final: 0.8245 (ptmm) REVERT: F 30 ARG cc_start: 0.8422 (tpt170) cc_final: 0.7290 (mpt180) REVERT: F 171 TYR cc_start: 0.8058 (t80) cc_final: 0.7603 (t80) REVERT: F 306 MET cc_start: 0.8857 (tmm) cc_final: 0.8493 (ttp) outliers start: 19 outliers final: 16 residues processed: 184 average time/residue: 0.2912 time to fit residues: 82.4739 Evaluate side-chains 186 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 168 time to evaluate : 1.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 388 MET Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain C residue 42 ASN Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 118 ASN Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 331 ILE Chi-restraints excluded: chain F residue 79 PHE Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain G residue 31 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 123 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 142 optimal weight: 4.9990 chunk 146 optimal weight: 4.9990 chunk 209 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 111 optimal weight: 9.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 GLN ** E 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 96 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.121764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.093206 restraints weight = 24618.243| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.12 r_work: 0.2891 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18072 Z= 0.175 Angle : 0.575 10.239 24474 Z= 0.290 Chirality : 0.045 0.158 2740 Planarity : 0.005 0.067 3074 Dihedral : 5.596 51.356 2524 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.28 % Favored : 94.54 % Rotamer: Outliers : 1.31 % Allowed : 13.34 % Favored : 85.35 % 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: -0.88 (0.18), residues: 2216 helix: 0.31 (0.17), residues: 1044 sheet: -0.95 (0.33), residues: 270 loop : -1.46 (0.20), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 22 HIS 0.005 0.001 HIS E 203 PHE 0.027 0.002 PHE F 79 TYR 0.011 0.002 TYR F 85 ARG 0.002 0.000 ARG E 147 Details of bonding type rmsd hydrogen bonds : bond 0.04474 ( 700) hydrogen bonds : angle 3.81555 ( 1992) covalent geometry : bond 0.00434 (18070) covalent geometry : angle 0.57457 (24474) Misc. bond : bond 0.00043 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4432 Ramachandran restraints generated. 2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 165 time to evaluate : 1.947 Fit side-chains REVERT: A 38 PHE cc_start: 0.6077 (m-80) cc_final: 0.5581 (m-80) REVERT: A 96 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8337 (pp) REVERT: A 421 LYS cc_start: 0.8737 (ptmt) cc_final: 0.8234 (ptmm) REVERT: B 30 ARG cc_start: 0.8420 (tpt170) cc_final: 0.7266 (mpt180) REVERT: B 171 TYR cc_start: 0.8089 (t80) cc_final: 0.7616 (t80) REVERT: B 256 ILE cc_start: 0.9151 (OUTLIER) cc_final: 0.8783 (mt) REVERT: B 306 MET cc_start: 0.8834 (tmm) cc_final: 0.8462 (ttp) REVERT: C 24 GLU cc_start: 0.8946 (mt-10) cc_final: 0.8670 (mt-10) REVERT: E 38 PHE cc_start: 0.6078 (m-80) cc_final: 0.5573 (m-80) REVERT: E 96 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8332 (pp) REVERT: E 421 LYS cc_start: 0.8710 (ptmt) cc_final: 0.8224 (ptmm) REVERT: F 30 ARG cc_start: 0.8435 (tpt170) cc_final: 0.7270 (mpt180) REVERT: F 171 TYR cc_start: 0.8083 (t80) cc_final: 0.7602 (t80) REVERT: F 256 ILE cc_start: 0.9153 (OUTLIER) cc_final: 0.8785 (mt) REVERT: F 306 MET cc_start: 0.8867 (tmm) cc_final: 0.8535 (ttp) outliers start: 25 outliers final: 20 residues processed: 182 average time/residue: 0.2880 time to fit residues: 80.5402 Evaluate side-chains 188 residues out of total 1926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 164 time to evaluate : 2.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain B residue 79 PHE Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain B residue 388 MET Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 42 ASN Chi-restraints excluded: chain E residue 96 LEU Chi-restraints excluded: chain E residue 118 ASN Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 331 ILE Chi-restraints excluded: chain F residue 79 PHE Chi-restraints excluded: chain F residue 256 ILE Chi-restraints excluded: chain F residue 287 THR Chi-restraints excluded: chain F residue 388 MET Chi-restraints excluded: chain F residue 466 LEU Chi-restraints excluded: chain G residue 31 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 125 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 152 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 150 optimal weight: 6.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 GLN ** E 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 96 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.123695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.095685 restraints weight = 24442.469| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 2.07 r_work: 0.2898 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18072 Z= 0.149 Angle : 0.542 9.126 24474 Z= 0.277 Chirality : 0.044 0.154 2740 Planarity : 0.005 0.069 3074 Dihedral : 5.563 51.327 2524 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.06 % Favored : 95.76 % Rotamer: Outliers : 1.37 % Allowed : 13.39 % Favored : 85.24 % 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: -0.77 (0.18), residues: 2216 helix: 0.41 (0.17), residues: 1032 sheet: -0.95 (0.33), residues: 270 loop : -1.38 (0.20), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 23 HIS 0.004 0.001 HIS E 203 PHE 0.026 0.002 PHE F 79 TYR 0.011 0.001 TYR B 85 ARG 0.002 0.000 ARG B 373 Details of bonding type rmsd hydrogen bonds : bond 0.04193 ( 700) hydrogen bonds : angle 3.77016 ( 1992) covalent geometry : bond 0.00367 (18070) covalent geometry : angle 0.54241 (24474) Misc. bond : bond 0.00033 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9540.61 seconds wall clock time: 169 minutes 5.71 seconds (10145.71 seconds total)