Starting phenix.real_space_refine on Thu Jul 31 21:31:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ssv_25414/07_2025/7ssv_25414.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ssv_25414/07_2025/7ssv_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_25414/07_2025/7ssv_25414.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ssv_25414/07_2025/7ssv_25414.map" model { file = "/net/cci-nas-00/data/ceres_data/7ssv_25414/07_2025/7ssv_25414.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ssv_25414/07_2025/7ssv_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 9.73, per 1000 atoms: 0.70 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: 3.48 Conformation dependent library (CDL) restraints added in 2.1 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: 1.52 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: 4.16 Time building geometry restraints manager: 4.16 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: 5.350 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: 0.560 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 34.570 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.470 ------------------------------------------------------------------------------- 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 14108 Z= 0.912 Angle : 1.720 12.153 19182 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 Details of bonding type rmsd hydrogen bonds : bond 0.25788 ( 723) hydrogen bonds : angle 8.20208 ( 2094) SS BOND : bond 0.01647 ( 3) SS BOND : angle 3.16523 ( 6) covalent geometry : bond 0.01756 (14105) covalent geometry : angle 1.71974 (19176) *********************** 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 : 1.420 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: 0.3152 time to fit residues: 122.7032 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 : 1.608 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.182013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.126288 restraints weight = 21279.060| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 3.62 r_work: 0.3168 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 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 14108 Z= 0.177 Angle : 0.665 6.289 19182 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 Details of bonding type rmsd hydrogen bonds : bond 0.06724 ( 723) hydrogen bonds : angle 5.02746 ( 2094) SS BOND : bond 0.00103 ( 3) SS BOND : angle 0.87124 ( 6) covalent geometry : bond 0.00405 (14105) covalent geometry : angle 0.66445 (19176) *********************** 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 : 1.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 LYS cc_start: 0.9045 (tttp) cc_final: 0.8014 (ttmm) REVERT: A 397 GLU cc_start: 0.8637 (mp0) cc_final: 0.8110 (mt-10) REVERT: A 422 ASP cc_start: 0.7425 (OUTLIER) cc_final: 0.7084 (p0) REVERT: A 470 LEU cc_start: 0.8171 (mp) cc_final: 0.7861 (mp) REVERT: A 489 ARG cc_start: 0.7803 (OUTLIER) cc_final: 0.7333 (tmm-80) REVERT: B 153 ARG cc_start: 0.9081 (OUTLIER) cc_final: 0.8415 (mtp180) REVERT: B 188 GLN cc_start: 0.8300 (mt0) cc_final: 0.7978 (mp10) REVERT: B 191 GLU cc_start: 0.7582 (mp0) cc_final: 0.7322 (mp0) REVERT: B 210 PRO cc_start: 0.7417 (Cg_endo) cc_final: 0.7137 (Cg_exo) REVERT: B 219 GLN cc_start: 0.8077 (OUTLIER) cc_final: 0.7747 (mm110) REVERT: B 367 ARG cc_start: 0.8547 (mpt180) cc_final: 0.7581 (mtp180) REVERT: C 213 ARG cc_start: 0.7646 (tmm160) cc_final: 0.7425 (tmm-80) REVERT: C 392 LYS cc_start: 0.8752 (tttp) cc_final: 0.8506 (ttpt) REVERT: D 380 HIS cc_start: 0.8958 (OUTLIER) cc_final: 0.8343 (m-70) outliers start: 59 outliers final: 30 residues processed: 208 average time/residue: 0.3221 time to fit residues: 95.1638 Evaluate side-chains 163 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 128 time to evaluate : 1.535 ------------------------------------------------------------------------------- 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 219 GLN 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 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 27 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 179 optimal weight: 50.0000 chunk 18 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.184983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.140009 restraints weight = 21324.536| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 3.05 r_work: 0.3267 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 14108 Z= 0.191 Angle : 0.610 6.735 19182 Z= 0.329 Chirality : 0.044 0.220 2216 Planarity : 0.006 0.063 2481 Dihedral : 5.398 58.556 2053 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 3.52 % Allowed : 17.38 % Favored : 79.09 % 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: -0.76 (0.19), residues: 1842 helix: 0.66 (0.17), residues: 929 sheet: -1.33 (0.39), residues: 173 loop : -1.80 (0.21), residues: 740 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 0.023 0.002 PHE C 406 TYR 0.017 0.002 TYR C 147 ARG 0.005 0.000 ARG A 135 Details of bonding type rmsd hydrogen bonds : bond 0.06228 ( 723) hydrogen bonds : angle 4.51613 ( 2094) SS BOND : bond 0.00233 ( 3) SS BOND : angle 0.80530 ( 6) covalent geometry : bond 0.00464 (14105) covalent geometry : angle 0.61007 (19176) *********************** 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 184 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 139 time to evaluate : 1.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 LYS cc_start: 0.9108 (tttp) cc_final: 0.8168 (ttmm) REVERT: A 397 GLU cc_start: 0.8488 (mp0) cc_final: 0.7972 (mt-10) REVERT: A 422 ASP cc_start: 0.7442 (OUTLIER) cc_final: 0.7053 (p0) REVERT: A 489 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7378 (tmm-80) REVERT: B 153 ARG cc_start: 0.9107 (OUTLIER) cc_final: 0.8422 (mtp180) REVERT: B 188 GLN cc_start: 0.8187 (mt0) cc_final: 0.7949 (mp10) REVERT: C 120 LYS cc_start: 0.8152 (mmtt) cc_final: 0.7557 (mmtt) REVERT: C 192 GLU cc_start: 0.8479 (pm20) cc_final: 0.8144 (pp20) REVERT: C 209 ARG cc_start: 0.7685 (pmt170) cc_final: 0.7315 (pmt170) REVERT: D 194 MET cc_start: 0.8081 (tpp) cc_final: 0.7655 (tpp) REVERT: D 380 HIS cc_start: 0.8923 (OUTLIER) cc_final: 0.8302 (m-70) outliers start: 45 outliers final: 27 residues processed: 176 average time/residue: 0.2655 time to fit residues: 68.0085 Evaluate side-chains 154 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 123 time to evaluate : 1.505 ------------------------------------------------------------------------------- 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 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 489 ARG Chi-restraints excluded: chain B residue 153 ARG Chi-restraints excluded: chain B residue 219 GLN Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 307 SER 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 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 108 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 145 optimal weight: 30.0000 chunk 103 optimal weight: 0.6980 chunk 71 optimal weight: 5.9990 chunk 120 optimal weight: 0.5980 chunk 83 optimal weight: 0.9980 chunk 171 optimal weight: 50.0000 chunk 68 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN A 188 GLN C 145 ASN D 164 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.185507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.141439 restraints weight = 21356.233| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 2.98 r_work: 0.3298 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14108 Z= 0.174 Angle : 0.583 8.015 19182 Z= 0.309 Chirality : 0.043 0.157 2216 Planarity : 0.006 0.070 2481 Dihedral : 4.809 55.338 2039 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.76 % Allowed : 18.01 % Favored : 78.23 % 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: -0.35 (0.20), residues: 1842 helix: 0.98 (0.18), residues: 929 sheet: -0.85 (0.42), residues: 161 loop : -1.64 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 436 HIS 0.004 0.001 HIS H 126 PHE 0.023 0.001 PHE C 406 TYR 0.019 0.002 TYR C 161 ARG 0.003 0.000 ARG A 135 Details of bonding type rmsd hydrogen bonds : bond 0.05646 ( 723) hydrogen bonds : angle 4.30390 ( 2094) SS BOND : bond 0.00222 ( 3) SS BOND : angle 0.60427 ( 6) covalent geometry : bond 0.00424 (14105) covalent geometry : angle 0.58339 (19176) *********************** 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 180 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 132 time to evaluate : 1.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 LYS cc_start: 0.9117 (tttp) cc_final: 0.8191 (ttmm) REVERT: A 397 GLU cc_start: 0.8361 (mp0) cc_final: 0.7907 (mt-10) REVERT: A 422 ASP cc_start: 0.7464 (OUTLIER) cc_final: 0.7073 (p0) REVERT: A 489 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.7314 (tmm-80) REVERT: B 153 ARG cc_start: 0.9080 (OUTLIER) cc_final: 0.8394 (mtp180) REVERT: B 188 GLN cc_start: 0.8176 (mt0) cc_final: 0.7937 (mp10) REVERT: C 120 LYS cc_start: 0.8182 (mmtt) cc_final: 0.7911 (mmmt) REVERT: C 121 THR cc_start: 0.8714 (p) cc_final: 0.8385 (t) REVERT: C 209 ARG cc_start: 0.7616 (pmt170) cc_final: 0.7295 (pmt170) REVERT: C 299 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.6937 (tm-30) REVERT: C 450 MET cc_start: 0.8926 (mtt) cc_final: 0.8696 (mtt) REVERT: D 380 HIS cc_start: 0.8880 (OUTLIER) cc_final: 0.8249 (m-70) outliers start: 48 outliers final: 31 residues processed: 174 average time/residue: 0.2999 time to fit residues: 76.3786 Evaluate side-chains 157 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 121 time to evaluate : 1.592 ------------------------------------------------------------------------------- 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 300 THR Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 377 LEU 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 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 471 THR Chi-restraints excluded: chain D residue 119 LEU 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 D residue 484 ASN Chi-restraints excluded: chain H residue 112 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 140 optimal weight: 10.0000 chunk 49 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 89 optimal weight: 0.0470 chunk 182 optimal weight: 6.9990 chunk 143 optimal weight: 40.0000 chunk 43 optimal weight: 1.9990 overall best weight: 0.9480 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.186664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.142901 restraints weight = 21508.428| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 3.09 r_work: 0.3303 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14108 Z= 0.146 Angle : 0.545 9.011 19182 Z= 0.290 Chirality : 0.042 0.161 2216 Planarity : 0.005 0.065 2481 Dihedral : 4.435 50.017 2036 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 4.39 % Allowed : 17.46 % Favored : 78.15 % 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: -0.01 (0.20), residues: 1842 helix: 1.25 (0.18), residues: 929 sheet: -0.67 (0.42), residues: 162 loop : -1.48 (0.22), residues: 751 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 0.023 0.001 PHE C 406 TYR 0.014 0.001 TYR C 161 ARG 0.006 0.000 ARG D 213 Details of bonding type rmsd hydrogen bonds : bond 0.05059 ( 723) hydrogen bonds : angle 4.06915 ( 2094) SS BOND : bond 0.00194 ( 3) SS BOND : angle 0.55295 ( 6) covalent geometry : bond 0.00348 (14105) covalent geometry : angle 0.54522 (19176) *********************** 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 183 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 127 time to evaluate : 1.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 325 ARG cc_start: 0.8112 (tpt90) cc_final: 0.7500 (tpt170) REVERT: A 392 LYS cc_start: 0.9102 (tttp) cc_final: 0.8178 (ttmm) REVERT: A 397 GLU cc_start: 0.8395 (mp0) cc_final: 0.7903 (mt-10) REVERT: A 422 ASP cc_start: 0.7424 (OUTLIER) cc_final: 0.7051 (p0) REVERT: A 489 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.7267 (tmm-80) REVERT: B 153 ARG cc_start: 0.9039 (OUTLIER) cc_final: 0.8348 (mtp180) REVERT: B 188 GLN cc_start: 0.8153 (mt0) cc_final: 0.7898 (mp10) REVERT: B 250 ILE cc_start: 0.9412 (tp) cc_final: 0.9197 (tp) REVERT: C 120 LYS cc_start: 0.8231 (mmtt) cc_final: 0.7754 (mmmt) REVERT: C 192 GLU cc_start: 0.8505 (pm20) cc_final: 0.8201 (pp20) REVERT: C 209 ARG cc_start: 0.7638 (pmt170) cc_final: 0.7333 (pmt170) REVERT: C 299 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.6933 (tm-30) REVERT: D 194 MET cc_start: 0.8071 (tpp) cc_final: 0.7597 (tpp) REVERT: D 380 HIS cc_start: 0.8892 (OUTLIER) cc_final: 0.8291 (m-70) outliers start: 56 outliers final: 33 residues processed: 179 average time/residue: 0.3283 time to fit residues: 87.8710 Evaluate side-chains 157 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 119 time to evaluate : 1.640 ------------------------------------------------------------------------------- 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 146 GLU 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 300 THR 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 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 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 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 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 129 optimal weight: 1.9990 chunk 143 optimal weight: 9.9990 chunk 119 optimal weight: 0.9980 chunk 180 optimal weight: 6.9990 chunk 146 optimal weight: 5.9990 chunk 168 optimal weight: 0.0870 chunk 106 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 173 optimal weight: 50.0000 overall best weight: 1.1962 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.186000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.143134 restraints weight = 21594.455| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 3.07 r_work: 0.3282 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14108 Z= 0.166 Angle : 0.560 7.361 19182 Z= 0.298 Chirality : 0.042 0.165 2216 Planarity : 0.005 0.065 2481 Dihedral : 4.378 47.649 2035 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.99 % Allowed : 18.25 % Favored : 77.76 % 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: 0.09 (0.20), residues: 1842 helix: 1.32 (0.18), residues: 929 sheet: -0.42 (0.41), residues: 169 loop : -1.46 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 436 HIS 0.004 0.001 HIS C 451 PHE 0.024 0.001 PHE C 406 TYR 0.015 0.001 TYR C 161 ARG 0.003 0.000 ARG A 325 Details of bonding type rmsd hydrogen bonds : bond 0.05337 ( 723) hydrogen bonds : angle 4.06724 ( 2094) SS BOND : bond 0.00220 ( 3) SS BOND : angle 0.51438 ( 6) covalent geometry : bond 0.00405 (14105) covalent geometry : angle 0.56029 (19176) *********************** 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 176 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 125 time to evaluate : 1.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 LEU cc_start: 0.8374 (mp) cc_final: 0.7819 (tt) REVERT: A 392 LYS cc_start: 0.9090 (tttp) cc_final: 0.8166 (ttmm) REVERT: A 397 GLU cc_start: 0.8465 (mp0) cc_final: 0.7960 (mt-10) REVERT: A 422 ASP cc_start: 0.7531 (OUTLIER) cc_final: 0.7160 (p0) REVERT: A 489 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.7266 (tmm-80) REVERT: B 188 GLN cc_start: 0.8151 (mt0) cc_final: 0.7918 (mp10) REVERT: B 250 ILE cc_start: 0.9405 (tp) cc_final: 0.9178 (tp) REVERT: C 120 LYS cc_start: 0.8193 (mmtt) cc_final: 0.7717 (mmmt) REVERT: C 121 THR cc_start: 0.8754 (p) cc_final: 0.8407 (t) REVERT: C 192 GLU cc_start: 0.8534 (pm20) cc_final: 0.8233 (pp20) REVERT: C 209 ARG cc_start: 0.7675 (pmt170) cc_final: 0.7333 (pmt170) REVERT: C 299 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.6921 (tm-30) REVERT: D 380 HIS cc_start: 0.8907 (OUTLIER) cc_final: 0.8347 (m-70) outliers start: 51 outliers final: 37 residues processed: 170 average time/residue: 0.2591 time to fit residues: 65.0411 Evaluate side-chains 160 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 119 time to evaluate : 1.641 ------------------------------------------------------------------------------- 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 300 THR 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 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 405 LEU Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 239 VAL 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 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 135 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 161 optimal weight: 30.0000 chunk 71 optimal weight: 2.9990 chunk 149 optimal weight: 40.0000 chunk 17 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 150 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 145 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.183571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.129769 restraints weight = 21425.833| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.95 r_work: 0.3207 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 14108 Z= 0.219 Angle : 0.603 9.229 19182 Z= 0.320 Chirality : 0.044 0.162 2216 Planarity : 0.006 0.069 2481 Dihedral : 4.306 45.006 2031 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 3.99 % Allowed : 18.40 % Favored : 77.60 % 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: 0.04 (0.20), residues: 1842 helix: 1.21 (0.18), residues: 929 sheet: -0.37 (0.39), residues: 179 loop : -1.43 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 436 HIS 0.004 0.001 HIS C 451 PHE 0.026 0.002 PHE C 406 TYR 0.014 0.002 TYR C 161 ARG 0.004 0.000 ARG A 325 Details of bonding type rmsd hydrogen bonds : bond 0.06073 ( 723) hydrogen bonds : angle 4.18463 ( 2094) SS BOND : bond 0.00307 ( 3) SS BOND : angle 0.61132 ( 6) covalent geometry : bond 0.00548 (14105) covalent geometry : angle 0.60273 (19176) *********************** 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 170 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 119 time to evaluate : 1.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 291 PHE cc_start: 0.7413 (m-80) cc_final: 0.7200 (m-80) REVERT: A 392 LYS cc_start: 0.9156 (tttp) cc_final: 0.8218 (ttmm) REVERT: A 397 GLU cc_start: 0.8703 (mp0) cc_final: 0.8159 (mt-10) REVERT: A 422 ASP cc_start: 0.7701 (OUTLIER) cc_final: 0.7343 (p0) REVERT: A 489 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.7267 (tmm-80) REVERT: B 188 GLN cc_start: 0.8211 (mt0) cc_final: 0.7923 (mp10) REVERT: C 120 LYS cc_start: 0.8188 (mmtt) cc_final: 0.7709 (mmmt) REVERT: C 121 THR cc_start: 0.8812 (p) cc_final: 0.8473 (t) REVERT: C 192 GLU cc_start: 0.8704 (pm20) cc_final: 0.8410 (pp20) REVERT: C 209 ARG cc_start: 0.7703 (pmt170) cc_final: 0.7286 (pmt170) REVERT: C 299 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7006 (tm-30) REVERT: D 380 HIS cc_start: 0.9035 (OUTLIER) cc_final: 0.8507 (m-70) outliers start: 51 outliers final: 37 residues processed: 163 average time/residue: 0.2595 time to fit residues: 62.2851 Evaluate side-chains 155 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 114 time to evaluate : 1.835 ------------------------------------------------------------------------------- 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 120 LYS Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 363 LEU 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 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 471 THR Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 239 VAL 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 H residue 112 ASP Chi-restraints excluded: chain H residue 132 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 129 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 145 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 chunk 125 optimal weight: 0.2980 chunk 39 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 134 optimal weight: 0.5980 chunk 116 optimal weight: 0.9980 chunk 164 optimal weight: 20.0000 chunk 160 optimal weight: 0.0010 overall best weight: 0.4186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.188346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.145374 restraints weight = 21418.705| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 3.04 r_work: 0.3333 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14108 Z= 0.114 Angle : 0.520 9.284 19182 Z= 0.274 Chirality : 0.041 0.154 2216 Planarity : 0.005 0.063 2481 Dihedral : 4.049 43.837 2031 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.90 % Allowed : 19.50 % Favored : 77.60 % 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: 0.48 (0.21), residues: 1842 helix: 1.59 (0.18), residues: 929 sheet: -0.21 (0.39), residues: 190 loop : -1.23 (0.24), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 436 HIS 0.001 0.000 HIS C 451 PHE 0.021 0.001 PHE D 186 TYR 0.014 0.001 TYR C 161 ARG 0.004 0.000 ARG A 325 Details of bonding type rmsd hydrogen bonds : bond 0.04274 ( 723) hydrogen bonds : angle 3.84445 ( 2094) SS BOND : bond 0.00145 ( 3) SS BOND : angle 0.39222 ( 6) covalent geometry : bond 0.00250 (14105) covalent geometry : angle 0.52016 (19176) *********************** 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 161 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 124 time to evaluate : 1.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8060 (mt) REVERT: A 392 LYS cc_start: 0.9038 (tttp) cc_final: 0.8135 (ttmm) REVERT: A 406 PHE cc_start: 0.8124 (OUTLIER) cc_final: 0.7347 (t80) REVERT: A 422 ASP cc_start: 0.7558 (OUTLIER) cc_final: 0.7171 (p0) REVERT: A 489 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.7209 (tmm-80) REVERT: B 188 GLN cc_start: 0.8164 (mt0) cc_final: 0.7928 (mp10) REVERT: C 120 LYS cc_start: 0.8235 (mmtt) cc_final: 0.7786 (mmmt) REVERT: C 121 THR cc_start: 0.8677 (p) cc_final: 0.8371 (t) REVERT: C 192 GLU cc_start: 0.8540 (pm20) cc_final: 0.8249 (pp20) REVERT: C 299 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.6848 (tm-30) REVERT: D 380 HIS cc_start: 0.8872 (OUTLIER) cc_final: 0.8308 (m-70) outliers start: 37 outliers final: 29 residues processed: 159 average time/residue: 0.2414 time to fit residues: 57.1337 Evaluate side-chains 153 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 118 time to evaluate : 1.421 ------------------------------------------------------------------------------- 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 406 PHE 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 410 ILE 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 347 LEU Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 336 ILE Chi-restraints excluded: chain D residue 343 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 132 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 87 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 80 optimal weight: 8.9990 chunk 135 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 33 optimal weight: 0.0370 chunk 50 optimal weight: 1.9990 overall best weight: 0.7462 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.187090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.143832 restraints weight = 21370.292| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 3.00 r_work: 0.3319 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.3957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14108 Z= 0.128 Angle : 0.527 8.890 19182 Z= 0.277 Chirality : 0.041 0.151 2216 Planarity : 0.005 0.068 2481 Dihedral : 3.976 43.828 2031 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.90 % Allowed : 19.58 % Favored : 77.53 % 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: 0.58 (0.21), residues: 1842 helix: 1.64 (0.18), residues: 929 sheet: -0.27 (0.36), residues: 229 loop : -1.14 (0.25), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.002 0.001 HIS C 451 PHE 0.019 0.001 PHE A 406 TYR 0.014 0.001 TYR C 161 ARG 0.004 0.000 ARG A 325 Details of bonding type rmsd hydrogen bonds : bond 0.04579 ( 723) hydrogen bonds : angle 3.82791 ( 2094) SS BOND : bond 0.00178 ( 3) SS BOND : angle 0.40320 ( 6) covalent geometry : bond 0.00299 (14105) covalent geometry : angle 0.52690 (19176) *********************** 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 162 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 125 time to evaluate : 1.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8080 (mt) REVERT: A 392 LYS cc_start: 0.9052 (tttp) cc_final: 0.8148 (ttmm) REVERT: A 422 ASP cc_start: 0.7559 (OUTLIER) cc_final: 0.7185 (p0) REVERT: A 489 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.7222 (tmm-80) REVERT: B 188 GLN cc_start: 0.8142 (mt0) cc_final: 0.7898 (mp10) REVERT: C 120 LYS cc_start: 0.8223 (mmtt) cc_final: 0.7785 (mmmt) REVERT: C 121 THR cc_start: 0.8694 (p) cc_final: 0.8381 (t) REVERT: C 192 GLU cc_start: 0.8509 (pm20) cc_final: 0.8246 (pp20) REVERT: C 299 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.6934 (tm-30) REVERT: D 380 HIS cc_start: 0.8872 (OUTLIER) cc_final: 0.8297 (m-70) outliers start: 37 outliers final: 31 residues processed: 160 average time/residue: 0.2387 time to fit residues: 56.9561 Evaluate side-chains 156 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 120 time to evaluate : 1.454 ------------------------------------------------------------------------------- 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 108 ILE Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 410 ILE 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 347 LEU Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 413 SER 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 6 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 138 optimal weight: 0.5980 chunk 38 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 11 optimal weight: 0.0570 chunk 45 optimal weight: 6.9990 chunk 173 optimal weight: 50.0000 chunk 1 optimal weight: 2.9990 chunk 111 optimal weight: 0.5980 overall best weight: 0.5898 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.187927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.144583 restraints weight = 21330.887| |-----------------------------------------------------------------------------| r_work (start): 0.3826 rms_B_bonded: 3.00 r_work: 0.3330 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.4071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14108 Z= 0.119 Angle : 0.523 8.805 19182 Z= 0.274 Chirality : 0.040 0.152 2216 Planarity : 0.005 0.068 2481 Dihedral : 3.882 43.697 2031 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.29 % Allowed : 19.26 % Favored : 77.45 % 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: 0.71 (0.21), residues: 1842 helix: 1.73 (0.18), residues: 929 sheet: -0.19 (0.36), residues: 230 loop : -1.06 (0.25), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.002 0.000 HIS C 451 PHE 0.020 0.001 PHE A 406 TYR 0.014 0.001 TYR C 161 ARG 0.008 0.000 ARG B 213 Details of bonding type rmsd hydrogen bonds : bond 0.04336 ( 723) hydrogen bonds : angle 3.76221 ( 2094) SS BOND : bond 0.00164 ( 3) SS BOND : angle 0.37423 ( 6) covalent geometry : bond 0.00275 (14105) covalent geometry : angle 0.52294 (19176) ********************** 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 168 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 126 time to evaluate : 1.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.8037 (mt) REVERT: A 191 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7644 (mt-10) REVERT: A 392 LYS cc_start: 0.9015 (tttp) cc_final: 0.8089 (ttmm) REVERT: A 406 PHE cc_start: 0.8129 (OUTLIER) cc_final: 0.7330 (t80) REVERT: A 422 ASP cc_start: 0.7560 (OUTLIER) cc_final: 0.7201 (p0) REVERT: A 489 ARG cc_start: 0.7705 (OUTLIER) cc_final: 0.7176 (tmm-80) REVERT: B 188 GLN cc_start: 0.8130 (mt0) cc_final: 0.7885 (mp10) REVERT: C 120 LYS cc_start: 0.8216 (mmtt) cc_final: 0.7780 (mmmt) REVERT: C 121 THR cc_start: 0.8687 (p) cc_final: 0.8368 (t) REVERT: C 192 GLU cc_start: 0.8497 (pm20) cc_final: 0.8257 (pp20) REVERT: C 299 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.6909 (tm-30) REVERT: D 380 HIS cc_start: 0.8878 (OUTLIER) cc_final: 0.8363 (m-70) outliers start: 42 outliers final: 31 residues processed: 164 average time/residue: 0.2430 time to fit residues: 59.4278 Evaluate side-chains 159 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 122 time to evaluate : 1.538 ------------------------------------------------------------------------------- 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 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 406 PHE Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 489 ARG Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 410 ILE 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 347 LEU Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 413 SER 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 58 optimal weight: 0.1980 chunk 177 optimal weight: 9.9990 chunk 10 optimal weight: 8.9990 chunk 171 optimal weight: 40.0000 chunk 162 optimal weight: 30.0000 chunk 62 optimal weight: 1.9990 chunk 94 optimal weight: 0.0670 chunk 24 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 145 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 overall best weight: 0.5720 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.188034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.144588 restraints weight = 21427.398| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 3.00 r_work: 0.3333 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.4119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14108 Z= 0.117 Angle : 0.521 8.775 19182 Z= 0.273 Chirality : 0.041 0.158 2216 Planarity : 0.005 0.070 2481 Dihedral : 3.838 43.771 2031 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.98 % Allowed : 19.58 % Favored : 77.45 % 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: 0.79 (0.21), residues: 1842 helix: 1.78 (0.18), residues: 929 sheet: -0.12 (0.36), residues: 230 loop : -1.01 (0.25), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.002 0.000 HIS C 451 PHE 0.020 0.001 PHE A 406 TYR 0.014 0.001 TYR C 161 ARG 0.010 0.000 ARG B 209 Details of bonding type rmsd hydrogen bonds : bond 0.04292 ( 723) hydrogen bonds : angle 3.73012 ( 2094) SS BOND : bond 0.00152 ( 3) SS BOND : angle 0.35607 ( 6) covalent geometry : bond 0.00270 (14105) covalent geometry : angle 0.52067 (19176) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8987.12 seconds wall clock time: 162 minutes 35.94 seconds (9755.94 seconds total)