Starting phenix.real_space_refine on Mon Dec 30 19:51:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ssv_25414/12_2024/7ssv_25414.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ssv_25414/12_2024/7ssv_25414.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ssv_25414/12_2024/7ssv_25414.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ssv_25414/12_2024/7ssv_25414.map" model { file = "/net/cci-nas-00/data/ceres_data/7ssv_25414/12_2024/7ssv_25414.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ssv_25414/12_2024/7ssv_25414.cif" } resolution = 3.39 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= 0.002 sd= 0.040 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 K 3 8.98 5 S 51 5.16 5 C 8938 2.51 5 N 2365 2.21 5 O 2458 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 59 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 13815 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2844 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 19, 'TRANS': 330} Chain breaks: 2 Chain: "B" Number of atoms: 2844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2844 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 19, 'TRANS': 330} Chain breaks: 2 Chain: "C" Number of atoms: 2844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2844 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 19, 'TRANS': 330} Chain breaks: 2 Chain: "D" Number of atoms: 2844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2844 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 19, 'TRANS': 330} Chain breaks: 2 Chain: "H" Number of atoms: 1389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 1389 Classifications: {'peptide': 261} Incomplete info: {'truncation_to_alanine': 197} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 246} Chain breaks: 2 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 639 Unresolved non-hydrogen angles: 835 Unresolved non-hydrogen dihedrals: 552 Unresolved non-hydrogen chiralities: 67 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 5, 'TYR:plan': 9, 'ASN:plan1': 9, 'TRP:plan': 7, 'ASP:plan': 7, 'PHE:plan': 5, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 304 Chain: "L" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1047 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 178} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 198} Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 548 Unresolved non-hydrogen angles: 709 Unresolved non-hydrogen dihedrals: 461 Unresolved non-hydrogen chiralities: 56 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 2, 'TYR:plan': 9, 'ASN:plan1': 8, 'TRP:plan': 3, 'ASP:plan': 7, 'PHE:plan': 4, 'GLU:plan': 9, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 260 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.16, per 1000 atoms: 0.74 Number of scatterers: 13815 At special positions: 0 Unit cell: (188.292, 121.836, 138.024, 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) K 3 19.00 S 51 16.00 O 2458 8.00 N 2365 7.00 C 8938 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS H 110 " - pdb=" SG CYS H 142 " distance=2.02 Simple disulfide: pdb=" SG CYS H 119 " - pdb=" SG CYS H 135 " distance=2.01 Simple disulfide: pdb=" SG CYS H 124 " - pdb=" SG CYS H 139 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.57 Conformation dependent library (CDL) restraints added in 2.0 seconds 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3506 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 18 sheets defined 55.1% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.61 Creating SS restraints... Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 132 through 137 Processing helix chain 'A' and resid 152 through 154 No H-bonds generated for 'chain 'A' and resid 152 through 154' Processing helix chain 'A' and resid 155 through 166 removed outlier: 3.855A pdb=" N ILE A 159 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 187 Processing helix chain 'A' and resid 190 through 202 Processing helix chain 'A' and resid 215 through 225 Processing helix chain 'A' and resid 231 through 254 Processing helix chain 'A' and resid 293 through 317 Processing helix chain 'A' and resid 321 through 325 removed outlier: 3.947A pdb=" N SER A 324 " --> pdb=" O ALA A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 348 Proline residue: A 338 - end of helix Processing helix chain 'A' and resid 361 through 369 Processing helix chain 'A' and resid 370 through 380 removed outlier: 3.584A pdb=" N ILE A 374 " --> pdb=" O VAL A 371 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS A 376 " --> pdb=" O ARG A 373 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ARG A 379 " --> pdb=" O LYS A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 391 removed outlier: 3.533A pdb=" N LEU A 387 " --> pdb=" O GLY A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 420 removed outlier: 4.403A pdb=" N LEU A 401 " --> pdb=" O GLU A 397 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER A 413 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N SER A 414 " --> pdb=" O ILE A 410 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA A 415 " --> pdb=" O LEU A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 433 Processing helix chain 'A' and resid 434 through 443 Processing helix chain 'A' and resid 454 through 474 removed outlier: 3.769A pdb=" N LYS A 458 " --> pdb=" O THR A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 489 removed outlier: 3.871A pdb=" N ILE A 479 " --> pdb=" O PRO A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 123 removed outlier: 3.605A pdb=" N LEU B 122 " --> pdb=" O GLN B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 155 removed outlier: 3.917A pdb=" N SER B 155 " --> pdb=" O ASN B 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 152 through 155' Processing helix chain 'B' and resid 156 through 166 Processing helix chain 'B' and resid 176 through 188 Processing helix chain 'B' and resid 190 through 202 Processing helix chain 'B' and resid 216 through 225 removed outlier: 3.547A pdb=" N TRP B 221 " --> pdb=" O GLN B 217 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU B 223 " --> pdb=" O GLN B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 230 removed outlier: 3.763A pdb=" N SER B 229 " --> pdb=" O TYR B 226 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N SER B 230 " --> pdb=" O PRO B 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 226 through 230' Processing helix chain 'B' and resid 231 through 256 removed outlier: 3.524A pdb=" N VAL B 249 " --> pdb=" O LEU B 245 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE B 250 " --> pdb=" O ILE B 246 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE B 251 " --> pdb=" O SER B 247 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU B 254 " --> pdb=" O ILE B 250 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR B 255 " --> pdb=" O PHE B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 316 Processing helix chain 'B' and resid 319 through 326 removed outlier: 3.596A pdb=" N ARG B 325 " --> pdb=" O ALA B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 348 removed outlier: 3.705A pdb=" N LEU B 330 " --> pdb=" O ASN B 326 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP B 332 " --> pdb=" O MET B 328 " (cutoff:3.500A) Proline residue: B 338 - end of helix Processing helix chain 'B' and resid 361 through 370 removed outlier: 4.069A pdb=" N ARG B 367 " --> pdb=" O LEU B 363 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LEU B 368 " --> pdb=" O ARG B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 380 Processing helix chain 'B' and resid 384 through 394 Processing helix chain 'B' and resid 395 through 420 removed outlier: 4.403A pdb=" N LEU B 401 " --> pdb=" O GLU B 397 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER B 413 " --> pdb=" O VAL B 409 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N SER B 414 " --> pdb=" O ILE B 410 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA B 415 " --> pdb=" O LEU B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 433 Processing helix chain 'B' and resid 434 through 443 Processing helix chain 'B' and resid 454 through 474 removed outlier: 3.769A pdb=" N LYS B 458 " --> pdb=" O THR B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 489 removed outlier: 3.871A pdb=" N ILE B 479 " --> pdb=" O PRO B 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 124 Processing helix chain 'C' and resid 132 through 137 Processing helix chain 'C' and resid 152 through 154 No H-bonds generated for 'chain 'C' and resid 152 through 154' Processing helix chain 'C' and resid 155 through 166 removed outlier: 4.181A pdb=" N ILE C 159 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 188 Processing helix chain 'C' and resid 190 through 202 Processing helix chain 'C' and resid 216 through 226 removed outlier: 3.973A pdb=" N TYR C 226 " --> pdb=" O LEU C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 255 removed outlier: 4.125A pdb=" N THR C 255 " --> pdb=" O PHE C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 316 removed outlier: 3.794A pdb=" N VAL C 297 " --> pdb=" O ASP C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 347 Proline residue: C 338 - end of helix Processing helix chain 'C' and resid 361 through 370 removed outlier: 3.755A pdb=" N VAL C 365 " --> pdb=" O ALA C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 380 removed outlier: 3.573A pdb=" N ILE C 374 " --> pdb=" O VAL C 371 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N PHE C 375 " --> pdb=" O PHE C 372 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS C 376 " --> pdb=" O ARG C 373 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU C 377 " --> pdb=" O ILE C 374 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG C 379 " --> pdb=" O LYS C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 394 Processing helix chain 'C' and resid 395 through 420 removed outlier: 4.403A pdb=" N LEU C 401 " --> pdb=" O GLU C 397 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N SER C 413 " --> pdb=" O VAL C 409 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N SER C 414 " --> pdb=" O ILE C 410 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA C 415 " --> pdb=" O LEU C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 433 Processing helix chain 'C' and resid 434 through 443 Processing helix chain 'C' and resid 454 through 474 removed outlier: 3.769A pdb=" N LYS C 458 " --> pdb=" O THR C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 489 removed outlier: 3.871A pdb=" N ILE C 479 " --> pdb=" O PRO C 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 124 Processing helix chain 'D' and resid 128 through 131 Processing helix chain 'D' and resid 132 through 137 Processing helix chain 'D' and resid 152 through 154 No H-bonds generated for 'chain 'D' and resid 152 through 154' Processing helix chain 'D' and resid 155 through 165 removed outlier: 4.088A pdb=" N ILE D 159 " --> pdb=" O SER D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 188 removed outlier: 3.593A pdb=" N ARG D 185 " --> pdb=" O SER D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 202 removed outlier: 3.569A pdb=" N LYS D 196 " --> pdb=" O GLU D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 226 removed outlier: 3.519A pdb=" N TYR D 226 " --> pdb=" O LEU D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 255 removed outlier: 3.648A pdb=" N ILE D 244 " --> pdb=" O SER D 240 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE D 250 " --> pdb=" O ILE D 246 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N THR D 255 " --> pdb=" O PHE D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 316 removed outlier: 3.634A pdb=" N VAL D 297 " --> pdb=" O ASP D 293 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N GLU D 299 " --> pdb=" O PHE D 295 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N SER D 307 " --> pdb=" O ILE D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 348 removed outlier: 3.911A pdb=" N LEU D 330 " --> pdb=" O ASN D 326 " (cutoff:3.500A) Proline residue: D 338 - end of helix Processing helix chain 'D' and resid 361 through 370 removed outlier: 4.073A pdb=" N VAL D 365 " --> pdb=" O ALA D 361 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE D 366 " --> pdb=" O ILE D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 372 No H-bonds generated for 'chain 'D' and resid 371 through 372' Processing helix chain 'D' and resid 373 through 377 removed outlier: 3.630A pdb=" N LYS D 376 " --> pdb=" O ARG D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 393 Processing helix chain 'D' and resid 395 through 420 removed outlier: 4.402A pdb=" N LEU D 401 " --> pdb=" O GLU D 397 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER D 413 " --> pdb=" O VAL D 409 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N SER D 414 " --> pdb=" O ILE D 410 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA D 415 " --> pdb=" O LEU D 411 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 433 Processing helix chain 'D' and resid 434 through 443 Processing helix chain 'D' and resid 454 through 474 removed outlier: 3.770A pdb=" N LYS D 458 " --> pdb=" O THR D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 489 removed outlier: 3.871A pdb=" N ILE D 479 " --> pdb=" O PRO D 475 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 67 removed outlier: 3.702A pdb=" N ARG H 66 " --> pdb=" O LEU H 63 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL H 67 " --> pdb=" O LYS H 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 63 through 67' Processing helix chain 'H' and resid 86 through 90 removed outlier: 3.760A pdb=" N THR H 90 " --> pdb=" O ALA H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 120 through 127 Processing helix chain 'H' and resid 127 through 133 Processing helix chain 'H' and resid 135 through 140 removed outlier: 3.658A pdb=" N CYS H 139 " --> pdb=" O CYS H 135 " (cutoff:3.500A) Processing helix chain 'H' and resid 239 through 241 No H-bonds generated for 'chain 'H' and resid 239 through 241' Processing helix chain 'L' and resid 28 through 32 removed outlier: 3.564A pdb=" N ASN L 31 " --> pdb=" O ASN L 28 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.994A pdb=" N ASP L 83 " --> pdb=" O GLN L 80 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLU L 84 " --> pdb=" O THR L 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 80 through 84' Processing helix chain 'L' and resid 125 through 131 Processing helix chain 'L' and resid 185 through 190 Processing sheet with id=AA1, first strand: chain 'A' and resid 113 through 118 removed outlier: 3.504A pdb=" N VAL A 106 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N TYR A 147 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N VAL A 107 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N PHE A 149 " --> pdb=" O VAL A 107 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ASN A 109 " --> pdb=" O PHE A 149 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 114 through 116 Processing sheet with id=AA3, first strand: chain 'C' and resid 113 through 118 removed outlier: 3.672A pdb=" N ILE C 110 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N PHE C 149 " --> pdb=" O VAL C 107 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ASN C 109 " --> pdb=" O PHE C 149 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 105 through 106 Processing sheet with id=AA5, first strand: chain 'D' and resid 113 through 114 removed outlier: 6.502A pdb=" N ASN D 109 " --> pdb=" O PHE D 149 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 3 through 8 Processing sheet with id=AA7, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.567A pdb=" N LEU H 12 " --> pdb=" O THR H 162 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N TRP H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N SER H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE H 48 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.567A pdb=" N LEU H 12 " --> pdb=" O THR H 162 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N SER H 97 " --> pdb=" O ASP H 153 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N HIS H 151 " --> pdb=" O HIS H 99 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 172 through 176 removed outlier: 3.649A pdb=" N LEU H 193 " --> pdb=" O PHE H 174 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU H 176 " --> pdb=" O GLY H 191 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N CYS H 192 " --> pdb=" O SER H 232 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP H 196 " --> pdb=" O TYR H 228 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N TYR H 228 " --> pdb=" O ASP H 196 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 172 through 176 removed outlier: 3.649A pdb=" N LEU H 193 " --> pdb=" O PHE H 174 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU H 176 " --> pdb=" O GLY H 191 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N CYS H 192 " --> pdb=" O SER H 232 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP H 196 " --> pdb=" O TYR H 228 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N TYR H 228 " --> pdb=" O ASP H 196 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 246 through 252 removed outlier: 4.174A pdb=" N TYR H 246 " --> pdb=" O VAL H 263 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N CYS H 248 " --> pdb=" O LYS H 261 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N LYS H 261 " --> pdb=" O CYS H 248 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N VAL H 250 " --> pdb=" O VAL H 259 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL H 259 " --> pdb=" O VAL H 250 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.721A pdb=" N VAL L 10 " --> pdb=" O THR L 108 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N LEU L 110 " --> pdb=" O VAL L 10 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N GLY L 12 " --> pdb=" O LEU L 110 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR L 88 " --> pdb=" O TYR L 37 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.721A pdb=" N VAL L 10 " --> pdb=" O THR L 108 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N LEU L 110 " --> pdb=" O VAL L 10 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N GLY L 12 " --> pdb=" O LEU L 110 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 18 through 23 removed outlier: 3.888A pdb=" N VAL L 18 " --> pdb=" O ILE L 76 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE L 76 " --> pdb=" O VAL L 18 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 18 through 23 removed outlier: 3.888A pdb=" N VAL L 18 " --> pdb=" O ILE L 76 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE L 76 " --> pdb=" O VAL L 18 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER L 71 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER L 68 " --> pdb=" O SER L 71 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 118 through 122 removed outlier: 3.551A pdb=" N ALA L 134 " --> pdb=" O LEU L 184 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU L 136 " --> pdb=" O LEU L 182 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU L 182 " --> pdb=" O LEU L 136 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N SER L 179 " --> pdb=" O THR L 167 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N THR L 167 " --> pdb=" O SER L 179 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N TYR L 181 " --> pdb=" O THR L 165 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N THR L 165 " --> pdb=" O TYR L 181 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N SER L 183 " --> pdb=" O VAL L 163 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N VAL L 163 " --> pdb=" O SER L 183 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 149 through 150 removed outlier: 4.143A pdb=" N THR L 149 " --> pdb=" O THR L 200 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N THR L 200 " --> pdb=" O THR L 149 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 157 through 159 removed outlier: 3.687A pdb=" N TRP L 152 " --> pdb=" O VAL L 159 " (cutoff:3.500A) 744 hydrogen bonds defined for protein. 2094 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: 4.23 Time building geometry restraints manager: 4.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 2252 1.31 - 1.44: 3937 1.44 - 1.57: 7840 1.57 - 1.70: 0 1.70 - 1.84: 76 Bond restraints: 14105 Sorted by residual: bond pdb=" CA ARG B 370 " pdb=" C ARG B 370 " ideal model delta sigma weight residual 1.522 1.410 0.112 1.38e-02 5.25e+03 6.62e+01 bond pdb=" C SER D 394 " pdb=" N MET D 395 " ideal model delta sigma weight residual 1.335 1.244 0.091 1.38e-02 5.25e+03 4.32e+01 bond pdb=" CA CYS H 119 " pdb=" C CYS H 119 " ideal model delta sigma weight residual 1.523 1.454 0.069 1.32e-02 5.74e+03 2.75e+01 bond pdb=" C ARG B 370 " pdb=" O ARG B 370 " ideal model delta sigma weight residual 1.236 1.175 0.061 1.29e-02 6.01e+03 2.25e+01 bond pdb=" CA SER D 413 " pdb=" CB SER D 413 " ideal model delta sigma weight residual 1.528 1.458 0.071 1.56e-02 4.11e+03 2.05e+01 ... (remaining 14100 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 16507 2.43 - 4.86: 2345 4.86 - 7.29: 261 7.29 - 9.72: 51 9.72 - 12.15: 12 Bond angle restraints: 19176 Sorted by residual: angle pdb=" CA PHE H 198 " pdb=" C PHE H 198 " pdb=" O PHE H 198 " ideal model delta sigma weight residual 120.28 110.45 9.83 1.03e+00 9.43e-01 9.11e+01 angle pdb=" CA PHE H 198 " pdb=" C PHE H 198 " pdb=" N PRO H 199 " ideal model delta sigma weight residual 117.75 126.67 -8.92 1.17e+00 7.31e-01 5.81e+01 angle pdb=" C CYS H 135 " pdb=" CA CYS H 135 " pdb=" CB CYS H 135 " ideal model delta sigma weight residual 111.85 100.81 11.04 1.47e+00 4.63e-01 5.64e+01 angle pdb=" CA ASP B 423 " pdb=" C ASP B 423 " pdb=" N PRO B 424 " ideal model delta sigma weight residual 117.82 123.26 -5.44 7.80e-01 1.64e+00 4.86e+01 angle pdb=" CA ASP A 423 " pdb=" C ASP A 423 " pdb=" N PRO A 424 " ideal model delta sigma weight residual 117.82 123.24 -5.42 7.80e-01 1.64e+00 4.82e+01 ... (remaining 19171 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.25: 7452 17.25 - 34.49: 661 34.49 - 51.74: 157 51.74 - 68.99: 40 68.99 - 86.23: 11 Dihedral angle restraints: 8321 sinusoidal: 2908 harmonic: 5413 Sorted by residual: dihedral pdb=" CB CYS H 110 " pdb=" SG CYS H 110 " pdb=" SG CYS H 142 " pdb=" CB CYS H 142 " ideal model delta sinusoidal sigma weight residual -86.00 -163.60 77.60 1 1.00e+01 1.00e-02 7.54e+01 dihedral pdb=" CB CYS H 124 " pdb=" SG CYS H 124 " pdb=" SG CYS H 139 " pdb=" CB CYS H 139 " ideal model delta sinusoidal sigma weight residual 93.00 163.91 -70.91 1 1.00e+01 1.00e-02 6.46e+01 dihedral pdb=" C THR C 444 " pdb=" N THR C 444 " pdb=" CA THR C 444 " pdb=" CB THR C 444 " ideal model delta harmonic sigma weight residual -122.00 -137.00 15.00 0 2.50e+00 1.60e-01 3.60e+01 ... (remaining 8318 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 1666 0.115 - 0.229: 464 0.229 - 0.344: 73 0.344 - 0.459: 9 0.459 - 0.573: 4 Chirality restraints: 2216 Sorted by residual: chirality pdb=" CA THR C 444 " pdb=" N THR C 444 " pdb=" C THR C 444 " pdb=" CB THR C 444 " both_signs ideal model delta sigma weight residual False 2.53 1.95 0.57 2.00e-01 2.50e+01 8.21e+00 chirality pdb=" CA THR D 444 " pdb=" N THR D 444 " pdb=" C THR D 444 " pdb=" CB THR D 444 " both_signs ideal model delta sigma weight residual False 2.53 1.95 0.57 2.00e-01 2.50e+01 8.16e+00 chirality pdb=" CA THR A 444 " pdb=" N THR A 444 " pdb=" C THR A 444 " pdb=" CB THR A 444 " both_signs ideal model delta sigma weight residual False 2.53 1.96 0.57 2.00e-01 2.50e+01 8.15e+00 ... (remaining 2213 not shown) Planarity restraints: 2481 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 222 " 0.022 2.00e-02 2.50e+03 4.40e-02 1.93e+01 pdb=" C LEU A 222 " -0.076 2.00e-02 2.50e+03 pdb=" O LEU A 222 " 0.028 2.00e-02 2.50e+03 pdb=" N LEU A 223 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 467 " -0.020 2.00e-02 2.50e+03 3.88e-02 1.51e+01 pdb=" C ALA B 467 " 0.067 2.00e-02 2.50e+03 pdb=" O ALA B 467 " -0.025 2.00e-02 2.50e+03 pdb=" N GLY B 468 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 467 " -0.020 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" C ALA A 467 " 0.067 2.00e-02 2.50e+03 pdb=" O ALA A 467 " -0.024 2.00e-02 2.50e+03 pdb=" N GLY A 468 " -0.022 2.00e-02 2.50e+03 ... (remaining 2478 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.80: 3687 2.80 - 3.38: 14437 3.38 - 3.97: 23297 3.97 - 4.55: 32134 4.55 - 5.14: 48384 Nonbonded interactions: 121939 Sorted by model distance: nonbonded pdb=" O THR A 255 " pdb=" OG1 THR A 255 " model vdw 2.215 3.040 nonbonded pdb=" O THR B 255 " pdb=" OG1 THR B 255 " model vdw 2.251 3.040 nonbonded pdb=" OD1 ASP D 332 " pdb=" NZ LYS D 376 " model vdw 2.282 3.120 nonbonded pdb=" N ASP C 178 " pdb=" OD1 ASP C 178 " model vdw 2.288 3.120 nonbonded pdb=" NH2 ARG C 170 " pdb=" OD2 ASP D 178 " model vdw 2.312 3.120 ... (remaining 121934 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 103 through 491) selection = chain 'B' selection = (chain 'C' and resid 103 through 491) selection = chain 'D' } 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: 3.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 34.510 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 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 : 0.018 0.183 14105 Z= 1.121 Angle : 1.720 12.153 19176 Z= 1.198 Chirality : 0.108 0.573 2216 Planarity : 0.009 0.087 2481 Dihedral : 14.839 86.233 4806 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 6.26 % Allowed : 12.29 % Favored : 81.44 % Cbeta Deviations : 1.14 % Peptide Plane: Cis-proline : 2.88 % 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: -3.22 (0.17), residues: 1842 helix: -1.79 (0.15), residues: 943 sheet: -2.46 (0.35), residues: 156 loop : -2.35 (0.19), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP C 221 HIS 0.013 0.004 HIS A 451 PHE 0.048 0.003 PHE H 122 TYR 0.023 0.003 TYR C 163 ARG 0.008 0.001 ARG C 114 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 227 time to evaluate : 1.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 GLN cc_start: 0.7949 (mt0) cc_final: 0.6972 (mt0) REVERT: A 308 PHE cc_start: 0.7940 (OUTLIER) cc_final: 0.7268 (t80) REVERT: A 392 LYS cc_start: 0.8669 (tttp) cc_final: 0.7975 (ttmm) REVERT: A 397 GLU cc_start: 0.8228 (mp0) cc_final: 0.7628 (mt-10) REVERT: A 422 ASP cc_start: 0.7182 (OUTLIER) cc_final: 0.6839 (p0) REVERT: A 489 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.7580 (tmm-80) REVERT: B 205 ARG cc_start: 0.6551 (mtt180) cc_final: 0.6324 (tpp-160) REVERT: B 210 PRO cc_start: 0.7624 (Cg_endo) cc_final: 0.7335 (Cg_exo) REVERT: B 367 ARG cc_start: 0.8281 (mpt180) cc_final: 0.7774 (mmm160) REVERT: B 405 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8451 (mt) REVERT: C 209 ARG cc_start: 0.7449 (pmt170) cc_final: 0.7181 (ptt-90) REVERT: C 405 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8172 (mp) REVERT: D 424 PRO cc_start: 0.6075 (Cg_exo) cc_final: 0.4999 (Cg_endo) outliers start: 80 outliers final: 20 residues processed: 282 average time/residue: 0.3282 time to fit residues: 126.7646 Evaluate side-chains 152 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 1.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 308 PHE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 489 ARG Chi-restraints excluded: chain B residue 153 ARG Chi-restraints excluded: chain B residue 219 GLN Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain C residue 153 ARG Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 422 ASP Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 430 SER Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain H residue 132 LEU Chi-restraints excluded: chain H residue 136 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 157 optimal weight: 50.0000 chunk 141 optimal weight: 50.0000 chunk 78 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 146 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 chunk 169 optimal weight: 7.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN A 145 ASN A 164 GLN A 484 ASN C 124 GLN C 145 ASN C 385 GLN C 484 ASN D 164 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14105 Z= 0.256 Angle : 0.664 6.289 19176 Z= 0.361 Chirality : 0.044 0.194 2216 Planarity : 0.007 0.066 2481 Dihedral : 6.540 57.165 2076 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 4.62 % Allowed : 15.51 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % 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: -1.41 (0.19), residues: 1842 helix: 0.07 (0.17), residues: 929 sheet: -2.00 (0.39), residues: 161 loop : -1.93 (0.20), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 436 HIS 0.002 0.001 HIS H 126 PHE 0.024 0.002 PHE C 140 TYR 0.013 0.002 TYR B 161 ARG 0.005 0.000 ARG A 170 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 158 time to evaluate : 1.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 LYS cc_start: 0.8597 (tttp) cc_final: 0.7901 (ttmm) REVERT: A 397 GLU cc_start: 0.7855 (mp0) cc_final: 0.7469 (mt-10) REVERT: A 422 ASP cc_start: 0.7160 (OUTLIER) cc_final: 0.6885 (p0) REVERT: A 470 LEU cc_start: 0.8225 (mp) cc_final: 0.7918 (mp) REVERT: A 489 ARG cc_start: 0.7637 (OUTLIER) cc_final: 0.7254 (tmm-80) REVERT: B 153 ARG cc_start: 0.8973 (OUTLIER) cc_final: 0.8280 (mtp180) REVERT: B 210 PRO cc_start: 0.7253 (Cg_endo) cc_final: 0.6989 (Cg_exo) REVERT: B 367 ARG cc_start: 0.8147 (mpt180) cc_final: 0.7690 (mtp180) REVERT: B 453 VAL cc_start: 0.8979 (OUTLIER) cc_final: 0.8769 (p) REVERT: D 380 HIS cc_start: 0.8622 (OUTLIER) cc_final: 0.7966 (m-70) outliers start: 59 outliers final: 30 residues processed: 208 average time/residue: 0.3009 time to fit residues: 88.6784 Evaluate side-chains 161 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 126 time to evaluate : 1.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 317 CYS Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 489 ARG Chi-restraints excluded: chain B residue 153 ARG Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 236 ILE Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 380 HIS Chi-restraints excluded: chain H residue 111 ILE Chi-restraints excluded: chain H residue 112 ASP Chi-restraints excluded: chain H residue 132 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 94 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 141 optimal weight: 50.0000 chunk 115 optimal weight: 10.0000 chunk 46 optimal weight: 0.8980 chunk 170 optimal weight: 40.0000 chunk 183 optimal weight: 6.9990 chunk 151 optimal weight: 6.9990 chunk 168 optimal weight: 8.9990 chunk 57 optimal weight: 3.9990 chunk 136 optimal weight: 0.9980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN C 145 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14105 Z= 0.348 Angle : 0.651 7.345 19176 Z= 0.351 Chirality : 0.045 0.176 2216 Planarity : 0.006 0.090 2481 Dihedral : 5.409 59.531 2050 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.92 % Allowed : 17.31 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % 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 (0.19), residues: 1842 helix: 0.50 (0.17), residues: 929 sheet: -1.30 (0.39), residues: 172 loop : -1.85 (0.21), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 436 HIS 0.005 0.001 HIS H 126 PHE 0.026 0.002 PHE C 406 TYR 0.019 0.002 TYR C 147 ARG 0.004 0.000 ARG C 214 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 137 time to evaluate : 1.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 LYS cc_start: 0.8630 (tttp) cc_final: 0.7920 (ttmm) REVERT: A 397 GLU cc_start: 0.7885 (mp0) cc_final: 0.7447 (mt-10) REVERT: A 422 ASP cc_start: 0.7311 (OUTLIER) cc_final: 0.6976 (p0) REVERT: A 489 ARG cc_start: 0.7727 (OUTLIER) cc_final: 0.7232 (tmm-80) REVERT: B 153 ARG cc_start: 0.8985 (OUTLIER) cc_final: 0.8376 (mtp180) REVERT: C 120 LYS cc_start: 0.8193 (mmtt) cc_final: 0.7608 (mmtt) REVERT: C 192 GLU cc_start: 0.8100 (pm20) cc_final: 0.7769 (pp20) REVERT: D 194 MET cc_start: 0.8088 (tpp) cc_final: 0.7655 (tpp) REVERT: D 380 HIS cc_start: 0.8685 (OUTLIER) cc_final: 0.8044 (m-70) outliers start: 50 outliers final: 33 residues processed: 179 average time/residue: 0.2656 time to fit residues: 69.7690 Evaluate side-chains 154 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 117 time to evaluate : 1.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 489 ARG Chi-restraints excluded: chain B residue 153 ARG Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 236 ILE Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 380 HIS Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain H residue 112 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 168 optimal weight: 0.4980 chunk 127 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 18 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 170 optimal weight: 0.9990 chunk 180 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 161 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN C 145 ASN D 164 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14105 Z= 0.203 Angle : 0.555 8.711 19176 Z= 0.296 Chirality : 0.042 0.216 2216 Planarity : 0.005 0.062 2481 Dihedral : 4.681 55.698 2036 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.45 % Allowed : 17.78 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % 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: -0.29 (0.20), residues: 1842 helix: 1.07 (0.18), residues: 929 sheet: -0.88 (0.42), residues: 161 loop : -1.66 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 436 HIS 0.003 0.001 HIS H 126 PHE 0.024 0.001 PHE A 197 TYR 0.018 0.001 TYR C 161 ARG 0.004 0.000 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 132 time to evaluate : 1.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 LYS cc_start: 0.8583 (tttp) cc_final: 0.7872 (ttmm) REVERT: A 397 GLU cc_start: 0.7759 (mp0) cc_final: 0.7357 (mt-10) REVERT: A 422 ASP cc_start: 0.7322 (OUTLIER) cc_final: 0.6958 (p0) REVERT: A 489 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.7157 (tmm-80) REVERT: B 153 ARG cc_start: 0.8884 (OUTLIER) cc_final: 0.8226 (mtp180) REVERT: C 120 LYS cc_start: 0.8121 (mmtt) cc_final: 0.7900 (mmmt) REVERT: C 299 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.6710 (tm-30) REVERT: D 194 MET cc_start: 0.8074 (tpp) cc_final: 0.7605 (tpp) REVERT: D 380 HIS cc_start: 0.8644 (OUTLIER) cc_final: 0.8001 (m-70) outliers start: 44 outliers final: 28 residues processed: 173 average time/residue: 0.2734 time to fit residues: 68.8661 Evaluate side-chains 153 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 120 time to evaluate : 1.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 489 ARG Chi-restraints excluded: chain B residue 153 ARG Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 336 ILE Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 380 HIS Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain H residue 112 ASP Chi-restraints excluded: chain H residue 132 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 150 optimal weight: 20.0000 chunk 102 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 134 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 154 optimal weight: 40.0000 chunk 124 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 162 optimal weight: 50.0000 chunk 45 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN C 145 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.075 14105 Z= 0.591 Angle : 0.740 8.540 19176 Z= 0.395 Chirality : 0.050 0.195 2216 Planarity : 0.006 0.071 2481 Dihedral : 4.919 48.943 2036 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 5.48 % Allowed : 17.38 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % 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 (0.20), residues: 1842 helix: 0.33 (0.17), residues: 969 sheet: -0.88 (0.41), residues: 172 loop : -1.82 (0.22), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 436 HIS 0.008 0.002 HIS C 451 PHE 0.032 0.002 PHE C 406 TYR 0.020 0.002 TYR C 147 ARG 0.006 0.001 ARG C 209 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 118 time to evaluate : 1.632 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 392 LYS cc_start: 0.8688 (tttp) cc_final: 0.7995 (ttmm) REVERT: A 397 GLU cc_start: 0.7890 (mp0) cc_final: 0.7486 (mt-10) REVERT: A 406 PHE cc_start: 0.7832 (OUTLIER) cc_final: 0.6881 (t80) REVERT: A 422 ASP cc_start: 0.7453 (OUTLIER) cc_final: 0.7136 (p0) REVERT: A 489 ARG cc_start: 0.7779 (OUTLIER) cc_final: 0.7252 (tmm-80) REVERT: C 120 LYS cc_start: 0.8234 (mmtt) cc_final: 0.7945 (mmmt) REVERT: C 121 THR cc_start: 0.8644 (p) cc_final: 0.8339 (t) REVERT: C 153 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.8322 (ptm160) REVERT: C 299 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.6809 (tm-30) REVERT: C 453 VAL cc_start: 0.9132 (OUTLIER) cc_final: 0.8845 (p) REVERT: D 194 MET cc_start: 0.8091 (tpp) cc_final: 0.7680 (tpp) REVERT: D 380 HIS cc_start: 0.8677 (OUTLIER) cc_final: 0.8136 (m-70) outliers start: 70 outliers final: 49 residues processed: 178 average time/residue: 0.2624 time to fit residues: 68.3258 Evaluate side-chains 170 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 114 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 406 PHE Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 489 ARG Chi-restraints excluded: chain B residue 120 LYS Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 341 ILE Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain C residue 153 ARG Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 307 SER Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 236 ILE Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 304 ILE Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 336 ILE Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 380 HIS Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain H residue 112 ASP Chi-restraints excluded: chain H residue 132 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 60 optimal weight: 0.7980 chunk 162 optimal weight: 50.0000 chunk 35 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 180 optimal weight: 40.0000 chunk 150 optimal weight: 4.9990 chunk 83 optimal weight: 0.5980 chunk 15 optimal weight: 0.0370 chunk 59 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 145 ASN C 145 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14105 Z= 0.200 Angle : 0.558 9.623 19176 Z= 0.297 Chirality : 0.042 0.178 2216 Planarity : 0.005 0.069 2481 Dihedral : 4.430 46.377 2032 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.68 % Allowed : 19.42 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.20), residues: 1842 helix: 1.20 (0.18), residues: 929 sheet: -0.61 (0.42), residues: 160 loop : -1.51 (0.22), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 436 HIS 0.001 0.000 HIS C 451 PHE 0.020 0.001 PHE C 406 TYR 0.016 0.001 TYR C 161 ARG 0.003 0.000 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 126 time to evaluate : 1.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 LYS cc_start: 0.8611 (tttp) cc_final: 0.7890 (ttmm) REVERT: A 397 GLU cc_start: 0.7767 (mp0) cc_final: 0.7354 (mt-10) REVERT: A 422 ASP cc_start: 0.7349 (OUTLIER) cc_final: 0.7016 (p0) REVERT: A 489 ARG cc_start: 0.7620 (OUTLIER) cc_final: 0.7136 (tmm-80) REVERT: C 120 LYS cc_start: 0.8166 (mmtt) cc_final: 0.7927 (mmmt) REVERT: C 299 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.6659 (tm-30) REVERT: C 453 VAL cc_start: 0.8943 (OUTLIER) cc_final: 0.8693 (p) REVERT: D 194 MET cc_start: 0.8084 (tpp) cc_final: 0.7582 (tpp) REVERT: D 380 HIS cc_start: 0.8621 (OUTLIER) cc_final: 0.8005 (m-70) outliers start: 47 outliers final: 36 residues processed: 169 average time/residue: 0.2505 time to fit residues: 63.1870 Evaluate side-chains 158 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 117 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 489 ARG Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 471 THR Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 336 ILE Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 380 HIS Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain H residue 112 ASP Chi-restraints excluded: chain H residue 132 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 174 optimal weight: 20.0000 chunk 20 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 152 optimal weight: 1.9990 chunk 101 optimal weight: 0.0770 chunk 180 optimal weight: 50.0000 chunk 112 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 83 optimal weight: 0.5980 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14105 Z= 0.185 Angle : 0.535 8.701 19176 Z= 0.283 Chirality : 0.042 0.192 2216 Planarity : 0.005 0.070 2481 Dihedral : 4.234 43.988 2032 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.29 % Allowed : 19.34 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % 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: 0.20 (0.20), residues: 1842 helix: 1.40 (0.18), residues: 929 sheet: -0.48 (0.42), residues: 161 loop : -1.37 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 436 HIS 0.002 0.001 HIS C 451 PHE 0.021 0.001 PHE C 406 TYR 0.016 0.001 TYR C 161 ARG 0.004 0.000 ARG B 185 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 124 time to evaluate : 1.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 LYS cc_start: 0.8606 (tttp) cc_final: 0.7921 (ttmm) REVERT: A 397 GLU cc_start: 0.7774 (mp0) cc_final: 0.7332 (mt-10) REVERT: A 422 ASP cc_start: 0.7410 (OUTLIER) cc_final: 0.7076 (p0) REVERT: A 489 ARG cc_start: 0.7568 (OUTLIER) cc_final: 0.7096 (tmm-80) REVERT: B 484 ASN cc_start: 0.8499 (OUTLIER) cc_final: 0.8135 (m-40) REVERT: C 120 LYS cc_start: 0.8142 (mmtt) cc_final: 0.7667 (mmmt) REVERT: C 299 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.6659 (tm-30) REVERT: D 194 MET cc_start: 0.8018 (tpp) cc_final: 0.7578 (tpp) REVERT: D 380 HIS cc_start: 0.8615 (OUTLIER) cc_final: 0.8034 (m-70) outliers start: 42 outliers final: 33 residues processed: 165 average time/residue: 0.2669 time to fit residues: 64.9940 Evaluate side-chains 156 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 118 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 489 ARG Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 336 ILE Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 380 HIS Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain H residue 112 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 111 optimal weight: 0.0980 chunk 71 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 114 optimal weight: 0.5980 chunk 122 optimal weight: 0.4980 chunk 89 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 141 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 145 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.3941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14105 Z= 0.177 Angle : 0.522 8.226 19176 Z= 0.276 Chirality : 0.041 0.254 2216 Planarity : 0.005 0.064 2481 Dihedral : 4.060 43.933 2032 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.29 % Allowed : 19.42 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % 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: 0.44 (0.21), residues: 1842 helix: 1.58 (0.18), residues: 929 sheet: -0.42 (0.37), residues: 209 loop : -1.24 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 436 HIS 0.002 0.000 HIS C 451 PHE 0.041 0.001 PHE D 186 TYR 0.016 0.001 TYR C 161 ARG 0.007 0.000 ARG D 151 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 127 time to evaluate : 1.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7852 (mt) REVERT: A 392 LYS cc_start: 0.8592 (tttp) cc_final: 0.7898 (ttmm) REVERT: A 422 ASP cc_start: 0.7439 (OUTLIER) cc_final: 0.7074 (p0) REVERT: A 489 ARG cc_start: 0.7500 (OUTLIER) cc_final: 0.7053 (tmm-80) REVERT: B 484 ASN cc_start: 0.8471 (OUTLIER) cc_final: 0.8125 (m-40) REVERT: C 120 LYS cc_start: 0.8134 (mmtt) cc_final: 0.7665 (mmmt) REVERT: C 121 THR cc_start: 0.8587 (p) cc_final: 0.8287 (t) REVERT: C 192 GLU cc_start: 0.8127 (pm20) cc_final: 0.7841 (pp20) REVERT: C 299 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.6683 (tm-30) REVERT: D 194 MET cc_start: 0.8095 (tpp) cc_final: 0.7651 (tpp) REVERT: D 380 HIS cc_start: 0.8616 (OUTLIER) cc_final: 0.8020 (m-70) outliers start: 42 outliers final: 29 residues processed: 166 average time/residue: 0.2574 time to fit residues: 63.2549 Evaluate side-chains 156 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 121 time to evaluate : 1.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 489 ARG Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 336 ILE Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 380 HIS Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain H residue 112 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 163 optimal weight: 30.0000 chunk 172 optimal weight: 50.0000 chunk 157 optimal weight: 9.9990 chunk 167 optimal weight: 8.9990 chunk 101 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 131 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 158 optimal weight: 50.0000 chunk 110 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 145 ASN C 145 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 14105 Z= 0.375 Angle : 0.614 7.447 19176 Z= 0.326 Chirality : 0.045 0.218 2216 Planarity : 0.006 0.071 2481 Dihedral : 4.193 44.338 2031 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 3.60 % Allowed : 19.34 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % 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: 0.20 (0.21), residues: 1842 helix: 1.27 (0.18), residues: 929 sheet: -0.33 (0.36), residues: 229 loop : -1.26 (0.25), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 436 HIS 0.005 0.001 HIS C 451 PHE 0.029 0.002 PHE D 186 TYR 0.014 0.002 TYR C 161 ARG 0.010 0.000 ARG B 213 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 121 time to evaluate : 1.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7930 (mt) REVERT: A 392 LYS cc_start: 0.8642 (tttp) cc_final: 0.7915 (ttmm) REVERT: A 397 GLU cc_start: 0.7841 (mp0) cc_final: 0.7253 (mt-10) REVERT: A 422 ASP cc_start: 0.7497 (OUTLIER) cc_final: 0.7190 (p0) REVERT: A 489 ARG cc_start: 0.7638 (OUTLIER) cc_final: 0.7154 (tmm-80) REVERT: B 484 ASN cc_start: 0.8533 (OUTLIER) cc_final: 0.8179 (m-40) REVERT: C 120 LYS cc_start: 0.8142 (mmtt) cc_final: 0.7671 (mmmt) REVERT: C 121 THR cc_start: 0.8660 (p) cc_final: 0.8365 (t) REVERT: C 299 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.6754 (tm-30) REVERT: D 380 HIS cc_start: 0.8680 (OUTLIER) cc_final: 0.8167 (m-70) outliers start: 46 outliers final: 35 residues processed: 162 average time/residue: 0.2521 time to fit residues: 61.1123 Evaluate side-chains 157 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 116 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 489 ARG Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 337 ILE Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 336 ILE Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 380 HIS Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain H residue 112 ASP Chi-restraints excluded: chain H residue 132 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 177 optimal weight: 20.0000 chunk 108 optimal weight: 2.9990 chunk 84 optimal weight: 0.5980 chunk 123 optimal weight: 0.4980 chunk 186 optimal weight: 20.0000 chunk 171 optimal weight: 40.0000 chunk 148 optimal weight: 40.0000 chunk 15 optimal weight: 0.7980 chunk 114 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 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 145 ASN B 145 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 14105 Z= 0.227 Angle : 0.559 10.175 19176 Z= 0.294 Chirality : 0.042 0.216 2216 Planarity : 0.006 0.070 2481 Dihedral : 4.094 44.098 2031 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.29 % Allowed : 19.73 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % 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: 0.40 (0.21), residues: 1842 helix: 1.47 (0.18), residues: 929 sheet: -0.27 (0.36), residues: 229 loop : -1.21 (0.25), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 436 HIS 0.003 0.001 HIS C 451 PHE 0.029 0.001 PHE D 186 TYR 0.015 0.001 TYR C 161 ARG 0.006 0.000 ARG C 209 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 116 time to evaluate : 1.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7902 (mt) REVERT: A 392 LYS cc_start: 0.8625 (tttp) cc_final: 0.7922 (ttmm) REVERT: A 397 GLU cc_start: 0.7744 (mp0) cc_final: 0.7232 (mt-10) REVERT: A 422 ASP cc_start: 0.7455 (OUTLIER) cc_final: 0.7118 (p0) REVERT: A 489 ARG cc_start: 0.7584 (OUTLIER) cc_final: 0.7100 (tmm-80) REVERT: B 484 ASN cc_start: 0.8510 (OUTLIER) cc_final: 0.8172 (m-40) REVERT: C 120 LYS cc_start: 0.8153 (mmtt) cc_final: 0.7682 (mmmt) REVERT: C 121 THR cc_start: 0.8623 (p) cc_final: 0.8331 (t) REVERT: C 299 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.6687 (tm-30) REVERT: D 380 HIS cc_start: 0.8640 (OUTLIER) cc_final: 0.8069 (m-70) outliers start: 42 outliers final: 32 residues processed: 155 average time/residue: 0.2542 time to fit residues: 58.7867 Evaluate side-chains 153 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 115 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 489 ARG Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 484 ASN Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 336 ILE Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 380 HIS Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain H residue 112 ASP Chi-restraints excluded: chain H residue 132 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 158 optimal weight: 30.0000 chunk 45 optimal weight: 5.9990 chunk 136 optimal weight: 0.9990 chunk 21 optimal weight: 7.9990 chunk 41 optimal weight: 0.9980 chunk 148 optimal weight: 40.0000 chunk 62 optimal weight: 0.7980 chunk 152 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 130 optimal weight: 0.3980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.185574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.142037 restraints weight = 21337.218| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 3.10 r_work: 0.3286 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.153 14105 Z= 0.297 Angle : 0.823 59.198 19176 Z= 0.485 Chirality : 0.042 0.194 2216 Planarity : 0.006 0.070 2481 Dihedral : 4.109 44.078 2031 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.51 % Favored : 95.44 % Rotamer: Outliers : 2.98 % Allowed : 20.05 % Favored : 76.98 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 2.88 % 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: 0.41 (0.21), residues: 1842 helix: 1.48 (0.18), residues: 929 sheet: -0.27 (0.36), residues: 229 loop : -1.21 (0.25), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 436 HIS 0.003 0.001 HIS C 451 PHE 0.026 0.001 PHE D 125 TYR 0.015 0.001 TYR C 161 ARG 0.006 0.000 ARG C 209 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2741.43 seconds wall clock time: 50 minutes 57.21 seconds (3057.21 seconds total)