Starting phenix.real_space_refine on Sat Sep 28 13:27:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dze_27795/09_2024/8dze_27795.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dze_27795/09_2024/8dze_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dze_27795/09_2024/8dze_27795.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dze_27795/09_2024/8dze_27795.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dze_27795/09_2024/8dze_27795.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dze_27795/09_2024/8dze_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-5461/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: 7.51, per 1000 atoms: 0.39 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: 4.81 Conformation dependent library (CDL) restraints added in 2.4 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: 2.45 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: 6.09 Time building geometry restraints manager: 5.58 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.040 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: 0.670 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 42.050 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.050 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:10.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.710 ------------------------------------------------------------------------------- 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 19626 Z= 0.480 Angle : 0.825 11.347 26604 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 *********************** 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 fitting. rotamer outliers: 13 poor density : 198 time to evaluate : 2.123 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: 1.2431 time to fit residues: 285.2286 Evaluate side-chains 188 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 171 time to evaluate : 2.292 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 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 19626 Z= 0.158 Angle : 0.499 5.478 26604 Z= 0.262 Chirality : 0.043 0.160 3066 Planarity : 0.004 0.036 3402 Dihedral : 10.615 160.543 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 *********************** 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 fitting. rotamer outliers: 45 poor density : 208 time to evaluate : 1.765 Fit side-chains REVERT: A 130 VAL cc_start: 0.8095 (t) cc_final: 0.7892 (t) REVERT: A 158 SER cc_start: 0.9049 (m) cc_final: 0.8817 (t) REVERT: B 120 GLU cc_start: 0.7202 (pp20) cc_final: 0.6925 (pp20) REVERT: B 164 TYR cc_start: 0.7486 (t80) cc_final: 0.7246 (t80) REVERT: B 220 TYR cc_start: 0.8021 (m-80) cc_final: 0.7808 (m-80) REVERT: B 405 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.8418 (mm-40) REVERT: B 525 LYS cc_start: 0.8170 (ttmm) cc_final: 0.7930 (ttmm) REVERT: C 164 TYR cc_start: 0.7629 (t80) cc_final: 0.7415 (t80) REVERT: C 320 ARG cc_start: 0.6899 (ttp80) cc_final: 0.6495 (ttm110) REVERT: D 130 VAL cc_start: 0.8107 (t) cc_final: 0.7905 (t) REVERT: D 158 SER cc_start: 0.9026 (m) cc_final: 0.8803 (t) REVERT: D 164 TYR cc_start: 0.7397 (t80) cc_final: 0.7196 (t80) REVERT: E 120 GLU cc_start: 0.7217 (pp20) cc_final: 0.6946 (pp20) REVERT: E 164 TYR cc_start: 0.7429 (t80) cc_final: 0.7194 (t80) REVERT: E 220 TYR cc_start: 0.8011 (m-80) cc_final: 0.7757 (m-80) REVERT: E 405 GLN cc_start: 0.8696 (OUTLIER) cc_final: 0.8386 (mm-40) REVERT: E 525 LYS cc_start: 0.8156 (ttmm) cc_final: 0.7924 (ttmm) REVERT: F 320 ARG cc_start: 0.6915 (ttp80) cc_final: 0.6478 (ttm110) outliers start: 45 outliers final: 32 residues processed: 244 average time/residue: 1.4082 time to fit residues: 384.3174 Evaluate side-chains 220 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 186 time to evaluate : 2.285 ------------------------------------------------------------------------------- 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 405 GLN 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 405 GLN 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 124 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 185 optimal weight: 0.0670 chunk 152 optimal weight: 6.9990 chunk 61 optimal weight: 0.0020 chunk 223 optimal weight: 10.0000 chunk 241 optimal weight: 2.9990 chunk 199 optimal weight: 3.9990 chunk 221 optimal weight: 0.6980 chunk 76 optimal weight: 5.9990 chunk 179 optimal weight: 3.9990 overall best weight: 0.9128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 356 HIS C 166 ASN D 166 ASN E 356 HIS F 166 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19626 Z= 0.172 Angle : 0.489 5.532 26604 Z= 0.258 Chirality : 0.042 0.161 3066 Planarity : 0.004 0.034 3402 Dihedral : 10.079 156.748 2897 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.53 % Favored : 92.22 % Rotamer: Outliers : 2.08 % Allowed : 14.98 % Favored : 82.94 % 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: 0.65 (0.17), residues: 2430 helix: 1.90 (0.16), residues: 1080 sheet: 1.64 (0.24), residues: 426 loop : -2.11 (0.18), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 359 HIS 0.003 0.001 HIS A 238 PHE 0.008 0.001 PHE B 382 TYR 0.010 0.001 TYR A 138 ARG 0.007 0.000 ARG B 110 *********************** 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 249 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 207 time to evaluate : 2.083 Fit side-chains REVERT: A 130 VAL cc_start: 0.8172 (t) cc_final: 0.7934 (t) REVERT: A 158 SER cc_start: 0.9073 (m) cc_final: 0.8868 (t) REVERT: B 120 GLU cc_start: 0.7291 (pp20) cc_final: 0.6974 (pp20) REVERT: B 164 TYR cc_start: 0.7548 (t80) cc_final: 0.7338 (t80) REVERT: B 220 TYR cc_start: 0.8030 (m-80) cc_final: 0.7763 (m-80) REVERT: B 525 LYS cc_start: 0.8173 (ttmm) cc_final: 0.7945 (ttmm) REVERT: C 121 MET cc_start: 0.8401 (ttp) cc_final: 0.8104 (ttp) REVERT: C 164 TYR cc_start: 0.7717 (t80) cc_final: 0.7483 (t80) REVERT: C 320 ARG cc_start: 0.7029 (ttp80) cc_final: 0.6599 (ttm110) REVERT: C 388 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.6697 (mp0) REVERT: D 130 VAL cc_start: 0.8228 (t) cc_final: 0.7996 (t) REVERT: D 164 TYR cc_start: 0.7480 (t80) cc_final: 0.7270 (t80) REVERT: E 120 GLU cc_start: 0.7326 (pp20) cc_final: 0.7066 (pp20) REVERT: E 164 TYR cc_start: 0.7552 (t80) cc_final: 0.7340 (t80) REVERT: E 220 TYR cc_start: 0.8036 (m-80) cc_final: 0.7793 (m-80) REVERT: E 525 LYS cc_start: 0.8167 (ttmm) cc_final: 0.7941 (ttmm) REVERT: F 120 GLU cc_start: 0.7534 (pp20) cc_final: 0.7330 (pp20) REVERT: F 320 ARG cc_start: 0.7040 (ttp80) cc_final: 0.6590 (ttm110) REVERT: F 388 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.6855 (mp0) outliers start: 42 outliers final: 33 residues processed: 228 average time/residue: 1.2127 time to fit residues: 313.7224 Evaluate side-chains 218 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 183 time to evaluate : 2.059 ------------------------------------------------------------------------------- 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 B residue 123 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 448 ASP Chi-restraints excluded: chain B residue 455 ILE Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 388 GLU 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 177 ASN 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 E residue 130 VAL 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 219 LEU Chi-restraints excluded: chain F residue 388 GLU Chi-restraints excluded: chain F residue 455 ILE Chi-restraints excluded: chain F residue 491 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 221 optimal weight: 0.7980 chunk 168 optimal weight: 8.9990 chunk 116 optimal weight: 1.9990 chunk 24 optimal weight: 0.3980 chunk 106 optimal weight: 4.9990 chunk 150 optimal weight: 1.9990 chunk 224 optimal weight: 6.9990 chunk 237 optimal weight: 0.9980 chunk 117 optimal weight: 4.9990 chunk 212 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 HIS A 166 ASN C 127 HIS C 166 ASN D 127 HIS D 166 ASN F 127 HIS F 166 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 19626 Z= 0.214 Angle : 0.514 5.529 26604 Z= 0.270 Chirality : 0.043 0.166 3066 Planarity : 0.004 0.035 3402 Dihedral : 9.845 154.215 2894 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.37 % Favored : 92.39 % Rotamer: Outliers : 2.98 % Allowed : 14.43 % 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: 0.69 (0.17), residues: 2430 helix: 1.96 (0.16), residues: 1092 sheet: 1.57 (0.24), residues: 426 loop : -2.12 (0.18), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 359 HIS 0.005 0.001 HIS F 239 PHE 0.007 0.001 PHE E 204 TYR 0.010 0.001 TYR A 138 ARG 0.004 0.000 ARG B 234 *********************** 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 251 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 191 time to evaluate : 2.166 Fit side-chains REVERT: A 130 VAL cc_start: 0.8308 (OUTLIER) cc_final: 0.8098 (t) REVERT: A 174 TYR cc_start: 0.6670 (t80) cc_final: 0.6352 (t80) REVERT: B 120 GLU cc_start: 0.7370 (pp20) cc_final: 0.7086 (pp20) REVERT: B 164 TYR cc_start: 0.7670 (t80) cc_final: 0.7398 (t80) REVERT: B 220 TYR cc_start: 0.8051 (m-80) cc_final: 0.7824 (m-80) REVERT: B 405 GLN cc_start: 0.8714 (OUTLIER) cc_final: 0.8387 (mm-40) REVERT: C 164 TYR cc_start: 0.7805 (t80) cc_final: 0.7564 (t80) REVERT: C 212 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.7848 (mmm160) REVERT: C 320 ARG cc_start: 0.7079 (ttp80) cc_final: 0.6625 (ttm110) REVERT: C 388 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.6909 (mp0) REVERT: D 130 VAL cc_start: 0.8266 (OUTLIER) cc_final: 0.8020 (t) REVERT: D 164 TYR cc_start: 0.7654 (t80) cc_final: 0.7442 (t80) REVERT: D 174 TYR cc_start: 0.6772 (t80) cc_final: 0.6156 (t80) REVERT: E 120 GLU cc_start: 0.7369 (pp20) cc_final: 0.7103 (pp20) REVERT: E 164 TYR cc_start: 0.7683 (t80) cc_final: 0.7408 (t80) REVERT: E 220 TYR cc_start: 0.8053 (m-80) cc_final: 0.7826 (m-80) REVERT: E 405 GLN cc_start: 0.8730 (OUTLIER) cc_final: 0.8370 (mm-40) REVERT: F 174 TYR cc_start: 0.6525 (t80) cc_final: 0.6019 (t80) REVERT: F 212 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.7711 (mmt180) REVERT: F 320 ARG cc_start: 0.7090 (ttp80) cc_final: 0.6592 (ttm110) REVERT: F 388 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.6960 (mp0) outliers start: 60 outliers final: 37 residues processed: 226 average time/residue: 1.2771 time to fit residues: 326.0153 Evaluate side-chains 220 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 175 time to evaluate : 2.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 145 MET 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 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 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 D residue 123 VAL Chi-restraints excluded: chain D residue 130 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 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 130 VAL Chi-restraints excluded: chain F residue 145 MET 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 455 ILE Chi-restraints excluded: chain F residue 491 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 198 optimal weight: 2.9990 chunk 134 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 177 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 202 optimal weight: 0.0370 chunk 164 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 121 optimal weight: 2.9990 chunk 213 optimal weight: 0.0030 chunk 60 optimal weight: 4.9990 overall best weight: 1.2074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN B 127 HIS C 166 ASN D 166 ASN E 127 HIS F 166 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 19626 Z= 0.211 Angle : 0.509 5.707 26604 Z= 0.268 Chirality : 0.043 0.169 3066 Planarity : 0.004 0.046 3402 Dihedral : 9.756 152.975 2890 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.82 % Favored : 91.93 % Rotamer: Outliers : 3.17 % Allowed : 14.53 % 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: 0.70 (0.17), residues: 2430 helix: 2.03 (0.16), residues: 1092 sheet: 1.47 (0.24), residues: 426 loop : -2.16 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 359 HIS 0.004 0.001 HIS A 239 PHE 0.008 0.001 PHE B 218 TYR 0.013 0.001 TYR A 278 ARG 0.004 0.000 ARG A 397 *********************** 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 250 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 186 time to evaluate : 2.424 Fit side-chains REVERT: A 130 VAL cc_start: 0.8371 (OUTLIER) cc_final: 0.8150 (t) REVERT: A 174 TYR cc_start: 0.6620 (t80) cc_final: 0.6046 (t80) REVERT: A 388 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.7021 (mp0) REVERT: B 120 GLU cc_start: 0.7403 (pp20) cc_final: 0.7143 (pp20) REVERT: B 164 TYR cc_start: 0.7708 (t80) cc_final: 0.7435 (t80) REVERT: B 174 TYR cc_start: 0.6459 (t80) cc_final: 0.6051 (t80) REVERT: B 405 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.8391 (mm-40) REVERT: C 164 TYR cc_start: 0.7845 (t80) cc_final: 0.7528 (t80) REVERT: C 212 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.7699 (mmm160) REVERT: C 320 ARG cc_start: 0.7088 (ttp80) cc_final: 0.6627 (ttm110) REVERT: C 388 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.6982 (mp0) REVERT: D 130 VAL cc_start: 0.8295 (OUTLIER) cc_final: 0.8053 (t) REVERT: D 145 MET cc_start: 0.8951 (OUTLIER) cc_final: 0.8635 (mmm) REVERT: D 164 TYR cc_start: 0.7821 (t80) cc_final: 0.7618 (t80) REVERT: D 174 TYR cc_start: 0.6629 (t80) cc_final: 0.6025 (t80) REVERT: D 388 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.6987 (mp0) REVERT: E 120 GLU cc_start: 0.7383 (pp20) cc_final: 0.7119 (pp20) REVERT: E 164 TYR cc_start: 0.7741 (t80) cc_final: 0.7476 (t80) REVERT: E 174 TYR cc_start: 0.6418 (t80) cc_final: 0.6012 (t80) REVERT: F 212 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.7737 (mmt180) REVERT: F 320 ARG cc_start: 0.7115 (ttp80) cc_final: 0.6613 (ttm110) REVERT: F 388 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.7005 (mp0) outliers start: 64 outliers final: 40 residues processed: 230 average time/residue: 1.4313 time to fit residues: 366.7434 Evaluate side-chains 216 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 166 time to evaluate : 2.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 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 176 ILE Chi-restraints excluded: chain B residue 217 ARG Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 405 GLN Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 455 ILE Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain C residue 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 130 VAL Chi-restraints excluded: chain D residue 145 MET 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 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 80 optimal weight: 0.7980 chunk 214 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 139 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 238 optimal weight: 0.8980 chunk 197 optimal weight: 2.9990 chunk 110 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 166 ASN F 166 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 19626 Z= 0.162 Angle : 0.492 6.024 26604 Z= 0.259 Chirality : 0.042 0.142 3066 Planarity : 0.003 0.044 3402 Dihedral : 9.664 154.291 2888 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.53 % Favored : 92.22 % Rotamer: Outliers : 3.12 % Allowed : 14.88 % Favored : 81.99 % 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 (0.17), residues: 2430 helix: 2.16 (0.16), residues: 1092 sheet: 1.39 (0.24), residues: 426 loop : -2.14 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 359 HIS 0.003 0.000 HIS D 239 PHE 0.008 0.001 PHE B 382 TYR 0.010 0.001 TYR D 138 ARG 0.009 0.000 ARG F 234 *********************** 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 236 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 173 time to evaluate : 2.159 Fit side-chains REVERT: A 130 VAL cc_start: 0.8329 (OUTLIER) cc_final: 0.8106 (t) REVERT: A 174 TYR cc_start: 0.6649 (t80) cc_final: 0.6039 (t80) REVERT: A 353 MET cc_start: 0.8855 (mtm) cc_final: 0.8596 (mtp) REVERT: A 388 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.7024 (mp0) REVERT: B 120 GLU cc_start: 0.7405 (pp20) cc_final: 0.7138 (pp20) REVERT: B 164 TYR cc_start: 0.7721 (t80) cc_final: 0.7502 (t80) REVERT: B 174 TYR cc_start: 0.6543 (t80) cc_final: 0.6122 (t80) REVERT: C 212 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.7683 (mmm160) REVERT: C 320 ARG cc_start: 0.7078 (ttp80) cc_final: 0.6633 (ttm110) REVERT: C 388 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.6967 (mp0) REVERT: D 130 VAL cc_start: 0.8269 (OUTLIER) cc_final: 0.8025 (t) REVERT: D 145 MET cc_start: 0.8931 (OUTLIER) cc_final: 0.8612 (mmm) REVERT: D 164 TYR cc_start: 0.7823 (t80) cc_final: 0.7572 (t80) REVERT: D 174 TYR cc_start: 0.6649 (t80) cc_final: 0.6036 (t80) REVERT: D 388 GLU cc_start: 0.7334 (OUTLIER) cc_final: 0.7003 (mp0) REVERT: E 120 GLU cc_start: 0.7385 (pp20) cc_final: 0.7112 (pp20) REVERT: E 164 TYR cc_start: 0.7772 (t80) cc_final: 0.7507 (t80) REVERT: E 174 TYR cc_start: 0.6443 (t80) cc_final: 0.5913 (t80) REVERT: F 212 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.7834 (mmm160) REVERT: F 320 ARG cc_start: 0.7093 (ttp80) cc_final: 0.6613 (ttm110) REVERT: F 388 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.7008 (mp0) outliers start: 63 outliers final: 42 residues processed: 216 average time/residue: 1.3836 time to fit residues: 334.6585 Evaluate side-chains 223 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 172 time to evaluate : 2.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 217 ARG Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 335 MET 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 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 491 LEU Chi-restraints excluded: chain C residue 492 LYS Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 340 ARG Chi-restraints excluded: chain D residue 345 ILE Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 388 GLU Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 455 ILE Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 217 ARG Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 335 MET Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 455 ILE Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain F residue 123 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 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 229 optimal weight: 0.4980 chunk 26 optimal weight: 0.9990 chunk 135 optimal weight: 0.7980 chunk 173 optimal weight: 6.9990 chunk 134 optimal weight: 5.9990 chunk 200 optimal weight: 0.2980 chunk 132 optimal weight: 3.9990 chunk 237 optimal weight: 0.0060 chunk 148 optimal weight: 0.6980 chunk 144 optimal weight: 0.0070 chunk 109 optimal weight: 3.9990 overall best weight: 0.3014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 166 ASN F 166 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 19626 Z= 0.121 Angle : 0.475 7.379 26604 Z= 0.248 Chirality : 0.041 0.135 3066 Planarity : 0.003 0.035 3402 Dihedral : 9.547 157.587 2886 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.28 % Favored : 92.47 % Rotamer: Outliers : 2.58 % Allowed : 15.48 % Favored : 81.94 % 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: 0.95 (0.18), residues: 2430 helix: 2.35 (0.16), residues: 1092 sheet: 1.44 (0.24), residues: 426 loop : -2.09 (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 F 238 PHE 0.008 0.001 PHE E 382 TYR 0.009 0.001 TYR D 138 ARG 0.009 0.000 ARG E 234 *********************** 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 239 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 187 time to evaluate : 2.280 Fit side-chains REVERT: A 147 LEU cc_start: 0.9366 (tp) cc_final: 0.9150 (tm) REVERT: A 174 TYR cc_start: 0.6646 (t80) cc_final: 0.6062 (t80) REVERT: A 353 MET cc_start: 0.8853 (mtm) cc_final: 0.8606 (mtp) REVERT: A 388 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.6960 (mp0) REVERT: B 120 GLU cc_start: 0.7402 (pp20) cc_final: 0.7120 (pp20) REVERT: B 164 TYR cc_start: 0.7703 (t80) cc_final: 0.7453 (t80) REVERT: B 174 TYR cc_start: 0.6509 (t80) cc_final: 0.6057 (t80) REVERT: C 164 TYR cc_start: 0.7808 (t80) cc_final: 0.7502 (t80) REVERT: C 320 ARG cc_start: 0.7056 (ttp80) cc_final: 0.6619 (ttm110) REVERT: C 388 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.6839 (mp0) REVERT: D 164 TYR cc_start: 0.7754 (t80) cc_final: 0.7552 (t80) REVERT: D 174 TYR cc_start: 0.6629 (t80) cc_final: 0.5999 (t80) REVERT: D 388 GLU cc_start: 0.7334 (OUTLIER) cc_final: 0.7039 (mp0) REVERT: E 120 GLU cc_start: 0.7377 (pp20) cc_final: 0.7092 (pp20) REVERT: E 164 TYR cc_start: 0.7720 (t80) cc_final: 0.7451 (t80) REVERT: F 320 ARG cc_start: 0.7065 (ttp80) cc_final: 0.6570 (ttm110) REVERT: F 388 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.6877 (mp0) outliers start: 52 outliers final: 34 residues processed: 223 average time/residue: 1.3273 time to fit residues: 330.3974 Evaluate side-chains 215 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 177 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain B residue 123 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 491 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 340 ARG Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 492 LYS Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 340 ARG Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 388 GLU Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain E residue 123 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 409 THR Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 176 ILE Chi-restraints excluded: chain F residue 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 146 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 141 optimal weight: 9.9990 chunk 71 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 150 optimal weight: 0.8980 chunk 161 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 186 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19626 Z= 0.181 Angle : 0.505 7.722 26604 Z= 0.262 Chirality : 0.042 0.142 3066 Planarity : 0.003 0.042 3402 Dihedral : 9.520 155.515 2886 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.61 % Favored : 92.14 % 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: 0.89 (0.17), residues: 2430 helix: 2.32 (0.16), residues: 1092 sheet: 1.38 (0.24), residues: 426 loop : -2.13 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 359 HIS 0.004 0.001 HIS A 239 PHE 0.008 0.001 PHE B 382 TYR 0.013 0.001 TYR D 138 ARG 0.010 0.000 ARG C 234 *********************** 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 234 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 185 time to evaluate : 2.137 Fit side-chains REVERT: A 147 LEU cc_start: 0.9383 (tp) cc_final: 0.9175 (tm) REVERT: A 174 TYR cc_start: 0.6685 (t80) cc_final: 0.6045 (t80) REVERT: A 388 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.7150 (mp0) REVERT: B 120 GLU cc_start: 0.7430 (pp20) cc_final: 0.7144 (pp20) REVERT: B 164 TYR cc_start: 0.7755 (t80) cc_final: 0.7521 (t80) REVERT: B 174 TYR cc_start: 0.6596 (t80) cc_final: 0.6138 (t80) REVERT: B 507 MET cc_start: 0.8114 (OUTLIER) cc_final: 0.7384 (mpt) REVERT: C 320 ARG cc_start: 0.7092 (ttp80) cc_final: 0.6642 (ttm110) REVERT: C 388 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.7006 (mp0) REVERT: C 489 MET cc_start: 0.9025 (ttp) cc_final: 0.8721 (ttp) REVERT: D 164 TYR cc_start: 0.7826 (t80) cc_final: 0.7618 (t80) REVERT: D 174 TYR cc_start: 0.6714 (t80) cc_final: 0.6080 (t80) REVERT: D 388 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.7180 (mp0) REVERT: E 120 GLU cc_start: 0.7400 (pp20) cc_final: 0.7130 (pp20) REVERT: E 164 TYR cc_start: 0.7788 (t80) cc_final: 0.7508 (t80) REVERT: E 174 TYR cc_start: 0.6490 (t80) cc_final: 0.5988 (t80) REVERT: E 507 MET cc_start: 0.8123 (OUTLIER) cc_final: 0.7380 (mpt) REVERT: F 212 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.7763 (mmt180) REVERT: F 320 ARG cc_start: 0.7101 (ttp80) cc_final: 0.6614 (ttm110) REVERT: F 388 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.7030 (mp0) outliers start: 49 outliers final: 40 residues processed: 219 average time/residue: 1.3849 time to fit residues: 336.5820 Evaluate side-chains 227 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 180 time to evaluate : 1.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain B residue 123 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 335 MET Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 340 ARG Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 492 LYS Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 340 ARG Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 388 GLU Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 489 MET Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain E residue 123 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 409 THR Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain E residue 507 MET Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 176 ILE Chi-restraints excluded: chain F residue 212 ARG Chi-restraints excluded: chain F residue 340 ARG Chi-restraints excluded: chain F residue 388 GLU Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 455 ILE 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 215 optimal weight: 1.9990 chunk 227 optimal weight: 0.8980 chunk 207 optimal weight: 0.8980 chunk 220 optimal weight: 0.9980 chunk 132 optimal weight: 6.9990 chunk 96 optimal weight: 0.5980 chunk 173 optimal weight: 6.9990 chunk 67 optimal weight: 0.9980 chunk 199 optimal weight: 0.9980 chunk 208 optimal weight: 3.9990 chunk 145 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19626 Z= 0.168 Angle : 0.504 7.982 26604 Z= 0.262 Chirality : 0.042 0.141 3066 Planarity : 0.003 0.040 3402 Dihedral : 9.510 155.384 2886 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.57 % Favored : 92.39 % Rotamer: Outliers : 2.23 % Allowed : 16.32 % Favored : 81.45 % 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: 2.34 (0.16), residues: 1092 sheet: 1.41 (0.24), 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 238 PHE 0.008 0.001 PHE B 382 TYR 0.014 0.001 TYR C 278 ARG 0.009 0.000 ARG C 234 *********************** 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 228 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 183 time to evaluate : 2.340 Fit side-chains REVERT: A 174 TYR cc_start: 0.6729 (t80) cc_final: 0.6135 (t80) REVERT: A 388 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.7169 (mp0) REVERT: B 120 GLU cc_start: 0.7443 (pp20) cc_final: 0.7154 (pp20) REVERT: B 174 TYR cc_start: 0.6645 (t80) cc_final: 0.6105 (t80) REVERT: C 320 ARG cc_start: 0.7026 (ttp80) cc_final: 0.6629 (ttm110) REVERT: C 388 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.7015 (mp0) REVERT: C 476 GLU cc_start: 0.6116 (mm-30) cc_final: 0.5666 (mt-10) REVERT: D 130 VAL cc_start: 0.8237 (OUTLIER) cc_final: 0.7994 (t) REVERT: D 174 TYR cc_start: 0.6748 (t80) cc_final: 0.6078 (t80) REVERT: D 388 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.7148 (mp0) REVERT: E 120 GLU cc_start: 0.7451 (pp20) cc_final: 0.7175 (pp20) REVERT: E 164 TYR cc_start: 0.7793 (t80) cc_final: 0.7562 (t80) REVERT: E 174 TYR cc_start: 0.6532 (t80) cc_final: 0.6033 (t80) REVERT: E 507 MET cc_start: 0.8128 (OUTLIER) cc_final: 0.7391 (mpt) REVERT: F 212 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.7803 (mmm160) REVERT: F 320 ARG cc_start: 0.7100 (ttp80) cc_final: 0.6616 (ttm110) REVERT: F 388 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.6999 (mp0) REVERT: F 455 ILE cc_start: 0.8761 (OUTLIER) cc_final: 0.8560 (mm) REVERT: F 476 GLU cc_start: 0.6185 (mm-30) cc_final: 0.5741 (mt-10) outliers start: 45 outliers final: 39 residues processed: 214 average time/residue: 1.3598 time to fit residues: 324.1772 Evaluate side-chains 218 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 171 time to evaluate : 1.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 145 MET 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 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 176 ILE Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 340 ARG Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 492 LYS Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 340 ARG Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 388 GLU Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain E residue 507 MET Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 176 ILE Chi-restraints excluded: chain F residue 212 ARG Chi-restraints excluded: chain F residue 340 ARG Chi-restraints excluded: chain F residue 388 GLU Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 455 ILE 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 233 optimal weight: 0.9990 chunk 142 optimal weight: 2.9990 chunk 110 optimal weight: 0.7980 chunk 162 optimal weight: 1.9990 chunk 245 optimal weight: 0.8980 chunk 225 optimal weight: 5.9990 chunk 195 optimal weight: 0.4980 chunk 20 optimal weight: 0.6980 chunk 150 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19626 Z= 0.166 Angle : 0.516 8.223 26604 Z= 0.267 Chirality : 0.042 0.142 3066 Planarity : 0.004 0.042 3402 Dihedral : 9.461 154.740 2886 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 2.28 % Allowed : 16.17 % 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: 0.93 (0.17), residues: 2430 helix: 2.35 (0.16), residues: 1092 sheet: 1.40 (0.24), residues: 426 loop : -2.12 (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 A 239 PHE 0.008 0.001 PHE B 382 TYR 0.014 0.001 TYR C 278 ARG 0.008 0.000 ARG C 234 ********************** 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 225 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 179 time to evaluate : 2.086 Fit side-chains REVERT: A 174 TYR cc_start: 0.6713 (t80) cc_final: 0.6133 (t80) REVERT: B 120 GLU cc_start: 0.7498 (pp20) cc_final: 0.7206 (pp20) REVERT: B 174 TYR cc_start: 0.6732 (t80) cc_final: 0.6192 (t80) REVERT: C 320 ARG cc_start: 0.7032 (ttp80) cc_final: 0.6648 (ttm110) REVERT: C 388 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.7018 (mp0) REVERT: C 476 GLU cc_start: 0.6293 (mm-30) cc_final: 0.5804 (mt-10) REVERT: D 130 VAL cc_start: 0.8252 (OUTLIER) cc_final: 0.8012 (t) REVERT: D 174 TYR cc_start: 0.6771 (t80) cc_final: 0.6089 (t80) REVERT: D 388 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.7154 (mp0) REVERT: E 120 GLU cc_start: 0.7483 (pp20) cc_final: 0.7201 (pp20) REVERT: E 174 TYR cc_start: 0.6553 (t80) cc_final: 0.6059 (t80) REVERT: F 174 TYR cc_start: 0.6625 (t80) cc_final: 0.6365 (t80) REVERT: F 212 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.7655 (mmm160) REVERT: F 320 ARG cc_start: 0.7106 (ttp80) cc_final: 0.6618 (ttm110) REVERT: F 388 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.7051 (mp0) REVERT: F 455 ILE cc_start: 0.8766 (OUTLIER) cc_final: 0.8561 (mm) REVERT: F 476 GLU cc_start: 0.6227 (mm-30) cc_final: 0.5746 (mt-10) outliers start: 46 outliers final: 42 residues processed: 209 average time/residue: 1.4632 time to fit residues: 339.9755 Evaluate side-chains 221 residues out of total 2106 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 173 time to evaluate : 2.171 ------------------------------------------------------------------------------- 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 145 MET 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 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 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 455 ILE Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 492 LYS Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 340 ARG Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 388 GLU Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 489 MET Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain E residue 155 THR 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 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 455 ILE 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 207 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 179 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 54 optimal weight: 0.2980 chunk 195 optimal weight: 0.0970 chunk 81 optimal weight: 4.9990 chunk 200 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 171 optimal weight: 10.0000 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.150442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.113431 restraints weight = 21851.242| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.25 r_work: 0.3194 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 19626 Z= 0.151 Angle : 0.502 8.488 26604 Z= 0.262 Chirality : 0.042 0.140 3066 Planarity : 0.004 0.038 3402 Dihedral : 9.422 154.696 2886 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 2.13 % Allowed : 16.52 % Favored : 81.35 % 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: 0.99 (0.17), residues: 2430 helix: 2.41 (0.16), residues: 1092 sheet: 1.42 (0.24), residues: 426 loop : -2.11 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 359 HIS 0.003 0.001 HIS C 238 PHE 0.008 0.001 PHE B 382 TYR 0.014 0.001 TYR C 278 ARG 0.008 0.000 ARG E 234 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6033.49 seconds wall clock time: 106 minutes 25.85 seconds (6385.85 seconds total)