Starting phenix.real_space_refine on Sun Aug 24 11:11:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dze_27795/08_2025/8dze_27795.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dze_27795/08_2025/8dze_27795.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8dze_27795/08_2025/8dze_27795.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dze_27795/08_2025/8dze_27795.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dze_27795/08_2025/8dze_27795.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dze_27795/08_2025/8dze_27795.map" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.061 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 6 6.06 5 P 18 5.49 5 S 84 5.16 5 C 12102 2.51 5 N 3390 2.21 5 O 3708 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19308 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3186 Classifications: {'peptide': 413} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 15, 'TRANS': 397} Chain breaks: 3 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 60 Planarities with less than four sites: {'ARG:plan': 4, 'GLN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 49 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' ZN': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2171 SG CYS A 403 90.435 129.403 30.842 1.00 67.86 S ATOM 2191 SG CYS A 406 94.137 129.562 30.333 1.00 74.08 S ATOM 2475 SG CYS A 445 92.459 132.497 31.856 1.00 91.66 S ATOM 2481 SG CYS A 446 92.806 129.072 33.819 1.00 87.17 S Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 2.97, per 1000 atoms: 0.15 Number of scatterers: 19308 At special positions: 0 Unit cell: (147.96, 143.64, 81, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 6 29.99 S 84 16.00 P 18 15.00 O 3708 8.00 N 3390 7.00 C 12102 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.62 Conformation dependent library (CDL) restraints added in 756.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 601 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 406 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 403 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 445 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 446 " pdb=" ZN B 601 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 406 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 403 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 445 " pdb="ZN ZN B 601 " - pdb=" SG CYS B 446 " pdb=" ZN C 601 " pdb="ZN ZN C 601 " - pdb=" SG CYS C 406 " pdb="ZN ZN C 601 " - pdb=" SG CYS C 403 " pdb="ZN ZN C 601 " - pdb=" SG CYS C 445 " pdb="ZN ZN C 601 " - pdb=" SG CYS C 446 " pdb=" ZN D 601 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 406 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 403 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 445 " pdb="ZN ZN D 601 " - pdb=" SG CYS D 446 " pdb=" ZN E 601 " pdb="ZN ZN E 601 " - pdb=" SG CYS E 406 " pdb="ZN ZN E 601 " - pdb=" SG CYS E 403 " pdb="ZN ZN E 601 " - pdb=" SG CYS E 445 " pdb="ZN ZN E 601 " - pdb=" SG CYS E 446 " pdb=" ZN F 601 " pdb="ZN ZN F 601 " - pdb=" SG CYS F 406 " pdb="ZN ZN F 601 " - pdb=" SG CYS F 403 " pdb="ZN ZN F 601 " - pdb=" SG CYS F 445 " pdb="ZN ZN F 601 " - pdb=" SG CYS F 446 " Number of angles added : 36 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4668 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 30 sheets defined 45.6% alpha, 25.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 107 through 122 Processing helix chain 'A' and resid 153 through 166 Processing helix chain 'A' and resid 238 through 251 Processing helix chain 'A' and resid 261 through 264 Processing helix chain 'A' and resid 265 through 282 removed outlier: 3.669A pdb=" N LYS A 282 " --> pdb=" O TYR A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 329 removed outlier: 3.556A pdb=" N SER A 329 " --> pdb=" O ALA A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 355 Processing helix chain 'A' and resid 368 through 376 removed outlier: 4.181A pdb=" N ASP A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 385 removed outlier: 3.848A pdb=" N LEU A 384 " --> pdb=" O ASP A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 416 removed outlier: 3.926A pdb=" N SER A 416 " --> pdb=" O GLU A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 429 Processing helix chain 'A' and resid 463 through 472 Processing helix chain 'A' and resid 478 through 485 Processing helix chain 'A' and resid 490 through 501 Processing helix chain 'A' and resid 505 through 513 Processing helix chain 'A' and resid 515 through 519 removed outlier: 3.530A pdb=" N ILE A 519 " --> pdb=" O ILE A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 533 Processing helix chain 'B' and resid 108 through 122 Processing helix chain 'B' and resid 153 through 166 Processing helix chain 'B' and resid 238 through 251 Processing helix chain 'B' and resid 261 through 264 Processing helix chain 'B' and resid 265 through 282 removed outlier: 3.669A pdb=" N LYS B 282 " --> pdb=" O TYR B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 329 removed outlier: 3.556A pdb=" N SER B 329 " --> pdb=" O ALA B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 355 Processing helix chain 'B' and resid 368 through 376 removed outlier: 4.181A pdb=" N ASP B 372 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 385 removed outlier: 3.849A pdb=" N LEU B 384 " --> pdb=" O ASP B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 416 removed outlier: 3.926A pdb=" N SER B 416 " --> pdb=" O GLU B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 429 Processing helix chain 'B' and resid 463 through 472 Processing helix chain 'B' and resid 478 through 485 Processing helix chain 'B' and resid 490 through 501 Processing helix chain 'B' and resid 505 through 513 Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.530A pdb=" N ILE B 519 " --> pdb=" O ILE B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 533 Processing helix chain 'C' and resid 108 through 122 Processing helix chain 'C' and resid 153 through 166 Processing helix chain 'C' and resid 238 through 251 Processing helix chain 'C' and resid 261 through 264 Processing helix chain 'C' and resid 265 through 282 removed outlier: 3.669A pdb=" N LYS C 282 " --> pdb=" O TYR C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 329 removed outlier: 3.556A pdb=" N SER C 329 " --> pdb=" O ALA C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 355 Processing helix chain 'C' and resid 368 through 376 removed outlier: 4.181A pdb=" N ASP C 372 " --> pdb=" O LEU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 385 removed outlier: 3.848A pdb=" N LEU C 384 " --> pdb=" O ASP C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 416 removed outlier: 3.925A pdb=" N SER C 416 " --> pdb=" O GLU C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 429 Processing helix chain 'C' and resid 463 through 472 Processing helix chain 'C' and resid 478 through 485 Processing helix chain 'C' and resid 490 through 501 Processing helix chain 'C' and resid 505 through 513 Processing helix chain 'C' and resid 515 through 519 removed outlier: 3.531A pdb=" N ILE C 519 " --> pdb=" O ILE C 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 533 Processing helix chain 'D' and resid 108 through 122 Processing helix chain 'D' and resid 153 through 166 Processing helix chain 'D' and resid 238 through 251 Processing helix chain 'D' and resid 261 through 264 Processing helix chain 'D' and resid 265 through 282 removed outlier: 3.670A pdb=" N LYS D 282 " --> pdb=" O TYR D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 329 removed outlier: 3.555A pdb=" N SER D 329 " --> pdb=" O ALA D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 355 Processing helix chain 'D' and resid 368 through 376 removed outlier: 4.182A pdb=" N ASP D 372 " --> pdb=" O LEU D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 385 removed outlier: 3.849A pdb=" N LEU D 384 " --> pdb=" O ASP D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 416 removed outlier: 3.925A pdb=" N SER D 416 " --> pdb=" O GLU D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 429 Processing helix chain 'D' and resid 463 through 472 Processing helix chain 'D' and resid 478 through 485 Processing helix chain 'D' and resid 490 through 501 Processing helix chain 'D' and resid 505 through 513 Processing helix chain 'D' and resid 515 through 519 removed outlier: 3.530A pdb=" N ILE D 519 " --> pdb=" O ILE D 516 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 533 Processing helix chain 'E' and resid 108 through 122 Processing helix chain 'E' and resid 153 through 166 Processing helix chain 'E' and resid 238 through 251 Processing helix chain 'E' and resid 261 through 264 Processing helix chain 'E' and resid 265 through 282 removed outlier: 3.669A pdb=" N LYS E 282 " --> pdb=" O TYR E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 329 removed outlier: 3.556A pdb=" N SER E 329 " --> pdb=" O ALA E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 341 through 355 Processing helix chain 'E' and resid 368 through 376 removed outlier: 4.181A pdb=" N ASP E 372 " --> pdb=" O LEU E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 380 through 385 removed outlier: 3.849A pdb=" N LEU E 384 " --> pdb=" O ASP E 380 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 416 removed outlier: 3.925A pdb=" N SER E 416 " --> pdb=" O GLU E 412 " (cutoff:3.500A) Processing helix chain 'E' and resid 421 through 429 Processing helix chain 'E' and resid 463 through 472 Processing helix chain 'E' and resid 478 through 485 Processing helix chain 'E' and resid 490 through 501 Processing helix chain 'E' and resid 505 through 513 Processing helix chain 'E' and resid 515 through 519 removed outlier: 3.531A pdb=" N ILE E 519 " --> pdb=" O ILE E 516 " (cutoff:3.500A) Processing helix chain 'E' and resid 520 through 533 Processing helix chain 'F' and resid 108 through 122 Processing helix chain 'F' and resid 153 through 166 Processing helix chain 'F' and resid 238 through 251 Processing helix chain 'F' and resid 261 through 264 Processing helix chain 'F' and resid 265 through 282 removed outlier: 3.669A pdb=" N LYS F 282 " --> pdb=" O TYR F 278 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 329 removed outlier: 3.556A pdb=" N SER F 329 " --> pdb=" O ALA F 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 341 through 355 Processing helix chain 'F' and resid 368 through 376 removed outlier: 4.181A pdb=" N ASP F 372 " --> pdb=" O LEU F 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 385 removed outlier: 3.848A pdb=" N LEU F 384 " --> pdb=" O ASP F 380 " (cutoff:3.500A) Processing helix chain 'F' and resid 409 through 416 removed outlier: 3.925A pdb=" N SER F 416 " --> pdb=" O GLU F 412 " (cutoff:3.500A) Processing helix chain 'F' and resid 421 through 429 Processing helix chain 'F' and resid 463 through 472 Processing helix chain 'F' and resid 478 through 485 Processing helix chain 'F' and resid 490 through 501 Processing helix chain 'F' and resid 505 through 513 Processing helix chain 'F' and resid 515 through 519 removed outlier: 3.531A pdb=" N ILE F 519 " --> pdb=" O ILE F 516 " (cutoff:3.500A) Processing helix chain 'F' and resid 520 through 533 Processing sheet with id=AA1, first strand: chain 'A' and resid 144 through 152 removed outlier: 5.069A pdb=" N MET A 145 " --> pdb=" O LYS A 141 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LYS A 141 " --> pdb=" O MET A 145 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N LEU A 147 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ILE A 139 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG A 212 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 144 through 152 removed outlier: 5.069A pdb=" N MET A 145 " --> pdb=" O LYS A 141 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LYS A 141 " --> pdb=" O MET A 145 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N LEU A 147 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ILE A 139 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG A 212 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 357 through 361 removed outlier: 6.084A pdb=" N ILE A 255 " --> pdb=" O ILE A 390 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY A 392 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU A 393 " --> pdb=" O VAL A 459 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL A 459 " --> pdb=" O LEU A 393 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ALA A 395 " --> pdb=" O ALA A 457 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ALA A 457 " --> pdb=" O ALA A 395 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ARG A 397 " --> pdb=" O ILE A 455 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ILE A 455 " --> pdb=" O ARG A 397 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N VAL A 399 " --> pdb=" O ARG A 453 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ARG A 453 " --> pdb=" O VAL A 399 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LYS A 401 " --> pdb=" O ASN A 451 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 288 through 290 removed outlier: 6.811A pdb=" N SER A 289 " --> pdb=" O LEU A 304 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 407 through 408 Processing sheet with id=AA6, first strand: chain 'B' and resid 144 through 152 removed outlier: 5.070A pdb=" N MET B 145 " --> pdb=" O LYS B 141 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LYS B 141 " --> pdb=" O MET B 145 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N LEU B 147 " --> pdb=" O ILE B 139 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ILE B 139 " --> pdb=" O LEU B 147 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG B 212 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 144 through 152 removed outlier: 5.070A pdb=" N MET B 145 " --> pdb=" O LYS B 141 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LYS B 141 " --> pdb=" O MET B 145 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N LEU B 147 " --> pdb=" O ILE B 139 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ILE B 139 " --> pdb=" O LEU B 147 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG B 212 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 357 through 361 removed outlier: 6.084A pdb=" N ILE B 255 " --> pdb=" O ILE B 390 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY B 392 " --> pdb=" O ILE B 255 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU B 393 " --> pdb=" O VAL B 459 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL B 459 " --> pdb=" O LEU B 393 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ALA B 395 " --> pdb=" O ALA B 457 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ALA B 457 " --> pdb=" O ALA B 395 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ARG B 397 " --> pdb=" O ILE B 455 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ILE B 455 " --> pdb=" O ARG B 397 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N VAL B 399 " --> pdb=" O ARG B 453 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ARG B 453 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LYS B 401 " --> pdb=" O ASN B 451 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 288 through 290 removed outlier: 6.811A pdb=" N SER B 289 " --> pdb=" O LEU B 304 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AB2, first strand: chain 'C' and resid 144 through 152 removed outlier: 5.070A pdb=" N MET C 145 " --> pdb=" O LYS C 141 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LYS C 141 " --> pdb=" O MET C 145 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N LEU C 147 " --> pdb=" O ILE C 139 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE C 139 " --> pdb=" O LEU C 147 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG C 212 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 144 through 152 removed outlier: 5.070A pdb=" N MET C 145 " --> pdb=" O LYS C 141 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LYS C 141 " --> pdb=" O MET C 145 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N LEU C 147 " --> pdb=" O ILE C 139 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE C 139 " --> pdb=" O LEU C 147 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG C 212 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 357 through 361 removed outlier: 6.085A pdb=" N ILE C 255 " --> pdb=" O ILE C 390 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY C 392 " --> pdb=" O ILE C 255 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU C 393 " --> pdb=" O VAL C 459 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL C 459 " --> pdb=" O LEU C 393 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ALA C 395 " --> pdb=" O ALA C 457 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ALA C 457 " --> pdb=" O ALA C 395 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ARG C 397 " --> pdb=" O ILE C 455 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ILE C 455 " --> pdb=" O ARG C 397 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL C 399 " --> pdb=" O ARG C 453 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ARG C 453 " --> pdb=" O VAL C 399 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LYS C 401 " --> pdb=" O ASN C 451 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 288 through 290 removed outlier: 6.812A pdb=" N SER C 289 " --> pdb=" O LEU C 304 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AB7, first strand: chain 'D' and resid 144 through 152 removed outlier: 5.069A pdb=" N MET D 145 " --> pdb=" O LYS D 141 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LYS D 141 " --> pdb=" O MET D 145 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N LEU D 147 " --> pdb=" O ILE D 139 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE D 139 " --> pdb=" O LEU D 147 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG D 212 " --> pdb=" O VAL D 130 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 144 through 152 removed outlier: 5.069A pdb=" N MET D 145 " --> pdb=" O LYS D 141 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LYS D 141 " --> pdb=" O MET D 145 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N LEU D 147 " --> pdb=" O ILE D 139 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE D 139 " --> pdb=" O LEU D 147 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG D 212 " --> pdb=" O VAL D 130 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 357 through 361 removed outlier: 6.084A pdb=" N ILE D 255 " --> pdb=" O ILE D 390 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY D 392 " --> pdb=" O ILE D 255 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU D 393 " --> pdb=" O VAL D 459 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL D 459 " --> pdb=" O LEU D 393 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ALA D 395 " --> pdb=" O ALA D 457 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ALA D 457 " --> pdb=" O ALA D 395 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ARG D 397 " --> pdb=" O ILE D 455 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ILE D 455 " --> pdb=" O ARG D 397 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL D 399 " --> pdb=" O ARG D 453 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ARG D 453 " --> pdb=" O VAL D 399 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LYS D 401 " --> pdb=" O ASN D 451 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 288 through 290 removed outlier: 6.811A pdb=" N SER D 289 " --> pdb=" O LEU D 304 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AC3, first strand: chain 'E' and resid 144 through 152 removed outlier: 5.069A pdb=" N MET E 145 " --> pdb=" O LYS E 141 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LYS E 141 " --> pdb=" O MET E 145 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N LEU E 147 " --> pdb=" O ILE E 139 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE E 139 " --> pdb=" O LEU E 147 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG E 212 " --> pdb=" O VAL E 130 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 144 through 152 removed outlier: 5.069A pdb=" N MET E 145 " --> pdb=" O LYS E 141 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LYS E 141 " --> pdb=" O MET E 145 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N LEU E 147 " --> pdb=" O ILE E 139 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE E 139 " --> pdb=" O LEU E 147 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG E 212 " --> pdb=" O VAL E 130 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 357 through 361 removed outlier: 6.085A pdb=" N ILE E 255 " --> pdb=" O ILE E 390 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY E 392 " --> pdb=" O ILE E 255 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU E 393 " --> pdb=" O VAL E 459 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL E 459 " --> pdb=" O LEU E 393 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ALA E 395 " --> pdb=" O ALA E 457 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ALA E 457 " --> pdb=" O ALA E 395 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ARG E 397 " --> pdb=" O ILE E 455 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ILE E 455 " --> pdb=" O ARG E 397 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL E 399 " --> pdb=" O ARG E 453 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ARG E 453 " --> pdb=" O VAL E 399 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LYS E 401 " --> pdb=" O ASN E 451 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 288 through 290 removed outlier: 6.812A pdb=" N SER E 289 " --> pdb=" O LEU E 304 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'E' and resid 407 through 408 Processing sheet with id=AC8, first strand: chain 'F' and resid 144 through 152 removed outlier: 5.071A pdb=" N MET F 145 " --> pdb=" O LYS F 141 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LYS F 141 " --> pdb=" O MET F 145 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N LEU F 147 " --> pdb=" O ILE F 139 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ILE F 139 " --> pdb=" O LEU F 147 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG F 212 " --> pdb=" O VAL F 130 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 144 through 152 removed outlier: 5.071A pdb=" N MET F 145 " --> pdb=" O LYS F 141 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LYS F 141 " --> pdb=" O MET F 145 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N LEU F 147 " --> pdb=" O ILE F 139 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ILE F 139 " --> pdb=" O LEU F 147 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG F 212 " --> pdb=" O VAL F 130 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 357 through 361 removed outlier: 6.084A pdb=" N ILE F 255 " --> pdb=" O ILE F 390 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY F 392 " --> pdb=" O ILE F 255 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU F 393 " --> pdb=" O VAL F 459 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL F 459 " --> pdb=" O LEU F 393 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ALA F 395 " --> pdb=" O ALA F 457 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ALA F 457 " --> pdb=" O ALA F 395 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ARG F 397 " --> pdb=" O ILE F 455 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ILE F 455 " --> pdb=" O ARG F 397 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL F 399 " --> pdb=" O ARG F 453 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ARG F 453 " --> pdb=" O VAL F 399 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LYS F 401 " --> pdb=" O ASN F 451 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 288 through 290 removed outlier: 6.812A pdb=" N SER F 289 " --> pdb=" O LEU F 304 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'F' and resid 407 through 408 1015 hydrogen bonds defined for protein. 2919 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.01 Time building geometry restraints manager: 2.09 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: 0.05 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: 1.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 17.480 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.010 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: 0.010 Load rotamer database and sin/cos tables:8.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 27.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.236 19650 Z= 0.381 Angle : 0.834 11.347 26640 Z= 0.370 Chirality : 0.047 0.331 3066 Planarity : 0.005 0.061 3402 Dihedral : 16.651 150.605 7380 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.04 % Favored : 92.72 % Rotamer: Outliers : 0.64 % Allowed : 17.21 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.16), residues: 2430 helix: 0.74 (0.15), residues: 1032 sheet: 2.20 (0.25), residues: 426 loop : -2.23 (0.17), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 110 TYR 0.008 0.001 TYR F 278 PHE 0.011 0.001 PHE C 382 TRP 0.006 0.001 TRP D 359 HIS 0.001 0.000 HIS E 238 Details of bonding type rmsd covalent geometry : bond 0.00762 (19626) covalent geometry : angle 0.82545 (26604) hydrogen bonds : bond 0.15067 ( 913) hydrogen bonds : angle 4.85350 ( 2919) metal coordination : bond 0.00573 ( 24) metal coordination : angle 3.39211 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 198 time to evaluate : 0.581 Fit side-chains REVERT: B 525 LYS cc_start: 0.8179 (ttmm) cc_final: 0.7937 (ttmm) REVERT: C 123 VAL cc_start: 0.8323 (m) cc_final: 0.7950 (m) REVERT: C 320 ARG cc_start: 0.6795 (ttp80) cc_final: 0.6351 (ttm110) REVERT: E 525 LYS cc_start: 0.8162 (ttmm) cc_final: 0.7924 (ttmm) REVERT: F 120 GLU cc_start: 0.7460 (pp20) cc_final: 0.7249 (pp20) REVERT: F 320 ARG cc_start: 0.6868 (ttp80) cc_final: 0.6428 (ttm110) outliers start: 13 outliers final: 17 residues processed: 202 average time/residue: 0.5574 time to fit residues: 126.8367 Evaluate side-chains 188 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 171 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ASN Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain D residue 177 ASN Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 177 ASN Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 409 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.4980 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.9980 chunk 235 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.155245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.118023 restraints weight = 22075.269| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.36 r_work: 0.3255 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.1012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19650 Z= 0.133 Angle : 0.531 5.472 26640 Z= 0.274 Chirality : 0.043 0.167 3066 Planarity : 0.004 0.036 3402 Dihedral : 10.603 158.762 2901 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.16 % Favored : 92.59 % Rotamer: Outliers : 2.48 % Allowed : 14.34 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.17), residues: 2430 helix: 1.75 (0.16), residues: 1044 sheet: 1.65 (0.24), residues: 432 loop : -2.14 (0.18), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 110 TYR 0.010 0.001 TYR E 138 PHE 0.008 0.001 PHE E 382 TRP 0.006 0.001 TRP A 359 HIS 0.005 0.001 HIS D 238 Details of bonding type rmsd covalent geometry : bond 0.00299 (19626) covalent geometry : angle 0.51925 (26604) hydrogen bonds : bond 0.03825 ( 913) hydrogen bonds : angle 3.78675 ( 2919) metal coordination : bond 0.00454 ( 24) metal coordination : angle 3.03143 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 208 time to evaluate : 0.711 Fit side-chains REVERT: A 158 SER cc_start: 0.8885 (m) cc_final: 0.8669 (t) REVERT: A 164 TYR cc_start: 0.7201 (t80) cc_final: 0.6998 (t80) REVERT: B 120 GLU cc_start: 0.7199 (pp20) cc_final: 0.6975 (pp20) REVERT: B 164 TYR cc_start: 0.7329 (t80) cc_final: 0.7059 (t80) REVERT: B 220 TYR cc_start: 0.8208 (m-80) cc_final: 0.7949 (m-80) REVERT: B 525 LYS cc_start: 0.8216 (ttmm) cc_final: 0.7986 (ttmm) REVERT: C 164 TYR cc_start: 0.7421 (t80) cc_final: 0.7187 (t80) REVERT: C 320 ARG cc_start: 0.7242 (ttp80) cc_final: 0.6495 (ttm110) REVERT: D 158 SER cc_start: 0.8896 (m) cc_final: 0.8687 (t) REVERT: D 164 TYR cc_start: 0.7119 (t80) cc_final: 0.6906 (t80) REVERT: E 121 MET cc_start: 0.7982 (ttp) cc_final: 0.7718 (ttp) REVERT: E 164 TYR cc_start: 0.7262 (t80) cc_final: 0.7003 (t80) REVERT: E 220 TYR cc_start: 0.8195 (m-80) cc_final: 0.7888 (m-80) REVERT: E 525 LYS cc_start: 0.8219 (ttmm) cc_final: 0.7988 (ttmm) REVERT: F 164 TYR cc_start: 0.7457 (t80) cc_final: 0.7253 (t80) REVERT: F 212 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7783 (mmt180) REVERT: F 320 ARG cc_start: 0.7252 (ttp80) cc_final: 0.6481 (ttm110) outliers start: 50 outliers final: 35 residues processed: 244 average time/residue: 0.6578 time to fit residues: 177.9674 Evaluate side-chains 220 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 184 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 177 ASN Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 448 ASP Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 177 ASN Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 448 ASP Chi-restraints excluded: chain B residue 455 ILE Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 448 ASP Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 177 ASN Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain E residue 145 MET Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 448 ASP Chi-restraints excluded: chain E residue 455 ILE Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain F residue 145 MET Chi-restraints excluded: chain F residue 212 ARG Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 448 ASP Chi-restraints excluded: chain F residue 455 ILE Chi-restraints excluded: chain F residue 491 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 195 optimal weight: 6.9990 chunk 197 optimal weight: 5.9990 chunk 159 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 136 optimal weight: 0.7980 chunk 200 optimal weight: 0.8980 chunk 223 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 B 356 HIS C 166 ASN C 356 HIS D 127 HIS D 166 ASN F 127 HIS F 166 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.152237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.114982 restraints weight = 22170.739| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.31 r_work: 0.3227 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 19650 Z= 0.131 Angle : 0.520 5.520 26640 Z= 0.269 Chirality : 0.043 0.165 3066 Planarity : 0.004 0.036 3402 Dihedral : 10.159 154.922 2897 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.45 % Favored : 92.30 % Rotamer: Outliers : 2.43 % Allowed : 14.48 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.17), residues: 2430 helix: 1.82 (0.16), residues: 1080 sheet: 1.60 (0.24), residues: 426 loop : -2.12 (0.18), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 110 TYR 0.010 0.001 TYR D 138 PHE 0.008 0.001 PHE B 204 TRP 0.006 0.001 TRP A 359 HIS 0.004 0.001 HIS A 239 Details of bonding type rmsd covalent geometry : bond 0.00307 (19626) covalent geometry : angle 0.50957 (26604) hydrogen bonds : bond 0.03438 ( 913) hydrogen bonds : angle 3.67846 ( 2919) metal coordination : bond 0.00500 ( 24) metal coordination : angle 2.91503 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 209 time to evaluate : 0.554 Fit side-chains REVERT: A 164 TYR cc_start: 0.7224 (t80) cc_final: 0.6982 (t80) REVERT: A 174 TYR cc_start: 0.6551 (t80) cc_final: 0.6217 (t80) REVERT: A 353 MET cc_start: 0.8807 (mtm) cc_final: 0.8591 (mtp) REVERT: A 397 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.7677 (mtt-85) REVERT: B 120 GLU cc_start: 0.7309 (pp20) cc_final: 0.7092 (pp20) REVERT: B 164 TYR cc_start: 0.7322 (t80) cc_final: 0.7088 (t80) REVERT: B 220 TYR cc_start: 0.8165 (m-80) cc_final: 0.7886 (m-80) REVERT: B 525 LYS cc_start: 0.8196 (ttmm) cc_final: 0.7966 (ttmm) REVERT: C 164 TYR cc_start: 0.7394 (t80) cc_final: 0.7134 (t80) REVERT: C 320 ARG cc_start: 0.7233 (ttp80) cc_final: 0.6473 (ttm110) REVERT: C 388 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7235 (mp0) REVERT: D 164 TYR cc_start: 0.7159 (t80) cc_final: 0.6923 (t80) REVERT: D 397 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.7598 (mtt-85) REVERT: E 120 GLU cc_start: 0.7248 (pp20) cc_final: 0.7041 (pp20) REVERT: E 164 TYR cc_start: 0.7325 (t80) cc_final: 0.7093 (t80) REVERT: E 220 TYR cc_start: 0.8167 (m-80) cc_final: 0.7838 (m-80) REVERT: E 525 LYS cc_start: 0.8226 (ttmm) cc_final: 0.7993 (ttmm) REVERT: F 164 TYR cc_start: 0.7410 (t80) cc_final: 0.7147 (t80) REVERT: F 320 ARG cc_start: 0.7244 (ttp80) cc_final: 0.6461 (ttm110) REVERT: F 388 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7350 (mp0) outliers start: 49 outliers final: 37 residues processed: 235 average time/residue: 0.5656 time to fit residues: 149.0607 Evaluate side-chains 224 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 183 time to evaluate : 0.454 ------------------------------------------------------------------------------- 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 347 LEU Chi-restraints excluded: chain A residue 397 ARG Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 455 ILE Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain C residue 455 ILE Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 145 MET Chi-restraints excluded: chain D residue 177 ASN Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 397 ARG 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 177 ASN 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 130 VAL Chi-restraints excluded: chain F residue 145 MET Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 388 GLU Chi-restraints excluded: chain F residue 455 ILE Chi-restraints excluded: chain F residue 491 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 77 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 236 optimal weight: 6.9990 chunk 41 optimal weight: 10.0000 chunk 105 optimal weight: 4.9990 chunk 205 optimal weight: 10.0000 chunk 240 optimal weight: 6.9990 chunk 137 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 193 optimal weight: 6.9990 chunk 68 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 127 HIS C 166 ASN D 166 ASN E 127 HIS E 356 HIS F 166 ASN F 356 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.142758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.104693 restraints weight = 22188.781| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.30 r_work: 0.3059 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 19650 Z= 0.273 Angle : 0.693 7.856 26640 Z= 0.352 Chirality : 0.050 0.246 3066 Planarity : 0.005 0.050 3402 Dihedral : 10.355 146.281 2894 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.70 % Favored : 91.98 % Rotamer: Outliers : 3.57 % Allowed : 13.84 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.17), residues: 2430 helix: 1.45 (0.16), residues: 1092 sheet: 0.58 (0.23), residues: 504 loop : -2.21 (0.19), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 234 TYR 0.015 0.001 TYR C 220 PHE 0.013 0.002 PHE A 204 TRP 0.011 0.002 TRP A 359 HIS 0.010 0.002 HIS F 239 Details of bonding type rmsd covalent geometry : bond 0.00681 (19626) covalent geometry : angle 0.67189 (26604) hydrogen bonds : bond 0.05019 ( 913) hydrogen bonds : angle 3.97772 ( 2919) metal coordination : bond 0.00740 ( 24) metal coordination : angle 4.68193 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 199 time to evaluate : 0.583 Fit side-chains REVERT: A 164 TYR cc_start: 0.7741 (t80) cc_final: 0.7431 (t80) REVERT: A 353 MET cc_start: 0.8913 (mtm) cc_final: 0.8674 (mtp) REVERT: A 388 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7839 (mp0) REVERT: A 397 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.7758 (mtt-85) REVERT: B 120 GLU cc_start: 0.7626 (pp20) cc_final: 0.7412 (pp20) REVERT: B 164 TYR cc_start: 0.7686 (t80) cc_final: 0.7444 (t80) REVERT: B 174 TYR cc_start: 0.6652 (t80) cc_final: 0.6158 (t80) REVERT: B 405 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.8224 (mm110) REVERT: B 530 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.7087 (ttm-80) REVERT: C 212 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.7912 (mmt180) REVERT: C 320 ARG cc_start: 0.7396 (ttp80) cc_final: 0.6549 (ttm110) REVERT: C 388 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7627 (mp0) REVERT: D 174 TYR cc_start: 0.6730 (t80) cc_final: 0.6173 (t80) REVERT: D 388 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7779 (mp0) REVERT: D 397 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.7803 (mtt-85) REVERT: E 120 GLU cc_start: 0.7609 (pp20) cc_final: 0.7390 (pp20) REVERT: E 164 TYR cc_start: 0.7695 (t80) cc_final: 0.7451 (t80) REVERT: E 174 TYR cc_start: 0.6639 (t80) cc_final: 0.6193 (t80) REVERT: E 220 TYR cc_start: 0.8359 (m-80) cc_final: 0.8094 (m-80) REVERT: E 405 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.8213 (mm-40) REVERT: E 530 ARG cc_start: 0.7433 (OUTLIER) cc_final: 0.7195 (ptt180) REVERT: F 164 TYR cc_start: 0.7732 (t80) cc_final: 0.7483 (t80) REVERT: F 212 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.7958 (mmt180) REVERT: F 320 ARG cc_start: 0.7478 (ttp80) cc_final: 0.6605 (ttm110) REVERT: F 388 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7687 (mp0) REVERT: F 489 MET cc_start: 0.9274 (ttm) cc_final: 0.8769 (ptm) outliers start: 72 outliers final: 32 residues processed: 256 average time/residue: 0.6652 time to fit residues: 187.3536 Evaluate side-chains 221 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 177 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 388 GLU Chi-restraints excluded: chain A residue 397 ARG Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain 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 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 B residue 530 ARG Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain C residue 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 D residue 123 VAL Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 388 GLU Chi-restraints excluded: chain D residue 397 ARG 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 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 E residue 530 ARG Chi-restraints excluded: chain F residue 123 VAL Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 145 MET Chi-restraints excluded: chain F residue 155 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 223 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 chunk 228 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 188 optimal weight: 3.9990 chunk 177 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 131 optimal weight: 0.1980 chunk 140 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN B 166 ASN C 166 ASN D 166 ASN E 166 ASN F 166 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.146827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.109280 restraints weight = 21828.542| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.27 r_work: 0.3136 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19650 Z= 0.124 Angle : 0.546 6.629 26640 Z= 0.279 Chirality : 0.043 0.161 3066 Planarity : 0.004 0.046 3402 Dihedral : 10.042 150.933 2878 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.33 % Allowed : 7.49 % Favored : 92.18 % Rotamer: Outliers : 3.32 % Allowed : 15.48 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.17), residues: 2430 helix: 1.86 (0.16), residues: 1092 sheet: 1.21 (0.23), residues: 426 loop : -2.26 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 397 TYR 0.011 0.001 TYR A 138 PHE 0.009 0.001 PHE D 382 TRP 0.007 0.001 TRP A 359 HIS 0.002 0.001 HIS A 239 Details of bonding type rmsd covalent geometry : bond 0.00286 (19626) covalent geometry : angle 0.52734 (26604) hydrogen bonds : bond 0.03323 ( 913) hydrogen bonds : angle 3.72124 ( 2919) metal coordination : bond 0.00460 ( 24) metal coordination : angle 3.86867 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 172 time to evaluate : 0.760 Fit side-chains REVERT: A 164 TYR cc_start: 0.7575 (t80) cc_final: 0.7371 (t80) REVERT: A 174 TYR cc_start: 0.6568 (t80) cc_final: 0.6094 (t80) REVERT: B 120 GLU cc_start: 0.7551 (pp20) cc_final: 0.7327 (pp20) REVERT: B 174 TYR cc_start: 0.6655 (t80) cc_final: 0.6222 (t80) REVERT: B 332 ASP cc_start: 0.7627 (OUTLIER) cc_final: 0.7378 (m-30) REVERT: B 476 GLU cc_start: 0.6602 (mm-30) cc_final: 0.5879 (tt0) REVERT: C 320 ARG cc_start: 0.7333 (ttp80) cc_final: 0.6566 (ttm110) REVERT: C 332 ASP cc_start: 0.7636 (OUTLIER) cc_final: 0.7366 (m-30) REVERT: C 365 ASN cc_start: 0.7708 (OUTLIER) cc_final: 0.7143 (m-40) REVERT: C 388 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7537 (mp0) REVERT: C 476 GLU cc_start: 0.6971 (mm-30) cc_final: 0.6150 (tt0) REVERT: D 174 TYR cc_start: 0.6587 (t80) cc_final: 0.6158 (t80) REVERT: E 174 TYR cc_start: 0.6637 (t80) cc_final: 0.6082 (t80) REVERT: E 220 TYR cc_start: 0.8254 (m-80) cc_final: 0.7960 (m-80) REVERT: E 332 ASP cc_start: 0.7664 (OUTLIER) cc_final: 0.7398 (m-30) REVERT: E 476 GLU cc_start: 0.6613 (mm-30) cc_final: 0.5883 (tt0) REVERT: E 530 ARG cc_start: 0.7314 (OUTLIER) cc_final: 0.7036 (ptt180) REVERT: F 212 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.7619 (mmt180) REVERT: F 320 ARG cc_start: 0.7371 (ttp80) cc_final: 0.6561 (ttm110) REVERT: F 332 ASP cc_start: 0.7603 (OUTLIER) cc_final: 0.7349 (m-30) REVERT: F 365 ASN cc_start: 0.7685 (OUTLIER) cc_final: 0.7110 (m-40) REVERT: F 388 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7613 (mp0) REVERT: F 476 GLU cc_start: 0.7007 (mm-30) cc_final: 0.6187 (tt0) REVERT: F 489 MET cc_start: 0.9168 (ttm) cc_final: 0.8899 (ttp) outliers start: 67 outliers final: 36 residues processed: 223 average time/residue: 0.7246 time to fit residues: 177.8841 Evaluate side-chains 207 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 161 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain B residue 365 ASN 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 332 ASP Chi-restraints excluded: chain C residue 340 ARG Chi-restraints excluded: chain C residue 365 ASN 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 409 THR Chi-restraints excluded: chain D residue 455 ILE Chi-restraints excluded: chain D residue 489 MET Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 332 ASP Chi-restraints excluded: chain E residue 335 MET Chi-restraints excluded: chain E residue 340 ARG Chi-restraints excluded: chain E residue 365 ASN Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 455 ILE Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain E residue 530 ARG Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 212 ARG Chi-restraints excluded: chain F residue 332 ASP Chi-restraints excluded: chain F residue 340 ARG Chi-restraints excluded: chain F residue 365 ASN Chi-restraints excluded: chain F residue 388 GLU Chi-restraints excluded: chain F residue 396 GLN 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 Chi-restraints excluded: chain F residue 531 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 181 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 189 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 73 optimal weight: 7.9990 chunk 180 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 191 optimal weight: 1.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN B 166 ASN C 166 ASN C 238 HIS D 166 ASN E 166 ASN F 166 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.144951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.107495 restraints weight = 21820.162| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.26 r_work: 0.3109 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 19650 Z= 0.160 Angle : 0.569 6.837 26640 Z= 0.289 Chirality : 0.044 0.186 3066 Planarity : 0.004 0.046 3402 Dihedral : 9.922 149.303 2878 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.19 % Favored : 91.69 % Rotamer: Outliers : 4.02 % Allowed : 15.13 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.17), residues: 2430 helix: 1.89 (0.16), residues: 1092 sheet: 0.43 (0.23), residues: 504 loop : -2.14 (0.20), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 234 TYR 0.010 0.001 TYR A 138 PHE 0.008 0.001 PHE B 218 TRP 0.007 0.001 TRP A 359 HIS 0.006 0.001 HIS C 239 Details of bonding type rmsd covalent geometry : bond 0.00390 (19626) covalent geometry : angle 0.55350 (26604) hydrogen bonds : bond 0.03684 ( 913) hydrogen bonds : angle 3.69382 ( 2919) metal coordination : bond 0.00509 ( 24) metal coordination : angle 3.59943 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 163 time to evaluate : 0.715 Fit side-chains REVERT: B 174 TYR cc_start: 0.6622 (t80) cc_final: 0.6141 (t80) REVERT: B 332 ASP cc_start: 0.7729 (OUTLIER) cc_final: 0.7487 (m-30) REVERT: B 476 GLU cc_start: 0.6667 (mm-30) cc_final: 0.6015 (tt0) REVERT: B 530 ARG cc_start: 0.7604 (OUTLIER) cc_final: 0.6912 (ttm-80) REVERT: C 212 ARG cc_start: 0.8494 (OUTLIER) cc_final: 0.7652 (mmt180) REVERT: C 320 ARG cc_start: 0.7341 (ttp80) cc_final: 0.6565 (ttm110) REVERT: C 332 ASP cc_start: 0.7732 (OUTLIER) cc_final: 0.7482 (m-30) REVERT: C 365 ASN cc_start: 0.7836 (OUTLIER) cc_final: 0.7326 (m-40) REVERT: C 388 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7685 (mp0) REVERT: E 174 TYR cc_start: 0.6666 (t80) cc_final: 0.6015 (t80) REVERT: E 212 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.7316 (mmm160) REVERT: E 220 TYR cc_start: 0.8271 (m-80) cc_final: 0.7999 (m-80) REVERT: E 332 ASP cc_start: 0.7727 (OUTLIER) cc_final: 0.7492 (m-30) REVERT: E 476 GLU cc_start: 0.6658 (mm-30) cc_final: 0.6003 (tt0) REVERT: E 530 ARG cc_start: 0.7320 (OUTLIER) cc_final: 0.7020 (ptt180) REVERT: F 212 ARG cc_start: 0.8525 (OUTLIER) cc_final: 0.7754 (mmt180) REVERT: F 320 ARG cc_start: 0.7398 (ttp80) cc_final: 0.6597 (ttm110) REVERT: F 332 ASP cc_start: 0.7729 (OUTLIER) cc_final: 0.7480 (m-30) REVERT: F 365 ASN cc_start: 0.7833 (OUTLIER) cc_final: 0.7277 (m-40) REVERT: F 388 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7697 (mp0) REVERT: F 489 MET cc_start: 0.9146 (ttm) cc_final: 0.8908 (ttp) outliers start: 81 outliers final: 45 residues processed: 216 average time/residue: 0.7242 time to fit residues: 172.2449 Evaluate side-chains 222 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 164 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 455 ILE Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 517 ASP Chi-restraints excluded: chain B residue 530 ARG Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 145 MET Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 212 ARG Chi-restraints excluded: chain C residue 332 ASP Chi-restraints excluded: chain C residue 340 ARG Chi-restraints excluded: chain C residue 365 ASN 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 121 MET Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 455 ILE Chi-restraints excluded: chain D residue 489 MET Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 212 ARG Chi-restraints excluded: chain E residue 217 ARG Chi-restraints excluded: chain E residue 332 ASP Chi-restraints excluded: chain E residue 335 MET Chi-restraints excluded: chain E residue 340 ARG Chi-restraints excluded: chain E residue 365 ASN Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 455 ILE Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain E residue 517 ASP Chi-restraints excluded: chain E residue 530 ARG 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 332 ASP Chi-restraints excluded: chain F residue 340 ARG Chi-restraints excluded: chain F residue 365 ASN 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 Chi-restraints excluded: chain F residue 531 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 86 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 230 optimal weight: 0.9980 chunk 7 optimal weight: 7.9990 chunk 233 optimal weight: 1.9990 chunk 89 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 chunk 90 optimal weight: 8.9990 chunk 88 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 234 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 166 ASN E 166 ASN F 166 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.145523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.108246 restraints weight = 21867.363| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.25 r_work: 0.3124 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19650 Z= 0.144 Angle : 0.556 6.232 26640 Z= 0.283 Chirality : 0.044 0.165 3066 Planarity : 0.004 0.046 3402 Dihedral : 9.882 150.002 2878 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.15 % Favored : 91.81 % Rotamer: Outliers : 3.52 % Allowed : 15.82 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.17), residues: 2430 helix: 1.95 (0.16), residues: 1092 sheet: 1.16 (0.23), residues: 426 loop : -2.27 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 234 TYR 0.011 0.001 TYR D 138 PHE 0.009 0.001 PHE B 218 TRP 0.008 0.001 TRP D 359 HIS 0.004 0.001 HIS F 239 Details of bonding type rmsd covalent geometry : bond 0.00347 (19626) covalent geometry : angle 0.54190 (26604) hydrogen bonds : bond 0.03426 ( 913) hydrogen bonds : angle 3.66442 ( 2919) metal coordination : bond 0.00457 ( 24) metal coordination : angle 3.39029 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 168 time to evaluate : 0.759 Fit side-chains REVERT: A 295 GLU cc_start: 0.2181 (OUTLIER) cc_final: 0.1894 (tm-30) REVERT: A 476 GLU cc_start: 0.7076 (mm-30) cc_final: 0.6099 (mt-10) REVERT: B 174 TYR cc_start: 0.6654 (t80) cc_final: 0.6119 (t80) REVERT: B 332 ASP cc_start: 0.7745 (OUTLIER) cc_final: 0.7496 (m-30) REVERT: B 405 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.8192 (mm-40) REVERT: B 476 GLU cc_start: 0.6658 (mm-30) cc_final: 0.6077 (tt0) REVERT: B 530 ARG cc_start: 0.7604 (OUTLIER) cc_final: 0.6859 (ttm-80) REVERT: C 212 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.7527 (mmm160) REVERT: C 320 ARG cc_start: 0.7261 (ttp80) cc_final: 0.6541 (ttm110) REVERT: C 332 ASP cc_start: 0.7773 (OUTLIER) cc_final: 0.7521 (m-30) REVERT: C 365 ASN cc_start: 0.7810 (OUTLIER) cc_final: 0.7285 (m-40) REVERT: C 388 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7671 (mp0) REVERT: D 476 GLU cc_start: 0.7054 (mm-30) cc_final: 0.6098 (mt-10) REVERT: E 174 TYR cc_start: 0.6657 (t80) cc_final: 0.6144 (t80) REVERT: E 220 TYR cc_start: 0.8225 (m-80) cc_final: 0.7926 (m-80) REVERT: E 332 ASP cc_start: 0.7745 (OUTLIER) cc_final: 0.7508 (m-30) REVERT: E 476 GLU cc_start: 0.6669 (mm-30) cc_final: 0.6065 (tt0) REVERT: E 530 ARG cc_start: 0.7327 (OUTLIER) cc_final: 0.6993 (ptt180) REVERT: F 212 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.7610 (mmt180) REVERT: F 320 ARG cc_start: 0.7392 (ttp80) cc_final: 0.6585 (ttm110) REVERT: F 332 ASP cc_start: 0.7809 (OUTLIER) cc_final: 0.7542 (m-30) REVERT: F 365 ASN cc_start: 0.7791 (OUTLIER) cc_final: 0.7220 (m-40) REVERT: F 388 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7671 (mp0) outliers start: 71 outliers final: 41 residues processed: 217 average time/residue: 0.7557 time to fit residues: 179.8918 Evaluate side-chains 219 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 164 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 335 MET Chi-restraints excluded: chain B residue 365 ASN 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 B residue 517 ASP Chi-restraints excluded: chain B residue 530 ARG Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 155 THR Chi-restraints excluded: chain C residue 212 ARG Chi-restraints excluded: chain C residue 332 ASP Chi-restraints excluded: chain C residue 340 ARG Chi-restraints excluded: chain C residue 365 ASN 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 121 MET Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 455 ILE Chi-restraints excluded: chain D residue 489 MET Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 217 ARG Chi-restraints excluded: chain E residue 332 ASP Chi-restraints excluded: chain E residue 335 MET Chi-restraints excluded: chain E residue 365 ASN Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 455 ILE Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain E residue 517 ASP Chi-restraints excluded: chain E residue 530 ARG Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 212 ARG Chi-restraints excluded: chain F residue 332 ASP Chi-restraints excluded: chain F residue 365 ASN 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 Chi-restraints excluded: chain F residue 531 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 205 optimal weight: 10.0000 chunk 72 optimal weight: 0.0040 chunk 12 optimal weight: 0.5980 chunk 70 optimal weight: 5.9990 chunk 232 optimal weight: 2.9990 chunk 123 optimal weight: 10.0000 chunk 162 optimal weight: 0.2980 chunk 90 optimal weight: 1.9990 chunk 54 optimal weight: 0.4980 chunk 233 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.149076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.112096 restraints weight = 21849.937| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.25 r_work: 0.3181 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 19650 Z= 0.097 Angle : 0.514 8.117 26640 Z= 0.262 Chirality : 0.042 0.137 3066 Planarity : 0.003 0.043 3402 Dihedral : 9.642 154.674 2878 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 2.53 % Allowed : 16.87 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.18), residues: 2430 helix: 2.19 (0.16), residues: 1092 sheet: 1.24 (0.23), residues: 426 loop : -2.20 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 397 TYR 0.009 0.001 TYR D 138 PHE 0.009 0.001 PHE D 382 TRP 0.009 0.001 TRP D 359 HIS 0.003 0.000 HIS F 238 Details of bonding type rmsd covalent geometry : bond 0.00211 (19626) covalent geometry : angle 0.50457 (26604) hydrogen bonds : bond 0.02688 ( 913) hydrogen bonds : angle 3.49997 ( 2919) metal coordination : bond 0.00343 ( 24) metal coordination : angle 2.73426 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 177 time to evaluate : 0.818 Fit side-chains REVERT: A 147 LEU cc_start: 0.9227 (tp) cc_final: 0.8941 (tm) REVERT: A 174 TYR cc_start: 0.6546 (t80) cc_final: 0.6128 (t80) REVERT: A 476 GLU cc_start: 0.6964 (mm-30) cc_final: 0.5966 (mt-10) REVERT: B 174 TYR cc_start: 0.6712 (t80) cc_final: 0.6146 (t80) REVERT: B 220 TYR cc_start: 0.8175 (m-80) cc_final: 0.7913 (m-80) REVERT: B 332 ASP cc_start: 0.7586 (OUTLIER) cc_final: 0.7368 (m-30) REVERT: B 476 GLU cc_start: 0.6593 (mm-30) cc_final: 0.5971 (tt0) REVERT: C 320 ARG cc_start: 0.7236 (ttp80) cc_final: 0.6528 (ttm110) REVERT: C 388 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7546 (mp0) REVERT: C 476 GLU cc_start: 0.6964 (mm-30) cc_final: 0.6218 (mt-10) REVERT: D 147 LEU cc_start: 0.9234 (tp) cc_final: 0.8958 (tm) REVERT: D 174 TYR cc_start: 0.6550 (t80) cc_final: 0.6132 (t80) REVERT: D 295 GLU cc_start: 0.2077 (OUTLIER) cc_final: 0.1813 (tm-30) REVERT: D 476 GLU cc_start: 0.6972 (mm-30) cc_final: 0.5969 (mt-10) REVERT: E 174 TYR cc_start: 0.6665 (t80) cc_final: 0.6117 (t80) REVERT: E 220 TYR cc_start: 0.8154 (m-80) cc_final: 0.7870 (m-80) REVERT: E 332 ASP cc_start: 0.7633 (OUTLIER) cc_final: 0.7419 (m-30) REVERT: E 476 GLU cc_start: 0.6573 (mm-30) cc_final: 0.5973 (tt0) REVERT: E 530 ARG cc_start: 0.7291 (OUTLIER) cc_final: 0.6956 (ptt180) REVERT: F 212 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.7588 (mmm160) REVERT: F 320 ARG cc_start: 0.7299 (ttp80) cc_final: 0.6506 (ttm110) REVERT: F 388 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7541 (mp0) REVERT: F 476 GLU cc_start: 0.6989 (mm-30) cc_final: 0.6261 (mt-10) outliers start: 51 outliers final: 33 residues processed: 216 average time/residue: 0.8512 time to fit residues: 201.1295 Evaluate side-chains 211 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 171 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 455 ILE Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 517 ASP Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 155 THR 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 121 MET Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 295 GLU Chi-restraints excluded: chain D residue 340 ARG Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 332 ASP Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 455 ILE Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain E residue 517 ASP Chi-restraints excluded: chain E residue 530 ARG Chi-restraints excluded: chain F residue 123 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 491 LEU Chi-restraints excluded: chain F residue 492 LYS Chi-restraints excluded: chain F residue 531 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 65 optimal weight: 4.9990 chunk 207 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 145 optimal weight: 0.7980 chunk 131 optimal weight: 0.0980 chunk 27 optimal weight: 3.9990 chunk 214 optimal weight: 4.9990 chunk 179 optimal weight: 3.9990 chunk 206 optimal weight: 0.7980 chunk 109 optimal weight: 0.9990 chunk 162 optimal weight: 0.2980 overall best weight: 0.5982 ------------------------------------------------------------------------------- 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 = 0.3731 r_free = 0.3731 target = 0.148845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.111859 restraints weight = 21718.452| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.24 r_work: 0.3174 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 19650 Z= 0.103 Angle : 0.525 8.680 26640 Z= 0.268 Chirality : 0.042 0.140 3066 Planarity : 0.004 0.045 3402 Dihedral : 9.547 155.251 2878 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 1.98 % Allowed : 17.26 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.18), residues: 2430 helix: 2.26 (0.16), residues: 1092 sheet: 1.24 (0.23), residues: 426 loop : -2.17 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 234 TYR 0.010 0.001 TYR E 278 PHE 0.008 0.001 PHE D 382 TRP 0.009 0.001 TRP E 359 HIS 0.002 0.001 HIS A 239 Details of bonding type rmsd covalent geometry : bond 0.00231 (19626) covalent geometry : angle 0.51673 (26604) hydrogen bonds : bond 0.02754 ( 913) hydrogen bonds : angle 3.54766 ( 2919) metal coordination : bond 0.00353 ( 24) metal coordination : angle 2.58999 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 175 time to evaluate : 0.789 Fit side-chains REVERT: A 147 LEU cc_start: 0.9257 (tp) cc_final: 0.8975 (tm) REVERT: A 174 TYR cc_start: 0.6576 (t80) cc_final: 0.6155 (t80) REVERT: A 476 GLU cc_start: 0.6974 (mm-30) cc_final: 0.5995 (mt-10) REVERT: B 174 TYR cc_start: 0.6745 (t80) cc_final: 0.6187 (t80) REVERT: B 220 TYR cc_start: 0.8172 (m-80) cc_final: 0.7906 (m-80) REVERT: B 332 ASP cc_start: 0.7670 (OUTLIER) cc_final: 0.7442 (m-30) REVERT: B 476 GLU cc_start: 0.6566 (mm-30) cc_final: 0.5978 (tt0) REVERT: C 320 ARG cc_start: 0.7243 (ttp80) cc_final: 0.6551 (ttm110) REVERT: C 332 ASP cc_start: 0.7672 (m-30) cc_final: 0.7442 (m-30) REVERT: C 388 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7566 (mp0) REVERT: C 476 GLU cc_start: 0.7048 (mm-30) cc_final: 0.6292 (mt-10) REVERT: C 489 MET cc_start: 0.9175 (ttp) cc_final: 0.8939 (ttp) REVERT: D 147 LEU cc_start: 0.9261 (tp) cc_final: 0.8990 (tm) REVERT: D 174 TYR cc_start: 0.6536 (t80) cc_final: 0.6080 (t80) REVERT: D 295 GLU cc_start: 0.2070 (OUTLIER) cc_final: 0.1805 (tm-30) REVERT: D 476 GLU cc_start: 0.6980 (mm-30) cc_final: 0.6010 (mt-10) REVERT: E 174 TYR cc_start: 0.6643 (t80) cc_final: 0.6056 (t80) REVERT: E 220 TYR cc_start: 0.8153 (m-80) cc_final: 0.7855 (m-80) REVERT: E 332 ASP cc_start: 0.7677 (OUTLIER) cc_final: 0.7453 (m-30) REVERT: E 476 GLU cc_start: 0.6542 (mm-30) cc_final: 0.5967 (tt0) REVERT: E 530 ARG cc_start: 0.7317 (OUTLIER) cc_final: 0.6984 (ptt180) REVERT: F 212 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.7512 (mmt180) REVERT: F 320 ARG cc_start: 0.7316 (ttp80) cc_final: 0.6526 (ttm110) REVERT: F 388 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7569 (mp0) REVERT: F 476 GLU cc_start: 0.7058 (mm-30) cc_final: 0.6325 (mt-10) outliers start: 40 outliers final: 32 residues processed: 208 average time/residue: 0.7874 time to fit residues: 179.9959 Evaluate side-chains 207 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 168 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 ARG Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 455 ILE Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 517 ASP Chi-restraints excluded: chain C residue 155 THR 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 C residue 531 ASP Chi-restraints excluded: chain D residue 295 GLU Chi-restraints excluded: chain D residue 340 ARG Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 332 ASP Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 455 ILE Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain E residue 517 ASP Chi-restraints excluded: chain E residue 530 ARG Chi-restraints excluded: chain F residue 155 THR 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 Chi-restraints excluded: chain F residue 531 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 79 optimal weight: 0.0070 chunk 45 optimal weight: 10.0000 chunk 163 optimal weight: 4.9990 chunk 161 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 143 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 21 optimal weight: 0.0770 chunk 178 optimal weight: 0.9990 chunk 238 optimal weight: 1.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 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 = 0.3735 r_free = 0.3735 target = 0.149059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.111909 restraints weight = 21801.611| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.26 r_work: 0.3173 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 19650 Z= 0.102 Angle : 0.521 8.555 26640 Z= 0.267 Chirality : 0.042 0.140 3066 Planarity : 0.004 0.043 3402 Dihedral : 9.508 155.426 2878 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 2.08 % Allowed : 17.26 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.18), residues: 2430 helix: 2.34 (0.16), residues: 1092 sheet: 0.48 (0.23), residues: 504 loop : -1.99 (0.20), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 397 TYR 0.010 0.001 TYR C 278 PHE 0.008 0.001 PHE D 382 TRP 0.007 0.001 TRP F 359 HIS 0.002 0.000 HIS C 239 Details of bonding type rmsd covalent geometry : bond 0.00230 (19626) covalent geometry : angle 0.51320 (26604) hydrogen bonds : bond 0.02724 ( 913) hydrogen bonds : angle 3.55582 ( 2919) metal coordination : bond 0.00347 ( 24) metal coordination : angle 2.52012 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4860 Ramachandran restraints generated. 2430 Oldfield, 0 Emsley, 2430 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 168 time to evaluate : 0.550 Fit side-chains REVERT: A 147 LEU cc_start: 0.9295 (tp) cc_final: 0.9042 (tm) REVERT: A 174 TYR cc_start: 0.6619 (t80) cc_final: 0.6193 (t80) REVERT: A 476 GLU cc_start: 0.6951 (mm-30) cc_final: 0.5983 (mt-10) REVERT: B 174 TYR cc_start: 0.6783 (t80) cc_final: 0.6228 (t80) REVERT: B 332 ASP cc_start: 0.7684 (OUTLIER) cc_final: 0.7461 (m-30) REVERT: B 476 GLU cc_start: 0.6547 (mm-30) cc_final: 0.5988 (tt0) REVERT: C 320 ARG cc_start: 0.7294 (ttp80) cc_final: 0.6608 (ttm110) REVERT: C 332 ASP cc_start: 0.7650 (m-30) cc_final: 0.7436 (m-30) REVERT: C 388 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7587 (mp0) REVERT: C 476 GLU cc_start: 0.7001 (mm-30) cc_final: 0.6262 (mt-10) REVERT: C 489 MET cc_start: 0.9198 (ttp) cc_final: 0.8952 (ttp) REVERT: D 147 LEU cc_start: 0.9307 (tp) cc_final: 0.9062 (tm) REVERT: D 174 TYR cc_start: 0.6581 (t80) cc_final: 0.6164 (t80) REVERT: D 476 GLU cc_start: 0.6961 (mm-30) cc_final: 0.5991 (mt-10) REVERT: E 174 TYR cc_start: 0.6685 (t80) cc_final: 0.6102 (t80) REVERT: E 220 TYR cc_start: 0.8180 (m-80) cc_final: 0.7873 (m-80) REVERT: E 332 ASP cc_start: 0.7690 (OUTLIER) cc_final: 0.7471 (m-30) REVERT: E 476 GLU cc_start: 0.6494 (mm-30) cc_final: 0.5945 (tt0) REVERT: E 530 ARG cc_start: 0.7361 (OUTLIER) cc_final: 0.6989 (ptt180) REVERT: F 166 ASN cc_start: 0.8133 (OUTLIER) cc_final: 0.7883 (p0) REVERT: F 212 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.7470 (mmt180) REVERT: F 320 ARG cc_start: 0.7375 (ttp80) cc_final: 0.6588 (ttm110) REVERT: F 388 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7597 (mp0) REVERT: F 476 GLU cc_start: 0.7002 (mm-30) cc_final: 0.6287 (mt-10) REVERT: F 492 LYS cc_start: 0.8105 (OUTLIER) cc_final: 0.7868 (ptpt) outliers start: 42 outliers final: 34 residues processed: 200 average time/residue: 0.7858 time to fit residues: 172.6034 Evaluate side-chains 206 residues out of total 2106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 164 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 328 ARG Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 145 MET Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 455 ILE Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 517 ASP Chi-restraints excluded: chain C residue 155 THR 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 C residue 531 ASP Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 340 ARG Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain E residue 130 VAL Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 332 ASP Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 455 ILE Chi-restraints excluded: chain E residue 491 LEU Chi-restraints excluded: chain E residue 517 ASP Chi-restraints excluded: chain E residue 530 ARG Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 166 ASN 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 492 LYS Chi-restraints excluded: chain F residue 531 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 23 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 235 optimal weight: 3.9990 chunk 200 optimal weight: 2.9990 chunk 131 optimal weight: 0.0010 chunk 26 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 33 optimal weight: 0.8980 chunk 239 optimal weight: 0.8980 chunk 176 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 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 = 0.3727 r_free = 0.3727 target = 0.148459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.111171 restraints weight = 21752.663| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.26 r_work: 0.3162 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 19650 Z= 0.108 Angle : 0.528 8.838 26640 Z= 0.270 Chirality : 0.042 0.141 3066 Planarity : 0.004 0.042 3402 Dihedral : 9.488 155.076 2878 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 2.03 % Allowed : 17.46 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.18), residues: 2430 helix: 2.36 (0.16), residues: 1092 sheet: 0.46 (0.23), residues: 504 loop : -1.98 (0.20), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 397 TYR 0.009 0.001 TYR C 278 PHE 0.008 0.001 PHE D 382 TRP 0.006 0.001 TRP F 359 HIS 0.003 0.001 HIS F 239 Details of bonding type rmsd covalent geometry : bond 0.00249 (19626) covalent geometry : angle 0.52022 (26604) hydrogen bonds : bond 0.02828 ( 913) hydrogen bonds : angle 3.56164 ( 2919) metal coordination : bond 0.00349 ( 24) metal coordination : angle 2.51803 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5176.55 seconds wall clock time: 89 minutes 10.53 seconds (5350.53 seconds total)