Starting phenix.real_space_refine on Thu Mar 5 12:19:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y72_72639/03_2026/9y72_72639.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y72_72639/03_2026/9y72_72639.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9y72_72639/03_2026/9y72_72639.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y72_72639/03_2026/9y72_72639.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9y72_72639/03_2026/9y72_72639.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y72_72639/03_2026/9y72_72639.map" } resolution = 2.51 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= 0.003 sd= 0.119 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 36 5.16 5 C 13740 2.51 5 N 3948 2.21 5 O 4200 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21924 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1827 Classifications: {'peptide': 241} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 231} Chain: "B" Number of atoms: 1827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1827 Classifications: {'peptide': 241} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 231} Chain: "C" Number of atoms: 1827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1827 Classifications: {'peptide': 241} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 231} Chain: "D" Number of atoms: 1827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1827 Classifications: {'peptide': 241} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 231} Chain: "E" Number of atoms: 1827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1827 Classifications: {'peptide': 241} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 231} Chain: "F" Number of atoms: 1827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1827 Classifications: {'peptide': 241} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 231} Chain: "G" Number of atoms: 1827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1827 Classifications: {'peptide': 241} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 231} Chain: "H" Number of atoms: 1827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1827 Classifications: {'peptide': 241} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 231} Chain: "I" Number of atoms: 1827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1827 Classifications: {'peptide': 241} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 231} Chain: "J" Number of atoms: 1827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1827 Classifications: {'peptide': 241} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 231} Chain: "K" Number of atoms: 1827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1827 Classifications: {'peptide': 241} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 231} Chain: "L" Number of atoms: 1827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1827 Classifications: {'peptide': 241} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 231} Time building chain proxies: 5.17, per 1000 atoms: 0.24 Number of scatterers: 21924 At special positions: 0 Unit cell: (126.684, 149.04, 113.436, 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 36 16.00 O 4200 8.00 N 3948 7.00 C 13740 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.78 Conformation dependent library (CDL) restraints added in 1.1 seconds 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5304 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 26 sheets defined 44.9% alpha, 14.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 322 through 339 removed outlier: 3.754A pdb=" N ARG A 333 " --> pdb=" O ALA A 329 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR A 339 " --> pdb=" O SER A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 369 removed outlier: 5.419A pdb=" N ALA A 362 " --> pdb=" O ALA A 358 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N ALA A 363 " --> pdb=" O ARG A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 389 Processing helix chain 'A' and resid 428 through 432 Processing helix chain 'A' and resid 433 through 450 Processing helix chain 'A' and resid 454 through 459 removed outlier: 4.080A pdb=" N LEU A 458 " --> pdb=" O PRO A 455 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER A 459 " --> pdb=" O ASP A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 472 removed outlier: 3.633A pdb=" N SER A 470 " --> pdb=" O ASN A 467 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLN A 471 " --> pdb=" O ILE A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 545 Processing helix chain 'B' and resid 322 through 338 removed outlier: 3.779A pdb=" N ARG B 333 " --> pdb=" O ALA B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 368 removed outlier: 5.398A pdb=" N ALA B 362 " --> pdb=" O ALA B 358 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N ALA B 363 " --> pdb=" O ARG B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 389 Processing helix chain 'B' and resid 428 through 432 Processing helix chain 'B' and resid 433 through 451 Processing helix chain 'B' and resid 454 through 459 removed outlier: 3.769A pdb=" N LEU B 458 " --> pdb=" O PRO B 455 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER B 459 " --> pdb=" O ASP B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 472 removed outlier: 3.987A pdb=" N GLN B 471 " --> pdb=" O ILE B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 545 Processing helix chain 'B' and resid 547 through 552 Processing helix chain 'C' and resid 322 through 339 removed outlier: 3.734A pdb=" N ARG C 333 " --> pdb=" O ALA C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 369 removed outlier: 5.500A pdb=" N ALA C 362 " --> pdb=" O ALA C 358 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N ALA C 363 " --> pdb=" O ARG C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 389 Processing helix chain 'C' and resid 433 through 451 Processing helix chain 'C' and resid 454 through 459 removed outlier: 3.951A pdb=" N LEU C 458 " --> pdb=" O PRO C 455 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER C 459 " --> pdb=" O ASP C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 472 removed outlier: 4.042A pdb=" N GLN C 471 " --> pdb=" O ILE C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 527 through 545 Processing helix chain 'D' and resid 322 through 339 removed outlier: 3.715A pdb=" N ARG D 333 " --> pdb=" O ALA D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 369 removed outlier: 5.522A pdb=" N ALA D 362 " --> pdb=" O ALA D 358 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N ALA D 363 " --> pdb=" O ARG D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 389 Processing helix chain 'D' and resid 433 through 451 Processing helix chain 'D' and resid 454 through 459 removed outlier: 3.850A pdb=" N LEU D 458 " --> pdb=" O PRO D 455 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER D 459 " --> pdb=" O ASP D 456 " (cutoff:3.500A) Processing helix chain 'D' and resid 467 through 471 removed outlier: 3.501A pdb=" N SER D 470 " --> pdb=" O ASN D 467 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLN D 471 " --> pdb=" O ILE D 468 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 467 through 471' Processing helix chain 'D' and resid 527 through 545 Processing helix chain 'E' and resid 322 through 339 removed outlier: 3.761A pdb=" N ARG E 333 " --> pdb=" O ALA E 329 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR E 339 " --> pdb=" O SER E 335 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 369 removed outlier: 5.365A pdb=" N ALA E 362 " --> pdb=" O ALA E 358 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N ALA E 363 " --> pdb=" O ARG E 359 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 389 Processing helix chain 'E' and resid 428 through 432 Processing helix chain 'E' and resid 433 through 450 Processing helix chain 'E' and resid 454 through 459 removed outlier: 4.086A pdb=" N LEU E 458 " --> pdb=" O PRO E 455 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER E 459 " --> pdb=" O ASP E 456 " (cutoff:3.500A) Processing helix chain 'E' and resid 467 through 472 removed outlier: 3.641A pdb=" N SER E 470 " --> pdb=" O ASN E 467 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLN E 471 " --> pdb=" O ILE E 468 " (cutoff:3.500A) Processing helix chain 'E' and resid 527 through 545 Processing helix chain 'F' and resid 322 through 339 removed outlier: 3.776A pdb=" N ARG F 333 " --> pdb=" O ALA F 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 368 removed outlier: 5.367A pdb=" N ALA F 362 " --> pdb=" O ALA F 358 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N ALA F 363 " --> pdb=" O ARG F 359 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 389 Processing helix chain 'F' and resid 428 through 432 Processing helix chain 'F' and resid 433 through 451 Processing helix chain 'F' and resid 454 through 459 removed outlier: 3.714A pdb=" N LEU F 458 " --> pdb=" O PRO F 455 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER F 459 " --> pdb=" O ASP F 456 " (cutoff:3.500A) Processing helix chain 'F' and resid 468 through 472 removed outlier: 4.015A pdb=" N GLN F 471 " --> pdb=" O ILE F 468 " (cutoff:3.500A) Processing helix chain 'F' and resid 527 through 545 Processing helix chain 'F' and resid 547 through 552 Processing helix chain 'G' and resid 322 through 339 removed outlier: 3.652A pdb=" N ARG G 333 " --> pdb=" O ALA G 329 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR G 339 " --> pdb=" O SER G 335 " (cutoff:3.500A) Processing helix chain 'G' and resid 350 through 369 removed outlier: 5.120A pdb=" N ALA G 362 " --> pdb=" O ALA G 358 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N ALA G 363 " --> pdb=" O ARG G 359 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU G 366 " --> pdb=" O ALA G 362 " (cutoff:3.500A) Processing helix chain 'G' and resid 374 through 389 Processing helix chain 'G' and resid 428 through 432 Processing helix chain 'G' and resid 433 through 450 Processing helix chain 'G' and resid 454 through 459 removed outlier: 4.092A pdb=" N LEU G 458 " --> pdb=" O PRO G 455 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER G 459 " --> pdb=" O ASP G 456 " (cutoff:3.500A) Processing helix chain 'G' and resid 467 through 472 removed outlier: 3.657A pdb=" N SER G 470 " --> pdb=" O ASN G 467 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLN G 471 " --> pdb=" O ILE G 468 " (cutoff:3.500A) Processing helix chain 'G' and resid 527 through 545 Processing helix chain 'G' and resid 547 through 552 Processing helix chain 'H' and resid 322 through 338 removed outlier: 3.625A pdb=" N ARG H 333 " --> pdb=" O ALA H 329 " (cutoff:3.500A) Processing helix chain 'H' and resid 350 through 368 removed outlier: 4.929A pdb=" N ALA H 362 " --> pdb=" O ALA H 358 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N ALA H 363 " --> pdb=" O ARG H 359 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU H 366 " --> pdb=" O ALA H 362 " (cutoff:3.500A) Processing helix chain 'H' and resid 374 through 389 Processing helix chain 'H' and resid 433 through 451 Processing helix chain 'H' and resid 454 through 459 removed outlier: 3.734A pdb=" N LEU H 458 " --> pdb=" O PRO H 455 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER H 459 " --> pdb=" O ASP H 456 " (cutoff:3.500A) Processing helix chain 'H' and resid 468 through 472 removed outlier: 4.017A pdb=" N GLN H 471 " --> pdb=" O ILE H 468 " (cutoff:3.500A) Processing helix chain 'H' and resid 527 through 545 Processing helix chain 'H' and resid 547 through 552 Processing helix chain 'I' and resid 322 through 339 removed outlier: 3.667A pdb=" N ARG I 333 " --> pdb=" O ALA I 329 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR I 339 " --> pdb=" O SER I 335 " (cutoff:3.500A) Processing helix chain 'I' and resid 350 through 369 removed outlier: 5.099A pdb=" N ALA I 362 " --> pdb=" O ALA I 358 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N ALA I 363 " --> pdb=" O ARG I 359 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU I 366 " --> pdb=" O ALA I 362 " (cutoff:3.500A) Processing helix chain 'I' and resid 374 through 389 Processing helix chain 'I' and resid 433 through 451 Processing helix chain 'I' and resid 454 through 459 removed outlier: 3.965A pdb=" N LEU I 458 " --> pdb=" O PRO I 455 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER I 459 " --> pdb=" O ASP I 456 " (cutoff:3.500A) Processing helix chain 'I' and resid 467 through 472 removed outlier: 4.038A pdb=" N GLN I 471 " --> pdb=" O ILE I 468 " (cutoff:3.500A) Processing helix chain 'I' and resid 527 through 545 Processing helix chain 'J' and resid 322 through 339 removed outlier: 3.658A pdb=" N ARG J 333 " --> pdb=" O ALA J 329 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR J 339 " --> pdb=" O SER J 335 " (cutoff:3.500A) Processing helix chain 'J' and resid 350 through 369 removed outlier: 5.012A pdb=" N ALA J 362 " --> pdb=" O ALA J 358 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N ALA J 363 " --> pdb=" O ARG J 359 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU J 366 " --> pdb=" O ALA J 362 " (cutoff:3.500A) Processing helix chain 'J' and resid 374 through 389 Processing helix chain 'J' and resid 433 through 451 Processing helix chain 'J' and resid 454 through 459 removed outlier: 3.881A pdb=" N LEU J 458 " --> pdb=" O PRO J 455 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER J 459 " --> pdb=" O ASP J 456 " (cutoff:3.500A) Processing helix chain 'J' and resid 467 through 471 removed outlier: 3.505A pdb=" N SER J 470 " --> pdb=" O ASN J 467 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLN J 471 " --> pdb=" O ILE J 468 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 467 through 471' Processing helix chain 'J' and resid 527 through 545 Processing helix chain 'K' and resid 322 through 339 removed outlier: 3.651A pdb=" N ARG K 333 " --> pdb=" O ALA K 329 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR K 339 " --> pdb=" O SER K 335 " (cutoff:3.500A) Processing helix chain 'K' and resid 350 through 369 removed outlier: 5.131A pdb=" N ALA K 362 " --> pdb=" O ALA K 358 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N ALA K 363 " --> pdb=" O ARG K 359 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU K 366 " --> pdb=" O ALA K 362 " (cutoff:3.500A) Processing helix chain 'K' and resid 374 through 389 Processing helix chain 'K' and resid 428 through 432 Processing helix chain 'K' and resid 433 through 451 Processing helix chain 'K' and resid 454 through 459 removed outlier: 4.089A pdb=" N LEU K 458 " --> pdb=" O PRO K 455 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER K 459 " --> pdb=" O ASP K 456 " (cutoff:3.500A) Processing helix chain 'K' and resid 467 through 472 removed outlier: 3.651A pdb=" N SER K 470 " --> pdb=" O ASN K 467 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLN K 471 " --> pdb=" O ILE K 468 " (cutoff:3.500A) Processing helix chain 'K' and resid 527 through 545 Processing helix chain 'K' and resid 547 through 552 Processing helix chain 'L' and resid 322 through 338 removed outlier: 3.624A pdb=" N ARG L 333 " --> pdb=" O ALA L 329 " (cutoff:3.500A) Processing helix chain 'L' and resid 350 through 369 removed outlier: 4.933A pdb=" N ALA L 362 " --> pdb=" O ALA L 358 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ALA L 363 " --> pdb=" O ARG L 359 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU L 366 " --> pdb=" O ALA L 362 " (cutoff:3.500A) Processing helix chain 'L' and resid 374 through 389 Processing helix chain 'L' and resid 428 through 432 Processing helix chain 'L' and resid 433 through 451 Processing helix chain 'L' and resid 454 through 459 removed outlier: 3.745A pdb=" N LEU L 458 " --> pdb=" O PRO L 455 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N SER L 459 " --> pdb=" O ASP L 456 " (cutoff:3.500A) Processing helix chain 'L' and resid 468 through 472 removed outlier: 4.013A pdb=" N GLN L 471 " --> pdb=" O ILE L 468 " (cutoff:3.500A) Processing helix chain 'L' and resid 527 through 545 Processing sheet with id=AA1, first strand: chain 'A' and resid 318 through 320 Processing sheet with id=AA2, first strand: chain 'A' and resid 341 through 349 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 341 through 349 current: chain 'A' and resid 425 through 426 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 425 through 426 current: chain 'A' and resid 486 through 489 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 486 through 489 current: chain 'A' and resid 507 through 522 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 507 through 522 current: chain 'E' and resid 341 through 349 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 341 through 349 current: chain 'E' and resid 425 through 426 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 425 through 426 current: chain 'E' and resid 486 through 489 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 486 through 489 current: chain 'E' and resid 507 through 522 No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 394 through 397 Processing sheet with id=AA4, first strand: chain 'A' and resid 415 through 417 Processing sheet with id=AA5, first strand: chain 'A' and resid 475 through 476 removed outlier: 3.688A pdb=" N PHE A 475 " --> pdb=" O THR B 345 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 341 through 349 current: chain 'B' and resid 420 through 422 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 420 through 422 current: chain 'B' and resid 486 through 489 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 486 through 489 current: chain 'B' and resid 507 through 522 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 507 through 522 current: chain 'D' and resid 425 through 426 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 425 through 426 current: chain 'D' and resid 486 through 489 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 486 through 489 current: chain 'D' and resid 507 through 522 Processing sheet with id=AA6, first strand: chain 'B' and resid 318 through 320 Processing sheet with id=AA7, first strand: chain 'C' and resid 341 through 349 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 341 through 349 current: chain 'C' and resid 425 through 426 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 425 through 426 current: chain 'C' and resid 486 through 489 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 486 through 489 current: chain 'C' and resid 507 through 522 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 507 through 522 current: chain 'F' and resid 420 through 422 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 420 through 422 current: chain 'F' and resid 486 through 489 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 486 through 489 current: chain 'F' and resid 507 through 522 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 415 through 417 Processing sheet with id=AA9, first strand: chain 'D' and resid 318 through 320 Processing sheet with id=AB1, first strand: chain 'D' and resid 394 through 397 Processing sheet with id=AB2, first strand: chain 'D' and resid 415 through 416 Processing sheet with id=AB3, first strand: chain 'E' and resid 318 through 320 Processing sheet with id=AB4, first strand: chain 'E' and resid 415 through 417 Processing sheet with id=AB5, first strand: chain 'G' and resid 318 through 320 Processing sheet with id=AB6, first strand: chain 'G' and resid 341 through 349 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 341 through 349 current: chain 'G' and resid 425 through 426 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 425 through 426 current: chain 'G' and resid 486 through 489 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 486 through 489 current: chain 'G' and resid 507 through 522 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 507 through 522 current: chain 'K' and resid 341 through 349 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 341 through 349 current: chain 'K' and resid 425 through 426 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 425 through 426 current: chain 'K' and resid 486 through 489 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 486 through 489 current: chain 'K' and resid 507 through 522 No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'G' and resid 394 through 397 Processing sheet with id=AB8, first strand: chain 'G' and resid 415 through 417 Processing sheet with id=AB9, first strand: chain 'G' and resid 475 through 476 removed outlier: 3.700A pdb=" N PHE G 475 " --> pdb=" O THR H 345 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 341 through 349 current: chain 'H' and resid 420 through 422 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 420 through 422 current: chain 'H' and resid 486 through 489 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 486 through 489 current: chain 'H' and resid 507 through 522 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 507 through 522 current: chain 'J' and resid 425 through 426 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 425 through 426 current: chain 'J' and resid 486 through 489 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 486 through 489 current: chain 'J' and resid 507 through 522 Processing sheet with id=AC1, first strand: chain 'H' and resid 318 through 320 Processing sheet with id=AC2, first strand: chain 'H' and resid 475 through 476 removed outlier: 3.700A pdb=" N PHE H 475 " --> pdb=" O THR I 345 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 341 through 349 current: chain 'I' and resid 425 through 426 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 425 through 426 current: chain 'I' and resid 486 through 489 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 486 through 489 current: chain 'I' and resid 507 through 522 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 507 through 522 current: chain 'L' and resid 341 through 349 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 341 through 349 current: chain 'L' and resid 420 through 422 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 420 through 422 current: chain 'L' and resid 486 through 489 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 486 through 489 current: chain 'L' and resid 507 through 522 Processing sheet with id=AC3, first strand: chain 'I' and resid 415 through 417 Processing sheet with id=AC4, first strand: chain 'J' and resid 318 through 320 Processing sheet with id=AC5, first strand: chain 'J' and resid 394 through 397 Processing sheet with id=AC6, first strand: chain 'J' and resid 415 through 416 Processing sheet with id=AC7, first strand: chain 'K' and resid 318 through 320 removed outlier: 3.592A pdb=" N GLU L 402 " --> pdb=" O ASN L 397 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 415 through 417 957 hydrogen bonds defined for protein. 2682 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.71 Time building geometry restraints manager: 2.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7576 1.34 - 1.46: 3016 1.46 - 1.57: 11620 1.57 - 1.69: 0 1.69 - 1.80: 60 Bond restraints: 22272 Sorted by residual: bond pdb=" CA SER F 508 " pdb=" CB SER F 508 " ideal model delta sigma weight residual 1.535 1.503 0.032 1.71e-02 3.42e+03 3.50e+00 bond pdb=" N SER F 508 " pdb=" CA SER F 508 " ideal model delta sigma weight residual 1.454 1.474 -0.019 1.33e-02 5.65e+03 2.10e+00 bond pdb=" C SER F 508 " pdb=" N ILE F 509 " ideal model delta sigma weight residual 1.331 1.317 0.014 1.27e-02 6.20e+03 1.19e+00 bond pdb=" CB PRO F 497 " pdb=" CG PRO F 497 " ideal model delta sigma weight residual 1.492 1.449 0.043 5.00e-02 4.00e+02 7.34e-01 bond pdb=" N PRO E 482 " pdb=" CA PRO E 482 " ideal model delta sigma weight residual 1.459 1.471 -0.012 1.40e-02 5.10e+03 6.87e-01 ... (remaining 22267 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 29658 1.34 - 2.67: 434 2.67 - 4.01: 105 4.01 - 5.35: 5 5.35 - 6.68: 2 Bond angle restraints: 30204 Sorted by residual: angle pdb=" CA SER F 508 " pdb=" C SER F 508 " pdb=" O SER F 508 " ideal model delta sigma weight residual 121.58 117.62 3.96 1.16e+00 7.43e-01 1.16e+01 angle pdb=" N SER F 508 " pdb=" CA SER F 508 " pdb=" C SER F 508 " ideal model delta sigma weight residual 109.41 104.88 4.53 1.52e+00 4.33e-01 8.88e+00 angle pdb=" CA LEU H 525 " pdb=" CB LEU H 525 " pdb=" CG LEU H 525 " ideal model delta sigma weight residual 116.30 122.98 -6.68 3.50e+00 8.16e-02 3.65e+00 angle pdb=" CA SER F 508 " pdb=" C SER F 508 " pdb=" N ILE F 509 " ideal model delta sigma weight residual 115.42 118.19 -2.77 1.64e+00 3.72e-01 2.86e+00 angle pdb=" CA LEU F 525 " pdb=" CB LEU F 525 " pdb=" CG LEU F 525 " ideal model delta sigma weight residual 116.30 121.68 -5.38 3.50e+00 8.16e-02 2.36e+00 ... (remaining 30199 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 11929 17.55 - 35.09: 1212 35.09 - 52.64: 254 52.64 - 70.18: 33 70.18 - 87.73: 24 Dihedral angle restraints: 13452 sinusoidal: 5208 harmonic: 8244 Sorted by residual: dihedral pdb=" CA ARG E 359 " pdb=" C ARG E 359 " pdb=" N ALA E 360 " pdb=" CA ALA E 360 " ideal model delta harmonic sigma weight residual -180.00 -163.71 -16.29 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CG ARG D 367 " pdb=" CD ARG D 367 " pdb=" NE ARG D 367 " pdb=" CZ ARG D 367 " ideal model delta sinusoidal sigma weight residual 180.00 135.18 44.82 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CA ARG A 359 " pdb=" C ARG A 359 " pdb=" N ALA A 360 " pdb=" CA ALA A 360 " ideal model delta harmonic sigma weight residual -180.00 -163.80 -16.20 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 13449 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 2269 0.029 - 0.059: 877 0.059 - 0.088: 220 0.088 - 0.117: 148 0.117 - 0.147: 38 Chirality restraints: 3552 Sorted by residual: chirality pdb=" CA VAL J 481 " pdb=" N VAL J 481 " pdb=" C VAL J 481 " pdb=" CB VAL J 481 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.39e-01 chirality pdb=" CA VAL D 481 " pdb=" N VAL D 481 " pdb=" C VAL D 481 " pdb=" CB VAL D 481 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.27e-01 chirality pdb=" CA VAL E 481 " pdb=" N VAL E 481 " pdb=" C VAL E 481 " pdb=" CB VAL E 481 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.14 2.00e-01 2.50e+01 5.25e-01 ... (remaining 3549 not shown) Planarity restraints: 3972 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 517 " -0.040 5.00e-02 4.00e+02 6.15e-02 6.05e+00 pdb=" N PRO B 518 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO B 518 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 518 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU F 517 " -0.040 5.00e-02 4.00e+02 6.04e-02 5.83e+00 pdb=" N PRO F 518 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO F 518 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO F 518 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER F 508 " -0.010 2.00e-02 2.50e+03 2.13e-02 4.52e+00 pdb=" C SER F 508 " 0.037 2.00e-02 2.50e+03 pdb=" O SER F 508 " -0.014 2.00e-02 2.50e+03 pdb=" N ILE F 509 " -0.013 2.00e-02 2.50e+03 ... (remaining 3969 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 3057 2.75 - 3.29: 20323 3.29 - 3.83: 38633 3.83 - 4.36: 48450 4.36 - 4.90: 79156 Nonbonded interactions: 189619 Sorted by model distance: nonbonded pdb=" OG1 THR D 464 " pdb=" OE1 GLN D 484 " model vdw 2.217 3.040 nonbonded pdb=" OG1 THR J 464 " pdb=" OE1 GLN J 484 " model vdw 2.218 3.040 nonbonded pdb=" OG1 THR I 464 " pdb=" OE1 GLN I 484 " model vdw 2.231 3.040 nonbonded pdb=" NH1 ARG L 357 " pdb=" O LEU L 372 " model vdw 2.252 3.120 nonbonded pdb=" OD1 ASP I 349 " pdb=" OG1 THR I 351 " model vdw 2.261 3.040 ... (remaining 189614 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 2.210 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: 0.020 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 20.030 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 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 : 0.004 0.043 22272 Z= 0.171 Angle : 0.467 6.684 30204 Z= 0.251 Chirality : 0.039 0.147 3552 Planarity : 0.004 0.062 3972 Dihedral : 14.928 87.727 8148 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Rotamer: Outliers : 0.31 % Allowed : 10.76 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 are not related in a simple way. whole: 1.81 (0.15), residues: 2868 helix: 1.89 (0.15), residues: 1152 sheet: 0.74 (0.19), residues: 744 loop : 0.94 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 496 TYR 0.007 0.001 TYR F 396 PHE 0.011 0.002 PHE B 534 HIS 0.003 0.001 HIS J 346 Details of bonding type rmsd covalent geometry : bond 0.00381 (22272) covalent geometry : angle 0.46713 (30204) hydrogen bonds : bond 0.18085 ( 957) hydrogen bonds : angle 5.87822 ( 2682) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 349 time to evaluate : 0.813 Fit side-chains REVERT: D 484 GLN cc_start: 0.8449 (mt0) cc_final: 0.8249 (mt0) REVERT: F 333 ARG cc_start: 0.8253 (ttp-170) cc_final: 0.7977 (ttp-110) REVERT: G 466 THR cc_start: 0.8889 (t) cc_final: 0.8598 (m) REVERT: J 333 ARG cc_start: 0.7723 (ttp80) cc_final: 0.7398 (ttm110) REVERT: L 361 LYS cc_start: 0.8266 (ptmm) cc_final: 0.7968 (ptpt) outliers start: 7 outliers final: 5 residues processed: 356 average time/residue: 0.7619 time to fit residues: 300.9318 Evaluate side-chains 278 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 273 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 525 LEU Chi-restraints excluded: chain G residue 411 LEU Chi-restraints excluded: chain H residue 525 LEU Chi-restraints excluded: chain L residue 335 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.0270 chunk 155 optimal weight: 0.2980 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 0.5980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN B 337 GLN E 337 GLN F 337 GLN G 337 GLN H 337 GLN K 337 GLN L 337 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.164061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.113028 restraints weight = 19472.497| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.74 r_work: 0.3043 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 22272 Z= 0.111 Angle : 0.466 10.262 30204 Z= 0.251 Chirality : 0.039 0.135 3552 Planarity : 0.004 0.038 3972 Dihedral : 4.545 58.528 3153 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Rotamer: Outliers : 2.69 % Allowed : 12.96 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 are not related in a simple way. whole: 2.34 (0.16), residues: 2868 helix: 2.26 (0.15), residues: 1152 sheet: 0.77 (0.19), residues: 744 loop : 1.55 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 357 TYR 0.006 0.001 TYR L 405 PHE 0.018 0.002 PHE J 534 HIS 0.003 0.000 HIS F 389 Details of bonding type rmsd covalent geometry : bond 0.00225 (22272) covalent geometry : angle 0.46585 (30204) hydrogen bonds : bond 0.05123 ( 957) hydrogen bonds : angle 4.60472 ( 2682) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 301 time to evaluate : 0.707 Fit side-chains REVERT: B 401 LYS cc_start: 0.7960 (mmtp) cc_final: 0.7638 (mttp) REVERT: E 352 LYS cc_start: 0.8940 (ttmt) cc_final: 0.8508 (tmtt) REVERT: F 333 ARG cc_start: 0.7916 (ttp-170) cc_final: 0.7611 (ttp-110) REVERT: F 401 LYS cc_start: 0.7879 (mmtp) cc_final: 0.7529 (mtmp) REVERT: G 334 GLU cc_start: 0.7083 (OUTLIER) cc_final: 0.6675 (mm-30) REVERT: G 401 LYS cc_start: 0.8241 (mmtm) cc_final: 0.7987 (mmtm) REVERT: H 334 GLU cc_start: 0.6851 (mm-30) cc_final: 0.6637 (mm-30) REVERT: I 352 LYS cc_start: 0.8376 (mttt) cc_final: 0.8058 (tttm) REVERT: I 418 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.6936 (mm-30) REVERT: I 466 THR cc_start: 0.8590 (OUTLIER) cc_final: 0.8329 (p) REVERT: J 333 ARG cc_start: 0.7448 (ttp80) cc_final: 0.6952 (ttm110) REVERT: J 352 LYS cc_start: 0.8374 (mttt) cc_final: 0.8047 (tttm) REVERT: J 417 THR cc_start: 0.6857 (m) cc_final: 0.6408 (p) REVERT: K 334 GLU cc_start: 0.7105 (OUTLIER) cc_final: 0.6673 (mm-30) REVERT: K 352 LYS cc_start: 0.8917 (ttmt) cc_final: 0.8496 (tmtt) REVERT: K 366 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7723 (pp20) REVERT: K 397 ASN cc_start: 0.8181 (t0) cc_final: 0.7976 (t0) REVERT: L 334 GLU cc_start: 0.6526 (mm-30) cc_final: 0.6191 (mm-30) outliers start: 61 outliers final: 24 residues processed: 343 average time/residue: 0.7327 time to fit residues: 281.1618 Evaluate side-chains 305 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 276 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain E residue 335 SER Chi-restraints excluded: chain E residue 347 GLU Chi-restraints excluded: chain E residue 366 GLU Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 466 THR Chi-restraints excluded: chain E residue 504 SER Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 525 LEU Chi-restraints excluded: chain G residue 334 GLU Chi-restraints excluded: chain G residue 335 SER Chi-restraints excluded: chain G residue 347 GLU Chi-restraints excluded: chain G residue 502 ASP Chi-restraints excluded: chain G residue 544 GLU Chi-restraints excluded: chain H residue 458 LEU Chi-restraints excluded: chain H residue 525 LEU Chi-restraints excluded: chain I residue 418 GLU Chi-restraints excluded: chain I residue 466 THR Chi-restraints excluded: chain J residue 539 LYS Chi-restraints excluded: chain K residue 334 GLU Chi-restraints excluded: chain K residue 335 SER Chi-restraints excluded: chain K residue 347 GLU Chi-restraints excluded: chain K residue 366 GLU Chi-restraints excluded: chain K residue 411 LEU Chi-restraints excluded: chain K residue 504 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 191 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 201 optimal weight: 10.0000 chunk 128 optimal weight: 4.9990 chunk 99 optimal weight: 0.4980 chunk 75 optimal weight: 7.9990 chunk 119 optimal weight: 1.9990 chunk 139 optimal weight: 0.0980 chunk 263 optimal weight: 1.9990 chunk 23 optimal weight: 0.0980 chunk 1 optimal weight: 9.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 GLN A 397 ASN B 337 GLN C 484 GLN D 484 GLN E 337 GLN F 337 GLN G 337 GLN H 337 GLN K 337 GLN L 337 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.163879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.112660 restraints weight = 19498.097| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.74 r_work: 0.3026 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 22272 Z= 0.114 Angle : 0.451 9.843 30204 Z= 0.241 Chirality : 0.039 0.136 3552 Planarity : 0.003 0.031 3972 Dihedral : 4.318 47.159 3150 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Rotamer: Outliers : 3.09 % Allowed : 13.27 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 are not related in a simple way. whole: 2.48 (0.16), residues: 2868 helix: 2.37 (0.15), residues: 1152 sheet: 0.77 (0.19), residues: 744 loop : 1.72 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 447 TYR 0.005 0.001 TYR H 396 PHE 0.016 0.002 PHE J 534 HIS 0.003 0.001 HIS H 389 Details of bonding type rmsd covalent geometry : bond 0.00242 (22272) covalent geometry : angle 0.45116 (30204) hydrogen bonds : bond 0.04871 ( 957) hydrogen bonds : angle 4.32131 ( 2682) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 296 time to evaluate : 0.790 Fit side-chains REVERT: A 352 LYS cc_start: 0.8998 (ttmt) cc_final: 0.8524 (tttt) REVERT: B 401 LYS cc_start: 0.8017 (mmtp) cc_final: 0.7683 (mttp) REVERT: B 443 ASP cc_start: 0.8260 (t70) cc_final: 0.7914 (t0) REVERT: C 466 THR cc_start: 0.8686 (OUTLIER) cc_final: 0.8428 (p) REVERT: E 352 LYS cc_start: 0.8988 (ttmt) cc_final: 0.8519 (tttt) REVERT: E 544 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7568 (tt0) REVERT: F 333 ARG cc_start: 0.7929 (ttp-170) cc_final: 0.7603 (ttp-110) REVERT: F 401 LYS cc_start: 0.8097 (mmtp) cc_final: 0.7715 (mtmp) REVERT: F 443 ASP cc_start: 0.8107 (t70) cc_final: 0.7744 (t70) REVERT: G 334 GLU cc_start: 0.7037 (OUTLIER) cc_final: 0.6659 (mm-30) REVERT: G 352 LYS cc_start: 0.8964 (ttmt) cc_final: 0.8536 (tmtt) REVERT: G 418 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7501 (pp20) REVERT: H 334 GLU cc_start: 0.6928 (mm-30) cc_final: 0.6584 (mm-30) REVERT: I 352 LYS cc_start: 0.8411 (mttt) cc_final: 0.8082 (tttm) REVERT: I 466 THR cc_start: 0.8644 (OUTLIER) cc_final: 0.8380 (p) REVERT: J 333 ARG cc_start: 0.7516 (ttp80) cc_final: 0.6793 (ttp80) REVERT: J 352 LYS cc_start: 0.8417 (mttt) cc_final: 0.8085 (tttm) REVERT: J 417 THR cc_start: 0.6897 (m) cc_final: 0.6480 (p) REVERT: J 466 THR cc_start: 0.8613 (OUTLIER) cc_final: 0.8314 (p) REVERT: J 548 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7400 (mp0) REVERT: K 334 GLU cc_start: 0.7044 (OUTLIER) cc_final: 0.6796 (pp20) REVERT: K 352 LYS cc_start: 0.8945 (ttmt) cc_final: 0.8515 (tmtt) REVERT: K 366 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7746 (pt0) REVERT: L 334 GLU cc_start: 0.6616 (mm-30) cc_final: 0.6237 (mm-30) REVERT: L 395 SER cc_start: 0.8613 (p) cc_final: 0.8389 (t) outliers start: 70 outliers final: 36 residues processed: 334 average time/residue: 0.6724 time to fit residues: 252.6066 Evaluate side-chains 322 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 277 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 347 GLU Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 387 LYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 502 ASP Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain C residue 466 THR Chi-restraints excluded: chain E residue 335 SER Chi-restraints excluded: chain E residue 347 GLU Chi-restraints excluded: chain E residue 387 LYS Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 466 THR Chi-restraints excluded: chain E residue 502 ASP Chi-restraints excluded: chain E residue 504 SER Chi-restraints excluded: chain E residue 544 GLU Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain G residue 334 GLU Chi-restraints excluded: chain G residue 335 SER Chi-restraints excluded: chain G residue 347 GLU Chi-restraints excluded: chain G residue 418 GLU Chi-restraints excluded: chain G residue 466 THR Chi-restraints excluded: chain G residue 502 ASP Chi-restraints excluded: chain G residue 504 SER Chi-restraints excluded: chain G residue 544 GLU Chi-restraints excluded: chain H residue 458 LEU Chi-restraints excluded: chain H residue 525 LEU Chi-restraints excluded: chain I residue 342 LEU Chi-restraints excluded: chain I residue 466 THR Chi-restraints excluded: chain I residue 539 LYS Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 466 THR Chi-restraints excluded: chain J residue 548 GLU Chi-restraints excluded: chain K residue 334 GLU Chi-restraints excluded: chain K residue 335 SER Chi-restraints excluded: chain K residue 347 GLU Chi-restraints excluded: chain K residue 366 GLU Chi-restraints excluded: chain K residue 411 LEU Chi-restraints excluded: chain K residue 502 ASP Chi-restraints excluded: chain K residue 504 SER Chi-restraints excluded: chain L residue 317 THR Chi-restraints excluded: chain L residue 468 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 33 optimal weight: 10.0000 chunk 233 optimal weight: 5.9990 chunk 231 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 277 optimal weight: 3.9990 chunk 188 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 128 optimal weight: 0.7980 chunk 75 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 214 optimal weight: 1.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 ASN B 337 GLN C 506 ASN D 484 GLN D 506 ASN E 397 ASN F 337 GLN G 337 GLN H 337 GLN I 484 GLN I 506 ASN J 506 ASN K 337 GLN K 397 ASN L 337 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.161012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.109894 restraints weight = 19364.110| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.87 r_work: 0.2983 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22272 Z= 0.174 Angle : 0.509 10.472 30204 Z= 0.269 Chirality : 0.040 0.140 3552 Planarity : 0.004 0.030 3972 Dihedral : 4.597 47.074 3148 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Rotamer: Outliers : 3.66 % Allowed : 13.71 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 are not related in a simple way. whole: 2.33 (0.16), residues: 2868 helix: 2.27 (0.15), residues: 1152 sheet: 0.73 (0.19), residues: 744 loop : 1.56 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 498 TYR 0.007 0.001 TYR H 396 PHE 0.014 0.002 PHE D 475 HIS 0.003 0.001 HIS B 389 Details of bonding type rmsd covalent geometry : bond 0.00392 (22272) covalent geometry : angle 0.50879 (30204) hydrogen bonds : bond 0.05348 ( 957) hydrogen bonds : angle 4.32097 ( 2682) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 280 time to evaluate : 0.745 Fit side-chains REVERT: A 337 GLN cc_start: 0.8050 (mt0) cc_final: 0.7047 (mt0) REVERT: B 401 LYS cc_start: 0.8044 (mmtp) cc_final: 0.7638 (mtmp) REVERT: C 466 THR cc_start: 0.8718 (OUTLIER) cc_final: 0.8442 (p) REVERT: D 466 THR cc_start: 0.8718 (OUTLIER) cc_final: 0.8400 (p) REVERT: E 337 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.7950 (mt0) REVERT: E 418 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7463 (mm-30) REVERT: E 466 THR cc_start: 0.8827 (OUTLIER) cc_final: 0.8546 (m) REVERT: F 333 ARG cc_start: 0.7875 (ttp-170) cc_final: 0.7556 (ttp-110) REVERT: F 334 GLU cc_start: 0.6869 (mm-30) cc_final: 0.6465 (mm-30) REVERT: F 401 LYS cc_start: 0.8100 (mmtp) cc_final: 0.7703 (mtmp) REVERT: G 334 GLU cc_start: 0.7025 (OUTLIER) cc_final: 0.6770 (pp20) REVERT: G 352 LYS cc_start: 0.9024 (ttmt) cc_final: 0.8543 (tmtt) REVERT: G 361 LYS cc_start: 0.8527 (ptmt) cc_final: 0.8249 (ptpt) REVERT: G 397 ASN cc_start: 0.8330 (t0) cc_final: 0.8100 (t0) REVERT: G 418 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7452 (pp20) REVERT: G 466 THR cc_start: 0.8829 (OUTLIER) cc_final: 0.8546 (m) REVERT: H 334 GLU cc_start: 0.6888 (mm-30) cc_final: 0.6481 (mm-30) REVERT: I 352 LYS cc_start: 0.8418 (mttt) cc_final: 0.8034 (tttm) REVERT: I 418 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.6949 (mm-30) REVERT: I 466 THR cc_start: 0.8688 (OUTLIER) cc_final: 0.8380 (p) REVERT: J 333 ARG cc_start: 0.7499 (ttp80) cc_final: 0.6739 (ttp80) REVERT: J 352 LYS cc_start: 0.8428 (mttt) cc_final: 0.8040 (tttm) REVERT: J 466 THR cc_start: 0.8669 (OUTLIER) cc_final: 0.8336 (p) REVERT: K 334 GLU cc_start: 0.7022 (OUTLIER) cc_final: 0.6767 (pp20) REVERT: K 352 LYS cc_start: 0.8977 (ttmt) cc_final: 0.8492 (tmtt) REVERT: K 361 LYS cc_start: 0.8528 (ptmt) cc_final: 0.8245 (ptpt) REVERT: K 366 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7701 (pt0) REVERT: K 544 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7769 (tt0) REVERT: L 334 GLU cc_start: 0.6661 (mm-30) cc_final: 0.6263 (mm-30) outliers start: 83 outliers final: 35 residues processed: 329 average time/residue: 0.6896 time to fit residues: 254.9737 Evaluate side-chains 318 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 269 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 387 LYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain C residue 466 THR Chi-restraints excluded: chain D residue 466 THR Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain E residue 335 SER Chi-restraints excluded: chain E residue 337 GLN Chi-restraints excluded: chain E residue 366 GLU Chi-restraints excluded: chain E residue 387 LYS Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 418 GLU Chi-restraints excluded: chain E residue 466 THR Chi-restraints excluded: chain E residue 504 SER Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 352 LYS Chi-restraints excluded: chain G residue 334 GLU Chi-restraints excluded: chain G residue 335 SER Chi-restraints excluded: chain G residue 418 GLU Chi-restraints excluded: chain G residue 466 THR Chi-restraints excluded: chain G residue 504 SER Chi-restraints excluded: chain G residue 544 GLU Chi-restraints excluded: chain H residue 352 LYS Chi-restraints excluded: chain H residue 458 LEU Chi-restraints excluded: chain H residue 525 LEU Chi-restraints excluded: chain H residue 544 GLU Chi-restraints excluded: chain I residue 418 GLU Chi-restraints excluded: chain I residue 466 THR Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 466 THR Chi-restraints excluded: chain K residue 334 GLU Chi-restraints excluded: chain K residue 335 SER Chi-restraints excluded: chain K residue 366 GLU Chi-restraints excluded: chain K residue 387 LYS Chi-restraints excluded: chain K residue 411 LEU Chi-restraints excluded: chain K residue 504 SER Chi-restraints excluded: chain K residue 544 GLU Chi-restraints excluded: chain L residue 317 THR Chi-restraints excluded: chain L residue 335 SER Chi-restraints excluded: chain L residue 352 LYS Chi-restraints excluded: chain L residue 468 ILE Chi-restraints excluded: chain L residue 544 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 69 optimal weight: 2.9990 chunk 97 optimal weight: 9.9990 chunk 179 optimal weight: 7.9990 chunk 100 optimal weight: 4.9990 chunk 105 optimal weight: 8.9990 chunk 270 optimal weight: 4.9990 chunk 235 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 183 optimal weight: 6.9990 chunk 123 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 ASN B 337 GLN D 313 HIS F 337 GLN H 337 GLN J 484 GLN K 337 GLN L 337 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.159839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.107960 restraints weight = 19161.973| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.81 r_work: 0.2952 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 22272 Z= 0.235 Angle : 0.570 11.032 30204 Z= 0.302 Chirality : 0.042 0.156 3552 Planarity : 0.004 0.040 3972 Dihedral : 4.902 51.671 3148 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Rotamer: Outliers : 3.79 % Allowed : 13.58 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 are not related in a simple way. whole: 2.10 (0.16), residues: 2868 helix: 2.08 (0.15), residues: 1152 sheet: 0.66 (0.19), residues: 744 loop : 1.39 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 357 TYR 0.008 0.001 TYR H 396 PHE 0.017 0.002 PHE J 475 HIS 0.004 0.001 HIS C 346 Details of bonding type rmsd covalent geometry : bond 0.00540 (22272) covalent geometry : angle 0.56982 (30204) hydrogen bonds : bond 0.05843 ( 957) hydrogen bonds : angle 4.39601 ( 2682) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 272 time to evaluate : 0.877 Fit side-chains REVERT: A 352 LYS cc_start: 0.9044 (ttmt) cc_final: 0.8558 (tmtt) REVERT: B 401 LYS cc_start: 0.8094 (mmtp) cc_final: 0.7735 (mttp) REVERT: D 466 THR cc_start: 0.8725 (OUTLIER) cc_final: 0.8401 (p) REVERT: E 337 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7963 (mt0) REVERT: E 352 LYS cc_start: 0.9045 (ttmt) cc_final: 0.8553 (tmtt) REVERT: E 397 ASN cc_start: 0.8450 (t0) cc_final: 0.8216 (t0) REVERT: E 418 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7519 (mm-30) REVERT: F 333 ARG cc_start: 0.7936 (ttp-170) cc_final: 0.7628 (ttp-110) REVERT: F 334 GLU cc_start: 0.6891 (mm-30) cc_final: 0.6411 (mt-10) REVERT: F 401 LYS cc_start: 0.8034 (mmtp) cc_final: 0.7610 (mtmp) REVERT: G 334 GLU cc_start: 0.7156 (OUTLIER) cc_final: 0.6892 (pp20) REVERT: G 352 LYS cc_start: 0.9049 (ttmt) cc_final: 0.8549 (tmtt) REVERT: G 361 LYS cc_start: 0.8545 (ptmt) cc_final: 0.8283 (ptpt) REVERT: G 418 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7434 (pp20) REVERT: G 466 THR cc_start: 0.8861 (OUTLIER) cc_final: 0.8564 (m) REVERT: H 334 GLU cc_start: 0.6926 (mm-30) cc_final: 0.6506 (mm-30) REVERT: I 352 LYS cc_start: 0.8447 (mttt) cc_final: 0.8103 (tttm) REVERT: I 418 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.6905 (mm-30) REVERT: J 333 ARG cc_start: 0.7563 (ttp80) cc_final: 0.7029 (ttm170) REVERT: J 352 LYS cc_start: 0.8442 (mttt) cc_final: 0.8107 (tttm) REVERT: J 417 THR cc_start: 0.6845 (m) cc_final: 0.6390 (p) REVERT: J 466 THR cc_start: 0.8728 (OUTLIER) cc_final: 0.8415 (p) REVERT: K 334 GLU cc_start: 0.7102 (OUTLIER) cc_final: 0.6853 (pp20) REVERT: K 361 LYS cc_start: 0.8559 (ptmt) cc_final: 0.8305 (ptpt) REVERT: K 366 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7732 (pt0) REVERT: K 544 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7883 (tt0) REVERT: L 334 GLU cc_start: 0.6822 (mm-30) cc_final: 0.6379 (mm-30) outliers start: 86 outliers final: 46 residues processed: 332 average time/residue: 0.6755 time to fit residues: 252.1943 Evaluate side-chains 313 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 256 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 387 LYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 352 LYS Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain C residue 466 THR Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 466 THR Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain E residue 335 SER Chi-restraints excluded: chain E residue 337 GLN Chi-restraints excluded: chain E residue 366 GLU Chi-restraints excluded: chain E residue 387 LYS Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 418 GLU Chi-restraints excluded: chain E residue 466 THR Chi-restraints excluded: chain E residue 504 SER Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 352 LYS Chi-restraints excluded: chain G residue 334 GLU Chi-restraints excluded: chain G residue 335 SER Chi-restraints excluded: chain G residue 418 GLU Chi-restraints excluded: chain G residue 466 THR Chi-restraints excluded: chain G residue 502 ASP Chi-restraints excluded: chain G residue 504 SER Chi-restraints excluded: chain G residue 544 GLU Chi-restraints excluded: chain H residue 352 LYS Chi-restraints excluded: chain H residue 458 LEU Chi-restraints excluded: chain H residue 468 ILE Chi-restraints excluded: chain H residue 525 LEU Chi-restraints excluded: chain H residue 544 GLU Chi-restraints excluded: chain I residue 418 GLU Chi-restraints excluded: chain I residue 466 THR Chi-restraints excluded: chain I residue 517 LEU Chi-restraints excluded: chain J residue 335 SER Chi-restraints excluded: chain J residue 466 THR Chi-restraints excluded: chain J residue 468 ILE Chi-restraints excluded: chain J residue 470 SER Chi-restraints excluded: chain J residue 517 LEU Chi-restraints excluded: chain K residue 334 GLU Chi-restraints excluded: chain K residue 335 SER Chi-restraints excluded: chain K residue 342 LEU Chi-restraints excluded: chain K residue 366 GLU Chi-restraints excluded: chain K residue 411 LEU Chi-restraints excluded: chain K residue 501 VAL Chi-restraints excluded: chain K residue 504 SER Chi-restraints excluded: chain K residue 544 GLU Chi-restraints excluded: chain L residue 317 THR Chi-restraints excluded: chain L residue 335 SER Chi-restraints excluded: chain L residue 352 LYS Chi-restraints excluded: chain L residue 468 ILE Chi-restraints excluded: chain L residue 544 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 74 optimal weight: 0.9990 chunk 119 optimal weight: 7.9990 chunk 117 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 98 optimal weight: 0.0370 chunk 35 optimal weight: 1.9990 chunk 25 optimal weight: 20.0000 chunk 92 optimal weight: 0.6980 chunk 141 optimal weight: 2.9990 chunk 173 optimal weight: 6.9990 chunk 26 optimal weight: 8.9990 overall best weight: 1.3464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 ASN B 337 GLN F 337 GLN G 337 GLN H 337 GLN K 337 GLN L 337 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.161734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.110345 restraints weight = 19250.020| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.81 r_work: 0.2995 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 22272 Z= 0.133 Angle : 0.475 9.655 30204 Z= 0.253 Chirality : 0.039 0.137 3552 Planarity : 0.003 0.030 3972 Dihedral : 4.531 53.065 3148 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % Rotamer: Outliers : 3.44 % Allowed : 14.42 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 are not related in a simple way. whole: 2.31 (0.16), residues: 2868 helix: 2.31 (0.15), residues: 1152 sheet: 0.63 (0.19), residues: 744 loop : 1.54 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 357 TYR 0.006 0.001 TYR H 396 PHE 0.014 0.002 PHE I 534 HIS 0.004 0.001 HIS B 389 Details of bonding type rmsd covalent geometry : bond 0.00290 (22272) covalent geometry : angle 0.47526 (30204) hydrogen bonds : bond 0.04909 ( 957) hydrogen bonds : angle 4.21336 ( 2682) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 273 time to evaluate : 0.853 Fit side-chains REVERT: A 352 LYS cc_start: 0.9015 (ttmt) cc_final: 0.8539 (tmtt) REVERT: A 401 LYS cc_start: 0.8223 (mmmt) cc_final: 0.7836 (mmtm) REVERT: A 544 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7675 (tt0) REVERT: B 401 LYS cc_start: 0.8042 (mmtp) cc_final: 0.7665 (mttp) REVERT: B 443 ASP cc_start: 0.8134 (t70) cc_final: 0.7782 (t0) REVERT: C 466 THR cc_start: 0.8645 (OUTLIER) cc_final: 0.8367 (p) REVERT: D 417 THR cc_start: 0.6768 (m) cc_final: 0.6348 (p) REVERT: D 466 THR cc_start: 0.8725 (OUTLIER) cc_final: 0.8384 (p) REVERT: E 337 GLN cc_start: 0.8161 (mt0) cc_final: 0.7920 (mt0) REVERT: E 352 LYS cc_start: 0.9028 (ttmt) cc_final: 0.8546 (tmtt) REVERT: F 333 ARG cc_start: 0.7855 (ttp-170) cc_final: 0.7581 (ttp-110) REVERT: F 334 GLU cc_start: 0.6916 (mm-30) cc_final: 0.6456 (mt-10) REVERT: F 401 LYS cc_start: 0.8079 (mmtp) cc_final: 0.7663 (mtmp) REVERT: G 334 GLU cc_start: 0.7082 (OUTLIER) cc_final: 0.6802 (pp20) REVERT: G 352 LYS cc_start: 0.9036 (ttmt) cc_final: 0.8547 (tmtt) REVERT: G 401 LYS cc_start: 0.8283 (mmtm) cc_final: 0.8068 (mmmt) REVERT: G 418 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7357 (pp20) REVERT: G 466 THR cc_start: 0.8839 (OUTLIER) cc_final: 0.8508 (m) REVERT: H 334 GLU cc_start: 0.6904 (mm-30) cc_final: 0.6548 (mm-30) REVERT: I 352 LYS cc_start: 0.8466 (mttt) cc_final: 0.8090 (tttm) REVERT: I 417 THR cc_start: 0.6553 (OUTLIER) cc_final: 0.6292 (p) REVERT: I 418 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.6912 (mm-30) REVERT: I 466 THR cc_start: 0.8634 (OUTLIER) cc_final: 0.8356 (p) REVERT: J 333 ARG cc_start: 0.7538 (ttp80) cc_final: 0.6263 (ttp80) REVERT: J 337 GLN cc_start: 0.7750 (OUTLIER) cc_final: 0.6023 (mp10) REVERT: J 352 LYS cc_start: 0.8457 (mttt) cc_final: 0.8069 (tttm) REVERT: J 417 THR cc_start: 0.6788 (m) cc_final: 0.6347 (p) REVERT: J 466 THR cc_start: 0.8710 (OUTLIER) cc_final: 0.8377 (p) REVERT: K 334 GLU cc_start: 0.7068 (OUTLIER) cc_final: 0.6780 (pp20) REVERT: K 352 LYS cc_start: 0.8986 (ttmt) cc_final: 0.8525 (tmtt) REVERT: K 366 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7704 (pt0) REVERT: K 397 ASN cc_start: 0.8456 (t0) cc_final: 0.8241 (t0) REVERT: K 401 LYS cc_start: 0.8295 (mmmt) cc_final: 0.7899 (mmtm) REVERT: K 544 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7819 (tt0) REVERT: L 334 GLU cc_start: 0.6849 (mm-30) cc_final: 0.6466 (mm-30) outliers start: 78 outliers final: 35 residues processed: 323 average time/residue: 0.6787 time to fit residues: 246.4385 Evaluate side-chains 313 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 264 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 387 LYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain C residue 466 THR Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 466 THR Chi-restraints excluded: chain E residue 335 SER Chi-restraints excluded: chain E residue 342 LEU Chi-restraints excluded: chain E residue 366 GLU Chi-restraints excluded: chain E residue 387 LYS Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 466 THR Chi-restraints excluded: chain E residue 504 SER Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 352 LYS Chi-restraints excluded: chain G residue 334 GLU Chi-restraints excluded: chain G residue 335 SER Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 411 LEU Chi-restraints excluded: chain G residue 418 GLU Chi-restraints excluded: chain G residue 466 THR Chi-restraints excluded: chain G residue 502 ASP Chi-restraints excluded: chain G residue 504 SER Chi-restraints excluded: chain H residue 317 THR Chi-restraints excluded: chain H residue 458 LEU Chi-restraints excluded: chain H residue 468 ILE Chi-restraints excluded: chain H residue 544 GLU Chi-restraints excluded: chain I residue 342 LEU Chi-restraints excluded: chain I residue 417 THR Chi-restraints excluded: chain I residue 418 GLU Chi-restraints excluded: chain I residue 466 THR Chi-restraints excluded: chain J residue 337 GLN Chi-restraints excluded: chain J residue 466 THR Chi-restraints excluded: chain K residue 334 GLU Chi-restraints excluded: chain K residue 335 SER Chi-restraints excluded: chain K residue 342 LEU Chi-restraints excluded: chain K residue 366 GLU Chi-restraints excluded: chain K residue 411 LEU Chi-restraints excluded: chain K residue 504 SER Chi-restraints excluded: chain K residue 544 GLU Chi-restraints excluded: chain L residue 468 ILE Chi-restraints excluded: chain L residue 544 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 238 optimal weight: 3.9990 chunk 226 optimal weight: 10.0000 chunk 244 optimal weight: 3.9990 chunk 285 optimal weight: 8.9990 chunk 95 optimal weight: 0.8980 chunk 199 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 233 optimal weight: 0.2980 chunk 168 optimal weight: 10.0000 chunk 257 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 ASN B 337 GLN F 337 GLN H 337 GLN L 337 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.163121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.110597 restraints weight = 19324.741| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.84 r_work: 0.2997 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 22272 Z= 0.123 Angle : 0.465 8.804 30204 Z= 0.246 Chirality : 0.039 0.136 3552 Planarity : 0.003 0.028 3972 Dihedral : 4.358 52.195 3146 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Rotamer: Outliers : 3.44 % Allowed : 14.99 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 are not related in a simple way. whole: 2.43 (0.16), residues: 2868 helix: 2.43 (0.15), residues: 1152 sheet: 0.65 (0.19), residues: 744 loop : 1.64 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 357 TYR 0.005 0.001 TYR H 396 PHE 0.014 0.002 PHE J 534 HIS 0.004 0.001 HIS J 389 Details of bonding type rmsd covalent geometry : bond 0.00266 (22272) covalent geometry : angle 0.46477 (30204) hydrogen bonds : bond 0.04711 ( 957) hydrogen bonds : angle 4.11525 ( 2682) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 279 time to evaluate : 0.819 Fit side-chains REVERT: A 352 LYS cc_start: 0.9000 (ttmt) cc_final: 0.8542 (tmtt) REVERT: A 401 LYS cc_start: 0.8190 (mmmt) cc_final: 0.7815 (mmtm) REVERT: B 401 LYS cc_start: 0.8049 (mmtp) cc_final: 0.7682 (mttp) REVERT: B 443 ASP cc_start: 0.8093 (t70) cc_final: 0.7739 (t0) REVERT: C 466 THR cc_start: 0.8630 (OUTLIER) cc_final: 0.8344 (p) REVERT: D 417 THR cc_start: 0.6746 (m) cc_final: 0.6342 (p) REVERT: D 466 THR cc_start: 0.8712 (OUTLIER) cc_final: 0.8366 (p) REVERT: E 337 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7803 (mt0) REVERT: E 352 LYS cc_start: 0.8998 (ttmt) cc_final: 0.8518 (tmtt) REVERT: F 334 GLU cc_start: 0.7002 (mm-30) cc_final: 0.6532 (mt-10) REVERT: F 401 LYS cc_start: 0.8124 (mmtp) cc_final: 0.7708 (mtmp) REVERT: G 334 GLU cc_start: 0.7077 (OUTLIER) cc_final: 0.6642 (mm-30) REVERT: G 352 LYS cc_start: 0.9020 (ttmt) cc_final: 0.8548 (tmtt) REVERT: G 401 LYS cc_start: 0.8229 (mmtm) cc_final: 0.8021 (mmmt) REVERT: G 466 THR cc_start: 0.8825 (OUTLIER) cc_final: 0.8529 (m) REVERT: H 334 GLU cc_start: 0.6811 (mm-30) cc_final: 0.6464 (mm-30) REVERT: I 352 LYS cc_start: 0.8458 (mttt) cc_final: 0.8070 (tttm) REVERT: I 417 THR cc_start: 0.6489 (OUTLIER) cc_final: 0.6287 (p) REVERT: I 418 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.6905 (mm-30) REVERT: I 466 THR cc_start: 0.8615 (OUTLIER) cc_final: 0.8328 (p) REVERT: J 333 ARG cc_start: 0.7507 (ttp80) cc_final: 0.6765 (ttp80) REVERT: J 352 LYS cc_start: 0.8460 (mttt) cc_final: 0.8073 (tttm) REVERT: J 417 THR cc_start: 0.6770 (m) cc_final: 0.6361 (p) REVERT: J 421 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7367 (tp) REVERT: J 466 THR cc_start: 0.8693 (OUTLIER) cc_final: 0.8342 (p) REVERT: K 334 GLU cc_start: 0.7095 (OUTLIER) cc_final: 0.6810 (pp20) REVERT: K 352 LYS cc_start: 0.8998 (ttmt) cc_final: 0.8527 (tmtt) REVERT: K 366 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7738 (pt0) REVERT: K 397 ASN cc_start: 0.8453 (t0) cc_final: 0.8180 (t0) REVERT: K 401 LYS cc_start: 0.8279 (mmmt) cc_final: 0.7870 (mmtm) REVERT: K 544 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7801 (tt0) REVERT: L 334 GLU cc_start: 0.6880 (mm-30) cc_final: 0.6497 (mm-30) outliers start: 78 outliers final: 36 residues processed: 328 average time/residue: 0.6729 time to fit residues: 249.1798 Evaluate side-chains 319 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 270 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 387 LYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 502 ASP Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain C residue 466 THR Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 466 THR Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain E residue 335 SER Chi-restraints excluded: chain E residue 337 GLN Chi-restraints excluded: chain E residue 347 GLU Chi-restraints excluded: chain E residue 366 GLU Chi-restraints excluded: chain E residue 387 LYS Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 466 THR Chi-restraints excluded: chain E residue 504 SER Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 352 LYS Chi-restraints excluded: chain G residue 334 GLU Chi-restraints excluded: chain G residue 335 SER Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 411 LEU Chi-restraints excluded: chain G residue 466 THR Chi-restraints excluded: chain G residue 502 ASP Chi-restraints excluded: chain G residue 504 SER Chi-restraints excluded: chain H residue 458 LEU Chi-restraints excluded: chain H residue 544 GLU Chi-restraints excluded: chain I residue 342 LEU Chi-restraints excluded: chain I residue 417 THR Chi-restraints excluded: chain I residue 418 GLU Chi-restraints excluded: chain I residue 466 THR Chi-restraints excluded: chain J residue 421 LEU Chi-restraints excluded: chain J residue 466 THR Chi-restraints excluded: chain J residue 468 ILE Chi-restraints excluded: chain K residue 334 GLU Chi-restraints excluded: chain K residue 335 SER Chi-restraints excluded: chain K residue 347 GLU Chi-restraints excluded: chain K residue 366 GLU Chi-restraints excluded: chain K residue 411 LEU Chi-restraints excluded: chain K residue 501 VAL Chi-restraints excluded: chain K residue 502 ASP Chi-restraints excluded: chain K residue 504 SER Chi-restraints excluded: chain K residue 544 GLU Chi-restraints excluded: chain L residue 544 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 19 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 chunk 166 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 202 optimal weight: 9.9990 chunk 151 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 215 optimal weight: 2.9990 chunk 234 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 ASN B 337 GLN C 326 GLN F 337 GLN H 337 GLN L 337 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.161572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.107188 restraints weight = 19212.075| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 1.66 r_work: 0.2988 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 22272 Z= 0.189 Angle : 0.526 9.808 30204 Z= 0.277 Chirality : 0.041 0.137 3552 Planarity : 0.004 0.029 3972 Dihedral : 4.648 52.536 3146 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Rotamer: Outliers : 3.35 % Allowed : 15.70 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 are not related in a simple way. whole: 2.28 (0.16), residues: 2868 helix: 2.28 (0.15), residues: 1152 sheet: 0.65 (0.19), residues: 744 loop : 1.51 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 357 TYR 0.007 0.001 TYR H 396 PHE 0.014 0.002 PHE J 475 HIS 0.003 0.001 HIS C 346 Details of bonding type rmsd covalent geometry : bond 0.00430 (22272) covalent geometry : angle 0.52611 (30204) hydrogen bonds : bond 0.05305 ( 957) hydrogen bonds : angle 4.21636 ( 2682) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 269 time to evaluate : 0.772 Fit side-chains REVERT: A 352 LYS cc_start: 0.9036 (ttmt) cc_final: 0.8568 (tmtt) REVERT: A 401 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7911 (mmtm) REVERT: B 401 LYS cc_start: 0.8062 (mmtp) cc_final: 0.7749 (mttp) REVERT: C 466 THR cc_start: 0.8721 (OUTLIER) cc_final: 0.8416 (p) REVERT: D 466 THR cc_start: 0.8740 (OUTLIER) cc_final: 0.8427 (p) REVERT: E 337 GLN cc_start: 0.8190 (OUTLIER) cc_final: 0.7952 (mt0) REVERT: E 352 LYS cc_start: 0.9054 (ttmt) cc_final: 0.8575 (tmtt) REVERT: E 466 THR cc_start: 0.8851 (OUTLIER) cc_final: 0.8569 (m) REVERT: E 544 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7881 (tt0) REVERT: F 334 GLU cc_start: 0.6972 (mm-30) cc_final: 0.6554 (mt-10) REVERT: F 401 LYS cc_start: 0.8068 (mmtp) cc_final: 0.7641 (mtmp) REVERT: G 334 GLU cc_start: 0.7112 (OUTLIER) cc_final: 0.6676 (mm-30) REVERT: G 352 LYS cc_start: 0.9057 (ttmt) cc_final: 0.8585 (tmtt) REVERT: G 361 LYS cc_start: 0.8465 (ptmt) cc_final: 0.8226 (ptpp) REVERT: G 466 THR cc_start: 0.8855 (OUTLIER) cc_final: 0.8572 (m) REVERT: H 334 GLU cc_start: 0.6848 (mm-30) cc_final: 0.6282 (mt-10) REVERT: I 352 LYS cc_start: 0.8433 (mttt) cc_final: 0.8129 (tttm) REVERT: I 417 THR cc_start: 0.6564 (OUTLIER) cc_final: 0.6287 (p) REVERT: I 418 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.6908 (mm-30) REVERT: I 466 THR cc_start: 0.8702 (OUTLIER) cc_final: 0.8396 (p) REVERT: J 333 ARG cc_start: 0.7531 (ttp80) cc_final: 0.7023 (ttm170) REVERT: J 352 LYS cc_start: 0.8431 (mttt) cc_final: 0.8123 (tttm) REVERT: J 417 THR cc_start: 0.6803 (m) cc_final: 0.6392 (p) REVERT: J 466 THR cc_start: 0.8721 (OUTLIER) cc_final: 0.8382 (p) REVERT: K 334 GLU cc_start: 0.7100 (OUTLIER) cc_final: 0.6837 (pp20) REVERT: K 352 LYS cc_start: 0.9023 (ttmt) cc_final: 0.8555 (tmtt) REVERT: K 361 LYS cc_start: 0.8467 (ptmt) cc_final: 0.8243 (ptpt) REVERT: K 366 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7769 (pt0) REVERT: K 544 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7814 (tt0) REVERT: L 334 GLU cc_start: 0.6944 (mm-30) cc_final: 0.6452 (mt-10) outliers start: 76 outliers final: 45 residues processed: 319 average time/residue: 0.6561 time to fit residues: 236.2271 Evaluate side-chains 321 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 261 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 387 LYS Chi-restraints excluded: chain A residue 401 LYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 502 ASP Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 352 LYS Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain C residue 466 THR Chi-restraints excluded: chain C residue 539 LYS Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 466 THR Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain E residue 335 SER Chi-restraints excluded: chain E residue 337 GLN Chi-restraints excluded: chain E residue 342 LEU Chi-restraints excluded: chain E residue 366 GLU Chi-restraints excluded: chain E residue 387 LYS Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 466 THR Chi-restraints excluded: chain E residue 504 SER Chi-restraints excluded: chain E residue 544 GLU Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 352 LYS Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain G residue 334 GLU Chi-restraints excluded: chain G residue 335 SER Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 387 LYS Chi-restraints excluded: chain G residue 411 LEU Chi-restraints excluded: chain G residue 466 THR Chi-restraints excluded: chain G residue 502 ASP Chi-restraints excluded: chain G residue 504 SER Chi-restraints excluded: chain H residue 458 LEU Chi-restraints excluded: chain H residue 468 ILE Chi-restraints excluded: chain H residue 544 GLU Chi-restraints excluded: chain I residue 417 THR Chi-restraints excluded: chain I residue 418 GLU Chi-restraints excluded: chain I residue 466 THR Chi-restraints excluded: chain J residue 361 LYS Chi-restraints excluded: chain J residue 466 THR Chi-restraints excluded: chain J residue 468 ILE Chi-restraints excluded: chain K residue 334 GLU Chi-restraints excluded: chain K residue 335 SER Chi-restraints excluded: chain K residue 342 LEU Chi-restraints excluded: chain K residue 366 GLU Chi-restraints excluded: chain K residue 387 LYS Chi-restraints excluded: chain K residue 411 LEU Chi-restraints excluded: chain K residue 501 VAL Chi-restraints excluded: chain K residue 502 ASP Chi-restraints excluded: chain K residue 504 SER Chi-restraints excluded: chain K residue 544 GLU Chi-restraints excluded: chain L residue 317 THR Chi-restraints excluded: chain L residue 335 SER Chi-restraints excluded: chain L residue 468 ILE Chi-restraints excluded: chain L residue 544 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 86 optimal weight: 8.9990 chunk 20 optimal weight: 0.8980 chunk 250 optimal weight: 4.9990 chunk 159 optimal weight: 4.9990 chunk 84 optimal weight: 7.9990 chunk 209 optimal weight: 6.9990 chunk 204 optimal weight: 0.9990 chunk 264 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 99 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 ASN B 337 GLN F 337 GLN H 337 GLN L 337 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.162192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.108583 restraints weight = 19389.317| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.78 r_work: 0.2989 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22272 Z= 0.155 Angle : 0.502 10.033 30204 Z= 0.265 Chirality : 0.040 0.137 3552 Planarity : 0.004 0.029 3972 Dihedral : 4.559 53.081 3146 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Rotamer: Outliers : 3.17 % Allowed : 16.23 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 are not related in a simple way. whole: 2.32 (0.16), residues: 2868 helix: 2.31 (0.15), residues: 1152 sheet: 0.66 (0.19), residues: 744 loop : 1.55 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 357 TYR 0.006 0.001 TYR H 396 PHE 0.014 0.002 PHE J 534 HIS 0.004 0.001 HIS D 389 Details of bonding type rmsd covalent geometry : bond 0.00346 (22272) covalent geometry : angle 0.50185 (30204) hydrogen bonds : bond 0.05040 ( 957) hydrogen bonds : angle 4.18568 ( 2682) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 260 time to evaluate : 0.839 Fit side-chains REVERT: A 352 LYS cc_start: 0.9034 (ttmt) cc_final: 0.8553 (tmtt) REVERT: A 401 LYS cc_start: 0.8227 (OUTLIER) cc_final: 0.7906 (mmtm) REVERT: B 401 LYS cc_start: 0.8059 (mmtp) cc_final: 0.7748 (mttp) REVERT: B 443 ASP cc_start: 0.8108 (t70) cc_final: 0.7760 (t0) REVERT: C 466 THR cc_start: 0.8666 (OUTLIER) cc_final: 0.8368 (p) REVERT: D 384 ASP cc_start: 0.8154 (m-30) cc_final: 0.7919 (m-30) REVERT: D 417 THR cc_start: 0.6779 (m) cc_final: 0.6363 (p) REVERT: D 466 THR cc_start: 0.8711 (OUTLIER) cc_final: 0.8373 (p) REVERT: E 337 GLN cc_start: 0.8174 (OUTLIER) cc_final: 0.7930 (mt0) REVERT: E 352 LYS cc_start: 0.9036 (ttmt) cc_final: 0.8549 (tmtt) REVERT: E 466 THR cc_start: 0.8815 (OUTLIER) cc_final: 0.8525 (m) REVERT: F 334 GLU cc_start: 0.6928 (mm-30) cc_final: 0.6534 (mt-10) REVERT: F 401 LYS cc_start: 0.8089 (mmtp) cc_final: 0.7666 (mtmp) REVERT: G 334 GLU cc_start: 0.7111 (OUTLIER) cc_final: 0.6669 (mm-30) REVERT: G 352 LYS cc_start: 0.9044 (ttmt) cc_final: 0.8553 (tmtt) REVERT: G 361 LYS cc_start: 0.8450 (ptmt) cc_final: 0.8200 (ptpp) REVERT: G 466 THR cc_start: 0.8819 (OUTLIER) cc_final: 0.8523 (m) REVERT: H 334 GLU cc_start: 0.6802 (mm-30) cc_final: 0.6250 (mt-10) REVERT: I 352 LYS cc_start: 0.8438 (mttt) cc_final: 0.8100 (tttm) REVERT: I 417 THR cc_start: 0.6571 (OUTLIER) cc_final: 0.6297 (p) REVERT: I 418 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.6885 (mm-30) REVERT: I 466 THR cc_start: 0.8662 (OUTLIER) cc_final: 0.8369 (p) REVERT: J 333 ARG cc_start: 0.7521 (ttp80) cc_final: 0.6786 (ttp80) REVERT: J 352 LYS cc_start: 0.8433 (mttt) cc_final: 0.8093 (tttm) REVERT: J 417 THR cc_start: 0.6806 (m) cc_final: 0.6412 (p) REVERT: J 466 THR cc_start: 0.8700 (OUTLIER) cc_final: 0.8367 (p) REVERT: K 334 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.6804 (pp20) REVERT: K 352 LYS cc_start: 0.8998 (ttmt) cc_final: 0.8530 (tmtt) REVERT: K 361 LYS cc_start: 0.8447 (ptmt) cc_final: 0.8218 (ptpt) REVERT: K 366 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7765 (pt0) REVERT: K 401 LYS cc_start: 0.8206 (mmmt) cc_final: 0.7932 (mmtm) REVERT: K 544 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7853 (tt0) REVERT: L 334 GLU cc_start: 0.6906 (mm-30) cc_final: 0.6432 (mt-10) outliers start: 72 outliers final: 44 residues processed: 306 average time/residue: 0.6789 time to fit residues: 233.8998 Evaluate side-chains 310 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 252 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 387 LYS Chi-restraints excluded: chain A residue 401 LYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 502 ASP Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 352 LYS Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain C residue 466 THR Chi-restraints excluded: chain C residue 539 LYS Chi-restraints excluded: chain D residue 334 GLU Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 466 THR Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain E residue 335 SER Chi-restraints excluded: chain E residue 337 GLN Chi-restraints excluded: chain E residue 342 LEU Chi-restraints excluded: chain E residue 366 GLU Chi-restraints excluded: chain E residue 387 LYS Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 466 THR Chi-restraints excluded: chain E residue 502 ASP Chi-restraints excluded: chain E residue 504 SER Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 352 LYS Chi-restraints excluded: chain F residue 468 ILE Chi-restraints excluded: chain G residue 334 GLU Chi-restraints excluded: chain G residue 335 SER Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 411 LEU Chi-restraints excluded: chain G residue 466 THR Chi-restraints excluded: chain G residue 502 ASP Chi-restraints excluded: chain G residue 504 SER Chi-restraints excluded: chain H residue 458 LEU Chi-restraints excluded: chain H residue 468 ILE Chi-restraints excluded: chain H residue 544 GLU Chi-restraints excluded: chain I residue 417 THR Chi-restraints excluded: chain I residue 418 GLU Chi-restraints excluded: chain I residue 466 THR Chi-restraints excluded: chain J residue 466 THR Chi-restraints excluded: chain J residue 468 ILE Chi-restraints excluded: chain K residue 334 GLU Chi-restraints excluded: chain K residue 335 SER Chi-restraints excluded: chain K residue 342 LEU Chi-restraints excluded: chain K residue 366 GLU Chi-restraints excluded: chain K residue 387 LYS Chi-restraints excluded: chain K residue 411 LEU Chi-restraints excluded: chain K residue 501 VAL Chi-restraints excluded: chain K residue 502 ASP Chi-restraints excluded: chain K residue 504 SER Chi-restraints excluded: chain K residue 544 GLU Chi-restraints excluded: chain L residue 317 THR Chi-restraints excluded: chain L residue 335 SER Chi-restraints excluded: chain L residue 468 ILE Chi-restraints excluded: chain L residue 544 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 216 optimal weight: 8.9990 chunk 259 optimal weight: 2.9990 chunk 178 optimal weight: 3.9990 chunk 286 optimal weight: 0.6980 chunk 146 optimal weight: 5.9990 chunk 82 optimal weight: 10.0000 chunk 204 optimal weight: 0.9990 chunk 209 optimal weight: 7.9990 chunk 264 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 9 optimal weight: 7.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 ASN B 337 GLN F 337 GLN H 337 GLN L 337 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.162504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.110819 restraints weight = 19270.750| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 1.80 r_work: 0.2997 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22272 Z= 0.142 Angle : 0.490 10.087 30204 Z= 0.258 Chirality : 0.039 0.137 3552 Planarity : 0.003 0.028 3972 Dihedral : 4.480 53.258 3146 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Rotamer: Outliers : 2.91 % Allowed : 16.58 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 are not related in a simple way. whole: 2.37 (0.16), residues: 2868 helix: 2.36 (0.15), residues: 1152 sheet: 0.65 (0.19), residues: 744 loop : 1.60 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 357 TYR 0.006 0.001 TYR H 396 PHE 0.014 0.002 PHE J 534 HIS 0.004 0.001 HIS D 389 Details of bonding type rmsd covalent geometry : bond 0.00314 (22272) covalent geometry : angle 0.49019 (30204) hydrogen bonds : bond 0.04896 ( 957) hydrogen bonds : angle 4.14597 ( 2682) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5736 Ramachandran restraints generated. 2868 Oldfield, 0 Emsley, 2868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 272 time to evaluate : 0.805 Fit side-chains REVERT: A 352 LYS cc_start: 0.9042 (ttmt) cc_final: 0.8574 (tmtt) REVERT: A 401 LYS cc_start: 0.8230 (mmmt) cc_final: 0.7917 (mmtm) REVERT: B 401 LYS cc_start: 0.8052 (mmtp) cc_final: 0.7741 (mttp) REVERT: B 443 ASP cc_start: 0.8121 (t70) cc_final: 0.7779 (t0) REVERT: C 466 THR cc_start: 0.8678 (OUTLIER) cc_final: 0.8385 (p) REVERT: D 417 THR cc_start: 0.6832 (m) cc_final: 0.6422 (p) REVERT: D 458 LEU cc_start: 0.8618 (mt) cc_final: 0.8416 (mm) REVERT: D 466 THR cc_start: 0.8729 (OUTLIER) cc_final: 0.8390 (p) REVERT: E 337 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.7922 (mt0) REVERT: E 352 LYS cc_start: 0.9044 (ttmt) cc_final: 0.8570 (tmtt) REVERT: E 466 THR cc_start: 0.8817 (OUTLIER) cc_final: 0.8530 (m) REVERT: F 334 GLU cc_start: 0.6934 (mm-30) cc_final: 0.6550 (mt-10) REVERT: F 401 LYS cc_start: 0.8088 (mmtp) cc_final: 0.7663 (mtmp) REVERT: G 334 GLU cc_start: 0.7120 (OUTLIER) cc_final: 0.6683 (mm-30) REVERT: G 352 LYS cc_start: 0.9048 (ttmt) cc_final: 0.8570 (tmtt) REVERT: G 361 LYS cc_start: 0.8443 (ptmt) cc_final: 0.8198 (ptpp) REVERT: G 401 LYS cc_start: 0.8184 (mmmt) cc_final: 0.7832 (mmtm) REVERT: G 466 THR cc_start: 0.8820 (OUTLIER) cc_final: 0.8526 (m) REVERT: H 334 GLU cc_start: 0.6815 (mm-30) cc_final: 0.6282 (mt-10) REVERT: I 352 LYS cc_start: 0.8428 (mttt) cc_final: 0.8118 (tttm) REVERT: I 417 THR cc_start: 0.6561 (OUTLIER) cc_final: 0.6306 (p) REVERT: I 418 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.6901 (mm-30) REVERT: I 466 THR cc_start: 0.8657 (OUTLIER) cc_final: 0.8367 (p) REVERT: J 333 ARG cc_start: 0.7509 (ttp80) cc_final: 0.6956 (ttm110) REVERT: J 352 LYS cc_start: 0.8431 (mttt) cc_final: 0.8122 (tttm) REVERT: J 417 THR cc_start: 0.6804 (m) cc_final: 0.6419 (p) REVERT: J 466 THR cc_start: 0.8712 (OUTLIER) cc_final: 0.8379 (p) REVERT: K 334 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6826 (pp20) REVERT: K 352 LYS cc_start: 0.9008 (ttmt) cc_final: 0.8548 (tmtt) REVERT: K 361 LYS cc_start: 0.8461 (ptmt) cc_final: 0.8242 (ptpt) REVERT: K 366 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7814 (pt0) REVERT: K 397 ASN cc_start: 0.8409 (t0) cc_final: 0.8185 (t0) REVERT: K 401 LYS cc_start: 0.8232 (mmmt) cc_final: 0.7913 (mmtm) REVERT: K 544 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7844 (tt0) REVERT: L 334 GLU cc_start: 0.6937 (mm-30) cc_final: 0.6452 (mt-10) outliers start: 66 outliers final: 44 residues processed: 314 average time/residue: 0.6665 time to fit residues: 236.1819 Evaluate side-chains 324 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 267 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 387 LYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 502 ASP Chi-restraints excluded: chain A residue 504 SER Chi-restraints excluded: chain B residue 335 SER Chi-restraints excluded: chain B residue 352 LYS Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain C residue 466 THR Chi-restraints excluded: chain C residue 539 LYS Chi-restraints excluded: chain D residue 421 LEU Chi-restraints excluded: chain D residue 466 THR Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain E residue 335 SER Chi-restraints excluded: chain E residue 337 GLN Chi-restraints excluded: chain E residue 342 LEU Chi-restraints excluded: chain E residue 366 GLU Chi-restraints excluded: chain E residue 387 LYS Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain E residue 466 THR Chi-restraints excluded: chain E residue 502 ASP Chi-restraints excluded: chain E residue 504 SER Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 352 LYS Chi-restraints excluded: chain G residue 334 GLU Chi-restraints excluded: chain G residue 335 SER Chi-restraints excluded: chain G residue 342 LEU Chi-restraints excluded: chain G residue 387 LYS Chi-restraints excluded: chain G residue 411 LEU Chi-restraints excluded: chain G residue 466 THR Chi-restraints excluded: chain G residue 502 ASP Chi-restraints excluded: chain G residue 504 SER Chi-restraints excluded: chain H residue 458 LEU Chi-restraints excluded: chain H residue 468 ILE Chi-restraints excluded: chain H residue 544 GLU Chi-restraints excluded: chain I residue 417 THR Chi-restraints excluded: chain I residue 418 GLU Chi-restraints excluded: chain I residue 466 THR Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 466 THR Chi-restraints excluded: chain J residue 468 ILE Chi-restraints excluded: chain K residue 334 GLU Chi-restraints excluded: chain K residue 335 SER Chi-restraints excluded: chain K residue 342 LEU Chi-restraints excluded: chain K residue 366 GLU Chi-restraints excluded: chain K residue 387 LYS Chi-restraints excluded: chain K residue 411 LEU Chi-restraints excluded: chain K residue 501 VAL Chi-restraints excluded: chain K residue 502 ASP Chi-restraints excluded: chain K residue 504 SER Chi-restraints excluded: chain K residue 544 GLU Chi-restraints excluded: chain L residue 317 THR Chi-restraints excluded: chain L residue 335 SER Chi-restraints excluded: chain L residue 468 ILE Chi-restraints excluded: chain L residue 544 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 60 optimal weight: 8.9990 chunk 128 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 155 optimal weight: 0.0870 chunk 199 optimal weight: 4.9990 chunk 167 optimal weight: 10.0000 chunk 257 optimal weight: 0.0270 chunk 230 optimal weight: 4.9990 chunk 270 optimal weight: 0.9980 overall best weight: 2.0220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 ASN B 337 GLN F 337 GLN H 337 GLN L 337 GLN L 452 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.161734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.107856 restraints weight = 19299.122| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 1.82 r_work: 0.2970 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 22272 Z= 0.168 Angle : 0.516 10.459 30204 Z= 0.271 Chirality : 0.040 0.136 3552 Planarity : 0.004 0.029 3972 Dihedral : 4.597 53.401 3146 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer: Outliers : 2.82 % Allowed : 16.75 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 are not related in a simple way. whole: 2.30 (0.16), residues: 2868 helix: 2.29 (0.15), residues: 1152 sheet: 0.65 (0.19), residues: 744 loop : 1.53 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 357 TYR 0.006 0.001 TYR H 396 PHE 0.014 0.002 PHE I 534 HIS 0.003 0.001 HIS D 389 Details of bonding type rmsd covalent geometry : bond 0.00378 (22272) covalent geometry : angle 0.51636 (30204) hydrogen bonds : bond 0.05136 ( 957) hydrogen bonds : angle 4.18727 ( 2682) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9043.32 seconds wall clock time: 154 minutes 5.18 seconds (9245.18 seconds total)