Starting phenix.real_space_refine on Sat Jan 25 09:15:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jzl_36746/01_2025/8jzl_36746.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jzl_36746/01_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8jzl_36746/01_2025/8jzl_36746.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jzl_36746/01_2025/8jzl_36746.map" model { file = "/net/cci-nas-00/data/ceres_data/8jzl_36746/01_2025/8jzl_36746.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jzl_36746/01_2025/8jzl_36746.cif" } resolution = 2.62 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: C, B, E, D, F Time building chain proxies: 10.79, per 1000 atoms: 0.47 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: 5.69 Conformation dependent library (CDL) restraints added in 2.8 seconds 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: 2.19 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: 7.46 Time building geometry restraints manager: 6.44 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: 0.15 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 18.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.180 Set scattering table: 0.050 Process input model: 45.120 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.900 ------------------------------------------------------------------------------- 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= 0.562 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.008 0.001 TRP E 227 HIS 0.006 0.001 HIS F 482 PHE 0.017 0.002 PHE C 502 TYR 0.015 0.002 TYR D 77 ARG 0.003 0.001 ARG C 81 *********************** 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 : 2.642 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: 0.8159 (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: 1.4008 time to fit residues: 379.5425 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 : 2.813 ------------------------------------------------------------------------------- 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 248 optimal weight: 9.9990 chunk 222 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 150 optimal weight: 8.9990 chunk 119 optimal weight: 0.9990 chunk 230 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 140 optimal weight: 3.9990 chunk 171 optimal weight: 0.9980 chunk 266 optimal weight: 0.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- 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 C 103 ASN C 432 HIS 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 = 0.3673 r_free = 0.3673 target = 0.112958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.068399 restraints weight = 47114.110| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 3.33 r_work: 0.2608 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 23628 Z= 0.162 Angle : 0.564 7.006 31944 Z= 0.292 Chirality : 0.040 0.163 3546 Planarity : 0.003 0.031 4164 Dihedral : 4.206 14.254 3140 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.69 % Allowed : 6.84 % Favored : 92.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.16), residues: 2976 helix: 2.57 (0.13), residues: 1518 sheet: 1.19 (0.25), residues: 420 loop : -1.11 (0.20), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 549 HIS 0.003 0.001 HIS D 485 PHE 0.011 0.001 PHE E 357 TYR 0.019 0.001 TYR D 77 ARG 0.006 0.000 ARG B 159 *********************** 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 234 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 217 time to evaluate : 2.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLN cc_start: 0.9267 (OUTLIER) cc_final: 0.8885 (mp10) REVERT: A 81 ARG cc_start: 0.8852 (ptp-110) cc_final: 0.8128 (ptp-110) REVERT: A 105 MET cc_start: 0.9284 (tpt) cc_final: 0.8853 (tmt) REVERT: A 547 ASN cc_start: 0.9313 (m-40) cc_final: 0.9053 (m110) REVERT: B 546 GLU cc_start: 0.8213 (tp30) cc_final: 0.7995 (tp30) REVERT: D 105 MET cc_start: 0.9057 (tpt) cc_final: 0.8163 (tmm) REVERT: D 220 ILE cc_start: 0.9307 (pt) cc_final: 0.9087 (pp) REVERT: D 551 SER cc_start: 0.9349 (t) cc_final: 0.8928 (p) REVERT: E 80 GLN cc_start: 0.9178 (OUTLIER) cc_final: 0.8905 (mp10) REVERT: E 547 ASN cc_start: 0.9351 (m-40) cc_final: 0.9151 (m-40) REVERT: F 471 ASP cc_start: 0.8970 (t0) cc_final: 0.8742 (t0) outliers start: 17 outliers final: 2 residues processed: 223 average time/residue: 1.4152 time to fit residues: 362.6100 Evaluate side-chains 196 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 192 time to evaluate : 2.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN 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 4 optimal weight: 30.0000 chunk 245 optimal weight: 50.0000 chunk 78 optimal weight: 1.9990 chunk 280 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 chunk 124 optimal weight: 0.9990 chunk 222 optimal weight: 0.0170 chunk 81 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 144 optimal weight: 7.9990 overall best weight: 1.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 325 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.112645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.067951 restraints weight = 47235.870| |-----------------------------------------------------------------------------| r_work (start): 0.2787 rms_B_bonded: 3.33 r_work: 0.2564 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 23628 Z= 0.190 Angle : 0.531 7.614 31944 Z= 0.270 Chirality : 0.039 0.171 3546 Planarity : 0.003 0.050 4164 Dihedral : 3.970 13.683 3140 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.40 % Allowed : 9.75 % Favored : 89.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.16), residues: 2976 helix: 2.60 (0.13), residues: 1566 sheet: 1.18 (0.25), residues: 420 loop : -1.06 (0.20), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 549 HIS 0.005 0.001 HIS A 485 PHE 0.008 0.001 PHE E 357 TYR 0.017 0.002 TYR A 77 ARG 0.006 0.000 ARG D 159 *********************** 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 222 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 212 time to evaluate : 2.665 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: 0.9252 (tpt) cc_final: 0.8661 (tmm) REVERT: A 267 GLU cc_start: 0.8753 (tp30) cc_final: 0.8428 (mm-30) REVERT: A 547 ASN cc_start: 0.9283 (m-40) cc_final: 0.9035 (m110) REVERT: D 105 MET cc_start: 0.9034 (tpt) cc_final: 0.8140 (tmm) REVERT: D 220 ILE cc_start: 0.9402 (pt) cc_final: 0.9175 (pp) REVERT: D 318 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8360 (mp0) REVERT: D 551 SER cc_start: 0.9319 (t) cc_final: 0.8901 (p) REVERT: F 471 ASP cc_start: 0.9026 (t0) cc_final: 0.8778 (t0) outliers start: 10 outliers final: 4 residues processed: 215 average time/residue: 1.4741 time to fit residues: 361.8152 Evaluate side-chains 191 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 186 time to evaluate : 2.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain B residue 160 ASP Chi-restraints excluded: chain D residue 318 GLU Chi-restraints excluded: chain D residue 333 MET Chi-restraints excluded: chain E residue 526 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 157 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 222 optimal weight: 0.9980 chunk 160 optimal weight: 0.9990 chunk 122 optimal weight: 2.9990 chunk 103 optimal weight: 10.0000 chunk 124 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 52 optimal weight: 30.0000 chunk 135 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 165 GLN E 540 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.113316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.068742 restraints weight = 47376.508| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 3.36 r_work: 0.2576 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 23628 Z= 0.157 Angle : 0.522 8.456 31944 Z= 0.262 Chirality : 0.038 0.166 3546 Planarity : 0.003 0.055 4164 Dihedral : 3.845 13.338 3138 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.69 % Allowed : 11.21 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.16), residues: 2976 helix: 2.91 (0.13), residues: 1524 sheet: 1.17 (0.25), residues: 420 loop : -1.00 (0.20), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 549 HIS 0.003 0.001 HIS B 482 PHE 0.007 0.001 PHE D 357 TYR 0.018 0.001 TYR A 77 ARG 0.006 0.000 ARG E 159 *********************** 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 219 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 202 time to evaluate : 2.699 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: 0.9295 (tpt) cc_final: 0.8705 (tmm) REVERT: A 267 GLU cc_start: 0.8750 (tp30) cc_final: 0.8279 (mm-30) REVERT: A 547 ASN cc_start: 0.9333 (m-40) cc_final: 0.9100 (m110) REVERT: D 105 MET cc_start: 0.9060 (tpt) cc_final: 0.8180 (tmm) REVERT: D 220 ILE cc_start: 0.9400 (pt) cc_final: 0.9184 (pp) REVERT: D 551 SER cc_start: 0.9318 (t) cc_final: 0.8898 (p) REVERT: E 80 GLN cc_start: 0.9151 (OUTLIER) cc_final: 0.8917 (mp10) REVERT: F 101 MET cc_start: 0.9057 (pmm) cc_final: 0.8785 (pmm) REVERT: F 318 GLU cc_start: 0.8955 (mt-10) cc_final: 0.8578 (mp0) REVERT: F 471 ASP cc_start: 0.9030 (t0) cc_final: 0.8791 (t0) outliers start: 17 outliers final: 3 residues processed: 208 average time/residue: 1.4926 time to fit residues: 354.2904 Evaluate side-chains 195 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 191 time to evaluate : 2.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain D residue 333 MET Chi-restraints excluded: chain E residue 80 GLN Chi-restraints excluded: chain F residue 231 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 163 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 13 optimal weight: 0.0970 chunk 285 optimal weight: 6.9990 chunk 251 optimal weight: 30.0000 chunk 63 optimal weight: 2.9990 chunk 100 optimal weight: 7.9990 chunk 79 optimal weight: 6.9990 chunk 289 optimal weight: 8.9990 chunk 246 optimal weight: 5.9990 chunk 232 optimal weight: 0.8980 overall best weight: 2.1982 ------------------------------------------------------------------------------- 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 = 0.3644 r_free = 0.3644 target = 0.111123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.066555 restraints weight = 47424.738| |-----------------------------------------------------------------------------| r_work (start): 0.2743 rms_B_bonded: 3.32 r_work: 0.2516 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 23628 Z= 0.254 Angle : 0.561 9.203 31944 Z= 0.284 Chirality : 0.040 0.175 3546 Planarity : 0.003 0.046 4164 Dihedral : 4.054 16.357 3138 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.89 % Allowed : 11.93 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.16), residues: 2976 helix: 2.74 (0.13), residues: 1560 sheet: 1.16 (0.26), residues: 402 loop : -0.87 (0.20), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 549 HIS 0.005 0.001 HIS E 482 PHE 0.011 0.001 PHE F 203 TYR 0.014 0.002 TYR A 77 ARG 0.007 0.000 ARG E 159 *********************** 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 223 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 201 time to evaluate : 2.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLN cc_start: 0.9233 (OUTLIER) cc_final: 0.8876 (mp10) REVERT: A 105 MET cc_start: 0.9281 (tpt) cc_final: 0.8679 (tmm) REVERT: A 267 GLU cc_start: 0.8763 (tp30) cc_final: 0.8259 (mm-30) REVERT: A 318 GLU cc_start: 0.9009 (mt-10) cc_final: 0.8637 (mp0) REVERT: A 547 ASN cc_start: 0.9317 (m-40) cc_final: 0.9096 (m110) REVERT: B 318 GLU cc_start: 0.9021 (mt-10) cc_final: 0.8577 (mp0) REVERT: B 368 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8410 (pp) REVERT: C 368 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8427 (pp) REVERT: D 220 ILE cc_start: 0.9397 (pt) cc_final: 0.9196 (pp) REVERT: D 551 SER cc_start: 0.9321 (t) cc_final: 0.8884 (p) REVERT: E 80 GLN cc_start: 0.9080 (OUTLIER) cc_final: 0.8780 (mp10) REVERT: E 85 THR cc_start: 0.9342 (m) cc_final: 0.9123 (p) REVERT: E 547 ASN cc_start: 0.9325 (m-40) cc_final: 0.9102 (m-40) REVERT: F 105 MET cc_start: 0.8755 (tpt) cc_final: 0.8303 (ppp) REVERT: F 318 GLU cc_start: 0.8974 (mt-10) cc_final: 0.8640 (mp0) REVERT: F 368 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8353 (pp) outliers start: 22 outliers final: 4 residues processed: 215 average time/residue: 1.4326 time to fit residues: 353.7086 Evaluate side-chains 201 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 192 time to evaluate : 2.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 GLN Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain E residue 80 GLN Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain F residue 231 VAL Chi-restraints excluded: chain F residue 368 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 71 optimal weight: 2.9990 chunk 267 optimal weight: 0.7980 chunk 182 optimal weight: 2.9990 chunk 247 optimal weight: 1.9990 chunk 147 optimal weight: 50.0000 chunk 97 optimal weight: 1.9990 chunk 187 optimal weight: 5.9990 chunk 190 optimal weight: 2.9990 chunk 232 optimal weight: 4.9990 chunk 95 optimal weight: 9.9990 chunk 132 optimal weight: 0.5980 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 = 0.3657 r_free = 0.3657 target = 0.111928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.067392 restraints weight = 47150.043| |-----------------------------------------------------------------------------| r_work (start): 0.2769 rms_B_bonded: 3.32 r_work: 0.2544 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23628 Z= 0.203 Angle : 0.542 8.581 31944 Z= 0.272 Chirality : 0.039 0.179 3546 Planarity : 0.003 0.044 4164 Dihedral : 3.938 14.373 3138 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.25 % Allowed : 12.14 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.16), residues: 2976 helix: 2.95 (0.13), residues: 1524 sheet: 1.15 (0.26), residues: 402 loop : -0.92 (0.20), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 549 HIS 0.005 0.001 HIS A 485 PHE 0.007 0.001 PHE F 203 TYR 0.013 0.001 TYR C 77 ARG 0.005 0.000 ARG A 159 *********************** 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 227 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 196 time to evaluate : 2.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLN cc_start: 0.9211 (OUTLIER) cc_final: 0.8855 (mp10) REVERT: A 105 MET cc_start: 0.9310 (tpt) cc_final: 0.8689 (tmm) REVERT: A 267 GLU cc_start: 0.8742 (tp30) cc_final: 0.8290 (mm-30) REVERT: A 318 GLU cc_start: 0.8999 (mt-10) cc_final: 0.8623 (mp0) REVERT: A 547 ASN cc_start: 0.9310 (m-40) cc_final: 0.9096 (m110) REVERT: B 318 GLU cc_start: 0.9017 (mt-10) cc_final: 0.8684 (mp0) REVERT: C 318 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8329 (mp0) REVERT: D 105 MET cc_start: 0.9104 (tpt) cc_final: 0.8844 (tpt) REVERT: E 80 GLN cc_start: 0.9232 (OUTLIER) cc_final: 0.8661 (mp10) REVERT: E 105 MET cc_start: 0.9432 (mmp) cc_final: 0.9028 (tpt) REVERT: E 318 GLU cc_start: 0.9017 (mt-10) cc_final: 0.8597 (mp0) REVERT: E 547 ASN cc_start: 0.9306 (m-40) cc_final: 0.9094 (m-40) REVERT: F 80 GLN cc_start: 0.8944 (mp10) cc_final: 0.8646 (mp10) REVERT: F 101 MET cc_start: 0.9425 (mpp) cc_final: 0.9105 (pmm) REVERT: F 318 GLU cc_start: 0.8960 (mt-10) cc_final: 0.8633 (mp0) outliers start: 31 outliers final: 7 residues processed: 219 average time/residue: 1.3908 time to fit residues: 350.4396 Evaluate side-chains 200 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 190 time to evaluate : 2.682 ------------------------------------------------------------------------------- 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 C residue 231 VAL Chi-restraints excluded: chain C 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 531 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 67 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 95 optimal weight: 10.0000 chunk 145 optimal weight: 9.9990 chunk 261 optimal weight: 7.9990 chunk 275 optimal weight: 4.9990 chunk 7 optimal weight: 10.0000 chunk 26 optimal weight: 0.5980 chunk 270 optimal weight: 0.9990 chunk 151 optimal weight: 4.9990 chunk 94 optimal weight: 7.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- 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 = 0.3636 r_free = 0.3636 target = 0.110674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.065949 restraints weight = 47490.862| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 3.33 r_work: 0.2572 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 23628 Z= 0.286 Angle : 0.575 9.371 31944 Z= 0.290 Chirality : 0.040 0.197 3546 Planarity : 0.003 0.043 4164 Dihedral : 4.076 16.113 3138 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.89 % Allowed : 12.74 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.16), residues: 2976 helix: 2.83 (0.13), residues: 1554 sheet: 1.13 (0.26), residues: 402 loop : -0.87 (0.20), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 549 HIS 0.005 0.001 HIS F 482 PHE 0.011 0.001 PHE F 203 TYR 0.013 0.001 TYR C 77 ARG 0.003 0.000 ARG A 81 *********************** 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: 22 poor density : 198 time to evaluate : 2.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLN cc_start: 0.9239 (OUTLIER) cc_final: 0.8860 (mp10) REVERT: A 105 MET cc_start: 0.9298 (tpt) cc_final: 0.8665 (tmm) REVERT: A 267 GLU cc_start: 0.8762 (tp30) cc_final: 0.8275 (mm-30) REVERT: A 318 GLU cc_start: 0.9014 (mt-10) cc_final: 0.8651 (mp0) REVERT: A 547 ASN cc_start: 0.9311 (m-40) cc_final: 0.9099 (m110) REVERT: B 318 GLU cc_start: 0.9051 (mt-10) cc_final: 0.8711 (mp0) REVERT: D 105 MET cc_start: 0.9130 (tpt) cc_final: 0.8911 (tpt) REVERT: E 80 GLN cc_start: 0.9211 (OUTLIER) cc_final: 0.8786 (mp10) REVERT: E 85 THR cc_start: 0.9325 (m) cc_final: 0.9093 (p) REVERT: E 105 MET cc_start: 0.9421 (mmp) cc_final: 0.8728 (tmm) REVERT: E 316 MET cc_start: 0.8672 (mtm) cc_final: 0.8460 (mtm) REVERT: E 318 GLU cc_start: 0.9054 (mt-10) cc_final: 0.8627 (mp0) REVERT: F 80 GLN cc_start: 0.8986 (mp10) cc_final: 0.8585 (mp10) REVERT: F 105 MET cc_start: 0.8790 (tpt) cc_final: 0.8352 (ppp) REVERT: F 318 GLU cc_start: 0.9000 (mt-10) cc_final: 0.8636 (mp0) outliers start: 22 outliers final: 12 residues processed: 216 average time/residue: 1.4343 time to fit residues: 356.0631 Evaluate side-chains 209 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 195 time to evaluate : 2.613 ------------------------------------------------------------------------------- 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 C residue 231 VAL Chi-restraints excluded: chain C residue 368 LEU 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 E residue 231 VAL Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain F residue 231 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 185 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 143 optimal weight: 4.9990 chunk 52 optimal weight: 8.9990 chunk 184 optimal weight: 0.6980 chunk 249 optimal weight: 8.9990 chunk 53 optimal weight: 7.9990 chunk 6 optimal weight: 8.9990 chunk 48 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- 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 = 0.3625 r_free = 0.3625 target = 0.110867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.066243 restraints weight = 47681.923| |-----------------------------------------------------------------------------| r_work (start): 0.2730 rms_B_bonded: 3.27 r_work: 0.2510 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 23628 Z= 0.285 Angle : 0.582 9.585 31944 Z= 0.293 Chirality : 0.040 0.196 3546 Planarity : 0.003 0.043 4164 Dihedral : 4.090 16.217 3138 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.93 % Allowed : 12.86 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.16), residues: 2976 helix: 3.02 (0.13), residues: 1512 sheet: 1.10 (0.26), residues: 402 loop : -0.94 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 549 HIS 0.006 0.001 HIS A 485 PHE 0.011 0.001 PHE F 203 TYR 0.013 0.001 TYR C 77 ARG 0.004 0.000 ARG A 81 *********************** 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 219 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 196 time to evaluate : 2.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLN cc_start: 0.9256 (OUTLIER) cc_final: 0.8865 (mp10) REVERT: A 105 MET cc_start: 0.9291 (tpt) cc_final: 0.8644 (tmm) REVERT: A 267 GLU cc_start: 0.8745 (tp30) cc_final: 0.8357 (mm-30) REVERT: A 318 GLU cc_start: 0.8986 (mt-10) cc_final: 0.8615 (mp0) REVERT: B 318 GLU cc_start: 0.9027 (mt-10) cc_final: 0.8601 (mp0) REVERT: D 105 MET cc_start: 0.9100 (tpt) cc_final: 0.8875 (tpt) REVERT: E 105 MET cc_start: 0.9427 (mmp) cc_final: 0.8716 (tmm) REVERT: E 316 MET cc_start: 0.8639 (mtm) cc_final: 0.8402 (mtm) REVERT: E 318 GLU cc_start: 0.9029 (mt-10) cc_final: 0.8695 (mp0) REVERT: F 80 GLN cc_start: 0.8999 (mp10) cc_final: 0.8638 (mp10) REVERT: F 101 MET cc_start: 0.9417 (mpp) cc_final: 0.9040 (pmm) REVERT: F 105 MET cc_start: 0.8815 (tpt) cc_final: 0.8352 (ppp) REVERT: F 318 GLU cc_start: 0.8995 (mt-10) cc_final: 0.8628 (mp0) outliers start: 23 outliers final: 14 residues processed: 214 average time/residue: 1.4548 time to fit residues: 356.9466 Evaluate side-chains 206 residues out of total 2478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 191 time to evaluate : 2.418 ------------------------------------------------------------------------------- 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 519 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 368 LEU 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 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 ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.3072 > 50: distance: 64 - 73: 3.317 distance: 73 - 74: 15.317 distance: 73 - 79: 10.186 distance: 74 - 75: 12.306 distance: 74 - 77: 11.753 distance: 75 - 76: 14.174 distance: 75 - 80: 5.694 distance: 77 - 78: 21.674 distance: 78 - 79: 15.722 distance: 80 - 81: 10.475 distance: 81 - 82: 20.186 distance: 81 - 84: 19.541 distance: 82 - 83: 22.726 distance: 82 - 89: 32.096 distance: 84 - 85: 9.425 distance: 85 - 86: 7.402 distance: 86 - 87: 5.185 distance: 86 - 88: 21.021 distance: 89 - 90: 6.666 distance: 90 - 91: 11.590 distance: 90 - 93: 14.603 distance: 91 - 92: 9.941 distance: 91 - 94: 4.359 distance: 94 - 95: 14.262 distance: 95 - 96: 12.022 distance: 95 - 98: 14.025 distance: 96 - 97: 15.249 distance: 96 - 105: 18.146 distance: 98 - 99: 13.550 distance: 99 - 100: 15.352 distance: 100 - 101: 14.925 distance: 101 - 102: 5.470 distance: 102 - 103: 7.634 distance: 102 - 104: 7.870 distance: 105 - 106: 9.455 distance: 105 - 111: 10.704 distance: 106 - 107: 10.075 distance: 106 - 109: 14.337 distance: 107 - 108: 7.082 distance: 107 - 112: 6.209 distance: 109 - 110: 7.763 distance: 110 - 111: 20.728 distance: 112 - 113: 10.776 distance: 113 - 114: 15.022 distance: 114 - 115: 18.529 distance: 114 - 116: 4.353 distance: 115 - 141: 15.458 distance: 116 - 117: 4.767 distance: 118 - 119: 10.424 distance: 118 - 120: 5.293 distance: 119 - 145: 10.998 distance: 121 - 122: 3.092 distance: 122 - 123: 13.387 distance: 122 - 134: 11.133 distance: 123 - 154: 13.508 distance: 125 - 126: 5.034 distance: 126 - 128: 3.391 distance: 134 - 135: 4.359 distance: 135 - 136: 9.213 distance: 135 - 138: 7.652 distance: 136 - 137: 5.128 distance: 136 - 141: 6.698 distance: 137 - 161: 6.894 distance: 138 - 139: 7.311 distance: 138 - 140: 15.183 distance: 141 - 142: 6.512 distance: 142 - 143: 6.105 distance: 143 - 144: 8.662 distance: 143 - 145: 4.879 distance: 144 - 169: 11.407