Starting phenix.real_space_refine on Sat Jul 4 07:41:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dze_27795/07_2026/8dze_27795.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dze_27795/07_2026/8dze_27795.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8dze_27795/07_2026/8dze_27795.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dze_27795/07_2026/8dze_27795.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dze_27795/07_2026/8dze_27795.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dze_27795/07_2026/8dze_27795.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8dze_27795/07_2026/8dze_27795.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dze_27795/07_2026/8dze_27795.cif" } resolution = 2.99 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= 0.061 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: 6 Type Number sf(0) Gaussians Zn 6 6.06 5 P 18 5.49 5 S 84 5.16 5 C 12102 2.51 5 N 3390 2.21 5 O 3708 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19308 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3186 Classifications: {'peptide': 413} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 15, 'TRANS': 397} Chain breaks: 3 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 60 Planarities with less than four sites: {'ARG:plan': 4, 'GLN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 49 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' ZN': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2171 SG CYS A 403 90.435 129.403 30.842 1.00 67.86 S ATOM 2191 SG CYS A 406 94.137 129.562 30.333 1.00 74.08 S ATOM 2475 SG CYS A 445 92.459 132.497 31.856 1.00 91.66 S ATOM 2481 SG CYS A 446 92.806 129.072 33.819 1.00 87.17 S Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 2.72, per 1000 atoms: 0.14 Number of scatterers: 19308 At special positions: 0 Unit cell: (147.96, 143.64, 81, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 6 29.99 S 84 16.00 P 18 15.00 O 3708 8.00 N 3390 7.00 C 12102 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.50 Conformation dependent library (CDL) restraints added in 823.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 601 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 406 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 403 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 445 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 446 " pdb=" ZN B 601 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 406 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 403 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 445 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 446 " pdb=" ZN C 601 " pdb="ZN ZN C 601 " - pdb=" SG CYS C 406 " pdb="ZN ZN C 601 " - pdb=" SG CYS C 403 " pdb="ZN ZN C 601 " - pdb=" SG CYS C 445 " pdb="ZN ZN C 601 " - pdb=" SG CYS C 446 " pdb=" ZN D 601 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 406 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 403 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 445 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 446 " pdb=" ZN E 601 " pdb="ZN ZN E 601 " - pdb=" SG CYS E 406 " pdb="ZN ZN E 601 " - pdb=" SG CYS E 403 " pdb="ZN ZN E 601 " - pdb=" SG CYS E 445 " pdb="ZN ZN E 601 " - pdb=" SG CYS E 446 " pdb=" ZN F 601 " pdb="ZN ZN F 601 " - pdb=" SG CYS F 406 " pdb="ZN ZN F 601 " - pdb=" SG CYS F 403 " pdb="ZN ZN F 601 " - pdb=" SG CYS F 445 " pdb="ZN ZN F 601 " - pdb=" SG CYS F 446 " Number of angles added : 36 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4668 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 30 sheets defined 45.6% alpha, 25.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 107 through 122 Processing helix chain 'A' and resid 153 through 166 Processing helix chain 'A' and resid 238 through 251 Processing helix chain 'A' and resid 261 through 264 Processing helix chain 'A' and resid 265 through 282 removed outlier: 3.669A pdb=" N LYS A 282 " --> pdb=" O TYR A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 329 removed outlier: 3.556A pdb=" N SER A 329 " --> pdb=" O ALA A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 355 Processing helix chain 'A' and resid 368 through 376 removed outlier: 4.181A pdb=" N ASP A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 385 removed outlier: 3.848A pdb=" N LEU A 384 " --> pdb=" O ASP A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 416 removed outlier: 3.926A pdb=" N SER A 416 " --> pdb=" O GLU A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 429 Processing helix chain 'A' and resid 463 through 472 Processing helix chain 'A' and resid 478 through 485 Processing helix chain 'A' and resid 490 through 501 Processing helix chain 'A' and resid 505 through 513 Processing helix chain 'A' and resid 515 through 519 removed outlier: 3.530A pdb=" N ILE A 519 " --> pdb=" O ILE A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 533 Processing helix chain 'B' and resid 108 through 122 Processing helix chain 'B' and resid 153 through 166 Processing helix chain 'B' and resid 238 through 251 Processing helix chain 'B' and resid 261 through 264 Processing helix chain 'B' and resid 265 through 282 removed outlier: 3.669A pdb=" N LYS B 282 " --> pdb=" O TYR B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 329 removed outlier: 3.556A pdb=" N SER B 329 " --> pdb=" O ALA B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 355 Processing helix chain 'B' and resid 368 through 376 removed outlier: 4.181A pdb=" N ASP B 372 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 385 removed outlier: 3.849A pdb=" N LEU B 384 " --> pdb=" O ASP B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 416 removed outlier: 3.926A pdb=" N SER B 416 " --> pdb=" O GLU B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 429 Processing helix chain 'B' and resid 463 through 472 Processing helix chain 'B' and resid 478 through 485 Processing helix chain 'B' and resid 490 through 501 Processing helix chain 'B' and resid 505 through 513 Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.530A pdb=" N ILE B 519 " --> pdb=" O ILE B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 533 Processing helix chain 'C' and resid 108 through 122 Processing helix chain 'C' and resid 153 through 166 Processing helix chain 'C' and resid 238 through 251 Processing helix chain 'C' and resid 261 through 264 Processing helix chain 'C' and resid 265 through 282 removed outlier: 3.669A pdb=" N LYS C 282 " --> pdb=" O TYR C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 329 removed outlier: 3.556A pdb=" N SER C 329 " --> pdb=" O ALA C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 355 Processing helix chain 'C' and resid 368 through 376 removed outlier: 4.181A pdb=" N ASP C 372 " --> pdb=" O LEU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 385 removed outlier: 3.848A pdb=" N LEU C 384 " --> pdb=" O ASP C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 416 removed outlier: 3.925A pdb=" N SER C 416 " --> pdb=" O GLU C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 429 Processing helix chain 'C' and resid 463 through 472 Processing helix chain 'C' and resid 478 through 485 Processing helix chain 'C' and resid 490 through 501 Processing helix chain 'C' and resid 505 through 513 Processing helix chain 'C' and resid 515 through 519 removed outlier: 3.531A pdb=" N ILE C 519 " --> pdb=" O ILE C 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 533 Processing helix chain 'D' and resid 108 through 122 Processing helix chain 'D' and resid 153 through 166 Processing helix chain 'D' and resid 238 through 251 Processing helix chain 'D' and resid 261 through 264 Processing helix chain 'D' and resid 265 through 282 removed outlier: 3.670A pdb=" N LYS D 282 " --> pdb=" O TYR D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 329 removed outlier: 3.555A pdb=" N SER D 329 " --> pdb=" O ALA D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 355 Processing helix chain 'D' and resid 368 through 376 removed outlier: 4.182A pdb=" N ASP D 372 " --> pdb=" O LEU D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 385 removed outlier: 3.849A pdb=" N LEU D 384 " --> pdb=" O ASP D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 416 removed outlier: 3.925A pdb=" N SER D 416 " --> pdb=" O GLU D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 429 Processing helix chain 'D' and resid 463 through 472 Processing helix chain 'D' and resid 478 through 485 Processing helix chain 'D' and resid 490 through 501 Processing helix chain 'D' and resid 505 through 513 Processing helix chain 'D' and resid 515 through 519 removed outlier: 3.530A pdb=" N ILE D 519 " --> pdb=" O ILE D 516 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 533 Processing helix chain 'E' and resid 108 through 122 Processing helix chain 'E' and resid 153 through 166 Processing helix chain 'E' and resid 238 through 251 Processing helix chain 'E' and resid 261 through 264 Processing helix chain 'E' and resid 265 through 282 removed outlier: 3.669A pdb=" N LYS E 282 " --> pdb=" O TYR E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 329 removed outlier: 3.556A pdb=" N SER E 329 " --> pdb=" O ALA E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 341 through 355 Processing helix chain 'E' and resid 368 through 376 removed outlier: 4.181A pdb=" N ASP E 372 " --> pdb=" O LEU E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 380 through 385 removed outlier: 3.849A pdb=" N LEU E 384 " --> pdb=" O ASP E 380 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 416 removed outlier: 3.925A pdb=" N SER E 416 " --> pdb=" O GLU E 412 " (cutoff:3.500A) Processing helix chain 'E' and resid 421 through 429 Processing helix chain 'E' and resid 463 through 472 Processing helix chain 'E' and resid 478 through 485 Processing helix chain 'E' and resid 490 through 501 Processing helix chain 'E' and resid 505 through 513 Processing helix chain 'E' and resid 515 through 519 removed outlier: 3.531A pdb=" N ILE E 519 " --> pdb=" O ILE E 516 " (cutoff:3.500A) Processing helix chain 'E' and resid 520 through 533 Processing helix chain 'F' and resid 108 through 122 Processing helix chain 'F' and resid 153 through 166 Processing helix chain 'F' and resid 238 through 251 Processing helix chain 'F' and resid 261 through 264 Processing helix chain 'F' and resid 265 through 282 removed outlier: 3.669A pdb=" N LYS F 282 " --> pdb=" O TYR F 278 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 329 removed outlier: 3.556A pdb=" N SER F 329 " --> pdb=" O ALA F 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 341 through 355 Processing helix chain 'F' and resid 368 through 376 removed outlier: 4.181A pdb=" N ASP F 372 " --> pdb=" O LEU F 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 385 removed outlier: 3.848A pdb=" N LEU F 384 " --> pdb=" O ASP F 380 " (cutoff:3.500A) Processing helix chain 'F' and resid 409 through 416 removed outlier: 3.925A pdb=" N SER F 416 " --> pdb=" O GLU F 412 " (cutoff:3.500A) Processing helix chain 'F' and resid 421 through 429 Processing helix chain 'F' and resid 463 through 472 Processing helix chain 'F' and resid 478 through 485 Processing helix chain 'F' and resid 490 through 501 Processing helix chain 'F' and resid 505 through 513 Processing helix chain 'F' and resid 515 through 519 removed outlier: 3.531A pdb=" N ILE F 519 " --> pdb=" O ILE F 516 " (cutoff:3.500A) Processing helix chain 'F' and resid 520 through 533 Processing sheet with id=AA1, first strand: chain 'A' and resid 144 through 152 removed outlier: 5.069A pdb=" N MET A 145 " --> pdb=" O LYS A 141 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LYS A 141 " --> pdb=" O MET A 145 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N LEU A 147 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ILE A 139 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG A 212 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 144 through 152 removed outlier: 5.069A pdb=" N MET A 145 " --> pdb=" O LYS A 141 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LYS A 141 " --> pdb=" O MET A 145 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N LEU A 147 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ILE A 139 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG A 212 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 357 through 361 removed outlier: 6.084A pdb=" N ILE A 255 " --> pdb=" O ILE A 390 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY A 392 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU A 393 " --> pdb=" O VAL A 459 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL A 459 " --> pdb=" O LEU A 393 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ALA A 395 " --> pdb=" O ALA A 457 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ALA A 457 " --> pdb=" O ALA A 395 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ARG A 397 " --> pdb=" O ILE A 455 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ILE A 455 " --> pdb=" O ARG A 397 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N VAL A 399 " --> pdb=" O ARG A 453 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ARG A 453 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LYS A 401 " --> pdb=" O ASN A 451 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 288 through 290 removed outlier: 6.811A pdb=" N SER A 289 " --> pdb=" O LEU A 304 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 407 through 408 Processing sheet with id=AA6, first strand: chain 'B' and resid 144 through 152 removed outlier: 5.070A pdb=" N MET B 145 " --> pdb=" O LYS B 141 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LYS B 141 " --> pdb=" O MET B 145 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N LEU B 147 " --> pdb=" O ILE B 139 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ILE B 139 " --> pdb=" O LEU B 147 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG B 212 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 144 through 152 removed outlier: 5.070A pdb=" N MET B 145 " --> pdb=" O LYS B 141 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LYS B 141 " --> pdb=" O MET B 145 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N LEU B 147 " --> pdb=" O ILE B 139 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ILE B 139 " --> pdb=" O LEU B 147 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG B 212 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 357 through 361 removed outlier: 6.084A pdb=" N ILE B 255 " --> pdb=" O ILE B 390 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY B 392 " --> pdb=" O ILE B 255 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU B 393 " --> pdb=" O VAL B 459 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL B 459 " --> pdb=" O LEU B 393 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ALA B 395 " --> pdb=" O ALA B 457 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ALA B 457 " --> pdb=" O ALA B 395 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ARG B 397 " --> pdb=" O ILE B 455 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ILE B 455 " --> pdb=" O ARG B 397 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N VAL B 399 " --> pdb=" O ARG B 453 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ARG B 453 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LYS B 401 " --> pdb=" O ASN B 451 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 288 through 290 removed outlier: 6.811A pdb=" N SER B 289 " --> pdb=" O LEU B 304 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AB2, first strand: chain 'C' and resid 144 through 152 removed outlier: 5.070A pdb=" N MET C 145 " --> pdb=" O LYS C 141 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LYS C 141 " --> pdb=" O MET C 145 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N LEU C 147 " --> pdb=" O ILE C 139 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE C 139 " --> pdb=" O LEU C 147 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG C 212 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 144 through 152 removed outlier: 5.070A pdb=" N MET C 145 " --> pdb=" O LYS C 141 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LYS C 141 " --> pdb=" O MET C 145 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N LEU C 147 " --> pdb=" O ILE C 139 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE C 139 " --> pdb=" O LEU C 147 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG C 212 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 357 through 361 removed outlier: 6.085A pdb=" N ILE C 255 " --> pdb=" O ILE C 390 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY C 392 " --> pdb=" O ILE C 255 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU C 393 " --> pdb=" O VAL C 459 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL C 459 " --> pdb=" O LEU C 393 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ALA C 395 " --> pdb=" O ALA C 457 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ALA C 457 " --> pdb=" O ALA C 395 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ARG C 397 " --> pdb=" O ILE C 455 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ILE C 455 " --> pdb=" O ARG C 397 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL C 399 " --> pdb=" O ARG C 453 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ARG C 453 " --> pdb=" O VAL C 399 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LYS C 401 " --> pdb=" O ASN C 451 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 288 through 290 removed outlier: 6.812A pdb=" N SER C 289 " --> pdb=" O LEU C 304 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AB7, first strand: chain 'D' and resid 144 through 152 removed outlier: 5.069A pdb=" N MET D 145 " --> pdb=" O LYS D 141 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LYS D 141 " --> pdb=" O MET D 145 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N LEU D 147 " --> pdb=" O ILE D 139 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE D 139 " --> pdb=" O LEU D 147 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG D 212 " --> pdb=" O VAL D 130 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 144 through 152 removed outlier: 5.069A pdb=" N MET D 145 " --> pdb=" O LYS D 141 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LYS D 141 " --> pdb=" O MET D 145 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N LEU D 147 " --> pdb=" O ILE D 139 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE D 139 " --> pdb=" O LEU D 147 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG D 212 " --> pdb=" O VAL D 130 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 357 through 361 removed outlier: 6.084A pdb=" N ILE D 255 " --> pdb=" O ILE D 390 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY D 392 " --> pdb=" O ILE D 255 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU D 393 " --> pdb=" O VAL D 459 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL D 459 " --> pdb=" O LEU D 393 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ALA D 395 " --> pdb=" O ALA D 457 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ALA D 457 " --> pdb=" O ALA D 395 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ARG D 397 " --> pdb=" O ILE D 455 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ILE D 455 " --> pdb=" O ARG D 397 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL D 399 " --> pdb=" O ARG D 453 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ARG D 453 " --> pdb=" O VAL D 399 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LYS D 401 " --> pdb=" O ASN D 451 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 288 through 290 removed outlier: 6.811A pdb=" N SER D 289 " --> pdb=" O LEU D 304 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AC3, first strand: chain 'E' and resid 144 through 152 removed outlier: 5.069A pdb=" N MET E 145 " --> pdb=" O LYS E 141 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LYS E 141 " --> pdb=" O MET E 145 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N LEU E 147 " --> pdb=" O ILE E 139 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE E 139 " --> pdb=" O LEU E 147 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG E 212 " --> pdb=" O VAL E 130 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 144 through 152 removed outlier: 5.069A pdb=" N MET E 145 " --> pdb=" O LYS E 141 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LYS E 141 " --> pdb=" O MET E 145 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N LEU E 147 " --> pdb=" O ILE E 139 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE E 139 " --> pdb=" O LEU E 147 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG E 212 " --> pdb=" O VAL E 130 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 357 through 361 removed outlier: 6.085A pdb=" N ILE E 255 " --> pdb=" O ILE E 390 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY E 392 " --> pdb=" O ILE E 255 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU E 393 " --> pdb=" O VAL E 459 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL E 459 " --> pdb=" O LEU E 393 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ALA E 395 " --> pdb=" O ALA E 457 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ALA E 457 " --> pdb=" O ALA E 395 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ARG E 397 " --> pdb=" O ILE E 455 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ILE E 455 " --> pdb=" O ARG E 397 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL E 399 " --> pdb=" O ARG E 453 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ARG E 453 " --> pdb=" O VAL E 399 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LYS E 401 " --> pdb=" O ASN E 451 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 288 through 290 removed outlier: 6.812A pdb=" N SER E 289 " --> pdb=" O LEU E 304 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'E' and resid 407 through 408 Processing sheet with id=AC8, first strand: chain 'F' and resid 144 through 152 removed outlier: 5.071A pdb=" N MET F 145 " --> pdb=" O LYS F 141 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LYS F 141 " --> pdb=" O MET F 145 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N LEU F 147 " --> pdb=" O ILE F 139 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ILE F 139 " --> pdb=" O LEU F 147 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG F 212 " --> pdb=" O VAL F 130 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 144 through 152 removed outlier: 5.071A pdb=" N MET F 145 " --> pdb=" O LYS F 141 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LYS F 141 " --> pdb=" O MET F 145 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N LEU F 147 " --> pdb=" O ILE F 139 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ILE F 139 " --> pdb=" O LEU F 147 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG F 212 " --> pdb=" O VAL F 130 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 357 through 361 removed outlier: 6.084A pdb=" N ILE F 255 " --> pdb=" O ILE F 390 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY F 392 " --> pdb=" O ILE F 255 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU F 393 " --> pdb=" O VAL F 459 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL F 459 " --> pdb=" O LEU F 393 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ALA F 395 " --> pdb=" O ALA F 457 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ALA F 457 " --> pdb=" O ALA F 395 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ARG F 397 " --> pdb=" O ILE F 455 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ILE F 455 " --> pdb=" O ARG F 397 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL F 399 " --> pdb=" O ARG F 453 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ARG F 453 " --> pdb=" O VAL F 399 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LYS F 401 " --> pdb=" O ASN F 451 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 288 through 290 removed outlier: 6.812A pdb=" N SER F 289 " --> pdb=" O LEU F 304 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'F' and resid 407 through 408 1015 hydrogen bonds defined for protein. 2919 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: 3.40 Time building geometry restraints manager: 2.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6492 1.34 - 1.46: 3958 1.46 - 1.58: 9008 1.58 - 1.70: 24 1.70 - 1.82: 144 Bond restraints: 19626 Sorted by residual: bond pdb=" C1' ANP D 602 " pdb=" C2' ANP D 602 " ideal model delta sigma weight residual 1.542 1.306 0.236 2.00e-02 2.50e+03 1.39e+02 bond pdb=" C1' ANP B 602 " pdb=" C2' ANP B 602 " ideal model delta sigma weight residual 1.542 1.306 0.236 2.00e-02 2.50e+03 1.39e+02 bond pdb=" C1' ANP C 602 " pdb=" C2' ANP C 602 " ideal model delta sigma weight residual 1.542 1.306 0.236 2.00e-02 2.50e+03 1.39e+02 bond pdb=" C1' ANP F 602 " pdb=" C2' ANP F 602 " ideal model delta sigma weight residual 1.542 1.306 0.236 2.00e-02 2.50e+03 1.39e+02 bond pdb=" C1' ANP E 602 " pdb=" C2' ANP E 602 " ideal model delta sigma weight residual 1.542 1.306 0.236 2.00e-02 2.50e+03 1.39e+02 ... (remaining 19621 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 26058 2.27 - 4.54: 360 4.54 - 6.81: 120 6.81 - 9.08: 42 9.08 - 11.35: 24 Bond angle restraints: 26604 Sorted by residual: angle pdb=" O3A ANP B 602 " pdb=" PA ANP B 602 " pdb=" O5' ANP B 602 " ideal model delta sigma weight residual 98.09 109.44 -11.35 3.00e+00 1.11e-01 1.43e+01 angle pdb=" O3A ANP C 602 " pdb=" PA ANP C 602 " pdb=" O5' ANP C 602 " ideal model delta sigma weight residual 98.09 109.43 -11.34 3.00e+00 1.11e-01 1.43e+01 angle pdb=" O3A ANP F 602 " pdb=" PA ANP F 602 " pdb=" O5' ANP F 602 " ideal model delta sigma weight residual 98.09 109.40 -11.31 3.00e+00 1.11e-01 1.42e+01 angle pdb=" O3A ANP E 602 " pdb=" PA ANP E 602 " pdb=" O5' ANP E 602 " ideal model delta sigma weight residual 98.09 109.39 -11.30 3.00e+00 1.11e-01 1.42e+01 angle pdb=" O3A ANP D 602 " pdb=" PA ANP D 602 " pdb=" O5' ANP D 602 " ideal model delta sigma weight residual 98.09 109.39 -11.30 3.00e+00 1.11e-01 1.42e+01 ... (remaining 26599 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.12: 11319 30.12 - 60.24: 537 60.24 - 90.36: 18 90.36 - 120.48: 0 120.48 - 150.60: 6 Dihedral angle restraints: 11880 sinusoidal: 4680 harmonic: 7200 Sorted by residual: dihedral pdb=" O1A ANP A 602 " pdb=" O3A ANP A 602 " pdb=" PA ANP A 602 " pdb=" PB ANP A 602 " ideal model delta sinusoidal sigma weight residual 83.11 -67.49 150.60 1 3.00e+01 1.11e-03 2.00e+01 dihedral pdb=" O1A ANP C 602 " pdb=" O3A ANP C 602 " pdb=" PA ANP C 602 " pdb=" PB ANP C 602 " ideal model delta sinusoidal sigma weight residual 83.11 -67.49 150.60 1 3.00e+01 1.11e-03 2.00e+01 dihedral pdb=" O1A ANP B 602 " pdb=" O3A ANP B 602 " pdb=" PA ANP B 602 " pdb=" PB ANP B 602 " ideal model delta sinusoidal sigma weight residual 83.11 -67.49 150.60 1 3.00e+01 1.11e-03 2.00e+01 ... (remaining 11877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 2625 0.066 - 0.133: 423 0.133 - 0.199: 6 0.199 - 0.265: 6 0.265 - 0.331: 6 Chirality restraints: 3066 Sorted by residual: chirality pdb=" C2' ANP E 602 " pdb=" C1' ANP E 602 " pdb=" C3' ANP E 602 " pdb=" O2' ANP E 602 " both_signs ideal model delta sigma weight residual False -2.72 -2.39 -0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" C2' ANP F 602 " pdb=" C1' ANP F 602 " pdb=" C3' ANP F 602 " pdb=" O2' ANP F 602 " both_signs ideal model delta sigma weight residual False -2.72 -2.39 -0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" C2' ANP C 602 " pdb=" C1' ANP C 602 " pdb=" C3' ANP C 602 " pdb=" O2' ANP C 602 " both_signs ideal model delta sigma weight residual False -2.72 -2.39 -0.33 2.00e-01 2.50e+01 2.72e+00 ... (remaining 3063 not shown) Planarity restraints: 3402 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU A 120 " 0.009 2.00e-02 2.50e+03 1.93e-02 3.73e+00 pdb=" CD GLU A 120 " -0.033 2.00e-02 2.50e+03 pdb=" OE1 GLU A 120 " 0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU A 120 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 120 " -0.009 2.00e-02 2.50e+03 1.92e-02 3.70e+00 pdb=" CD GLU B 120 " 0.033 2.00e-02 2.50e+03 pdb=" OE1 GLU B 120 " -0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU B 120 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU D 120 " -0.009 2.00e-02 2.50e+03 1.92e-02 3.70e+00 pdb=" CD GLU D 120 " 0.033 2.00e-02 2.50e+03 pdb=" OE1 GLU D 120 " -0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU D 120 " -0.012 2.00e-02 2.50e+03 ... (remaining 3399 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 4862 2.81 - 3.33: 17670 3.33 - 3.86: 29976 3.86 - 4.38: 35664 4.38 - 4.90: 63258 Nonbonded interactions: 151430 Sorted by model distance: nonbonded pdb=" O THR D 350 " pdb=" OG1 THR D 354 " model vdw 2.289 3.040 nonbonded pdb=" O THR E 350 " pdb=" OG1 THR E 354 " model vdw 2.289 3.040 nonbonded pdb=" O THR C 350 " pdb=" OG1 THR C 354 " model vdw 2.289 3.040 nonbonded pdb=" O THR F 350 " pdb=" OG1 THR F 354 " model vdw 2.290 3.040 nonbonded pdb=" O THR B 350 " pdb=" OG1 THR B 354 " model vdw 2.290 3.040 ... (remaining 151425 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 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: 0.360 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 18.040 Find NCS groups from input model: 0.190 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:6.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.236 19650 Z= 0.381 Angle : 0.834 11.347 26640 Z= 0.370 Chirality : 0.047 0.331 3066 Planarity : 0.005 0.061 3402 Dihedral : 15.759 150.605 7212 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.04 % Favored : 92.72 % Rotamer: Outliers : 0.64 % Allowed : 17.21 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.16 (0.16), residues: 2430 helix: 0.74 (0.15), residues: 1032 sheet: 2.20 (0.25), residues: 426 loop : -2.23 (0.17), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 110 TYR 0.008 0.001 TYR F 278 PHE 0.011 0.001 PHE C 382 TRP 0.006 0.001 TRP D 359 HIS 0.001 0.000 HIS E 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00762 / 0.38 (19626) covalent geometry : angle 0.82545 / 0.37 (26604) hydrogen bonds : bond 0.15067 / 10.18 ( 913) hydrogen bonds : angle 4.85350 / 3.43 ( 2919) metal coordination : bond 0.00573 / 0.33 ( 24) metal coordination : angle 3.39211 / 2.29 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 198 time to evaluate : 0.701 Fit side-chains REVERT: B 525 LYS cc_start: 0.8179 (ttmm) cc_final: 0.7937 (ttmm) REVERT: C 123 VAL cc_start: 0.8323 (m) cc_final: 0.7950 (m) REVERT: C 320 ARG cc_start: 0.6795 (ttp80) cc_final: 0.6351 (ttm110) REVERT: E 525 LYS cc_start: 0.8162 (ttmm) cc_final: 0.7924 (ttmm) REVERT: F 120 GLU cc_start: 0.7460 (pp20) cc_final: 0.7249 (pp20) REVERT: F 320 ARG cc_start: 0.6868 (ttp80) cc_final: 0.6428 (ttm110) outliers start: 13 outliers final: 17 residues processed: 202 average time/residue: 0.5510 time to fit residues: 125.9180 Evaluate side-chains 188 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 171 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ASN Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain D residue 177 ASN Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 177 ASN Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 409 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.4980 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.9980 chunk 235 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 256 ASN A 356 HIS A 439 ASN B 256 ASN B 356 HIS B 439 ASN C 256 ASN C 439 ASN D 256 ASN D 356 HIS D 439 ASN E 256 ASN E 439 ASN F 256 ASN F 439 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.155409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.118773 restraints weight = 22103.435| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.26 r_work: 0.3268 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19650 Z= 0.128 Angle : 0.525 5.445 26640 Z= 0.271 Chirality : 0.043 0.142 3066 Planarity : 0.004 0.038 3402 Dihedral : 9.160 164.439 2733 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.16 % Favored : 92.59 % Rotamer: Outliers : 2.43 % Allowed : 14.19 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.48 (0.17), residues: 2430 helix: 1.77 (0.16), residues: 1044 sheet: 1.64 (0.24), residues: 432 loop : -2.13 (0.18), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 110 TYR 0.009 0.001 TYR E 138 PHE 0.008 0.001 PHE B 382 TRP 0.005 0.001 TRP D 359 HIS 0.005 0.001 HIS D 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (19626) covalent geometry : angle 0.51337 / 0.27 (26604) hydrogen bonds : bond 0.03656 / 2.46 ( 913) hydrogen bonds : angle 3.77235 / 2.64 ( 2919) metal coordination : bond 0.00497 / 0.27 ( 24) metal coordination : angle 2.98306 / 1.99 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 207 time to evaluate : 0.703 Fit side-chains REVERT: A 158 SER cc_start: 0.8886 (m) cc_final: 0.8663 (t) REVERT: B 120 GLU cc_start: 0.7198 (pp20) cc_final: 0.6972 (pp20) REVERT: B 164 TYR cc_start: 0.7328 (t80) cc_final: 0.7066 (t80) REVERT: B 220 TYR cc_start: 0.8191 (m-80) cc_final: 0.7939 (m-80) REVERT: B 525 LYS cc_start: 0.8215 (ttmm) cc_final: 0.7984 (ttmm) REVERT: C 164 TYR cc_start: 0.7428 (t80) cc_final: 0.7199 (t80) REVERT: C 320 ARG cc_start: 0.7274 (ttp80) cc_final: 0.6542 (ttm110) REVERT: D 158 SER cc_start: 0.8902 (m) cc_final: 0.8685 (t) REVERT: D 164 TYR cc_start: 0.7125 (t80) cc_final: 0.6920 (t80) REVERT: E 121 MET cc_start: 0.7993 (ttp) cc_final: 0.7727 (ttp) REVERT: E 164 TYR cc_start: 0.7261 (t80) cc_final: 0.7013 (t80) REVERT: E 220 TYR cc_start: 0.8190 (m-80) cc_final: 0.7895 (m-80) REVERT: E 525 LYS cc_start: 0.8214 (ttmm) cc_final: 0.7984 (ttmm) REVERT: F 320 ARG cc_start: 0.7240 (ttp80) cc_final: 0.6476 (ttm110) outliers start: 49 outliers final: 33 residues processed: 243 average time/residue: 0.6638 time to fit residues: 179.7623 Evaluate side-chains 217 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 184 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ASN Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 448 ASP Chi-restraints excluded: chain B residue 455 ILE Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 448 ASP Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 177 ASN Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 448 ASP Chi-restraints excluded: chain E residue 455 ILE Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain F residue 145 MET Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 448 ASP Chi-restraints excluded: chain F residue 455 ILE Chi-restraints excluded: chain F residue 491 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 195 optimal weight: 2.9990 chunk 197 optimal weight: 5.9990 chunk 159 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 48 optimal weight: 0.4980 chunk 136 optimal weight: 0.8980 chunk 200 optimal weight: 0.7980 chunk 223 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 166 ASN C 166 ASN C 356 HIS D 166 ASN E 356 HIS F 166 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.154271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.117335 restraints weight = 22213.179| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.31 r_work: 0.3261 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 19650 Z= 0.108 Angle : 0.498 5.520 26640 Z= 0.258 Chirality : 0.042 0.138 3066 Planarity : 0.004 0.051 3402 Dihedral : 8.928 158.620 2727 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.37 % Favored : 92.39 % Rotamer: Outliers : 2.33 % Allowed : 14.83 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.17), residues: 2430 helix: 1.90 (0.16), residues: 1080 sheet: 1.61 (0.24), residues: 426 loop : -2.10 (0.18), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 110 TYR 0.010 0.001 TYR D 138 PHE 0.008 0.001 PHE C 382 TRP 0.006 0.001 TRP D 359 HIS 0.003 0.001 HIS A 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (19626) covalent geometry : angle 0.48809 / 0.26 (26604) hydrogen bonds : bond 0.03143 / 2.12 ( 913) hydrogen bonds : angle 3.65463 / 2.56 ( 2919) metal coordination : bond 0.00450 / 0.24 ( 24) metal coordination : angle 2.72182 / 1.81 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 204 time to evaluate : 0.758 Fit side-chains REVERT: A 158 SER cc_start: 0.8901 (m) cc_final: 0.8694 (t) REVERT: A 397 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.7701 (mtt-85) REVERT: B 120 GLU cc_start: 0.7256 (pp20) cc_final: 0.6995 (pp20) REVERT: B 164 TYR cc_start: 0.7319 (t80) cc_final: 0.7108 (t80) REVERT: B 220 TYR cc_start: 0.8136 (m-80) cc_final: 0.7829 (m-80) REVERT: B 525 LYS cc_start: 0.8179 (ttmm) cc_final: 0.7956 (ttmm) REVERT: C 164 TYR cc_start: 0.7400 (t80) cc_final: 0.7166 (t80) REVERT: C 220 TYR cc_start: 0.8125 (m-80) cc_final: 0.7920 (m-80) REVERT: C 320 ARG cc_start: 0.7214 (ttp80) cc_final: 0.6461 (ttm110) REVERT: C 388 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7155 (mp0) REVERT: D 158 SER cc_start: 0.8905 (m) cc_final: 0.8698 (t) REVERT: D 164 TYR cc_start: 0.7144 (t80) cc_final: 0.6930 (t80) REVERT: D 353 MET cc_start: 0.8825 (mtm) cc_final: 0.8560 (mtp) REVERT: E 120 GLU cc_start: 0.7220 (pp20) cc_final: 0.7014 (pp20) REVERT: E 164 TYR cc_start: 0.7300 (t80) cc_final: 0.7087 (t80) REVERT: E 220 TYR cc_start: 0.8152 (m-80) cc_final: 0.7864 (m-80) REVERT: E 525 LYS cc_start: 0.8212 (ttmm) cc_final: 0.7985 (ttmm) REVERT: F 320 ARG cc_start: 0.7230 (ttp80) cc_final: 0.6463 (ttm110) REVERT: F 388 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7325 (mp0) outliers start: 47 outliers final: 37 residues processed: 230 average time/residue: 0.5803 time to fit residues: 150.3758 Evaluate side-chains 223 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 183 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 177 ASN Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 397 ARG Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 455 ILE Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 455 ILE Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 177 ASN Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 448 ASP Chi-restraints excluded: chain E residue 455 ILE Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain F residue 145 MET Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 388 GLU Chi-restraints excluded: chain F residue 455 ILE Chi-restraints excluded: chain F residue 491 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 77 optimal weight: 0.7980 chunk 91 optimal weight: 6.9990 chunk 236 optimal weight: 3.9990 chunk 41 optimal weight: 10.0000 chunk 105 optimal weight: 4.9990 chunk 205 optimal weight: 10.0000 chunk 240 optimal weight: 6.9990 chunk 137 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 193 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 127 HIS A 166 ASN B 127 HIS C 127 HIS C 166 ASN D 127 HIS D 166 ASN E 127 HIS F 127 HIS F 166 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.146992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.109523 restraints weight = 22143.343| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.28 r_work: 0.3148 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 19650 Z= 0.195 Angle : 0.584 6.248 26640 Z= 0.299 Chirality : 0.045 0.159 3066 Planarity : 0.004 0.040 3402 Dihedral : 8.716 150.492 2724 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.49 % Favored : 92.18 % Rotamer: Outliers : 2.93 % Allowed : 14.63 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.52 (0.17), residues: 2430 helix: 1.80 (0.16), residues: 1092 sheet: 1.46 (0.23), residues: 426 loop : -2.17 (0.18), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 234 TYR 0.012 0.001 TYR A 138 PHE 0.010 0.001 PHE F 204 TRP 0.009 0.002 TRP D 359 HIS 0.007 0.001 HIS F 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.20 (19626) covalent geometry : angle 0.56912 / 0.30 (26604) hydrogen bonds : bond 0.03992 / 2.68 ( 913) hydrogen bonds : angle 3.75051 / 2.62 ( 2919) metal coordination : bond 0.00609 / 0.33 ( 24) metal coordination : angle 3.60237 / 2.37 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 190 time to evaluate : 0.694 Fit side-chains REVERT: A 174 TYR cc_start: 0.6505 (t80) cc_final: 0.5871 (t80) REVERT: A 397 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.7688 (mtt-85) REVERT: B 120 GLU cc_start: 0.7475 (pp20) cc_final: 0.7231 (pp20) REVERT: B 164 TYR cc_start: 0.7545 (t80) cc_final: 0.7285 (t80) REVERT: B 174 TYR cc_start: 0.6338 (t80) cc_final: 0.5887 (t80) REVERT: B 220 TYR cc_start: 0.8286 (m-80) cc_final: 0.8010 (m-80) REVERT: B 405 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.8256 (mm-40) REVERT: C 164 TYR cc_start: 0.7618 (t80) cc_final: 0.7339 (t80) REVERT: C 320 ARG cc_start: 0.7358 (ttp80) cc_final: 0.6553 (ttm110) REVERT: C 388 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7486 (mp0) REVERT: D 164 TYR cc_start: 0.7443 (t80) cc_final: 0.7202 (t80) REVERT: D 174 TYR cc_start: 0.6567 (t80) cc_final: 0.5940 (t80) REVERT: E 120 GLU cc_start: 0.7439 (pp20) cc_final: 0.7236 (pp20) REVERT: E 164 TYR cc_start: 0.7559 (t80) cc_final: 0.7300 (t80) REVERT: E 174 TYR cc_start: 0.6348 (t80) cc_final: 0.5943 (t80) REVERT: E 220 TYR cc_start: 0.8269 (m-80) cc_final: 0.8033 (m-80) REVERT: E 405 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.8278 (mm-40) REVERT: F 174 TYR cc_start: 0.6463 (t80) cc_final: 0.6200 (t80) REVERT: F 320 ARG cc_start: 0.7374 (ttp80) cc_final: 0.6550 (ttm110) REVERT: F 388 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7511 (mp0) REVERT: F 489 MET cc_start: 0.9121 (ttm) cc_final: 0.8832 (ttp) outliers start: 59 outliers final: 38 residues processed: 229 average time/residue: 0.6379 time to fit residues: 163.0063 Evaluate side-chains 208 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 165 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 397 ARG Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 405 GLN Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 455 ILE Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 455 ILE Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 217 ARG Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 405 GLN Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 448 ASP Chi-restraints excluded: chain E residue 455 ILE Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 145 MET Chi-restraints excluded: chain F residue 388 GLU Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 455 ILE Chi-restraints excluded: chain F residue 491 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 223 optimal weight: 8.9990 chunk 158 optimal weight: 0.5980 chunk 228 optimal weight: 4.9990 chunk 62 optimal weight: 0.0000 chunk 48 optimal weight: 4.9990 chunk 188 optimal weight: 3.9990 chunk 177 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 131 optimal weight: 0.0770 chunk 140 optimal weight: 0.7980 overall best weight: 0.4942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 166 ASN C 166 ASN D 166 ASN F 166 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.150823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.113795 restraints weight = 21938.880| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.25 r_work: 0.3199 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 19650 Z= 0.097 Angle : 0.501 5.914 26640 Z= 0.257 Chirality : 0.041 0.143 3066 Planarity : 0.003 0.032 3402 Dihedral : 8.650 151.983 2720 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.24 % Favored : 92.51 % Rotamer: Outliers : 2.53 % Allowed : 15.13 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.77 (0.17), residues: 2430 helix: 2.12 (0.16), residues: 1092 sheet: 1.43 (0.23), residues: 426 loop : -2.10 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 397 TYR 0.010 0.001 TYR A 138 PHE 0.009 0.001 PHE D 382 TRP 0.006 0.001 TRP C 359 HIS 0.002 0.000 HIS D 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.10 (19626) covalent geometry : angle 0.48745 / 0.26 (26604) hydrogen bonds : bond 0.02892 / 1.94 ( 913) hydrogen bonds : angle 3.58210 / 2.51 ( 2919) metal coordination : bond 0.00397 / 0.21 ( 24) metal coordination : angle 3.14050 / 2.09 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 185 time to evaluate : 0.771 Fit side-chains REVERT: A 174 TYR cc_start: 0.6423 (t80) cc_final: 0.5901 (t80) REVERT: A 388 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7583 (mp0) REVERT: B 120 GLU cc_start: 0.7389 (pp20) cc_final: 0.7155 (pp20) REVERT: B 164 TYR cc_start: 0.7471 (t80) cc_final: 0.7195 (t80) REVERT: B 174 TYR cc_start: 0.6393 (t80) cc_final: 0.5882 (t80) REVERT: B 220 TYR cc_start: 0.8163 (m-80) cc_final: 0.7915 (m-80) REVERT: C 164 TYR cc_start: 0.7511 (t80) cc_final: 0.7192 (t80) REVERT: C 320 ARG cc_start: 0.7292 (ttp80) cc_final: 0.6533 (ttm110) REVERT: C 388 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7467 (mp0) REVERT: D 164 TYR cc_start: 0.7472 (t80) cc_final: 0.7242 (t80) REVERT: D 174 TYR cc_start: 0.6666 (t80) cc_final: 0.5955 (t80) REVERT: D 388 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7559 (mp0) REVERT: E 120 GLU cc_start: 0.7334 (pp20) cc_final: 0.7125 (pp20) REVERT: E 164 TYR cc_start: 0.7479 (t80) cc_final: 0.7216 (t80) REVERT: E 174 TYR cc_start: 0.6319 (t80) cc_final: 0.5722 (t80) REVERT: E 220 TYR cc_start: 0.8136 (m-80) cc_final: 0.7900 (m-80) REVERT: F 320 ARG cc_start: 0.7327 (ttp80) cc_final: 0.6551 (ttm110) REVERT: F 388 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7498 (mp0) outliers start: 51 outliers final: 41 residues processed: 219 average time/residue: 0.6491 time to fit residues: 159.5180 Evaluate side-chains 218 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 173 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 455 ILE Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 492 LYS Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 340 ARG Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 388 GLU Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 455 ILE Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 217 ARG Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 335 MET Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 448 ASP Chi-restraints excluded: chain E residue 455 ILE Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 176 ILE Chi-restraints excluded: chain F residue 388 GLU Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 491 LEU Chi-restraints excluded: chain F residue 492 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 181 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 189 optimal weight: 0.3980 chunk 25 optimal weight: 3.9990 chunk 131 optimal weight: 0.0670 chunk 105 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 chunk 180 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 chunk 191 optimal weight: 0.7980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 166 ASN C 166 ASN D 166 ASN F 166 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.150848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.113722 restraints weight = 21755.011| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.27 r_work: 0.3206 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 19650 Z= 0.097 Angle : 0.498 6.171 26640 Z= 0.255 Chirality : 0.041 0.139 3066 Planarity : 0.003 0.033 3402 Dihedral : 8.587 152.043 2718 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.61 % Favored : 92.10 % Rotamer: Outliers : 3.12 % Allowed : 15.38 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.87 (0.17), residues: 2430 helix: 2.24 (0.16), residues: 1092 sheet: 1.41 (0.24), residues: 426 loop : -2.08 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 397 TYR 0.009 0.001 TYR A 138 PHE 0.008 0.001 PHE B 382 TRP 0.007 0.001 TRP C 359 HIS 0.002 0.000 HIS D 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 (19626) covalent geometry : angle 0.48619 / 0.25 (26604) hydrogen bonds : bond 0.02762 / 1.85 ( 913) hydrogen bonds : angle 3.50941 / 2.46 ( 2919) metal coordination : bond 0.00404 / 0.23 ( 24) metal coordination : angle 2.95333 / 1.96 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 183 time to evaluate : 0.739 Fit side-chains REVERT: A 174 TYR cc_start: 0.6472 (t80) cc_final: 0.5897 (t80) REVERT: A 388 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7607 (mp0) REVERT: B 120 GLU cc_start: 0.7384 (pp20) cc_final: 0.7147 (pp20) REVERT: B 164 TYR cc_start: 0.7474 (t80) cc_final: 0.7183 (t80) REVERT: B 174 TYR cc_start: 0.6406 (t80) cc_final: 0.5902 (t80) REVERT: B 220 TYR cc_start: 0.8102 (m-80) cc_final: 0.7889 (m-80) REVERT: C 164 TYR cc_start: 0.7485 (t80) cc_final: 0.7237 (t80) REVERT: C 320 ARG cc_start: 0.7268 (ttp80) cc_final: 0.6504 (ttm110) REVERT: C 328 ARG cc_start: 0.7082 (OUTLIER) cc_final: 0.6314 (mtp180) REVERT: C 388 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7469 (mp0) REVERT: D 164 TYR cc_start: 0.7483 (t80) cc_final: 0.7224 (t80) REVERT: D 174 TYR cc_start: 0.6548 (t80) cc_final: 0.5852 (t80) REVERT: D 388 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7607 (mp0) REVERT: E 120 GLU cc_start: 0.7359 (pp20) cc_final: 0.7129 (pp20) REVERT: E 164 TYR cc_start: 0.7477 (t80) cc_final: 0.7181 (t80) REVERT: E 174 TYR cc_start: 0.6322 (t80) cc_final: 0.5828 (t80) REVERT: E 220 TYR cc_start: 0.8092 (m-80) cc_final: 0.7842 (m-80) REVERT: F 212 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7599 (mmm160) REVERT: F 320 ARG cc_start: 0.7302 (ttp80) cc_final: 0.6517 (ttm110) REVERT: F 388 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7504 (mp0) outliers start: 63 outliers final: 43 residues processed: 222 average time/residue: 0.6177 time to fit residues: 154.4380 Evaluate side-chains 223 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 174 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 455 ILE Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 328 ARG Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 492 LYS Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 340 ARG Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 388 GLU Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 217 ARG Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 335 MET Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 455 ILE Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 176 ILE Chi-restraints excluded: chain F residue 212 ARG Chi-restraints excluded: chain F residue 388 GLU Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 491 LEU Chi-restraints excluded: chain F residue 492 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 86 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 230 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 233 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 234 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 166 ASN C 166 ASN D 166 ASN F 166 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.148966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.111533 restraints weight = 21896.296| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.28 r_work: 0.3168 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 19650 Z= 0.122 Angle : 0.521 7.291 26640 Z= 0.266 Chirality : 0.042 0.145 3066 Planarity : 0.003 0.036 3402 Dihedral : 8.522 149.437 2718 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.49 % Favored : 92.26 % Rotamer: Outliers : 2.88 % Allowed : 15.38 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.83 (0.17), residues: 2430 helix: 2.23 (0.16), residues: 1092 sheet: 1.36 (0.23), residues: 426 loop : -2.12 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 397 TYR 0.010 0.001 TYR D 138 PHE 0.008 0.001 PHE D 382 TRP 0.006 0.001 TRP A 359 HIS 0.004 0.001 HIS C 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (19626) covalent geometry : angle 0.50995 / 0.27 (26604) hydrogen bonds : bond 0.03101 / 2.09 ( 913) hydrogen bonds : angle 3.53471 / 2.48 ( 2919) metal coordination : bond 0.00437 / 0.23 ( 24) metal coordination : angle 3.00224 / 1.97 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 182 time to evaluate : 0.745 Fit side-chains REVERT: A 174 TYR cc_start: 0.6573 (t80) cc_final: 0.5989 (t80) REVERT: A 318 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.7012 (tp30) REVERT: A 388 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7817 (mp0) REVERT: B 120 GLU cc_start: 0.7485 (pp20) cc_final: 0.7240 (pp20) REVERT: B 164 TYR cc_start: 0.7604 (t80) cc_final: 0.7360 (t80) REVERT: B 174 TYR cc_start: 0.6565 (t80) cc_final: 0.6073 (t80) REVERT: B 220 TYR cc_start: 0.8165 (m-80) cc_final: 0.7939 (m-80) REVERT: C 320 ARG cc_start: 0.7347 (ttp80) cc_final: 0.6589 (ttm110) REVERT: C 388 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7588 (mp0) REVERT: D 164 TYR cc_start: 0.7566 (t80) cc_final: 0.7331 (t80) REVERT: D 174 TYR cc_start: 0.6579 (t80) cc_final: 0.5923 (t80) REVERT: D 388 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7760 (mp0) REVERT: E 120 GLU cc_start: 0.7452 (pp20) cc_final: 0.7206 (pp20) REVERT: E 164 TYR cc_start: 0.7593 (t80) cc_final: 0.7358 (t80) REVERT: E 174 TYR cc_start: 0.6466 (t80) cc_final: 0.5925 (t80) REVERT: E 220 TYR cc_start: 0.8131 (m-80) cc_final: 0.7909 (m-80) REVERT: E 507 MET cc_start: 0.8184 (OUTLIER) cc_final: 0.7508 (mpt) REVERT: F 212 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.7755 (mmt180) REVERT: F 320 ARG cc_start: 0.7360 (ttp80) cc_final: 0.6595 (ttm110) REVERT: F 388 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7615 (mp0) outliers start: 58 outliers final: 45 residues processed: 219 average time/residue: 0.5988 time to fit residues: 146.7256 Evaluate side-chains 225 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 173 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 455 ILE Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain C residue 476 GLU Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 492 LYS Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 340 ARG Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 388 GLU Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 455 ILE Chi-restraints excluded: chain D residue 489 MET Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 217 ARG Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 335 MET Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 448 ASP Chi-restraints excluded: chain E residue 455 ILE Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain E residue 507 MET Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 176 ILE Chi-restraints excluded: chain F residue 212 ARG Chi-restraints excluded: chain F residue 388 GLU Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 476 GLU Chi-restraints excluded: chain F residue 491 LEU Chi-restraints excluded: chain F residue 492 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 205 optimal weight: 10.0000 chunk 72 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 232 optimal weight: 0.9990 chunk 123 optimal weight: 10.0000 chunk 162 optimal weight: 1.9990 chunk 90 optimal weight: 0.0040 chunk 54 optimal weight: 0.9990 chunk 233 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.149480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.112069 restraints weight = 21908.612| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.28 r_work: 0.3171 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 19650 Z= 0.107 Angle : 0.511 7.832 26640 Z= 0.260 Chirality : 0.042 0.142 3066 Planarity : 0.003 0.043 3402 Dihedral : 8.504 149.633 2718 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.11 % Favored : 91.85 % Rotamer: Outliers : 2.83 % Allowed : 15.58 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.88 (0.17), residues: 2430 helix: 2.30 (0.16), residues: 1092 sheet: 1.38 (0.23), residues: 426 loop : -2.12 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 234 TYR 0.010 0.001 TYR D 138 PHE 0.008 0.001 PHE B 382 TRP 0.006 0.001 TRP A 359 HIS 0.003 0.000 HIS C 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (19626) covalent geometry : angle 0.49978 / 0.26 (26604) hydrogen bonds : bond 0.02897 / 1.95 ( 913) hydrogen bonds : angle 3.50705 / 2.46 ( 2919) metal coordination : bond 0.00393 / 0.21 ( 24) metal coordination : angle 2.92211 / 1.95 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 180 time to evaluate : 0.793 Fit side-chains REVERT: A 174 TYR cc_start: 0.6577 (t80) cc_final: 0.5982 (t80) REVERT: A 318 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.7010 (tp30) REVERT: A 388 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7812 (mp0) REVERT: B 120 GLU cc_start: 0.7471 (pp20) cc_final: 0.7224 (pp20) REVERT: B 164 TYR cc_start: 0.7608 (t80) cc_final: 0.7352 (t80) REVERT: B 174 TYR cc_start: 0.6566 (t80) cc_final: 0.5969 (t80) REVERT: B 220 TYR cc_start: 0.8140 (m-80) cc_final: 0.7929 (m-80) REVERT: C 320 ARG cc_start: 0.7331 (ttp80) cc_final: 0.6570 (ttm110) REVERT: C 388 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7583 (mp0) REVERT: D 147 LEU cc_start: 0.9243 (tp) cc_final: 0.8957 (tm) REVERT: D 164 TYR cc_start: 0.7548 (t80) cc_final: 0.7296 (t80) REVERT: D 174 TYR cc_start: 0.6591 (t80) cc_final: 0.5922 (t80) REVERT: D 388 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7773 (mp0) REVERT: E 120 GLU cc_start: 0.7450 (pp20) cc_final: 0.7202 (pp20) REVERT: E 164 TYR cc_start: 0.7579 (t80) cc_final: 0.7327 (t80) REVERT: E 174 TYR cc_start: 0.6472 (t80) cc_final: 0.5914 (t80) REVERT: E 220 TYR cc_start: 0.8118 (m-80) cc_final: 0.7917 (m-80) REVERT: F 212 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.7692 (mmm160) REVERT: F 320 ARG cc_start: 0.7344 (ttp80) cc_final: 0.6571 (ttm110) REVERT: F 388 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7605 (mp0) outliers start: 57 outliers final: 43 residues processed: 222 average time/residue: 0.6757 time to fit residues: 167.7561 Evaluate side-chains 226 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 177 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 455 ILE Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 340 ARG Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 492 LYS Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 340 ARG Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 388 GLU Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 455 ILE Chi-restraints excluded: chain D residue 489 MET Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 217 ARG Chi-restraints excluded: chain E residue 335 MET Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 455 ILE Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 176 ILE Chi-restraints excluded: chain F residue 212 ARG Chi-restraints excluded: chain F residue 340 ARG Chi-restraints excluded: chain F residue 388 GLU Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 491 LEU Chi-restraints excluded: chain F residue 492 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 65 optimal weight: 4.9990 chunk 207 optimal weight: 6.9990 chunk 117 optimal weight: 5.9990 chunk 145 optimal weight: 0.6980 chunk 131 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 214 optimal weight: 0.9980 chunk 179 optimal weight: 4.9990 chunk 206 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 162 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 166 ASN E 166 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.149000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.111614 restraints weight = 21813.038| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.27 r_work: 0.3158 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19650 Z= 0.113 Angle : 0.521 7.692 26640 Z= 0.264 Chirality : 0.042 0.143 3066 Planarity : 0.003 0.041 3402 Dihedral : 8.450 148.950 2714 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 3.03 % Allowed : 15.67 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.86 (0.17), residues: 2430 helix: 2.28 (0.16), residues: 1092 sheet: 1.36 (0.23), residues: 426 loop : -2.13 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 234 TYR 0.010 0.001 TYR A 138 PHE 0.008 0.001 PHE B 382 TRP 0.006 0.001 TRP D 359 HIS 0.003 0.001 HIS C 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 (19626) covalent geometry : angle 0.51131 / 0.26 (26604) hydrogen bonds : bond 0.02930 / 1.96 ( 913) hydrogen bonds : angle 3.50076 / 2.46 ( 2919) metal coordination : bond 0.00407 / 0.22 ( 24) metal coordination : angle 2.80326 / 1.85 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 176 time to evaluate : 0.745 Fit side-chains REVERT: A 147 LEU cc_start: 0.9260 (tp) cc_final: 0.8999 (tm) REVERT: A 174 TYR cc_start: 0.6602 (t80) cc_final: 0.6036 (t80) REVERT: A 388 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7811 (mp0) REVERT: B 120 GLU cc_start: 0.7474 (pp20) cc_final: 0.7227 (pp20) REVERT: B 164 TYR cc_start: 0.7584 (t80) cc_final: 0.7318 (t80) REVERT: B 174 TYR cc_start: 0.6603 (t80) cc_final: 0.6056 (t80) REVERT: B 220 TYR cc_start: 0.8169 (m-80) cc_final: 0.7949 (m-80) REVERT: B 507 MET cc_start: 0.8169 (OUTLIER) cc_final: 0.7484 (mpt) REVERT: B 530 ARG cc_start: 0.7599 (OUTLIER) cc_final: 0.6855 (ttm-80) REVERT: C 320 ARG cc_start: 0.7334 (ttp80) cc_final: 0.6567 (ttm110) REVERT: C 388 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7600 (mp0) REVERT: C 476 GLU cc_start: 0.6856 (mm-30) cc_final: 0.5982 (tt0) REVERT: D 147 LEU cc_start: 0.9279 (tp) cc_final: 0.9009 (tm) REVERT: D 174 TYR cc_start: 0.6629 (t80) cc_final: 0.5987 (t80) REVERT: D 388 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7765 (mp0) REVERT: E 120 GLU cc_start: 0.7480 (pp20) cc_final: 0.7235 (pp20) REVERT: E 164 TYR cc_start: 0.7581 (t80) cc_final: 0.7322 (t80) REVERT: E 174 TYR cc_start: 0.6535 (t80) cc_final: 0.6009 (t80) REVERT: E 220 TYR cc_start: 0.8146 (m-80) cc_final: 0.7931 (m-80) REVERT: F 212 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.7617 (mmt180) REVERT: F 320 ARG cc_start: 0.7346 (ttp80) cc_final: 0.6567 (ttm110) REVERT: F 388 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7597 (mp0) REVERT: F 476 GLU cc_start: 0.6969 (mm-30) cc_final: 0.6152 (tt0) outliers start: 61 outliers final: 44 residues processed: 217 average time/residue: 0.6968 time to fit residues: 168.2899 Evaluate side-chains 220 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 169 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain B residue 340 ARG Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 455 ILE Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 530 ARG Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 340 ARG Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 492 LYS Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 340 ARG Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 388 GLU Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 455 ILE Chi-restraints excluded: chain D residue 489 MET Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 217 ARG Chi-restraints excluded: chain E residue 335 MET Chi-restraints excluded: chain E residue 340 ARG Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 455 ILE Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 176 ILE Chi-restraints excluded: chain F residue 212 ARG Chi-restraints excluded: chain F residue 340 ARG Chi-restraints excluded: chain F residue 388 GLU Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 491 LEU Chi-restraints excluded: chain F residue 492 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 79 optimal weight: 1.9990 chunk 45 optimal weight: 7.9990 chunk 163 optimal weight: 1.9990 chunk 161 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 chunk 26 optimal weight: 0.0570 chunk 143 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 178 optimal weight: 1.9990 chunk 238 optimal weight: 3.9990 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.149897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.112268 restraints weight = 21959.781| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.33 r_work: 0.3158 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 19650 Z= 0.105 Angle : 0.523 8.125 26640 Z= 0.265 Chirality : 0.042 0.141 3066 Planarity : 0.003 0.039 3402 Dihedral : 8.401 149.186 2714 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 2.43 % Allowed : 16.17 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.91 (0.17), residues: 2430 helix: 2.32 (0.16), residues: 1092 sheet: 1.39 (0.23), residues: 426 loop : -2.10 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 234 TYR 0.010 0.001 TYR A 138 PHE 0.008 0.001 PHE E 382 TRP 0.007 0.001 TRP A 359 HIS 0.003 0.000 HIS C 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (19626) covalent geometry : angle 0.51392 / 0.26 (26604) hydrogen bonds : bond 0.02791 / 1.87 ( 913) hydrogen bonds : angle 3.58021 / 2.52 ( 2919) metal coordination : bond 0.00375 / 0.20 ( 24) metal coordination : angle 2.70869 / 1.80 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 175 time to evaluate : 0.764 Fit side-chains REVERT: A 147 LEU cc_start: 0.9264 (tp) cc_final: 0.9024 (tm) REVERT: A 174 TYR cc_start: 0.6540 (t80) cc_final: 0.5981 (t80) REVERT: B 120 GLU cc_start: 0.7467 (pp20) cc_final: 0.7221 (pp20) REVERT: B 164 TYR cc_start: 0.7548 (t80) cc_final: 0.7333 (t80) REVERT: B 174 TYR cc_start: 0.6640 (t80) cc_final: 0.6056 (t80) REVERT: B 220 TYR cc_start: 0.8150 (m-80) cc_final: 0.7910 (m-80) REVERT: C 320 ARG cc_start: 0.7265 (ttp80) cc_final: 0.6574 (ttm110) REVERT: C 388 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7575 (mp0) REVERT: C 476 GLU cc_start: 0.6854 (mm-30) cc_final: 0.5952 (tt0) REVERT: D 147 LEU cc_start: 0.9271 (tp) cc_final: 0.9010 (tm) REVERT: D 174 TYR cc_start: 0.6617 (t80) cc_final: 0.5972 (t80) REVERT: D 388 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7742 (mp0) REVERT: E 120 GLU cc_start: 0.7473 (pp20) cc_final: 0.7225 (pp20) REVERT: E 164 TYR cc_start: 0.7522 (t80) cc_final: 0.7306 (t80) REVERT: E 174 TYR cc_start: 0.6527 (t80) cc_final: 0.5924 (t80) REVERT: E 220 TYR cc_start: 0.8114 (m-80) cc_final: 0.7884 (m-80) REVERT: F 212 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.7715 (mmt180) REVERT: F 320 ARG cc_start: 0.7335 (ttp80) cc_final: 0.6557 (ttm110) REVERT: F 388 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7581 (mp0) REVERT: F 476 GLU cc_start: 0.6942 (mm-30) cc_final: 0.6065 (tt0) outliers start: 49 outliers final: 46 residues processed: 210 average time/residue: 0.6473 time to fit residues: 152.1836 Evaluate side-chains 215 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 165 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain B residue 340 ARG Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 455 ILE Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 340 ARG Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 492 LYS Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 340 ARG Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 388 GLU Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 489 MET Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 217 ARG Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 335 MET Chi-restraints excluded: chain E residue 340 ARG Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 455 ILE Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 176 ILE Chi-restraints excluded: chain F residue 212 ARG Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 340 ARG Chi-restraints excluded: chain F residue 388 GLU Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 491 LEU Chi-restraints excluded: chain F residue 492 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 23 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 235 optimal weight: 0.8980 chunk 200 optimal weight: 0.7980 chunk 131 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 82 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 239 optimal weight: 0.7980 chunk 176 optimal weight: 0.9980 chunk 91 optimal weight: 6.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.149172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.111974 restraints weight = 21920.542| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.26 r_work: 0.3169 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 19650 Z= 0.114 Angle : 0.530 8.581 26640 Z= 0.270 Chirality : 0.042 0.143 3066 Planarity : 0.003 0.041 3402 Dihedral : 8.358 148.191 2714 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 2.53 % Allowed : 16.07 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.90 (0.17), residues: 2430 helix: 2.31 (0.16), residues: 1092 sheet: 1.36 (0.23), residues: 426 loop : -2.10 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 234 TYR 0.010 0.001 TYR A 138 PHE 0.008 0.001 PHE B 382 TRP 0.006 0.001 TRP D 359 HIS 0.003 0.001 HIS C 239 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 (19626) covalent geometry : angle 0.52181 / 0.27 (26604) hydrogen bonds : bond 0.02935 / 1.97 ( 913) hydrogen bonds : angle 3.65649 / 2.56 ( 2919) metal coordination : bond 0.00377 / 0.20 ( 24) metal coordination : angle 2.62453 / 1.74 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5575.63 seconds wall clock time: 95 minutes 55.79 seconds (5755.79 seconds total)