Starting phenix.real_space_refine on Sun Oct 12 09:27:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jzl_36746/10_2025/8jzl_36746.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jzl_36746/10_2025/8jzl_36746.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jzl_36746/10_2025/8jzl_36746.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jzl_36746/10_2025/8jzl_36746.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jzl_36746/10_2025/8jzl_36746.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jzl_36746/10_2025/8jzl_36746.map" } resolution = 2.62 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= -0.000 sd= 0.007 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: 4 Type Number sf(0) Gaussians S 90 5.16 5 C 14538 2.51 5 N 4212 2.21 5 O 4344 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23184 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3864 Classifications: {'peptide': 498} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 478} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 3.45, per 1000 atoms: 0.15 Number of scatterers: 23184 At special positions: 0 Unit cell: (156.782, 144.896, 125.086, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 90 16.00 O 4344 8.00 N 4212 7.00 C 14538 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: 2.02 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 715.3 nanoseconds 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5544 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 12 sheets defined 56.0% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 72 through 92 removed outlier: 3.588A pdb=" N LEU A 76 " --> pdb=" O SER A 72 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG A 81 " --> pdb=" O TYR A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 111 removed outlier: 3.844A pdb=" N VAL A 110 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS A 111 " --> pdb=" O LEU A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 143 removed outlier: 4.647A pdb=" N LYS A 128 " --> pdb=" O ALA A 124 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N LYS A 129 " --> pdb=" O LYS A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 169 removed outlier: 3.518A pdb=" N GLN A 169 " --> pdb=" O GLN A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 280 Processing helix chain 'A' and resid 281 through 290 Processing helix chain 'A' and resid 312 through 328 removed outlier: 3.725A pdb=" N MET A 316 " --> pdb=" O LYS A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 367 Processing helix chain 'A' and resid 371 through 388 removed outlier: 3.623A pdb=" N SER A 377 " --> pdb=" O LYS A 373 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TYR A 378 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU A 381 " --> pdb=" O SER A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 406 Processing helix chain 'A' and resid 411 through 429 Processing helix chain 'A' and resid 430 through 433 Processing helix chain 'A' and resid 439 through 452 removed outlier: 3.770A pdb=" N ARG A 444 " --> pdb=" O LYS A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 483 removed outlier: 3.848A pdb=" N GLN A 483 " --> pdb=" O ILE A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 509 removed outlier: 3.631A pdb=" N LEU A 507 " --> pdb=" O GLN A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 520 Processing helix chain 'A' and resid 532 through 536 removed outlier: 3.596A pdb=" N ASN A 536 " --> pdb=" O GLU A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 543 removed outlier: 4.131A pdb=" N ARG A 542 " --> pdb=" O SER A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 553 Processing helix chain 'A' and resid 555 through 559 removed outlier: 3.752A pdb=" N ILE A 559 " --> pdb=" O SER A 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 92 removed outlier: 3.588A pdb=" N LEU B 76 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG B 81 " --> pdb=" O TYR B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 111 removed outlier: 3.844A pdb=" N VAL B 110 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS B 111 " --> pdb=" O LEU B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 143 removed outlier: 4.648A pdb=" N LYS B 128 " --> pdb=" O ALA B 124 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N LYS B 129 " --> pdb=" O LYS B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 169 removed outlier: 3.519A pdb=" N GLN B 169 " --> pdb=" O GLN B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 280 Processing helix chain 'B' and resid 281 through 290 Processing helix chain 'B' and resid 312 through 328 removed outlier: 3.725A pdb=" N MET B 316 " --> pdb=" O LYS B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 367 Processing helix chain 'B' and resid 371 through 388 removed outlier: 3.624A pdb=" N SER B 377 " --> pdb=" O LYS B 373 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TYR B 378 " --> pdb=" O ALA B 374 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU B 381 " --> pdb=" O SER B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 406 Processing helix chain 'B' and resid 411 through 429 Processing helix chain 'B' and resid 430 through 433 Processing helix chain 'B' and resid 439 through 452 removed outlier: 3.770A pdb=" N ARG B 444 " --> pdb=" O LYS B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 483 removed outlier: 3.848A pdb=" N GLN B 483 " --> pdb=" O ILE B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 509 removed outlier: 3.632A pdb=" N LEU B 507 " --> pdb=" O GLN B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 520 Processing helix chain 'B' and resid 532 through 536 removed outlier: 3.595A pdb=" N ASN B 536 " --> pdb=" O GLU B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 543 removed outlier: 4.131A pdb=" N ARG B 542 " --> pdb=" O SER B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 553 Processing helix chain 'B' and resid 555 through 559 removed outlier: 3.752A pdb=" N ILE B 559 " --> pdb=" O SER B 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 92 removed outlier: 3.588A pdb=" N LEU C 76 " --> pdb=" O SER C 72 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG C 81 " --> pdb=" O TYR C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 111 removed outlier: 3.844A pdb=" N VAL C 110 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS C 111 " --> pdb=" O LEU C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 143 removed outlier: 4.647A pdb=" N LYS C 128 " --> pdb=" O ALA C 124 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N LYS C 129 " --> pdb=" O LYS C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 169 removed outlier: 3.519A pdb=" N GLN C 169 " --> pdb=" O GLN C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 280 Processing helix chain 'C' and resid 281 through 290 Processing helix chain 'C' and resid 312 through 328 removed outlier: 3.726A pdb=" N MET C 316 " --> pdb=" O LYS C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 367 Processing helix chain 'C' and resid 371 through 388 removed outlier: 3.624A pdb=" N SER C 377 " --> pdb=" O LYS C 373 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TYR C 378 " --> pdb=" O ALA C 374 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLU C 381 " --> pdb=" O SER C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 406 Processing helix chain 'C' and resid 411 through 429 Processing helix chain 'C' and resid 430 through 433 Processing helix chain 'C' and resid 439 through 452 removed outlier: 3.771A pdb=" N ARG C 444 " --> pdb=" O LYS C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 483 removed outlier: 3.849A pdb=" N GLN C 483 " --> pdb=" O ILE C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 509 removed outlier: 3.632A pdb=" N LEU C 507 " --> pdb=" O GLN C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 520 Processing helix chain 'C' and resid 532 through 536 removed outlier: 3.595A pdb=" N ASN C 536 " --> pdb=" O GLU C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 543 removed outlier: 4.130A pdb=" N ARG C 542 " --> pdb=" O SER C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 545 through 553 Processing helix chain 'C' and resid 555 through 559 removed outlier: 3.752A pdb=" N ILE C 559 " --> pdb=" O SER C 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 92 removed outlier: 3.587A pdb=" N LEU D 76 " --> pdb=" O SER D 72 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG D 81 " --> pdb=" O TYR D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 111 removed outlier: 3.844A pdb=" N VAL D 110 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS D 111 " --> pdb=" O LEU D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 143 removed outlier: 4.647A pdb=" N LYS D 128 " --> pdb=" O ALA D 124 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N LYS D 129 " --> pdb=" O LYS D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 169 removed outlier: 3.519A pdb=" N GLN D 169 " --> pdb=" O GLN D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 280 Processing helix chain 'D' and resid 281 through 290 Processing helix chain 'D' and resid 312 through 328 removed outlier: 3.725A pdb=" N MET D 316 " --> pdb=" O LYS D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 367 Processing helix chain 'D' and resid 371 through 388 removed outlier: 3.623A pdb=" N SER D 377 " --> pdb=" O LYS D 373 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N TYR D 378 " --> pdb=" O ALA D 374 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU D 381 " --> pdb=" O SER D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 406 Processing helix chain 'D' and resid 411 through 429 Processing helix chain 'D' and resid 430 through 433 Processing helix chain 'D' and resid 439 through 452 removed outlier: 3.771A pdb=" N ARG D 444 " --> pdb=" O LYS D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 483 removed outlier: 3.850A pdb=" N GLN D 483 " --> pdb=" O ILE D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 495 through 509 removed outlier: 3.631A pdb=" N LEU D 507 " --> pdb=" O GLN D 503 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 520 Processing helix chain 'D' and resid 532 through 536 removed outlier: 3.595A pdb=" N ASN D 536 " --> pdb=" O GLU D 533 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 543 removed outlier: 4.130A pdb=" N ARG D 542 " --> pdb=" O SER D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 553 Processing helix chain 'D' and resid 555 through 559 removed outlier: 3.752A pdb=" N ILE D 559 " --> pdb=" O SER D 556 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 92 removed outlier: 3.589A pdb=" N LEU E 76 " --> pdb=" O SER E 72 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG E 81 " --> pdb=" O TYR E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 111 removed outlier: 3.844A pdb=" N VAL E 110 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS E 111 " --> pdb=" O LEU E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 143 removed outlier: 4.647A pdb=" N LYS E 128 " --> pdb=" O ALA E 124 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N LYS E 129 " --> pdb=" O LYS E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 169 removed outlier: 3.518A pdb=" N GLN E 169 " --> pdb=" O GLN E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 280 Processing helix chain 'E' and resid 281 through 290 Processing helix chain 'E' and resid 312 through 328 removed outlier: 3.725A pdb=" N MET E 316 " --> pdb=" O LYS E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 through 367 Processing helix chain 'E' and resid 371 through 388 removed outlier: 3.624A pdb=" N SER E 377 " --> pdb=" O LYS E 373 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TYR E 378 " --> pdb=" O ALA E 374 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLU E 381 " --> pdb=" O SER E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 398 through 406 Processing helix chain 'E' and resid 411 through 429 Processing helix chain 'E' and resid 430 through 433 Processing helix chain 'E' and resid 439 through 452 removed outlier: 3.770A pdb=" N ARG E 444 " --> pdb=" O LYS E 440 " (cutoff:3.500A) Processing helix chain 'E' and resid 465 through 483 removed outlier: 3.849A pdb=" N GLN E 483 " --> pdb=" O ILE E 479 " (cutoff:3.500A) Processing helix chain 'E' and resid 495 through 509 removed outlier: 3.632A pdb=" N LEU E 507 " --> pdb=" O GLN E 503 " (cutoff:3.500A) Processing helix chain 'E' and resid 510 through 520 Processing helix chain 'E' and resid 532 through 536 removed outlier: 3.595A pdb=" N ASN E 536 " --> pdb=" O GLU E 533 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 543 removed outlier: 4.131A pdb=" N ARG E 542 " --> pdb=" O SER E 538 " (cutoff:3.500A) Processing helix chain 'E' and resid 545 through 553 Processing helix chain 'E' and resid 555 through 559 removed outlier: 3.753A pdb=" N ILE E 559 " --> pdb=" O SER E 556 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 92 removed outlier: 3.589A pdb=" N LEU F 76 " --> pdb=" O SER F 72 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG F 81 " --> pdb=" O TYR F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 111 removed outlier: 3.844A pdb=" N VAL F 110 " --> pdb=" O GLU F 106 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS F 111 " --> pdb=" O LEU F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 143 removed outlier: 4.647A pdb=" N LYS F 128 " --> pdb=" O ALA F 124 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N LYS F 129 " --> pdb=" O LYS F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 169 removed outlier: 3.518A pdb=" N GLN F 169 " --> pdb=" O GLN F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 280 Processing helix chain 'F' and resid 281 through 290 Processing helix chain 'F' and resid 312 through 328 removed outlier: 3.725A pdb=" N MET F 316 " --> pdb=" O LYS F 312 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 367 Processing helix chain 'F' and resid 371 through 388 removed outlier: 3.623A pdb=" N SER F 377 " --> pdb=" O LYS F 373 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TYR F 378 " --> pdb=" O ALA F 374 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLU F 381 " --> pdb=" O SER F 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 398 through 406 Processing helix chain 'F' and resid 411 through 429 Processing helix chain 'F' and resid 430 through 433 Processing helix chain 'F' and resid 439 through 452 removed outlier: 3.771A pdb=" N ARG F 444 " --> pdb=" O LYS F 440 " (cutoff:3.500A) Processing helix chain 'F' and resid 465 through 483 removed outlier: 3.849A pdb=" N GLN F 483 " --> pdb=" O ILE F 479 " (cutoff:3.500A) Processing helix chain 'F' and resid 495 through 509 removed outlier: 3.631A pdb=" N LEU F 507 " --> pdb=" O GLN F 503 " (cutoff:3.500A) Processing helix chain 'F' and resid 510 through 520 Processing helix chain 'F' and resid 532 through 536 removed outlier: 3.594A pdb=" N ASN F 536 " --> pdb=" O GLU F 533 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 543 removed outlier: 4.131A pdb=" N ARG F 542 " --> pdb=" O SER F 538 " (cutoff:3.500A) Processing helix chain 'F' and resid 545 through 553 Processing helix chain 'F' and resid 555 through 559 removed outlier: 3.753A pdb=" N ILE F 559 " --> pdb=" O SER F 556 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 174 through 180 removed outlier: 5.071A pdb=" N HIS A 184 " --> pdb=" O HIS A 234 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL A 233 " --> pdb=" O THR A 241 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N THR A 241 " --> pdb=" O VAL A 233 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLU A 235 " --> pdb=" O ASP A 239 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ASP A 239 " --> pdb=" O GLU A 235 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL A 294 " --> pdb=" O LYS A 351 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ASP A 353 " --> pdb=" O VAL A 294 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU A 296 " --> pdb=" O ASP A 353 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N ALA A 355 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU A 298 " --> pdb=" O ALA A 355 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N PHE A 357 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N SER A 300 " --> pdb=" O PHE A 357 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 196 through 197 removed outlier: 3.902A pdb=" N ILE A 197 " --> pdb=" O LYS A 200 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LYS A 200 " --> pdb=" O ILE A 197 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 174 through 180 removed outlier: 5.070A pdb=" N HIS B 184 " --> pdb=" O HIS B 234 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL B 233 " --> pdb=" O THR B 241 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N THR B 241 " --> pdb=" O VAL B 233 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLU B 235 " --> pdb=" O ASP B 239 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ASP B 239 " --> pdb=" O GLU B 235 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL B 294 " --> pdb=" O LYS B 351 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ASP B 353 " --> pdb=" O VAL B 294 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU B 296 " --> pdb=" O ASP B 353 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N ALA B 355 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU B 298 " --> pdb=" O ALA B 355 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N PHE B 357 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N SER B 300 " --> pdb=" O PHE B 357 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 196 through 197 removed outlier: 3.901A pdb=" N ILE B 197 " --> pdb=" O LYS B 200 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LYS B 200 " --> pdb=" O ILE B 197 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 174 through 180 removed outlier: 5.071A pdb=" N HIS C 184 " --> pdb=" O HIS C 234 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL C 233 " --> pdb=" O THR C 241 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N THR C 241 " --> pdb=" O VAL C 233 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLU C 235 " --> pdb=" O ASP C 239 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ASP C 239 " --> pdb=" O GLU C 235 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL C 294 " --> pdb=" O LYS C 351 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ASP C 353 " --> pdb=" O VAL C 294 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU C 296 " --> pdb=" O ASP C 353 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N ALA C 355 " --> pdb=" O LEU C 296 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU C 298 " --> pdb=" O ALA C 355 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N PHE C 357 " --> pdb=" O LEU C 298 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N SER C 300 " --> pdb=" O PHE C 357 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 196 through 197 removed outlier: 3.901A pdb=" N ILE C 197 " --> pdb=" O LYS C 200 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LYS C 200 " --> pdb=" O ILE C 197 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 174 through 180 removed outlier: 5.070A pdb=" N HIS D 184 " --> pdb=" O HIS D 234 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL D 233 " --> pdb=" O THR D 241 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N THR D 241 " --> pdb=" O VAL D 233 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLU D 235 " --> pdb=" O ASP D 239 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ASP D 239 " --> pdb=" O GLU D 235 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL D 294 " --> pdb=" O LYS D 351 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ASP D 353 " --> pdb=" O VAL D 294 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU D 296 " --> pdb=" O ASP D 353 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N ALA D 355 " --> pdb=" O LEU D 296 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU D 298 " --> pdb=" O ALA D 355 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N PHE D 357 " --> pdb=" O LEU D 298 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N SER D 300 " --> pdb=" O PHE D 357 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 196 through 197 removed outlier: 3.902A pdb=" N ILE D 197 " --> pdb=" O LYS D 200 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LYS D 200 " --> pdb=" O ILE D 197 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'E' and resid 174 through 180 removed outlier: 5.070A pdb=" N HIS E 184 " --> pdb=" O HIS E 234 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL E 233 " --> pdb=" O THR E 241 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N THR E 241 " --> pdb=" O VAL E 233 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLU E 235 " --> pdb=" O ASP E 239 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ASP E 239 " --> pdb=" O GLU E 235 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL E 294 " --> pdb=" O LYS E 351 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ASP E 353 " --> pdb=" O VAL E 294 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU E 296 " --> pdb=" O ASP E 353 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N ALA E 355 " --> pdb=" O LEU E 296 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU E 298 " --> pdb=" O ALA E 355 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N PHE E 357 " --> pdb=" O LEU E 298 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N SER E 300 " --> pdb=" O PHE E 357 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 196 through 197 removed outlier: 3.902A pdb=" N ILE E 197 " --> pdb=" O LYS E 200 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LYS E 200 " --> pdb=" O ILE E 197 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'F' and resid 174 through 180 removed outlier: 5.071A pdb=" N HIS F 184 " --> pdb=" O HIS F 234 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL F 233 " --> pdb=" O THR F 241 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N THR F 241 " --> pdb=" O VAL F 233 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLU F 235 " --> pdb=" O ASP F 239 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ASP F 239 " --> pdb=" O GLU F 235 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL F 294 " --> pdb=" O LYS F 351 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ASP F 353 " --> pdb=" O VAL F 294 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU F 296 " --> pdb=" O ASP F 353 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N ALA F 355 " --> pdb=" O LEU F 296 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU F 298 " --> pdb=" O ALA F 355 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N PHE F 357 " --> pdb=" O LEU F 298 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N SER F 300 " --> pdb=" O PHE F 357 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 196 through 197 removed outlier: 3.901A pdb=" N ILE F 197 " --> pdb=" O LYS F 200 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LYS F 200 " --> pdb=" O ILE F 197 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 1320 hydrogen bonds defined for protein. 3816 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: 4.27 Time building geometry restraints manager: 2.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 7772 1.33 - 1.45: 2449 1.45 - 1.57: 13245 1.57 - 1.68: 0 1.68 - 1.80: 162 Bond restraints: 23628 Sorted by residual: bond pdb=" C LEU E 251 " pdb=" N SER E 252 " ideal model delta sigma weight residual 1.333 1.298 0.035 1.59e-02 3.96e+03 4.75e+00 bond pdb=" C LEU D 251 " pdb=" N SER D 252 " ideal model delta sigma weight residual 1.333 1.298 0.035 1.59e-02 3.96e+03 4.73e+00 bond pdb=" C LEU A 251 " pdb=" N SER A 252 " ideal model delta sigma weight residual 1.333 1.298 0.035 1.59e-02 3.96e+03 4.73e+00 bond pdb=" C LEU F 251 " pdb=" N SER F 252 " ideal model delta sigma weight residual 1.333 1.298 0.034 1.59e-02 3.96e+03 4.70e+00 bond pdb=" C LEU C 251 " pdb=" N SER C 252 " ideal model delta sigma weight residual 1.333 1.298 0.034 1.59e-02 3.96e+03 4.70e+00 ... (remaining 23623 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 30939 1.65 - 3.30: 863 3.30 - 4.95: 100 4.95 - 6.60: 36 6.60 - 8.25: 6 Bond angle restraints: 31944 Sorted by residual: angle pdb=" C LEU F 76 " pdb=" N TYR F 77 " pdb=" CA TYR F 77 " ideal model delta sigma weight residual 120.82 125.22 -4.40 1.50e+00 4.44e-01 8.59e+00 angle pdb=" C LEU C 76 " pdb=" N TYR C 77 " pdb=" CA TYR C 77 " ideal model delta sigma weight residual 120.82 125.21 -4.39 1.50e+00 4.44e-01 8.56e+00 angle pdb=" C LEU D 76 " pdb=" N TYR D 77 " pdb=" CA TYR D 77 " ideal model delta sigma weight residual 120.82 125.20 -4.38 1.50e+00 4.44e-01 8.51e+00 angle pdb=" C LEU E 76 " pdb=" N TYR E 77 " pdb=" CA TYR E 77 " ideal model delta sigma weight residual 120.82 125.14 -4.32 1.50e+00 4.44e-01 8.31e+00 angle pdb=" C LEU B 76 " pdb=" N TYR B 77 " pdb=" CA TYR B 77 " ideal model delta sigma weight residual 120.82 125.14 -4.32 1.50e+00 4.44e-01 8.29e+00 ... (remaining 31939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 13174 17.48 - 34.96: 980 34.96 - 52.44: 168 52.44 - 69.92: 42 69.92 - 87.40: 12 Dihedral angle restraints: 14376 sinusoidal: 5796 harmonic: 8580 Sorted by residual: dihedral pdb=" CA TYR D 254 " pdb=" C TYR D 254 " pdb=" N HIS D 255 " pdb=" CA HIS D 255 " ideal model delta harmonic sigma weight residual -180.00 -161.52 -18.48 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA TYR B 254 " pdb=" C TYR B 254 " pdb=" N HIS B 255 " pdb=" CA HIS B 255 " ideal model delta harmonic sigma weight residual -180.00 -161.54 -18.46 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA TYR A 254 " pdb=" C TYR A 254 " pdb=" N HIS A 255 " pdb=" CA HIS A 255 " ideal model delta harmonic sigma weight residual -180.00 -161.56 -18.44 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 14373 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1871 0.031 - 0.062: 1120 0.062 - 0.093: 368 0.093 - 0.124: 134 0.124 - 0.154: 53 Chirality restraints: 3546 Sorted by residual: chirality pdb=" CA GLU A 318 " pdb=" N GLU A 318 " pdb=" C GLU A 318 " pdb=" CB GLU A 318 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.96e-01 chirality pdb=" CA GLU D 318 " pdb=" N GLU D 318 " pdb=" C GLU D 318 " pdb=" CB GLU D 318 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.92e-01 chirality pdb=" CA GLU F 318 " pdb=" N GLU F 318 " pdb=" C GLU F 318 " pdb=" CB GLU F 318 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.85e-01 ... (remaining 3543 not shown) Planarity restraints: 4164 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS E 351 " 0.023 5.00e-02 4.00e+02 3.41e-02 1.86e+00 pdb=" N PRO E 352 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO E 352 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO E 352 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS F 351 " -0.023 5.00e-02 4.00e+02 3.40e-02 1.85e+00 pdb=" N PRO F 352 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO F 352 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO F 352 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 351 " -0.023 5.00e-02 4.00e+02 3.40e-02 1.85e+00 pdb=" N PRO C 352 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO C 352 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 352 " -0.019 5.00e-02 4.00e+02 ... (remaining 4161 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 8046 2.86 - 3.37: 22625 3.37 - 3.88: 37210 3.88 - 4.39: 42374 4.39 - 4.90: 72167 Nonbonded interactions: 182422 Sorted by model distance: nonbonded pdb=" O LYS A 464 " pdb=" NE2 GLN A 515 " model vdw 2.353 3.120 nonbonded pdb=" O LYS F 464 " pdb=" NE2 GLN F 515 " model vdw 2.353 3.120 nonbonded pdb=" O LYS C 464 " pdb=" NE2 GLN C 515 " model vdw 2.354 3.120 nonbonded pdb=" O LYS E 464 " pdb=" NE2 GLN E 515 " model vdw 2.354 3.120 nonbonded pdb=" O LYS D 464 " pdb=" NE2 GLN D 515 " model vdw 2.354 3.120 ... (remaining 182417 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: 0.08 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: 11.200 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: 0.030 Extract box with map and model: 0.590 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 19.560 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 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 : 0.009 0.040 23628 Z= 0.373 Angle : 0.670 8.247 31944 Z= 0.357 Chirality : 0.045 0.154 3546 Planarity : 0.003 0.034 4164 Dihedral : 12.906 87.398 8832 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.16), residues: 2976 helix: 1.93 (0.13), residues: 1542 sheet: 1.15 (0.26), residues: 396 loop : -1.09 (0.20), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 81 TYR 0.015 0.002 TYR D 77 PHE 0.017 0.002 PHE C 502 TRP 0.008 0.001 TRP E 227 HIS 0.006 0.001 HIS F 482 Details of bonding type rmsd covalent geometry : bond 0.00854 (23628) covalent geometry : angle 0.67041 (31944) hydrogen bonds : bond 0.15965 ( 1320) hydrogen bonds : angle 6.10736 ( 3816) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASN cc_start: 0.9232 (m110) cc_final: 0.8920 (m-40) REVERT: A 105 MET cc_start: 0.9170 (tpt) cc_final: 0.8908 (tmt) REVERT: A 547 ASN cc_start: 0.9250 (m-40) cc_final: 0.8981 (m110) REVERT: B 546 GLU cc_start: 0.8600 (tp30) cc_final: 0.8399 (tp30) REVERT: C 465 ASP cc_start: 0.8410 (m-30) cc_final: 0.8155 (m-30) REVERT: D 105 MET cc_start: 0.9272 (tpt) cc_final: 0.8421 (tmm) REVERT: D 220 ILE cc_start: 0.9376 (pt) cc_final: 0.9161 (pp) REVERT: E 105 MET cc_start: 0.9148 (tpt) cc_final: 0.8245 (tmm) REVERT: E 547 ASN cc_start: 0.9360 (m-40) cc_final: 0.9115 (m-40) REVERT: F 543 VAL cc_start: 0.8805 (t) cc_final: 0.8506 (p) outliers start: 0 outliers final: 1 residues processed: 235 average time/residue: 0.6242 time to fit residues: 168.8642 Evaluate side-chains 173 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 172 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 548 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 0.0270 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 overall best weight: 1.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN A 432 HIS A 540 GLN B 103 ASN B 325 GLN B 432 HIS B 515 GLN C 103 ASN D 103 ASN D 432 HIS E 103 ASN E 432 HIS E 515 GLN F 103 ASN F 432 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.112734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.067898 restraints weight = 47170.278| |-----------------------------------------------------------------------------| r_work (start): 0.2784 rms_B_bonded: 3.34 r_work: 0.2563 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23628 Z= 0.134 Angle : 0.574 7.101 31944 Z= 0.296 Chirality : 0.040 0.158 3546 Planarity : 0.003 0.035 4164 Dihedral : 4.266 14.429 3140 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.69 % Allowed : 7.16 % Favored : 92.15 % 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: 1.75 (0.16), residues: 2976 helix: 2.58 (0.13), residues: 1518 sheet: 1.20 (0.26), residues: 402 loop : -1.06 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 159 TYR 0.020 0.002 TYR D 77 PHE 0.011 0.001 PHE E 357 TRP 0.013 0.001 TRP F 549 HIS 0.004 0.001 HIS C 255 Details of bonding type rmsd covalent geometry : bond 0.00292 (23628) covalent geometry : angle 0.57397 (31944) hydrogen bonds : bond 0.04204 ( 1320) hydrogen bonds : angle 4.41038 ( 3816) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 214 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLN cc_start: 0.9279 (OUTLIER) cc_final: 0.8915 (mp10) REVERT: A 81 ARG cc_start: 0.8884 (ptp-110) cc_final: 0.8119 (ptp-110) REVERT: A 105 MET cc_start: 0.9267 (tpt) cc_final: 0.8853 (tmt) REVERT: A 547 ASN cc_start: 0.9295 (m-40) cc_final: 0.9044 (m110) REVERT: B 546 GLU cc_start: 0.8184 (tp30) cc_final: 0.7963 (tp30) REVERT: C 316 MET cc_start: 0.8733 (mtt) cc_final: 0.8504 (mtt) REVERT: C 318 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8352 (mp0) REVERT: D 105 MET cc_start: 0.9096 (tpt) cc_final: 0.8185 (tmm) REVERT: D 220 ILE cc_start: 0.9355 (pt) cc_final: 0.9126 (pp) REVERT: D 551 SER cc_start: 0.9336 (t) cc_final: 0.8911 (p) REVERT: E 80 GLN cc_start: 0.9181 (OUTLIER) cc_final: 0.8897 (mp10) REVERT: F 471 ASP cc_start: 0.9044 (t0) cc_final: 0.8778 (t0) outliers start: 17 outliers final: 2 residues processed: 219 average time/residue: 0.6985 time to fit residues: 174.6615 Evaluate side-chains 198 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 193 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain D residue 333 MET Chi-restraints excluded: chain E residue 80 GLN Chi-restraints excluded: chain E residue 548 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 237 optimal weight: 5.9990 chunk 19 optimal weight: 0.1980 chunk 123 optimal weight: 0.8980 chunk 73 optimal weight: 5.9990 chunk 260 optimal weight: 8.9990 chunk 246 optimal weight: 20.0000 chunk 225 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 207 optimal weight: 5.9990 chunk 265 optimal weight: 3.9990 chunk 292 optimal weight: 8.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 432 HIS F 325 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.111914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.066929 restraints weight = 47531.476| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 3.36 r_work: 0.2598 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23628 Z= 0.147 Angle : 0.547 7.801 31944 Z= 0.279 Chirality : 0.040 0.178 3546 Planarity : 0.003 0.049 4164 Dihedral : 4.072 14.826 3140 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.44 % Allowed : 9.75 % Favored : 89.81 % 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: 1.85 (0.16), residues: 2976 helix: 2.58 (0.13), residues: 1560 sheet: 1.18 (0.26), residues: 402 loop : -1.01 (0.20), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 159 TYR 0.016 0.001 TYR A 77 PHE 0.008 0.001 PHE D 357 TRP 0.013 0.001 TRP C 549 HIS 0.005 0.001 HIS E 485 Details of bonding type rmsd covalent geometry : bond 0.00341 (23628) covalent geometry : angle 0.54680 (31944) hydrogen bonds : bond 0.04080 ( 1320) hydrogen bonds : angle 4.15320 ( 3816) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 204 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.9256 (tpt) cc_final: 0.8646 (tmm) REVERT: A 547 ASN cc_start: 0.9302 (m-40) cc_final: 0.9063 (m110) REVERT: B 105 MET cc_start: 0.8828 (tpt) cc_final: 0.8613 (tpt) REVERT: C 318 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8282 (mp0) REVERT: D 105 MET cc_start: 0.9031 (tpt) cc_final: 0.8130 (tmm) REVERT: D 220 ILE cc_start: 0.9437 (pt) cc_final: 0.9214 (pp) REVERT: D 551 SER cc_start: 0.9353 (t) cc_final: 0.8915 (p) REVERT: E 80 GLN cc_start: 0.9123 (OUTLIER) cc_final: 0.8919 (mp10) REVERT: F 318 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8356 (mp0) outliers start: 11 outliers final: 2 residues processed: 207 average time/residue: 0.7197 time to fit residues: 169.3265 Evaluate side-chains 190 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 185 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain E residue 80 GLN Chi-restraints excluded: chain F residue 318 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 34 optimal weight: 0.3980 chunk 243 optimal weight: 7.9990 chunk 14 optimal weight: 0.8980 chunk 7 optimal weight: 8.9990 chunk 148 optimal weight: 20.0000 chunk 117 optimal weight: 5.9990 chunk 107 optimal weight: 9.9990 chunk 258 optimal weight: 6.9990 chunk 242 optimal weight: 0.9980 chunk 203 optimal weight: 20.0000 chunk 19 optimal weight: 0.7980 overall best weight: 1.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 325 GLN E 165 GLN E 540 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.111817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.067046 restraints weight = 47415.804| |-----------------------------------------------------------------------------| r_work (start): 0.2760 rms_B_bonded: 3.34 r_work: 0.2536 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23628 Z= 0.142 Angle : 0.548 8.365 31944 Z= 0.276 Chirality : 0.039 0.164 3546 Planarity : 0.003 0.031 4164 Dihedral : 4.002 14.737 3138 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.89 % Allowed : 11.29 % Favored : 87.82 % 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: 1.95 (0.16), residues: 2976 helix: 2.69 (0.13), residues: 1566 sheet: 1.15 (0.26), residues: 402 loop : -0.99 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 159 TYR 0.018 0.001 TYR A 77 PHE 0.008 0.001 PHE F 203 TRP 0.012 0.001 TRP A 549 HIS 0.004 0.001 HIS F 482 Details of bonding type rmsd covalent geometry : bond 0.00330 (23628) covalent geometry : angle 0.54758 (31944) hydrogen bonds : bond 0.03695 ( 1320) hydrogen bonds : angle 4.04589 ( 3816) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 193 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 MET cc_start: 0.9292 (tpt) cc_final: 0.8651 (tmm) REVERT: A 547 ASN cc_start: 0.9315 (m-40) cc_final: 0.9088 (m110) REVERT: B 105 MET cc_start: 0.8846 (tpt) cc_final: 0.8644 (tpt) REVERT: B 318 GLU cc_start: 0.9023 (mt-10) cc_final: 0.8565 (mp0) REVERT: C 318 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8322 (mp0) REVERT: C 368 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8408 (pp) REVERT: D 220 ILE cc_start: 0.9406 (pt) cc_final: 0.9201 (pp) REVERT: E 80 GLN cc_start: 0.9237 (OUTLIER) cc_final: 0.8772 (mp10) REVERT: E 105 MET cc_start: 0.9446 (mmp) cc_final: 0.9022 (tpt) REVERT: F 101 MET cc_start: 0.9077 (pmm) cc_final: 0.8824 (pmm) REVERT: F 368 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8337 (pp) outliers start: 22 outliers final: 4 residues processed: 205 average time/residue: 0.7061 time to fit residues: 165.0772 Evaluate side-chains 193 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 185 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain E residue 80 GLN Chi-restraints excluded: chain E residue 526 VAL Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 368 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 20 optimal weight: 0.9980 chunk 202 optimal weight: 20.0000 chunk 279 optimal weight: 4.9990 chunk 249 optimal weight: 4.9990 chunk 286 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 113 optimal weight: 6.9990 chunk 200 optimal weight: 6.9990 chunk 187 optimal weight: 6.9990 chunk 46 optimal weight: 10.0000 chunk 288 optimal weight: 0.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.109826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.064637 restraints weight = 47413.763| |-----------------------------------------------------------------------------| r_work (start): 0.2707 rms_B_bonded: 3.33 r_work: 0.2482 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 23628 Z= 0.242 Angle : 0.611 8.996 31944 Z= 0.310 Chirality : 0.042 0.174 3546 Planarity : 0.003 0.031 4164 Dihedral : 4.327 17.403 3138 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.42 % Allowed : 11.89 % Favored : 86.69 % 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: 1.89 (0.16), residues: 2976 helix: 2.67 (0.13), residues: 1560 sheet: 1.06 (0.26), residues: 402 loop : -1.03 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 159 TYR 0.015 0.002 TYR C 77 PHE 0.014 0.002 PHE F 203 TRP 0.011 0.001 TRP C 549 HIS 0.006 0.001 HIS E 482 Details of bonding type rmsd covalent geometry : bond 0.00569 (23628) covalent geometry : angle 0.61072 (31944) hydrogen bonds : bond 0.04571 ( 1320) hydrogen bonds : angle 4.14649 ( 3816) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 196 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLN cc_start: 0.9226 (OUTLIER) cc_final: 0.8875 (mp10) REVERT: A 105 MET cc_start: 0.9296 (tpt) cc_final: 0.8637 (tmm) REVERT: A 318 GLU cc_start: 0.9035 (mt-10) cc_final: 0.8688 (mp0) REVERT: A 547 ASN cc_start: 0.9302 (m-40) cc_final: 0.9083 (m110) REVERT: B 105 MET cc_start: 0.8895 (tpt) cc_final: 0.8658 (tpt) REVERT: B 318 GLU cc_start: 0.9013 (mt-10) cc_final: 0.8688 (mp0) REVERT: C 368 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8547 (pp) REVERT: D 105 MET cc_start: 0.9100 (tpt) cc_final: 0.8838 (tpt) REVERT: E 80 GLN cc_start: 0.9237 (OUTLIER) cc_final: 0.8884 (mp10) REVERT: E 318 GLU cc_start: 0.9024 (mt-10) cc_final: 0.8588 (mp0) REVERT: E 368 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8543 (pp) REVERT: E 515 GLN cc_start: 0.7766 (OUTLIER) cc_final: 0.7209 (mt0) REVERT: F 80 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.8725 (mp10) REVERT: F 318 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8256 (mp0) REVERT: F 368 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8543 (pp) outliers start: 35 outliers final: 5 residues processed: 219 average time/residue: 0.7014 time to fit residues: 175.1334 Evaluate side-chains 199 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 186 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain D residue 519 THR Chi-restraints excluded: chain E residue 80 GLN Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 515 GLN Chi-restraints excluded: chain F residue 80 GLN Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 318 GLU Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 519 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 115 optimal weight: 4.9990 chunk 194 optimal weight: 7.9990 chunk 139 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 169 optimal weight: 0.9980 chunk 119 optimal weight: 0.7980 chunk 176 optimal weight: 1.9990 chunk 99 optimal weight: 8.9990 chunk 216 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 GLN ** 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 = 0.3658 r_free = 0.3658 target = 0.112088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.067394 restraints weight = 47448.272| |-----------------------------------------------------------------------------| r_work (start): 0.2771 rms_B_bonded: 3.28 r_work: 0.2553 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23628 Z= 0.118 Angle : 0.540 8.442 31944 Z= 0.272 Chirality : 0.039 0.181 3546 Planarity : 0.003 0.029 4164 Dihedral : 3.984 14.795 3138 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.97 % Allowed : 13.11 % Favored : 85.92 % 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: 2.08 (0.16), residues: 2976 helix: 2.94 (0.13), residues: 1524 sheet: 1.14 (0.26), residues: 402 loop : -0.99 (0.20), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 159 TYR 0.013 0.001 TYR C 77 PHE 0.008 0.001 PHE A 357 TRP 0.013 0.001 TRP A 549 HIS 0.003 0.001 HIS E 482 Details of bonding type rmsd covalent geometry : bond 0.00271 (23628) covalent geometry : angle 0.53950 (31944) hydrogen bonds : bond 0.03390 ( 1320) hydrogen bonds : angle 3.96441 ( 3816) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 199 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLN cc_start: 0.9262 (OUTLIER) cc_final: 0.8886 (mp10) REVERT: A 105 MET cc_start: 0.9280 (tpt) cc_final: 0.8655 (tmm) REVERT: A 159 ARG cc_start: 0.7794 (ttt-90) cc_final: 0.7564 (tmt170) REVERT: A 547 ASN cc_start: 0.9321 (m-40) cc_final: 0.9095 (m110) REVERT: B 105 MET cc_start: 0.8885 (tpt) cc_final: 0.8649 (tpt) REVERT: B 318 GLU cc_start: 0.9018 (mt-10) cc_final: 0.8608 (mp0) REVERT: D 105 MET cc_start: 0.9097 (tpt) cc_final: 0.8828 (tpt) REVERT: E 80 GLN cc_start: 0.9267 (OUTLIER) cc_final: 0.8990 (mp10) REVERT: F 80 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.8540 (mp10) REVERT: F 101 MET cc_start: 0.9433 (mpp) cc_final: 0.9104 (pmm) REVERT: F 318 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8249 (mp0) outliers start: 24 outliers final: 9 residues processed: 216 average time/residue: 0.6514 time to fit residues: 161.8262 Evaluate side-chains 204 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 191 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain D residue 519 THR Chi-restraints excluded: chain E residue 80 GLN Chi-restraints excluded: chain F residue 80 GLN Chi-restraints excluded: chain F residue 197 ILE Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 318 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 267 optimal weight: 1.9990 chunk 154 optimal weight: 5.9990 chunk 43 optimal weight: 8.9990 chunk 119 optimal weight: 0.5980 chunk 277 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 142 optimal weight: 10.0000 chunk 53 optimal weight: 20.0000 chunk 108 optimal weight: 3.9990 chunk 64 optimal weight: 0.3980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 483 GLN ** 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 = 0.3645 r_free = 0.3645 target = 0.111192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.066452 restraints weight = 47405.844| |-----------------------------------------------------------------------------| r_work (start): 0.2751 rms_B_bonded: 3.33 r_work: 0.2526 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 23628 Z= 0.155 Angle : 0.562 9.327 31944 Z= 0.283 Chirality : 0.039 0.197 3546 Planarity : 0.003 0.029 4164 Dihedral : 4.016 15.555 3138 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.17 % Allowed : 13.31 % Favored : 85.52 % 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: 2.14 (0.16), residues: 2976 helix: 2.98 (0.13), residues: 1518 sheet: 1.11 (0.26), residues: 402 loop : -0.90 (0.20), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 159 TYR 0.013 0.001 TYR C 77 PHE 0.009 0.001 PHE F 203 TRP 0.011 0.001 TRP A 549 HIS 0.005 0.001 HIS E 482 Details of bonding type rmsd covalent geometry : bond 0.00364 (23628) covalent geometry : angle 0.56198 (31944) hydrogen bonds : bond 0.03695 ( 1320) hydrogen bonds : angle 3.97014 ( 3816) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 191 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLN cc_start: 0.9241 (OUTLIER) cc_final: 0.8867 (mp10) REVERT: A 105 MET cc_start: 0.9291 (tpt) cc_final: 0.8650 (tmm) REVERT: A 159 ARG cc_start: 0.7741 (ttt-90) cc_final: 0.7473 (tmt170) REVERT: A 318 GLU cc_start: 0.9026 (mt-10) cc_final: 0.8668 (mp0) REVERT: A 547 ASN cc_start: 0.9308 (m-40) cc_final: 0.9091 (m110) REVERT: B 105 MET cc_start: 0.8912 (tpt) cc_final: 0.8660 (tpt) REVERT: B 318 GLU cc_start: 0.9042 (mt-10) cc_final: 0.8704 (mp0) REVERT: C 318 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8299 (mp0) REVERT: D 105 MET cc_start: 0.9103 (tpt) cc_final: 0.8827 (tpt) REVERT: D 318 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8198 (mp0) REVERT: E 80 GLN cc_start: 0.9244 (OUTLIER) cc_final: 0.8899 (mp10) REVERT: E 316 MET cc_start: 0.8607 (mtm) cc_final: 0.8399 (mtm) REVERT: E 318 GLU cc_start: 0.9046 (mt-10) cc_final: 0.8715 (mp0) REVERT: F 318 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8197 (mp0) outliers start: 29 outliers final: 13 residues processed: 216 average time/residue: 0.6610 time to fit residues: 164.4804 Evaluate side-chains 209 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 191 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain D residue 318 GLU Chi-restraints excluded: chain D residue 519 THR Chi-restraints excluded: chain E residue 80 GLN Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain F residue 197 ILE Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 318 GLU Chi-restraints excluded: chain F residue 519 THR Chi-restraints excluded: chain F residue 531 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 186 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 211 optimal weight: 7.9990 chunk 194 optimal weight: 0.0370 chunk 123 optimal weight: 3.9990 chunk 212 optimal weight: 8.9990 chunk 130 optimal weight: 3.9990 chunk 233 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 263 optimal weight: 4.9990 overall best weight: 1.7662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 80 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.111588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.067069 restraints weight = 47477.591| |-----------------------------------------------------------------------------| r_work (start): 0.2750 rms_B_bonded: 3.28 r_work: 0.2531 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23628 Z= 0.143 Angle : 0.556 9.537 31944 Z= 0.282 Chirality : 0.039 0.196 3546 Planarity : 0.003 0.029 4164 Dihedral : 3.979 15.200 3138 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.13 % Allowed : 13.35 % Favored : 85.52 % 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: 2.16 (0.16), residues: 2976 helix: 3.05 (0.13), residues: 1518 sheet: 1.12 (0.26), residues: 402 loop : -0.98 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 159 TYR 0.013 0.001 TYR C 77 PHE 0.008 0.001 PHE F 203 TRP 0.011 0.001 TRP E 549 HIS 0.005 0.001 HIS A 485 Details of bonding type rmsd covalent geometry : bond 0.00335 (23628) covalent geometry : angle 0.55574 (31944) hydrogen bonds : bond 0.03557 ( 1320) hydrogen bonds : angle 3.94464 ( 3816) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 187 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLN cc_start: 0.9237 (OUTLIER) cc_final: 0.8855 (mp10) REVERT: A 105 MET cc_start: 0.9293 (tpt) cc_final: 0.8654 (tmm) REVERT: A 159 ARG cc_start: 0.7712 (ttt-90) cc_final: 0.7448 (tmt170) REVERT: A 316 MET cc_start: 0.8721 (mtm) cc_final: 0.8293 (mtm) REVERT: A 318 GLU cc_start: 0.9013 (mt-10) cc_final: 0.8640 (mp0) REVERT: A 547 ASN cc_start: 0.9302 (m-40) cc_final: 0.9093 (m110) REVERT: B 105 MET cc_start: 0.8928 (tpt) cc_final: 0.8678 (tpt) REVERT: B 318 GLU cc_start: 0.9015 (mt-10) cc_final: 0.8584 (mp0) REVERT: C 318 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8232 (mp0) REVERT: D 105 MET cc_start: 0.9103 (tpt) cc_final: 0.8823 (tpt) REVERT: D 318 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8123 (mp0) REVERT: E 80 GLN cc_start: 0.9272 (OUTLIER) cc_final: 0.8992 (mp10) REVERT: E 316 MET cc_start: 0.8627 (mtm) cc_final: 0.8338 (mtm) REVERT: E 318 GLU cc_start: 0.9018 (mt-10) cc_final: 0.8692 (mp0) REVERT: F 80 GLN cc_start: 0.8921 (OUTLIER) cc_final: 0.8604 (mp10) REVERT: F 101 MET cc_start: 0.9410 (mpp) cc_final: 0.9035 (pmm) REVERT: F 105 MET cc_start: 0.8813 (tpt) cc_final: 0.8366 (ppp) REVERT: F 318 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8133 (mp0) outliers start: 28 outliers final: 18 residues processed: 208 average time/residue: 0.6845 time to fit residues: 163.0698 Evaluate side-chains 209 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 185 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain B residue 80 GLN Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain D residue 318 GLU Chi-restraints excluded: chain D residue 519 THR Chi-restraints excluded: chain E residue 80 GLN Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain F residue 80 GLN Chi-restraints excluded: chain F residue 197 ILE Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 318 GLU Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 519 THR Chi-restraints excluded: chain F residue 531 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 277 optimal weight: 0.8980 chunk 171 optimal weight: 2.9990 chunk 222 optimal weight: 0.7980 chunk 142 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 228 optimal weight: 2.9990 chunk 193 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 53 optimal weight: 8.9990 chunk 263 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 483 GLN ** 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 = 0.3631 r_free = 0.3631 target = 0.111002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.066525 restraints weight = 48060.389| |-----------------------------------------------------------------------------| r_work (start): 0.2739 rms_B_bonded: 3.29 r_work: 0.2518 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 23628 Z= 0.163 Angle : 0.577 9.756 31944 Z= 0.290 Chirality : 0.040 0.209 3546 Planarity : 0.003 0.026 4164 Dihedral : 4.022 15.579 3138 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.09 % Allowed : 13.83 % Favored : 85.07 % 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: 2.10 (0.16), residues: 2976 helix: 2.86 (0.13), residues: 1554 sheet: 1.09 (0.26), residues: 420 loop : -0.94 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 159 TYR 0.014 0.001 TYR B 77 PHE 0.010 0.001 PHE F 203 TRP 0.011 0.001 TRP E 549 HIS 0.005 0.001 HIS A 485 Details of bonding type rmsd covalent geometry : bond 0.00383 (23628) covalent geometry : angle 0.57681 (31944) hydrogen bonds : bond 0.03713 ( 1320) hydrogen bonds : angle 3.96711 ( 3816) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 191 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLN cc_start: 0.9238 (OUTLIER) cc_final: 0.8857 (mp10) REVERT: A 105 MET cc_start: 0.9293 (tpt) cc_final: 0.8645 (tmm) REVERT: A 159 ARG cc_start: 0.7710 (ttt-90) cc_final: 0.7425 (tmt170) REVERT: A 316 MET cc_start: 0.8746 (mtm) cc_final: 0.8294 (mtm) REVERT: A 318 GLU cc_start: 0.9011 (mt-10) cc_final: 0.8652 (mp0) REVERT: A 447 MET cc_start: 0.9076 (mtp) cc_final: 0.8858 (mtm) REVERT: A 547 ASN cc_start: 0.9300 (m-40) cc_final: 0.9093 (m110) REVERT: B 318 GLU cc_start: 0.9016 (mt-10) cc_final: 0.8673 (mp0) REVERT: C 318 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8271 (mp0) REVERT: D 105 MET cc_start: 0.9108 (tpt) cc_final: 0.8874 (tpt) REVERT: D 316 MET cc_start: 0.8871 (mtm) cc_final: 0.8321 (mtm) REVERT: D 318 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8151 (mp0) REVERT: E 318 GLU cc_start: 0.9025 (mt-10) cc_final: 0.8702 (mp0) REVERT: F 105 MET cc_start: 0.8818 (tpt) cc_final: 0.8380 (ppp) REVERT: F 318 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8207 (mp0) outliers start: 27 outliers final: 19 residues processed: 213 average time/residue: 0.6768 time to fit residues: 165.4011 Evaluate side-chains 209 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 186 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 531 SER Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 531 SER Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain D residue 318 GLU Chi-restraints excluded: chain D residue 519 THR Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain F residue 197 ILE Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 318 GLU Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 519 THR Chi-restraints excluded: chain F residue 531 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 103 optimal weight: 20.0000 chunk 135 optimal weight: 0.8980 chunk 219 optimal weight: 4.9990 chunk 157 optimal weight: 3.9990 chunk 197 optimal weight: 7.9990 chunk 235 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 269 optimal weight: 0.9990 chunk 107 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 145 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 GLN ** 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 = 0.3657 r_free = 0.3657 target = 0.112672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.068348 restraints weight = 47593.421| |-----------------------------------------------------------------------------| r_work (start): 0.2782 rms_B_bonded: 3.29 r_work: 0.2564 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 23628 Z= 0.110 Angle : 0.553 9.942 31944 Z= 0.277 Chirality : 0.039 0.223 3546 Planarity : 0.003 0.026 4164 Dihedral : 3.860 14.878 3138 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.85 % Allowed : 14.00 % Favored : 85.15 % 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: 2.07 (0.16), residues: 2976 helix: 2.81 (0.13), residues: 1560 sheet: 0.96 (0.25), residues: 432 loop : -0.92 (0.21), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 159 TYR 0.012 0.001 TYR C 77 PHE 0.007 0.001 PHE B 357 TRP 0.013 0.001 TRP E 549 HIS 0.004 0.001 HIS A 485 Details of bonding type rmsd covalent geometry : bond 0.00254 (23628) covalent geometry : angle 0.55265 (31944) hydrogen bonds : bond 0.03161 ( 1320) hydrogen bonds : angle 3.91669 ( 3816) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5952 Ramachandran restraints generated. 2976 Oldfield, 0 Emsley, 2976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 192 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLN cc_start: 0.9201 (OUTLIER) cc_final: 0.8841 (mp10) REVERT: A 105 MET cc_start: 0.9280 (tpt) cc_final: 0.8646 (tmm) REVERT: A 159 ARG cc_start: 0.7729 (ttt-90) cc_final: 0.7470 (tmt170) REVERT: A 318 GLU cc_start: 0.9015 (mt-10) cc_final: 0.8671 (mp0) REVERT: A 547 ASN cc_start: 0.9292 (m-40) cc_final: 0.9085 (m110) REVERT: B 316 MET cc_start: 0.8890 (mtm) cc_final: 0.8396 (mtm) REVERT: B 318 GLU cc_start: 0.9006 (mt-10) cc_final: 0.8662 (mp0) REVERT: C 471 ASP cc_start: 0.8971 (t0) cc_final: 0.8743 (t0) REVERT: D 105 MET cc_start: 0.9106 (tpt) cc_final: 0.8867 (tpt) REVERT: E 316 MET cc_start: 0.8648 (mtm) cc_final: 0.8246 (mtm) REVERT: E 318 GLU cc_start: 0.8983 (mt-10) cc_final: 0.8669 (mp0) REVERT: F 101 MET cc_start: 0.9417 (mpp) cc_final: 0.8983 (pmm) REVERT: F 105 MET cc_start: 0.8803 (tpt) cc_final: 0.8330 (ppp) REVERT: F 318 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8230 (mp0) REVERT: F 471 ASP cc_start: 0.8964 (t0) cc_final: 0.8748 (t0) outliers start: 21 outliers final: 12 residues processed: 210 average time/residue: 0.6787 time to fit residues: 164.0499 Evaluate side-chains 197 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 183 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 531 SER Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain D residue 519 THR Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain F residue 197 ILE Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 318 GLU Chi-restraints excluded: chain F residue 519 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 253 optimal weight: 20.0000 chunk 249 optimal weight: 6.9990 chunk 130 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 92 optimal weight: 8.9990 chunk 22 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 275 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 236 optimal weight: 6.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 483 GLN ** 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 = 0.3639 r_free = 0.3639 target = 0.111488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.066820 restraints weight = 47888.951| |-----------------------------------------------------------------------------| r_work (start): 0.2747 rms_B_bonded: 3.31 r_work: 0.2527 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 23628 Z= 0.154 Angle : 0.579 9.914 31944 Z= 0.292 Chirality : 0.040 0.220 3546 Planarity : 0.003 0.025 4164 Dihedral : 3.958 15.393 3138 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.93 % Allowed : 14.20 % Favored : 84.87 % 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: 2.11 (0.16), residues: 2976 helix: 2.85 (0.13), residues: 1554 sheet: 0.93 (0.25), residues: 432 loop : -0.84 (0.21), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 159 TYR 0.012 0.001 TYR C 77 PHE 0.009 0.001 PHE F 203 TRP 0.011 0.001 TRP E 549 HIS 0.005 0.001 HIS A 485 Details of bonding type rmsd covalent geometry : bond 0.00362 (23628) covalent geometry : angle 0.57914 (31944) hydrogen bonds : bond 0.03632 ( 1320) hydrogen bonds : angle 3.95520 ( 3816) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10032.45 seconds wall clock time: 171 minutes 29.87 seconds (10289.87 seconds total)