Starting phenix.real_space_refine on Tue Jun 17 02:14:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dze_27795/06_2025/8dze_27795.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dze_27795/06_2025/8dze_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8dze_27795/06_2025/8dze_27795.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dze_27795/06_2025/8dze_27795.map" model { file = "/net/cci-nas-00/data/ceres_data/8dze_27795/06_2025/8dze_27795.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dze_27795/06_2025/8dze_27795.cif" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.061 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 4, 'GLU:plan': 3, 'ASP:plan': 2} 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: C, B, E, D, F Time building chain proxies: 7.40, per 1000 atoms: 0.38 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: 4.31 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 2.44 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: 6.84 Time building geometry restraints manager: 5.17 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: 11379 30.12 - 60.24: 645 60.24 - 90.36: 18 90.36 - 120.48: 0 120.48 - 150.60: 6 Dihedral angle restraints: 12048 sinusoidal: 4848 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 12045 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: 0.15 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' 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: 1.440 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: 0.710 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 42.880 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:15.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 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 : 16.651 150.605 7380 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (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 TRP 0.006 0.001 TRP D 359 HIS 0.001 0.000 HIS E 238 PHE 0.011 0.001 PHE C 382 TYR 0.008 0.001 TYR F 278 ARG 0.015 0.001 ARG E 110 Details of bonding type rmsd hydrogen bonds : bond 0.15067 ( 913) hydrogen bonds : angle 4.85350 ( 2919) metal coordination : bond 0.00573 ( 24) metal coordination : angle 3.39211 ( 36) covalent geometry : bond 0.00762 (19626) covalent geometry : angle 0.82545 (26604) *********************** 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 : 2.071 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: 1.2473 time to fit residues: 285.1902 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 : 1.974 ------------------------------------------------------------------------------- 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 207 optimal weight: 7.9990 chunk 186 optimal weight: 0.9990 chunk 103 optimal weight: 0.0060 chunk 63 optimal weight: 0.8980 chunk 125 optimal weight: 7.9990 chunk 99 optimal weight: 7.9990 chunk 192 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 117 optimal weight: 0.7980 chunk 143 optimal weight: 3.9990 chunk 223 optimal weight: 7.9990 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN A 356 HIS A 439 ASN B 256 ASN B 439 ASN C 256 ASN C 356 HIS 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 = 0.3835 r_free = 0.3835 target = 0.157460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.120407 restraints weight = 21955.559| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.37 r_work: 0.3289 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.0908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 19650 Z= 0.111 Angle : 0.510 5.478 26640 Z= 0.263 Chirality : 0.043 0.160 3066 Planarity : 0.004 0.036 3402 Dihedral : 10.614 160.541 2901 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.04 % Favored : 92.72 % Rotamer: Outliers : 2.23 % Allowed : 14.53 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.17), residues: 2430 helix: 1.78 (0.16), residues: 1044 sheet: 1.68 (0.24), residues: 432 loop : -2.11 (0.18), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 359 HIS 0.004 0.001 HIS D 238 PHE 0.006 0.001 PHE C 382 TYR 0.009 0.001 TYR E 138 ARG 0.006 0.000 ARG B 110 Details of bonding type rmsd hydrogen bonds : bond 0.03647 ( 913) hydrogen bonds : angle 3.76664 ( 2919) metal coordination : bond 0.00450 ( 24) metal coordination : angle 2.89355 ( 36) covalent geometry : bond 0.00241 (19626) covalent geometry : angle 0.49879 (26604) *********************** 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 253 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 208 time to evaluate : 2.183 Fit side-chains REVERT: A 158 SER cc_start: 0.8873 (m) cc_final: 0.8647 (t) REVERT: B 120 GLU cc_start: 0.7154 (pp20) cc_final: 0.6911 (pp20) REVERT: B 164 TYR cc_start: 0.7278 (t80) cc_final: 0.7027 (t80) REVERT: B 220 TYR cc_start: 0.8170 (m-80) cc_final: 0.7910 (m-80) REVERT: B 525 LYS cc_start: 0.8194 (ttmm) cc_final: 0.7967 (ttmm) REVERT: C 164 TYR cc_start: 0.7365 (t80) cc_final: 0.7141 (t80) REVERT: C 320 ARG cc_start: 0.7107 (ttp80) cc_final: 0.6385 (ttm110) REVERT: D 158 SER cc_start: 0.8867 (m) cc_final: 0.8643 (t) REVERT: E 120 GLU cc_start: 0.7177 (pp20) cc_final: 0.6936 (pp20) REVERT: E 164 TYR cc_start: 0.7215 (t80) cc_final: 0.6969 (t80) REVERT: E 220 TYR cc_start: 0.8154 (m-80) cc_final: 0.7850 (m-80) REVERT: E 525 LYS cc_start: 0.8191 (ttmm) cc_final: 0.7966 (ttmm) REVERT: F 164 TYR cc_start: 0.7440 (t80) cc_final: 0.7234 (t80) REVERT: F 320 ARG cc_start: 0.7122 (ttp80) cc_final: 0.6370 (ttm110) outliers start: 45 outliers final: 32 residues processed: 244 average time/residue: 1.4849 time to fit residues: 404.6034 Evaluate side-chains 220 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 188 time to evaluate : 2.213 ------------------------------------------------------------------------------- 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 177 ASN 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 491 LEU Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 428 ILE 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 177 ASN Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 448 ASP 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 491 LEU Chi-restraints excluded: chain F residue 176 ILE 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 170 optimal weight: 10.0000 chunk 63 optimal weight: 0.6980 chunk 208 optimal weight: 7.9990 chunk 98 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 225 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 218 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 HIS B 127 HIS B 356 HIS C 127 HIS C 166 ASN D 127 HIS D 166 ASN E 356 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 = 0.3755 r_free = 0.3755 target = 0.150746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.113424 restraints weight = 21896.284| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.29 r_work: 0.3199 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 19650 Z= 0.161 Angle : 0.546 5.714 26640 Z= 0.282 Chirality : 0.044 0.180 3066 Planarity : 0.004 0.041 3402 Dihedral : 10.124 152.998 2897 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.41 % Favored : 92.35 % Rotamer: Outliers : 2.43 % Allowed : 14.73 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.17), residues: 2430 helix: 1.78 (0.16), residues: 1080 sheet: 1.58 (0.24), residues: 426 loop : -2.14 (0.18), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 359 HIS 0.005 0.001 HIS C 239 PHE 0.008 0.001 PHE E 204 TYR 0.011 0.001 TYR A 138 ARG 0.007 0.000 ARG B 234 Details of bonding type rmsd hydrogen bonds : bond 0.03763 ( 913) hydrogen bonds : angle 3.71938 ( 2919) metal coordination : bond 0.00618 ( 24) metal coordination : angle 2.95857 ( 36) covalent geometry : bond 0.00388 (19626) covalent geometry : angle 0.53546 (26604) *********************** 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 259 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 210 time to evaluate : 4.277 Fit side-chains REVERT: A 174 TYR cc_start: 0.6496 (t80) cc_final: 0.6097 (t80) REVERT: A 353 MET cc_start: 0.8838 (mtm) cc_final: 0.8552 (mtp) REVERT: B 120 GLU cc_start: 0.7347 (pp20) cc_final: 0.7122 (pp20) REVERT: B 164 TYR cc_start: 0.7417 (t80) cc_final: 0.7181 (t80) REVERT: B 220 TYR cc_start: 0.8216 (m-80) cc_final: 0.7947 (m-80) REVERT: C 164 TYR cc_start: 0.7449 (t80) cc_final: 0.7180 (t80) REVERT: C 320 ARG cc_start: 0.7253 (ttp80) cc_final: 0.6492 (ttm110) REVERT: C 388 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7289 (mp0) REVERT: D 174 TYR cc_start: 0.6612 (t80) cc_final: 0.6302 (t80) REVERT: D 353 MET cc_start: 0.8859 (mtm) cc_final: 0.8639 (mtp) REVERT: E 120 GLU cc_start: 0.7361 (pp20) cc_final: 0.7143 (pp20) REVERT: E 164 TYR cc_start: 0.7395 (t80) cc_final: 0.7149 (t80) REVERT: E 220 TYR cc_start: 0.8200 (m-80) cc_final: 0.7929 (m-80) REVERT: F 164 TYR cc_start: 0.7456 (t80) cc_final: 0.7180 (t80) REVERT: F 174 TYR cc_start: 0.6366 (t80) cc_final: 0.5963 (t80) REVERT: F 320 ARG cc_start: 0.7283 (ttp80) cc_final: 0.6459 (ttm110) REVERT: F 388 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7419 (mp0) outliers start: 49 outliers final: 35 residues processed: 236 average time/residue: 1.8614 time to fit residues: 497.5533 Evaluate side-chains 216 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 179 time to evaluate : 2.370 ------------------------------------------------------------------------------- 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 409 THR Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 350 THR 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 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 123 VAL Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 350 THR 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 145 MET Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 388 GLU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 170 optimal weight: 9.9990 chunk 203 optimal weight: 0.0870 chunk 231 optimal weight: 0.9990 chunk 185 optimal weight: 5.9990 chunk 198 optimal weight: 2.9990 chunk 228 optimal weight: 4.9990 chunk 95 optimal weight: 0.9980 chunk 151 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 89 optimal weight: 0.7980 chunk 201 optimal weight: 0.9980 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3763 r_free = 0.3763 target = 0.151418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.114270 restraints weight = 22007.934| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.29 r_work: 0.3217 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.1617 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= 0.106 Angle : 0.504 6.361 26640 Z= 0.260 Chirality : 0.042 0.153 3066 Planarity : 0.003 0.033 3402 Dihedral : 9.885 155.086 2892 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.95 % Favored : 92.80 % Rotamer: Outliers : 2.18 % Allowed : 15.23 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.17), residues: 2430 helix: 2.01 (0.16), residues: 1092 sheet: 1.50 (0.24), residues: 426 loop : -2.09 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 359 HIS 0.003 0.000 HIS F 239 PHE 0.008 0.001 PHE D 382 TYR 0.010 0.001 TYR A 138 ARG 0.005 0.000 ARG B 234 Details of bonding type rmsd hydrogen bonds : bond 0.03016 ( 913) hydrogen bonds : angle 3.59068 ( 2919) metal coordination : bond 0.00406 ( 24) metal coordination : angle 3.09197 ( 36) covalent geometry : bond 0.00238 (19626) covalent geometry : angle 0.49123 (26604) *********************** 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 233 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 189 time to evaluate : 2.672 Fit side-chains REVERT: A 174 TYR cc_start: 0.6526 (t80) cc_final: 0.5922 (t80) REVERT: A 388 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7563 (mp0) REVERT: B 120 GLU cc_start: 0.7349 (pp20) cc_final: 0.7115 (pp20) REVERT: B 164 TYR cc_start: 0.7414 (t80) cc_final: 0.7135 (t80) REVERT: B 220 TYR cc_start: 0.8155 (m-80) cc_final: 0.7883 (m-80) REVERT: C 164 TYR cc_start: 0.7469 (t80) cc_final: 0.7218 (t80) REVERT: C 212 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.7672 (mmm160) REVERT: C 320 ARG cc_start: 0.7257 (ttp80) cc_final: 0.6493 (ttm110) REVERT: C 388 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7393 (mp0) REVERT: D 388 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7529 (mp0) REVERT: E 120 GLU cc_start: 0.7361 (pp20) cc_final: 0.7125 (pp20) REVERT: E 164 TYR cc_start: 0.7419 (t80) cc_final: 0.7142 (t80) REVERT: E 220 TYR cc_start: 0.8132 (m-80) cc_final: 0.7863 (m-80) REVERT: F 164 TYR cc_start: 0.7454 (t80) cc_final: 0.7116 (t80) REVERT: F 174 TYR cc_start: 0.6403 (t80) cc_final: 0.6024 (t80) REVERT: F 212 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.7698 (mmm160) REVERT: F 320 ARG cc_start: 0.7266 (ttp80) cc_final: 0.6480 (ttm110) REVERT: F 388 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7433 (mp0) outliers start: 44 outliers final: 31 residues processed: 221 average time/residue: 1.7923 time to fit residues: 448.6793 Evaluate side-chains 211 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 174 time to evaluate : 2.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 LEU 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 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 145 MET Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 212 ARG 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 388 GLU Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain E residue 219 LEU 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 145 MET 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 388 GLU Chi-restraints excluded: chain F residue 409 THR 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 11 optimal weight: 0.2980 chunk 129 optimal weight: 8.9990 chunk 22 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 chunk 50 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 169 optimal weight: 0.8980 chunk 123 optimal weight: 10.0000 chunk 80 optimal weight: 0.6980 chunk 192 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3765 r_free = 0.3765 target = 0.151600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.114398 restraints weight = 22002.341| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.30 r_work: 0.3215 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1719 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= 0.102 Angle : 0.491 5.986 26640 Z= 0.253 Chirality : 0.042 0.152 3066 Planarity : 0.003 0.043 3402 Dihedral : 9.692 155.630 2890 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.49 % Favored : 92.26 % Rotamer: Outliers : 2.63 % Allowed : 15.08 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.17), residues: 2430 helix: 2.17 (0.16), residues: 1092 sheet: 1.47 (0.24), residues: 426 loop : -2.07 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 359 HIS 0.003 0.000 HIS A 239 PHE 0.008 0.001 PHE B 382 TYR 0.011 0.001 TYR A 278 ARG 0.005 0.000 ARG F 397 Details of bonding type rmsd hydrogen bonds : bond 0.02847 ( 913) hydrogen bonds : angle 3.50387 ( 2919) metal coordination : bond 0.00412 ( 24) metal coordination : angle 2.96278 ( 36) covalent geometry : bond 0.00231 (19626) covalent geometry : angle 0.47954 (26604) *********************** 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 244 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 191 time to evaluate : 2.208 Fit side-chains REVERT: A 174 TYR cc_start: 0.6555 (t80) cc_final: 0.5954 (t80) REVERT: B 120 GLU cc_start: 0.7397 (pp20) cc_final: 0.7131 (pp20) REVERT: B 164 TYR cc_start: 0.7481 (t80) cc_final: 0.7249 (t80) REVERT: B 220 TYR cc_start: 0.8156 (m-80) cc_final: 0.7872 (m-80) REVERT: C 164 TYR cc_start: 0.7531 (t80) cc_final: 0.7243 (t80) REVERT: C 212 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.7566 (mmm160) REVERT: C 320 ARG cc_start: 0.7290 (ttp80) cc_final: 0.6548 (ttm110) REVERT: C 388 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7423 (mp0) REVERT: D 174 TYR cc_start: 0.6698 (t80) cc_final: 0.6017 (t80) REVERT: D 388 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7580 (mp0) REVERT: E 120 GLU cc_start: 0.7405 (pp20) cc_final: 0.7183 (pp20) REVERT: E 164 TYR cc_start: 0.7474 (t80) cc_final: 0.7240 (t80) REVERT: E 220 TYR cc_start: 0.8128 (m-80) cc_final: 0.7857 (m-80) REVERT: F 164 TYR cc_start: 0.7534 (t80) cc_final: 0.7232 (t80) REVERT: F 174 TYR cc_start: 0.6432 (t80) cc_final: 0.6069 (t80) REVERT: F 212 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.7709 (mmm160) REVERT: F 320 ARG cc_start: 0.7326 (ttp80) cc_final: 0.6554 (ttm110) REVERT: F 388 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7514 (mp0) outliers start: 53 outliers final: 38 residues processed: 226 average time/residue: 1.5032 time to fit residues: 385.4384 Evaluate side-chains 215 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 172 time to evaluate : 1.978 ------------------------------------------------------------------------------- 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 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 155 THR 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 212 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 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 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 123 VAL Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 155 THR 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 145 MET 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 148 optimal weight: 0.0980 chunk 132 optimal weight: 7.9990 chunk 158 optimal weight: 5.9990 chunk 198 optimal weight: 0.9990 chunk 113 optimal weight: 4.9990 chunk 151 optimal weight: 2.9990 chunk 129 optimal weight: 10.0000 chunk 195 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 187 optimal weight: 3.9990 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN C 166 ASN D 166 ASN E 127 HIS F 166 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.144884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.107280 restraints weight = 22185.882| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.27 r_work: 0.3108 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 19650 Z= 0.222 Angle : 0.606 6.955 26640 Z= 0.307 Chirality : 0.046 0.200 3066 Planarity : 0.004 0.050 3402 Dihedral : 9.908 148.849 2886 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.82 % Favored : 91.93 % Rotamer: Outliers : 3.62 % Allowed : 14.53 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.17), residues: 2430 helix: 1.89 (0.16), residues: 1092 sheet: 0.55 (0.23), residues: 504 loop : -2.10 (0.19), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 482 HIS 0.006 0.001 HIS C 239 PHE 0.012 0.002 PHE B 204 TYR 0.013 0.001 TYR E 138 ARG 0.010 0.001 ARG F 234 Details of bonding type rmsd hydrogen bonds : bond 0.04085 ( 913) hydrogen bonds : angle 3.77601 ( 2919) metal coordination : bond 0.00616 ( 24) metal coordination : angle 3.97837 ( 36) covalent geometry : bond 0.00555 (19626) covalent geometry : angle 0.58833 (26604) *********************** 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: 73 poor density : 173 time to evaluate : 2.507 Fit side-chains REVERT: A 174 TYR cc_start: 0.6602 (t80) cc_final: 0.6066 (t80) REVERT: A 318 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.7060 (tp30) REVERT: A 388 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7836 (mp0) REVERT: B 120 GLU cc_start: 0.7563 (pp20) cc_final: 0.7330 (pp20) REVERT: B 164 TYR cc_start: 0.7656 (t80) cc_final: 0.7416 (t80) REVERT: B 174 TYR cc_start: 0.6689 (t80) cc_final: 0.6234 (t80) REVERT: B 220 TYR cc_start: 0.8292 (m-80) cc_final: 0.8051 (m-80) REVERT: B 405 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.8189 (mm-40) REVERT: C 212 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.7768 (mmt180) REVERT: C 320 ARG cc_start: 0.7337 (ttp80) cc_final: 0.6567 (ttm110) REVERT: C 388 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7638 (mp0) REVERT: D 174 TYR cc_start: 0.6659 (t80) cc_final: 0.6049 (t80) REVERT: D 388 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7885 (mp0) REVERT: E 120 GLU cc_start: 0.7589 (pp20) cc_final: 0.7365 (pp20) REVERT: E 164 TYR cc_start: 0.7670 (t80) cc_final: 0.7427 (t80) REVERT: E 174 TYR cc_start: 0.6604 (t80) cc_final: 0.6123 (t80) REVERT: E 220 TYR cc_start: 0.8290 (m-80) cc_final: 0.8050 (m-80) REVERT: E 405 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.8178 (mm-40) REVERT: F 164 TYR cc_start: 0.7683 (t80) cc_final: 0.7414 (t80) REVERT: F 212 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.7888 (mmt180) REVERT: F 320 ARG cc_start: 0.7431 (ttp80) cc_final: 0.6630 (ttm110) REVERT: F 388 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7716 (mp0) outliers start: 73 outliers final: 42 residues processed: 228 average time/residue: 1.5203 time to fit residues: 385.2282 Evaluate side-chains 217 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 166 time to evaluate : 1.961 ------------------------------------------------------------------------------- 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 345 ILE 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 155 THR Chi-restraints excluded: chain B residue 217 ARG Chi-restraints excluded: chain B residue 350 THR 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 212 ARG 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 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 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 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 155 THR Chi-restraints excluded: chain E residue 217 ARG Chi-restraints excluded: chain E residue 350 THR Chi-restraints excluded: chain E residue 405 GLN 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 145 MET 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 455 ILE 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 108 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 226 optimal weight: 0.1980 chunk 91 optimal weight: 6.9990 chunk 72 optimal weight: 0.0070 chunk 213 optimal weight: 8.9990 chunk 159 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 242 optimal weight: 0.8980 chunk 195 optimal weight: 0.3980 chunk 81 optimal weight: 0.9990 overall best weight: 0.5000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN B 166 ASN C 166 ASN E 166 ASN F 166 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.149532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.112269 restraints weight = 21826.819| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.27 r_work: 0.3173 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2203 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= 0.100 Angle : 0.511 6.743 26640 Z= 0.261 Chirality : 0.042 0.141 3066 Planarity : 0.003 0.044 3402 Dihedral : 9.723 153.353 2882 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.94 % Favored : 91.81 % Rotamer: Outliers : 2.98 % Allowed : 15.72 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.18), residues: 2430 helix: 2.17 (0.16), residues: 1092 sheet: 1.33 (0.23), residues: 426 loop : -2.13 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 359 HIS 0.002 0.000 HIS B 238 PHE 0.008 0.001 PHE B 382 TYR 0.010 0.001 TYR D 138 ARG 0.006 0.000 ARG F 397 Details of bonding type rmsd hydrogen bonds : bond 0.02792 ( 913) hydrogen bonds : angle 3.57057 ( 2919) metal coordination : bond 0.00375 ( 24) metal coordination : angle 3.19181 ( 36) covalent geometry : bond 0.00220 (19626) covalent geometry : angle 0.49730 (26604) *********************** 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 234 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 174 time to evaluate : 1.972 Fit side-chains REVERT: A 174 TYR cc_start: 0.6617 (t80) cc_final: 0.6099 (t80) REVERT: B 120 GLU cc_start: 0.7450 (pp20) cc_final: 0.7215 (pp20) REVERT: B 164 TYR cc_start: 0.7599 (t80) cc_final: 0.7357 (t80) REVERT: B 174 TYR cc_start: 0.6595 (t80) cc_final: 0.6095 (t80) REVERT: B 220 TYR cc_start: 0.8213 (m-80) cc_final: 0.7940 (m-80) REVERT: B 332 ASP cc_start: 0.7567 (OUTLIER) cc_final: 0.7337 (m-30) REVERT: C 320 ARG cc_start: 0.7285 (ttp80) cc_final: 0.6603 (ttm110) REVERT: C 328 ARG cc_start: 0.7201 (OUTLIER) cc_final: 0.6683 (ttp-170) REVERT: C 388 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7552 (mp0) REVERT: C 476 GLU cc_start: 0.6829 (mm-30) cc_final: 0.5949 (mt-10) REVERT: D 174 TYR cc_start: 0.6584 (t80) cc_final: 0.6031 (t80) REVERT: E 120 GLU cc_start: 0.7483 (pp20) cc_final: 0.7251 (pp20) REVERT: E 164 TYR cc_start: 0.7608 (t80) cc_final: 0.7356 (t80) REVERT: E 174 TYR cc_start: 0.6544 (t80) cc_final: 0.5968 (t80) REVERT: E 220 TYR cc_start: 0.8203 (m-80) cc_final: 0.7932 (m-80) REVERT: E 332 ASP cc_start: 0.7571 (OUTLIER) cc_final: 0.7340 (m-30) REVERT: F 320 ARG cc_start: 0.7359 (ttp80) cc_final: 0.6587 (ttm110) REVERT: F 328 ARG cc_start: 0.7170 (OUTLIER) cc_final: 0.6367 (mtp180) REVERT: F 388 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7633 (mp0) REVERT: F 476 GLU cc_start: 0.6835 (mm-30) cc_final: 0.5945 (mt-10) outliers start: 60 outliers final: 33 residues processed: 208 average time/residue: 1.4745 time to fit residues: 340.8611 Evaluate side-chains 200 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 161 time to evaluate : 1.986 ------------------------------------------------------------------------------- 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 409 THR 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 332 ASP 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 491 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain C residue 328 ARG 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 123 VAL Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 328 ARG Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 217 ARG Chi-restraints excluded: chain E residue 332 ASP 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 328 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 35 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 187 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 195 optimal weight: 0.9990 chunk 199 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 21 optimal weight: 0.1980 chunk 170 optimal weight: 1.9990 chunk 141 optimal weight: 0.5980 chunk 236 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 166 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.148945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.111580 restraints weight = 21799.801| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.27 r_work: 0.3168 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 19650 Z= 0.108 Angle : 0.513 7.119 26640 Z= 0.262 Chirality : 0.042 0.142 3066 Planarity : 0.003 0.042 3402 Dihedral : 9.596 153.663 2882 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.90 % Favored : 92.06 % Rotamer: Outliers : 2.43 % Allowed : 16.02 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.17), residues: 2430 helix: 2.24 (0.16), residues: 1092 sheet: 1.35 (0.23), residues: 426 loop : -2.13 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 359 HIS 0.003 0.001 HIS C 239 PHE 0.008 0.001 PHE D 382 TYR 0.009 0.001 TYR D 138 ARG 0.007 0.000 ARG F 234 Details of bonding type rmsd hydrogen bonds : bond 0.02875 ( 913) hydrogen bonds : angle 3.51980 ( 2919) metal coordination : bond 0.00394 ( 24) metal coordination : angle 2.83107 ( 36) covalent geometry : bond 0.00246 (19626) covalent geometry : angle 0.50231 (26604) *********************** 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 223 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 174 time to evaluate : 2.017 Fit side-chains REVERT: A 147 LEU cc_start: 0.9277 (tp) cc_final: 0.8972 (tm) REVERT: A 174 TYR cc_start: 0.6559 (t80) cc_final: 0.6066 (t80) REVERT: B 120 GLU cc_start: 0.7483 (pp20) cc_final: 0.7248 (pp20) REVERT: B 174 TYR cc_start: 0.6617 (t80) cc_final: 0.6109 (t80) REVERT: B 220 TYR cc_start: 0.8210 (m-80) cc_final: 0.7928 (m-80) REVERT: B 332 ASP cc_start: 0.7551 (OUTLIER) cc_final: 0.7337 (m-30) REVERT: C 212 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.7681 (mmm160) REVERT: C 320 ARG cc_start: 0.7290 (ttp80) cc_final: 0.6603 (ttm110) REVERT: C 388 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7606 (mp0) REVERT: C 476 GLU cc_start: 0.6847 (mm-30) cc_final: 0.6045 (mt-10) REVERT: D 147 LEU cc_start: 0.9280 (tp) cc_final: 0.9008 (tm) REVERT: D 174 TYR cc_start: 0.6613 (t80) cc_final: 0.6006 (t80) REVERT: E 120 GLU cc_start: 0.7537 (pp20) cc_final: 0.7297 (pp20) REVERT: E 164 TYR cc_start: 0.7633 (t80) cc_final: 0.7375 (t80) REVERT: E 174 TYR cc_start: 0.6556 (t80) cc_final: 0.5987 (t80) REVERT: E 220 TYR cc_start: 0.8193 (m-80) cc_final: 0.7911 (m-80) REVERT: E 530 ARG cc_start: 0.7414 (OUTLIER) cc_final: 0.7181 (ptt180) REVERT: F 212 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.7784 (mmm160) REVERT: F 320 ARG cc_start: 0.7358 (ttp80) cc_final: 0.6585 (ttm110) REVERT: F 388 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7634 (mp0) REVERT: F 476 GLU cc_start: 0.6850 (mm-30) cc_final: 0.6040 (mt-10) outliers start: 49 outliers final: 39 residues processed: 204 average time/residue: 1.4938 time to fit residues: 339.3205 Evaluate side-chains 216 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 171 time to evaluate : 1.997 ------------------------------------------------------------------------------- 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 155 THR Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 332 ASP 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 491 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain C residue 212 ARG 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 347 LEU 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 155 THR 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 E residue 530 ARG Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 155 THR 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 242 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 211 optimal weight: 7.9990 chunk 43 optimal weight: 4.9990 chunk 84 optimal weight: 0.9980 chunk 241 optimal weight: 1.9990 chunk 169 optimal weight: 0.5980 chunk 201 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 231 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.149558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.112294 restraints weight = 21831.355| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.27 r_work: 0.3176 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2267 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= 0.104 Angle : 0.508 8.167 26640 Z= 0.259 Chirality : 0.042 0.142 3066 Planarity : 0.003 0.050 3402 Dihedral : 9.546 154.442 2882 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % Rotamer: Outliers : 2.18 % Allowed : 16.27 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.17), residues: 2430 helix: 2.32 (0.16), residues: 1092 sheet: 1.33 (0.23), residues: 426 loop : -2.10 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 359 HIS 0.003 0.001 HIS F 239 PHE 0.008 0.001 PHE E 382 TYR 0.009 0.001 TYR D 138 ARG 0.006 0.000 ARG F 234 Details of bonding type rmsd hydrogen bonds : bond 0.02782 ( 913) hydrogen bonds : angle 3.48575 ( 2919) metal coordination : bond 0.00374 ( 24) metal coordination : angle 2.73143 ( 36) covalent geometry : bond 0.00238 (19626) covalent geometry : angle 0.49831 (26604) *********************** 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 221 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 177 time to evaluate : 1.999 Fit side-chains REVERT: A 147 LEU cc_start: 0.9271 (tp) cc_final: 0.8978 (tm) REVERT: A 174 TYR cc_start: 0.6563 (t80) cc_final: 0.6114 (t80) REVERT: B 120 GLU cc_start: 0.7497 (pp20) cc_final: 0.7261 (pp20) REVERT: B 174 TYR cc_start: 0.6668 (t80) cc_final: 0.6169 (t80) REVERT: B 220 TYR cc_start: 0.8175 (m-80) cc_final: 0.7960 (m-80) REVERT: C 212 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.7662 (mmm160) REVERT: C 320 ARG cc_start: 0.7286 (ttp80) cc_final: 0.6597 (ttm110) REVERT: C 388 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7667 (mp0) REVERT: C 476 GLU cc_start: 0.6848 (mm-30) cc_final: 0.6040 (mt-10) REVERT: D 147 LEU cc_start: 0.9293 (tp) cc_final: 0.9040 (tm) REVERT: D 174 TYR cc_start: 0.6637 (t80) cc_final: 0.6019 (t80) REVERT: E 120 GLU cc_start: 0.7581 (pp20) cc_final: 0.7337 (pp20) REVERT: E 174 TYR cc_start: 0.6555 (t80) cc_final: 0.5969 (t80) REVERT: E 220 TYR cc_start: 0.8167 (m-80) cc_final: 0.7907 (m-80) REVERT: F 212 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.7756 (mmm160) REVERT: F 320 ARG cc_start: 0.7356 (ttp80) cc_final: 0.6583 (ttm110) REVERT: F 388 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7678 (mp0) outliers start: 44 outliers final: 43 residues processed: 207 average time/residue: 1.4991 time to fit residues: 345.1642 Evaluate side-chains 211 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 164 time to evaluate : 1.983 ------------------------------------------------------------------------------- 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 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 155 THR 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 130 VAL Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain C residue 212 ARG 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 347 LEU 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 155 THR 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 130 VAL Chi-restraints excluded: chain F residue 155 THR 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 160 optimal weight: 0.6980 chunk 213 optimal weight: 0.2980 chunk 42 optimal weight: 0.7980 chunk 114 optimal weight: 7.9990 chunk 186 optimal weight: 0.9980 chunk 153 optimal weight: 0.8980 chunk 127 optimal weight: 8.9990 chunk 139 optimal weight: 0.6980 chunk 154 optimal weight: 1.9990 chunk 207 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.149753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.112597 restraints weight = 21778.944| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.26 r_work: 0.3184 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 19650 Z= 0.104 Angle : 0.517 8.572 26640 Z= 0.265 Chirality : 0.042 0.141 3066 Planarity : 0.003 0.047 3402 Dihedral : 9.474 154.920 2882 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 2.38 % Allowed : 15.77 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.17), residues: 2430 helix: 2.33 (0.16), residues: 1092 sheet: 1.36 (0.23), residues: 426 loop : -2.08 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 359 HIS 0.003 0.000 HIS C 238 PHE 0.008 0.001 PHE B 382 TYR 0.009 0.001 TYR D 138 ARG 0.006 0.000 ARG F 234 Details of bonding type rmsd hydrogen bonds : bond 0.02750 ( 913) hydrogen bonds : angle 3.63026 ( 2919) metal coordination : bond 0.00345 ( 24) metal coordination : angle 2.52419 ( 36) covalent geometry : bond 0.00233 (19626) covalent geometry : angle 0.50929 (26604) ********************** 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 223 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 175 time to evaluate : 2.268 Fit side-chains REVERT: A 147 LEU cc_start: 0.9293 (tp) cc_final: 0.9016 (tm) REVERT: A 174 TYR cc_start: 0.6588 (t80) cc_final: 0.6088 (t80) REVERT: B 120 GLU cc_start: 0.7555 (pp20) cc_final: 0.7312 (pp20) REVERT: B 174 TYR cc_start: 0.6692 (t80) cc_final: 0.6113 (t80) REVERT: B 220 TYR cc_start: 0.8164 (m-80) cc_final: 0.7900 (m-80) REVERT: C 212 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.7660 (mmm160) REVERT: C 320 ARG cc_start: 0.7289 (ttp80) cc_final: 0.6606 (ttm110) REVERT: C 388 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7665 (mp0) REVERT: D 147 LEU cc_start: 0.9294 (tp) cc_final: 0.9049 (tm) REVERT: D 174 TYR cc_start: 0.6639 (t80) cc_final: 0.6073 (t80) REVERT: E 120 GLU cc_start: 0.7573 (pp20) cc_final: 0.7331 (pp20) REVERT: E 174 TYR cc_start: 0.6612 (t80) cc_final: 0.6045 (t80) REVERT: E 220 TYR cc_start: 0.8142 (m-80) cc_final: 0.7878 (m-80) REVERT: F 212 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.7759 (mmm160) REVERT: F 320 ARG cc_start: 0.7353 (ttp80) cc_final: 0.6582 (ttm110) REVERT: F 388 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7663 (mp0) REVERT: F 476 GLU cc_start: 0.6960 (mm-30) cc_final: 0.6149 (mt-10) outliers start: 48 outliers final: 42 residues processed: 210 average time/residue: 1.5157 time to fit residues: 354.0703 Evaluate side-chains 218 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 172 time to evaluate : 1.979 ------------------------------------------------------------------------------- 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 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 155 THR Chi-restraints excluded: chain B residue 219 LEU 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 130 VAL Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain C residue 212 ARG 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 328 ARG Chi-restraints excluded: chain D residue 347 LEU 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 155 THR Chi-restraints excluded: chain E residue 217 ARG Chi-restraints excluded: chain E residue 219 LEU 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 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 64 optimal weight: 2.9990 chunk 244 optimal weight: 2.9990 chunk 210 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 13 optimal weight: 0.3980 chunk 86 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 230 optimal weight: 1.9990 chunk 205 optimal weight: 0.7980 chunk 208 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.146403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.108752 restraints weight = 21988.550| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.28 r_work: 0.3132 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19650 Z= 0.155 Angle : 0.564 8.460 26640 Z= 0.288 Chirality : 0.044 0.156 3066 Planarity : 0.004 0.050 3402 Dihedral : 9.560 150.817 2882 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 2.08 % Allowed : 16.22 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.18), residues: 2430 helix: 2.19 (0.16), residues: 1092 sheet: 0.51 (0.23), residues: 504 loop : -1.98 (0.20), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 482 HIS 0.005 0.001 HIS F 239 PHE 0.009 0.001 PHE E 204 TYR 0.011 0.001 TYR A 138 ARG 0.006 0.000 ARG F 234 Details of bonding type rmsd hydrogen bonds : bond 0.03491 ( 913) hydrogen bonds : angle 3.75047 ( 2919) metal coordination : bond 0.00448 ( 24) metal coordination : angle 3.10326 ( 36) covalent geometry : bond 0.00375 (19626) covalent geometry : angle 0.55293 (26604) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13097.23 seconds wall clock time: 230 minutes 24.66 seconds (13824.66 seconds total)