Starting phenix.real_space_refine on Wed Mar 4 13:10:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ssv_25414/03_2026/7ssv_25414.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ssv_25414/03_2026/7ssv_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 { model { file = "/net/cci-nas-00/data/ceres_data/7ssv_25414/03_2026/7ssv_25414.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ssv_25414/03_2026/7ssv_25414.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ssv_25414/03_2026/7ssv_25414.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ssv_25414/03_2026/7ssv_25414.map" } resolution = 3.39 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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, 'ARG:plan': 3, 'GLU:plan': 7, 'TRP:plan': 7, 'TYR:plan': 9, 'PHE:plan': 5, 'ASP:plan': 7, 'ASN:plan1': 9, 'HIS:plan': 5} 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: {'ASN:plan1': 8, 'GLN:plan1': 10, 'TYR:plan': 9, 'TRP:plan': 3, 'ASP:plan': 7, 'ARG:plan': 3, 'PHE:plan': 4, 'GLU:plan': 9, 'HIS:plan': 2} 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: 3.22, per 1000 atoms: 0.23 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: 1.23 Conformation dependent library (CDL) restraints added in 528.7 milliseconds 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: 0.49 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: 2.27 Time building geometry restraints manager: 1.58 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: 5.500 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 13.240 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.590 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.22 (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 ARG 0.008 0.001 ARG C 114 TYR 0.023 0.003 TYR C 163 PHE 0.048 0.003 PHE H 122 TRP 0.018 0.003 TRP C 221 HIS 0.013 0.004 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.01756 (14105) covalent geometry : angle 1.71974 (19176) SS BOND : bond 0.01647 ( 3) SS BOND : angle 3.16523 ( 6) hydrogen bonds : bond 0.25788 ( 723) hydrogen bonds : angle 8.20208 ( 2094) *********************** 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 : 0.543 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: 0.6971 (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: 0.6325 (tpp-160) REVERT: B 210 PRO cc_start: 0.7624 (Cg_endo) cc_final: 0.7336 (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: 0.1408 time to fit residues: 54.2299 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 : 0.486 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.0980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 D 484 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.183012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.127899 restraints weight = 20892.011| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 3.40 r_work: 0.3197 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14108 Z= 0.161 Angle : 0.649 6.364 19182 Z= 0.353 Chirality : 0.044 0.199 2216 Planarity : 0.006 0.064 2481 Dihedral : 6.502 58.082 2076 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.54 % Allowed : 15.43 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.19), residues: 1842 helix: 0.13 (0.17), residues: 929 sheet: -2.05 (0.38), residues: 166 loop : -1.92 (0.20), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 170 TYR 0.014 0.002 TYR B 161 PHE 0.025 0.002 PHE C 140 TRP 0.009 0.001 TRP C 436 HIS 0.002 0.001 HIS C 488 Details of bonding type rmsd covalent geometry : bond 0.00351 (14105) covalent geometry : angle 0.64933 (19176) SS BOND : bond 0.00079 ( 3) SS BOND : angle 0.90249 ( 6) hydrogen bonds : bond 0.06444 ( 723) hydrogen bonds : angle 4.99984 ( 2094) *********************** 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 220 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 162 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 TYR cc_start: 0.7763 (m-80) cc_final: 0.6971 (m-80) REVERT: A 392 LYS cc_start: 0.9013 (tttp) cc_final: 0.7983 (ttmm) REVERT: A 397 GLU cc_start: 0.8600 (mp0) cc_final: 0.8101 (mt-10) REVERT: A 422 ASP cc_start: 0.7427 (OUTLIER) cc_final: 0.7084 (p0) REVERT: A 470 LEU cc_start: 0.8160 (mp) cc_final: 0.7840 (mp) REVERT: A 489 ARG cc_start: 0.7828 (OUTLIER) cc_final: 0.7368 (tmm-80) REVERT: B 153 ARG cc_start: 0.9080 (OUTLIER) cc_final: 0.8602 (mtp180) REVERT: B 188 GLN cc_start: 0.8270 (mt0) cc_final: 0.7947 (mp10) REVERT: B 210 PRO cc_start: 0.7378 (Cg_endo) cc_final: 0.7120 (Cg_exo) REVERT: B 367 ARG cc_start: 0.8521 (mpt180) cc_final: 0.7567 (mtp180) REVERT: C 209 ARG cc_start: 0.7738 (pmt170) cc_final: 0.7450 (ptt-90) REVERT: C 213 ARG cc_start: 0.7703 (tmm160) cc_final: 0.7436 (tmm-80) REVERT: C 392 LYS cc_start: 0.8734 (tttp) cc_final: 0.8484 (ttpt) REVERT: D 380 HIS cc_start: 0.8944 (OUTLIER) cc_final: 0.8296 (m-70) outliers start: 58 outliers final: 30 residues processed: 211 average time/residue: 0.1238 time to fit residues: 37.1422 Evaluate side-chains 164 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 130 time to evaluate : 0.433 ------------------------------------------------------------------------------- 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 363 LEU 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 D residue 422 ASP 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 175 optimal weight: 30.0000 chunk 97 optimal weight: 0.2980 chunk 11 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 182 optimal weight: 40.0000 chunk 55 optimal weight: 0.0980 chunk 37 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 C 164 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.186890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.143810 restraints weight = 21641.692| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 3.09 r_work: 0.3312 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2946 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= 0.161 Angle : 0.578 6.103 19182 Z= 0.312 Chirality : 0.043 0.225 2216 Planarity : 0.006 0.061 2481 Dihedral : 5.299 52.131 2053 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.52 % Allowed : 16.60 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.20), residues: 1842 helix: 0.79 (0.17), residues: 929 sheet: -1.36 (0.40), residues: 166 loop : -1.72 (0.21), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 151 TYR 0.014 0.001 TYR C 147 PHE 0.031 0.001 PHE D 186 TRP 0.010 0.001 TRP A 436 HIS 0.003 0.001 HIS H 126 Details of bonding type rmsd covalent geometry : bond 0.00376 (14105) covalent geometry : angle 0.57832 (19176) SS BOND : bond 0.00192 ( 3) SS BOND : angle 0.76966 ( 6) hydrogen bonds : bond 0.05751 ( 723) hydrogen bonds : angle 4.45521 ( 2094) *********************** 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 188 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 143 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 TYR cc_start: 0.7742 (m-80) cc_final: 0.7072 (m-80) REVERT: A 392 LYS cc_start: 0.9114 (tttp) cc_final: 0.8199 (ttmm) REVERT: A 397 GLU cc_start: 0.8420 (mp0) cc_final: 0.7932 (mt-10) REVERT: A 422 ASP cc_start: 0.7338 (OUTLIER) cc_final: 0.6935 (p0) REVERT: A 489 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.7349 (tmm-80) REVERT: B 153 ARG cc_start: 0.9180 (OUTLIER) cc_final: 0.8581 (mtp180) REVERT: B 188 GLN cc_start: 0.8214 (mt0) cc_final: 0.7969 (mp10) REVERT: B 367 ARG cc_start: 0.8495 (mpt180) cc_final: 0.7512 (mmm160) REVERT: C 120 LYS cc_start: 0.8125 (mmtt) cc_final: 0.7512 (mmtt) REVERT: C 192 GLU cc_start: 0.8449 (pm20) cc_final: 0.8122 (pp20) REVERT: D 194 MET cc_start: 0.8157 (tpp) cc_final: 0.7673 (tpp) REVERT: D 198 ARG cc_start: 0.7717 (mtt180) cc_final: 0.7412 (mtt180) REVERT: D 380 HIS cc_start: 0.8898 (OUTLIER) cc_final: 0.8253 (m-70) outliers start: 45 outliers final: 24 residues processed: 179 average time/residue: 0.1271 time to fit residues: 32.5685 Evaluate side-chains 157 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 129 time to evaluate : 0.505 ------------------------------------------------------------------------------- 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 B residue 363 LEU 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 471 THR Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 380 HIS Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain H residue 112 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 152 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 chunk 88 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 142 optimal weight: 50.0000 chunk 169 optimal weight: 40.0000 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 C 164 GLN D 164 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.184745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.141235 restraints weight = 21553.010| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 3.15 r_work: 0.3257 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 14108 Z= 0.204 Angle : 0.608 7.324 19182 Z= 0.323 Chirality : 0.044 0.170 2216 Planarity : 0.006 0.063 2481 Dihedral : 4.913 59.086 2041 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 4.15 % Allowed : 17.46 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.20), residues: 1842 helix: 0.93 (0.18), residues: 929 sheet: -0.83 (0.42), residues: 160 loop : -1.66 (0.22), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 135 TYR 0.019 0.002 TYR C 161 PHE 0.026 0.002 PHE C 406 TRP 0.011 0.001 TRP A 436 HIS 0.005 0.001 HIS H 126 Details of bonding type rmsd covalent geometry : bond 0.00505 (14105) covalent geometry : angle 0.60820 (19176) SS BOND : bond 0.00244 ( 3) SS BOND : angle 0.64785 ( 6) hydrogen bonds : bond 0.06123 ( 723) hydrogen bonds : angle 4.36730 ( 2094) *********************** 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 184 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 131 time to evaluate : 0.540 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 392 LYS cc_start: 0.9117 (tttp) cc_final: 0.8201 (ttmm) REVERT: A 397 GLU cc_start: 0.8448 (mp0) cc_final: 0.7979 (mt-10) REVERT: A 422 ASP cc_start: 0.7481 (OUTLIER) cc_final: 0.7077 (p0) REVERT: A 489 ARG cc_start: 0.7960 (OUTLIER) cc_final: 0.7361 (tmm-80) REVERT: B 188 GLN cc_start: 0.8209 (mt0) cc_final: 0.7991 (mp10) REVERT: C 299 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.6989 (tm-30) REVERT: D 380 HIS cc_start: 0.8915 (OUTLIER) cc_final: 0.8302 (m-70) outliers start: 53 outliers final: 35 residues processed: 176 average time/residue: 0.1144 time to fit residues: 29.6364 Evaluate side-chains 158 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 119 time to evaluate : 0.537 ------------------------------------------------------------------------------- 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 469 VAL Chi-restraints excluded: chain A residue 489 ARG Chi-restraints excluded: chain B residue 246 ILE Chi-restraints excluded: chain B residue 300 THR Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 377 LEU 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 307 SER Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 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 256 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 182 optimal weight: 10.0000 chunk 75 optimal weight: 0.5980 chunk 38 optimal weight: 0.4980 chunk 29 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 125 optimal weight: 0.6980 chunk 116 optimal weight: 0.5980 chunk 172 optimal weight: 50.0000 chunk 46 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4312 r_free = 0.4312 target = 0.188012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.145079 restraints weight = 21682.916| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 3.07 r_work: 0.3336 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14108 Z= 0.122 Angle : 0.525 7.424 19182 Z= 0.280 Chirality : 0.041 0.141 2216 Planarity : 0.005 0.060 2481 Dihedral : 4.314 57.511 2032 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.99 % Allowed : 17.85 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.20), residues: 1842 helix: 1.31 (0.18), residues: 929 sheet: -0.63 (0.43), residues: 161 loop : -1.43 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 135 TYR 0.014 0.001 TYR C 161 PHE 0.021 0.001 PHE C 406 TRP 0.011 0.001 TRP A 436 HIS 0.002 0.001 HIS H 126 Details of bonding type rmsd covalent geometry : bond 0.00276 (14105) covalent geometry : angle 0.52535 (19176) SS BOND : bond 0.00153 ( 3) SS BOND : angle 0.50107 ( 6) hydrogen bonds : bond 0.04636 ( 723) hydrogen bonds : angle 4.02935 ( 2094) *********************** 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 185 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 134 time to evaluate : 0.534 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: 0.8121 (tpt90) cc_final: 0.7548 (tpt170) REVERT: A 392 LYS cc_start: 0.9084 (tttp) cc_final: 0.8174 (ttmm) REVERT: A 397 GLU cc_start: 0.8385 (mp0) cc_final: 0.7883 (mt-10) REVERT: A 422 ASP cc_start: 0.7411 (OUTLIER) cc_final: 0.7017 (p0) REVERT: A 489 ARG cc_start: 0.7825 (OUTLIER) cc_final: 0.7249 (tmm-80) REVERT: B 188 GLN cc_start: 0.8158 (mt0) cc_final: 0.7931 (mp10) REVERT: B 250 ILE cc_start: 0.9405 (tp) cc_final: 0.9203 (tp) REVERT: C 120 LYS cc_start: 0.8124 (mmtt) cc_final: 0.7794 (mmmt) REVERT: C 192 GLU cc_start: 0.8453 (pm20) cc_final: 0.8129 (pp20) REVERT: C 299 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.6972 (tm-30) REVERT: D 194 MET cc_start: 0.8109 (tpp) cc_final: 0.7637 (tpp) REVERT: D 380 HIS cc_start: 0.8892 (OUTLIER) cc_final: 0.8249 (m-70) outliers start: 51 outliers final: 31 residues processed: 180 average time/residue: 0.1165 time to fit residues: 30.9825 Evaluate side-chains 157 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 122 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 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 246 ILE Chi-restraints excluded: chain B residue 327 ILE 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 307 SER Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 336 ILE Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 380 HIS Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain H residue 112 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 42 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 147 optimal weight: 30.0000 chunk 156 optimal weight: 50.0000 chunk 8 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 146 optimal weight: 40.0000 chunk 111 optimal weight: 0.0050 chunk 89 optimal weight: 0.2980 chunk 120 optimal weight: 2.9990 chunk 174 optimal weight: 40.0000 overall best weight: 1.2600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN B 145 ASN C 145 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.185663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.141592 restraints weight = 21390.251| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 3.14 r_work: 0.3278 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14108 Z= 0.173 Angle : 0.571 8.293 19182 Z= 0.304 Chirality : 0.043 0.170 2216 Planarity : 0.005 0.065 2481 Dihedral : 4.255 51.653 2031 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.76 % Allowed : 18.48 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.20), residues: 1842 helix: 1.28 (0.18), residues: 929 sheet: -0.51 (0.40), residues: 181 loop : -1.41 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 144 TYR 0.015 0.001 TYR C 161 PHE 0.030 0.001 PHE D 186 TRP 0.011 0.001 TRP A 436 HIS 0.004 0.001 HIS C 451 Details of bonding type rmsd covalent geometry : bond 0.00422 (14105) covalent geometry : angle 0.57092 (19176) SS BOND : bond 0.00231 ( 3) SS BOND : angle 0.53797 ( 6) hydrogen bonds : bond 0.05633 ( 723) hydrogen bonds : angle 4.08055 ( 2094) *********************** 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 171 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 123 time to evaluate : 0.678 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: 0.8113 (tpt90) cc_final: 0.7505 (tpt170) REVERT: A 392 LYS cc_start: 0.9104 (tttp) cc_final: 0.8169 (ttmm) REVERT: A 397 GLU cc_start: 0.8438 (mp0) cc_final: 0.7883 (mt-10) REVERT: A 422 ASP cc_start: 0.7478 (OUTLIER) cc_final: 0.7115 (p0) REVERT: A 489 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.7263 (tmm-80) REVERT: B 188 GLN cc_start: 0.8189 (mt0) cc_final: 0.7945 (mp10) REVERT: C 120 LYS cc_start: 0.8179 (mmtt) cc_final: 0.7551 (mmmt) REVERT: C 121 THR cc_start: 0.8745 (p) cc_final: 0.8400 (t) REVERT: C 192 GLU cc_start: 0.8545 (pm20) cc_final: 0.8245 (pp20) REVERT: C 209 ARG cc_start: 0.7741 (pmt170) cc_final: 0.7414 (pmt170) REVERT: C 299 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.6928 (tm-30) REVERT: C 453 VAL cc_start: 0.8994 (OUTLIER) cc_final: 0.8659 (p) REVERT: D 380 HIS cc_start: 0.8897 (OUTLIER) cc_final: 0.8354 (m-70) outliers start: 48 outliers final: 33 residues processed: 165 average time/residue: 0.1249 time to fit residues: 30.1615 Evaluate side-chains 154 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 116 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 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 327 ILE Chi-restraints excluded: chain B residue 377 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 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 453 VAL Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 236 ILE Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 336 ILE Chi-restraints excluded: chain D residue 343 LEU Chi-restraints excluded: chain D residue 374 ILE Chi-restraints excluded: chain D residue 380 HIS Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain H residue 112 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 87 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 61 optimal weight: 0.5980 chunk 54 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 134 optimal weight: 0.0970 chunk 138 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 chunk 107 optimal weight: 3.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN B 145 ASN C 145 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.187997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.134649 restraints weight = 21425.356| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 2.76 r_work: 0.3331 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.3779 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= 0.121 Angle : 0.527 10.131 19182 Z= 0.278 Chirality : 0.041 0.160 2216 Planarity : 0.005 0.065 2481 Dihedral : 4.122 49.070 2031 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.68 % Allowed : 18.87 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.21), residues: 1842 helix: 1.56 (0.18), residues: 929 sheet: -0.35 (0.39), residues: 190 loop : -1.30 (0.23), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 105 TYR 0.016 0.001 TYR A 147 PHE 0.019 0.001 PHE C 406 TRP 0.010 0.001 TRP A 436 HIS 0.002 0.000 HIS C 451 Details of bonding type rmsd covalent geometry : bond 0.00275 (14105) covalent geometry : angle 0.52667 (19176) SS BOND : bond 0.00152 ( 3) SS BOND : angle 0.36698 ( 6) hydrogen bonds : bond 0.04605 ( 723) hydrogen bonds : angle 3.89385 ( 2094) *********************** 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 169 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 122 time to evaluate : 0.541 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 392 LYS cc_start: 0.9107 (tttp) cc_final: 0.8156 (ttmm) REVERT: A 422 ASP cc_start: 0.7657 (OUTLIER) cc_final: 0.7260 (p0) REVERT: A 489 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.7210 (tmm-80) REVERT: B 188 GLN cc_start: 0.8210 (mt0) cc_final: 0.7928 (mp10) REVERT: B 250 ILE cc_start: 0.9420 (tp) cc_final: 0.9212 (tp) REVERT: C 120 LYS cc_start: 0.8100 (mmtt) cc_final: 0.7483 (mmmt) REVERT: C 121 THR cc_start: 0.8722 (p) cc_final: 0.8397 (t) REVERT: C 192 GLU cc_start: 0.8635 (pm20) cc_final: 0.8380 (pp20) REVERT: C 299 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.6961 (tm-30) REVERT: C 453 VAL cc_start: 0.8969 (OUTLIER) cc_final: 0.8674 (p) REVERT: D 337 ILE cc_start: 0.9249 (mm) cc_final: 0.9047 (mt) REVERT: D 380 HIS cc_start: 0.9001 (OUTLIER) cc_final: 0.8479 (m-70) outliers start: 47 outliers final: 35 residues processed: 164 average time/residue: 0.1156 time to fit residues: 28.0745 Evaluate side-chains 161 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 121 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 489 ARG Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 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 307 SER Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 256 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 99 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 74 optimal weight: 0.0980 chunk 86 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 58 optimal weight: 0.5980 chunk 183 optimal weight: 7.9990 chunk 9 optimal weight: 0.6980 chunk 109 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4311 r_free = 0.4311 target = 0.187723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.143588 restraints weight = 21438.647| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 2.99 r_work: 0.3322 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3858 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= 0.123 Angle : 0.522 9.516 19182 Z= 0.275 Chirality : 0.041 0.154 2216 Planarity : 0.005 0.066 2481 Dihedral : 4.034 46.636 2031 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.92 % Allowed : 18.56 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.21), residues: 1842 helix: 1.65 (0.18), residues: 929 sheet: -0.15 (0.39), residues: 189 loop : -1.23 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 325 TYR 0.015 0.001 TYR C 161 PHE 0.022 0.001 PHE C 406 TRP 0.010 0.001 TRP A 436 HIS 0.002 0.001 HIS C 451 Details of bonding type rmsd covalent geometry : bond 0.00286 (14105) covalent geometry : angle 0.52249 (19176) SS BOND : bond 0.00156 ( 3) SS BOND : angle 0.39773 ( 6) hydrogen bonds : bond 0.04582 ( 723) hydrogen bonds : angle 3.83364 ( 2094) *********************** 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 176 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 126 time to evaluate : 0.490 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 392 LYS cc_start: 0.9065 (tttp) cc_final: 0.8143 (ttmm) REVERT: A 422 ASP cc_start: 0.7562 (OUTLIER) cc_final: 0.7178 (p0) REVERT: A 489 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.7230 (tmm-80) REVERT: B 188 GLN cc_start: 0.8132 (mt0) cc_final: 0.7889 (mp10) REVERT: C 120 LYS cc_start: 0.8148 (mmtt) cc_final: 0.7524 (mmmt) REVERT: C 121 THR cc_start: 0.8676 (p) cc_final: 0.8357 (t) REVERT: C 192 GLU cc_start: 0.8497 (pm20) cc_final: 0.8251 (pp20) REVERT: C 299 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.6910 (tm-30) REVERT: C 453 VAL cc_start: 0.8928 (OUTLIER) cc_final: 0.8612 (p) REVERT: D 380 HIS cc_start: 0.8849 (OUTLIER) cc_final: 0.8283 (m-70) outliers start: 50 outliers final: 36 residues processed: 170 average time/residue: 0.1176 time to fit residues: 29.4958 Evaluate side-chains 161 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 120 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 145 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 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 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 405 LEU Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 256 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 9 optimal weight: 0.5980 chunk 74 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 133 optimal weight: 0.9990 chunk 142 optimal weight: 50.0000 chunk 11 optimal weight: 2.9990 chunk 175 optimal weight: 0.0970 chunk 20 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4312 r_free = 0.4312 target = 0.188032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.144908 restraints weight = 21583.019| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 3.15 r_work: 0.3327 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.3929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14108 Z= 0.120 Angle : 0.523 9.278 19182 Z= 0.276 Chirality : 0.041 0.155 2216 Planarity : 0.005 0.068 2481 Dihedral : 3.973 44.293 2031 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.37 % Allowed : 19.11 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.21), residues: 1842 helix: 1.71 (0.18), residues: 929 sheet: -0.05 (0.39), residues: 189 loop : -1.15 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 325 TYR 0.015 0.001 TYR C 161 PHE 0.021 0.001 PHE C 406 TRP 0.010 0.001 TRP A 436 HIS 0.002 0.000 HIS C 451 Details of bonding type rmsd covalent geometry : bond 0.00276 (14105) covalent geometry : angle 0.52275 (19176) SS BOND : bond 0.00144 ( 3) SS BOND : angle 0.36251 ( 6) hydrogen bonds : bond 0.04436 ( 723) hydrogen bonds : angle 3.78459 ( 2094) *********************** 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 172 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 129 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 LYS cc_start: 0.9052 (tttp) cc_final: 0.8148 (ttmm) REVERT: A 422 ASP cc_start: 0.7566 (OUTLIER) cc_final: 0.7184 (p0) REVERT: A 489 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.7219 (tmm-80) REVERT: B 127 GLU cc_start: 0.8283 (pm20) cc_final: 0.7525 (pp20) REVERT: B 188 GLN cc_start: 0.8138 (mt0) cc_final: 0.7887 (mp10) REVERT: C 120 LYS cc_start: 0.8131 (mmtt) cc_final: 0.7515 (mmmt) REVERT: C 121 THR cc_start: 0.8681 (p) cc_final: 0.8358 (t) REVERT: C 192 GLU cc_start: 0.8496 (pm20) cc_final: 0.8262 (pp20) REVERT: C 299 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.6949 (tm-30) REVERT: C 453 VAL cc_start: 0.8918 (OUTLIER) cc_final: 0.8608 (p) REVERT: D 380 HIS cc_start: 0.8863 (OUTLIER) cc_final: 0.8296 (m-70) outliers start: 43 outliers final: 36 residues processed: 166 average time/residue: 0.1215 time to fit residues: 29.8248 Evaluate side-chains 163 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 122 time to evaluate : 0.538 ------------------------------------------------------------------------------- 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 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 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 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 405 LEU Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 256 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 39 optimal weight: 0.7980 chunk 174 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 150 optimal weight: 20.0000 chunk 75 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 131 optimal weight: 0.6980 chunk 123 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.4307 r_free = 0.4307 target = 0.187569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.143977 restraints weight = 21382.550| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 3.09 r_work: 0.3319 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14108 Z= 0.131 Angle : 0.540 9.612 19182 Z= 0.284 Chirality : 0.041 0.153 2216 Planarity : 0.005 0.072 2481 Dihedral : 3.937 43.715 2031 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.29 % Allowed : 19.03 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.21), residues: 1842 helix: 1.72 (0.18), residues: 929 sheet: -0.21 (0.35), residues: 229 loop : -1.06 (0.25), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 209 TYR 0.015 0.001 TYR C 161 PHE 0.022 0.001 PHE C 406 TRP 0.010 0.001 TRP A 436 HIS 0.002 0.001 HIS C 451 Details of bonding type rmsd covalent geometry : bond 0.00311 (14105) covalent geometry : angle 0.53978 (19176) SS BOND : bond 0.00171 ( 3) SS BOND : angle 0.35842 ( 6) hydrogen bonds : bond 0.04590 ( 723) hydrogen bonds : angle 3.78258 ( 2094) ********************** 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 163 residues out of total 1652 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 121 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 LYS cc_start: 0.9047 (tttp) cc_final: 0.8131 (ttmm) REVERT: A 422 ASP cc_start: 0.7579 (OUTLIER) cc_final: 0.7208 (p0) REVERT: A 489 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.7208 (tmm-80) REVERT: B 188 GLN cc_start: 0.8141 (mt0) cc_final: 0.7871 (mp10) REVERT: C 120 LYS cc_start: 0.8142 (mmtt) cc_final: 0.7544 (mmmt) REVERT: C 192 GLU cc_start: 0.8506 (pm20) cc_final: 0.8283 (pp20) REVERT: C 209 ARG cc_start: 0.7746 (pmt170) cc_final: 0.7400 (pmt170) REVERT: C 299 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.6927 (tm-30) REVERT: C 453 VAL cc_start: 0.8944 (OUTLIER) cc_final: 0.8624 (p) REVERT: D 380 HIS cc_start: 0.8856 (OUTLIER) cc_final: 0.8332 (m-70) outliers start: 42 outliers final: 36 residues processed: 157 average time/residue: 0.1015 time to fit residues: 24.1297 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 : 0.534 ------------------------------------------------------------------------------- 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 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 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 405 LEU Chi-restraints excluded: chain C residue 413 SER Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 256 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 16 optimal weight: 2.9990 chunk 131 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 chunk 183 optimal weight: 40.0000 chunk 22 optimal weight: 5.9990 chunk 94 optimal weight: 0.9980 chunk 73 optimal weight: 0.0270 chunk 78 optimal weight: 0.0980 chunk 63 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 overall best weight: 0.5640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN B 145 ASN C 145 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.188514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.146472 restraints weight = 21472.222| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 3.09 r_work: 0.3342 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.4079 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= 0.119 Angle : 0.530 9.146 19182 Z= 0.278 Chirality : 0.041 0.152 2216 Planarity : 0.005 0.070 2481 Dihedral : 3.873 43.645 2031 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.37 % Allowed : 18.95 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.21), residues: 1842 helix: 1.82 (0.18), residues: 929 sheet: -0.15 (0.36), residues: 229 loop : -1.01 (0.25), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 209 TYR 0.015 0.001 TYR C 161 PHE 0.021 0.001 PHE C 406 TRP 0.010 0.001 TRP A 436 HIS 0.002 0.000 HIS C 451 Details of bonding type rmsd covalent geometry : bond 0.00275 (14105) covalent geometry : angle 0.52956 (19176) SS BOND : bond 0.00155 ( 3) SS BOND : angle 0.33726 ( 6) hydrogen bonds : bond 0.04301 ( 723) hydrogen bonds : angle 3.72316 ( 2094) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3977.84 seconds wall clock time: 68 minutes 24.66 seconds (4104.66 seconds total)