Starting phenix.real_space_refine on Sat Aug 23 21:36:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jwe_36680/08_2025/8jwe_36680.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jwe_36680/08_2025/8jwe_36680.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jwe_36680/08_2025/8jwe_36680.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jwe_36680/08_2025/8jwe_36680.map" model { file = "/net/cci-nas-00/data/ceres_data/8jwe_36680/08_2025/8jwe_36680.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jwe_36680/08_2025/8jwe_36680.cif" } resolution = 2.74 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= 0.001 sd= 0.154 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 70 5.16 5 C 9583 2.51 5 N 2485 2.21 5 O 2723 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14861 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2123 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 9, 'TRANS': 271} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 165 Unresolved non-hydrogen angles: 208 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'PHE:plan': 5, 'ARG:plan': 6, 'ASN:plan1': 2, 'GLN:plan1': 1, 'TYR:plan': 1, 'GLU:plan': 7, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 114 Restraints were copied for chains: B, C, D, E, F, G Time building chain proxies: 2.06, per 1000 atoms: 0.14 Number of scatterers: 14861 At special positions: 0 Unit cell: (105.04, 107.06, 133.32, 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 70 16.00 O 2723 8.00 N 2485 7.00 C 9583 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: 1.03 Conformation dependent library (CDL) restraints added in 592.1 milliseconds Enol-peptide restraints added in 1.2 microseconds 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3850 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 9 sheets defined 48.4% alpha, 16.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 446 through 462 removed outlier: 4.802A pdb=" N GLU A 452 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG A 457 " --> pdb=" O GLU A 453 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N MET A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE A 460 " --> pdb=" O LEU A 456 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LYS A 461 " --> pdb=" O ARG A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.838A pdb=" N GLY A 478 " --> pdb=" O ALA A 474 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ARG A 479 " --> pdb=" O ALA A 475 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 474 through 479' Processing helix chain 'A' and resid 479 through 494 removed outlier: 3.860A pdb=" N ALA A 484 " --> pdb=" O ILE A 480 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N PHE A 485 " --> pdb=" O THR A 481 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A 489 " --> pdb=" O PHE A 485 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A 490 " --> pdb=" O THR A 486 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS A 491 " --> pdb=" O GLU A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 522 removed outlier: 3.678A pdb=" N LEU A 516 " --> pdb=" O GLN A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 534 removed outlier: 3.566A pdb=" N LEU A 531 " --> pdb=" O VAL A 527 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU A 534 " --> pdb=" O LEU A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 551 removed outlier: 3.690A pdb=" N GLN A 547 " --> pdb=" O PHE A 543 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL A 549 " --> pdb=" O SER A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 571 Processing helix chain 'A' and resid 612 through 616 Processing helix chain 'A' and resid 642 through 659 Processing helix chain 'A' and resid 695 through 717 removed outlier: 3.529A pdb=" N ARG A 712 " --> pdb=" O LEU A 708 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU A 715 " --> pdb=" O LYS A 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 462 removed outlier: 4.802A pdb=" N GLU B 452 " --> pdb=" O ASN B 448 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG B 457 " --> pdb=" O GLU B 453 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N MET B 459 " --> pdb=" O LEU B 455 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE B 460 " --> pdb=" O LEU B 456 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LYS B 461 " --> pdb=" O ARG B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 479 removed outlier: 3.838A pdb=" N GLY B 478 " --> pdb=" O ALA B 474 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ARG B 479 " --> pdb=" O ALA B 475 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 474 through 479' Processing helix chain 'B' and resid 479 through 494 removed outlier: 3.861A pdb=" N ALA B 484 " --> pdb=" O ILE B 480 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N PHE B 485 " --> pdb=" O THR B 481 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL B 489 " --> pdb=" O PHE B 485 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL B 490 " --> pdb=" O THR B 486 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS B 491 " --> pdb=" O GLU B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 522 removed outlier: 3.678A pdb=" N LEU B 516 " --> pdb=" O GLN B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 534 removed outlier: 3.566A pdb=" N LEU B 531 " --> pdb=" O VAL B 527 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU B 534 " --> pdb=" O LEU B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 551 removed outlier: 3.690A pdb=" N GLN B 547 " --> pdb=" O PHE B 543 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL B 549 " --> pdb=" O SER B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 571 Processing helix chain 'B' and resid 612 through 616 Processing helix chain 'B' and resid 642 through 659 Processing helix chain 'B' and resid 695 through 717 removed outlier: 3.530A pdb=" N ARG B 712 " --> pdb=" O LEU B 708 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU B 715 " --> pdb=" O LYS B 711 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 462 removed outlier: 4.802A pdb=" N GLU C 452 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG C 457 " --> pdb=" O GLU C 453 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N MET C 459 " --> pdb=" O LEU C 455 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE C 460 " --> pdb=" O LEU C 456 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LYS C 461 " --> pdb=" O ARG C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 479 removed outlier: 3.838A pdb=" N GLY C 478 " --> pdb=" O ALA C 474 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ARG C 479 " --> pdb=" O ALA C 475 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 474 through 479' Processing helix chain 'C' and resid 479 through 494 removed outlier: 3.861A pdb=" N ALA C 484 " --> pdb=" O ILE C 480 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N PHE C 485 " --> pdb=" O THR C 481 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL C 489 " --> pdb=" O PHE C 485 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL C 490 " --> pdb=" O THR C 486 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS C 491 " --> pdb=" O GLU C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 522 removed outlier: 3.678A pdb=" N LEU C 516 " --> pdb=" O GLN C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 534 removed outlier: 3.566A pdb=" N LEU C 531 " --> pdb=" O VAL C 527 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU C 534 " --> pdb=" O LEU C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 551 removed outlier: 3.691A pdb=" N GLN C 547 " --> pdb=" O PHE C 543 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL C 549 " --> pdb=" O SER C 545 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 571 Processing helix chain 'C' and resid 612 through 616 Processing helix chain 'C' and resid 642 through 659 Processing helix chain 'C' and resid 695 through 717 removed outlier: 3.530A pdb=" N ARG C 712 " --> pdb=" O LEU C 708 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU C 715 " --> pdb=" O LYS C 711 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 462 removed outlier: 4.803A pdb=" N GLU D 452 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG D 457 " --> pdb=" O GLU D 453 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N MET D 459 " --> pdb=" O LEU D 455 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE D 460 " --> pdb=" O LEU D 456 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LYS D 461 " --> pdb=" O ARG D 457 " (cutoff:3.500A) Processing helix chain 'D' and resid 474 through 479 removed outlier: 3.837A pdb=" N GLY D 478 " --> pdb=" O ALA D 474 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ARG D 479 " --> pdb=" O ALA D 475 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 474 through 479' Processing helix chain 'D' and resid 479 through 494 removed outlier: 3.861A pdb=" N ALA D 484 " --> pdb=" O ILE D 480 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N PHE D 485 " --> pdb=" O THR D 481 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL D 489 " --> pdb=" O PHE D 485 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL D 490 " --> pdb=" O THR D 486 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS D 491 " --> pdb=" O GLU D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 508 through 522 removed outlier: 3.679A pdb=" N LEU D 516 " --> pdb=" O GLN D 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 534 removed outlier: 3.567A pdb=" N LEU D 531 " --> pdb=" O VAL D 527 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU D 534 " --> pdb=" O LEU D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 551 removed outlier: 3.690A pdb=" N GLN D 547 " --> pdb=" O PHE D 543 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL D 549 " --> pdb=" O SER D 545 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 571 Processing helix chain 'D' and resid 612 through 616 Processing helix chain 'D' and resid 642 through 659 Processing helix chain 'D' and resid 695 through 717 removed outlier: 3.530A pdb=" N ARG D 712 " --> pdb=" O LEU D 708 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU D 715 " --> pdb=" O LYS D 711 " (cutoff:3.500A) Processing helix chain 'E' and resid 446 through 462 removed outlier: 4.802A pdb=" N GLU E 452 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG E 457 " --> pdb=" O GLU E 453 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N MET E 459 " --> pdb=" O LEU E 455 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE E 460 " --> pdb=" O LEU E 456 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LYS E 461 " --> pdb=" O ARG E 457 " (cutoff:3.500A) Processing helix chain 'E' and resid 474 through 479 removed outlier: 3.838A pdb=" N GLY E 478 " --> pdb=" O ALA E 474 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ARG E 479 " --> pdb=" O ALA E 475 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 474 through 479' Processing helix chain 'E' and resid 479 through 494 removed outlier: 3.861A pdb=" N ALA E 484 " --> pdb=" O ILE E 480 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N PHE E 485 " --> pdb=" O THR E 481 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL E 489 " --> pdb=" O PHE E 485 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL E 490 " --> pdb=" O THR E 486 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS E 491 " --> pdb=" O GLU E 487 " (cutoff:3.500A) Processing helix chain 'E' and resid 508 through 522 removed outlier: 3.678A pdb=" N LEU E 516 " --> pdb=" O GLN E 512 " (cutoff:3.500A) Processing helix chain 'E' and resid 525 through 534 removed outlier: 3.567A pdb=" N LEU E 531 " --> pdb=" O VAL E 527 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU E 534 " --> pdb=" O LEU E 530 " (cutoff:3.500A) Processing helix chain 'E' and resid 543 through 551 removed outlier: 3.690A pdb=" N GLN E 547 " --> pdb=" O PHE E 543 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL E 549 " --> pdb=" O SER E 545 " (cutoff:3.500A) Processing helix chain 'E' and resid 555 through 571 Processing helix chain 'E' and resid 612 through 616 Processing helix chain 'E' and resid 642 through 659 Processing helix chain 'E' and resid 695 through 717 removed outlier: 3.530A pdb=" N ARG E 712 " --> pdb=" O LEU E 708 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU E 715 " --> pdb=" O LYS E 711 " (cutoff:3.500A) Processing helix chain 'F' and resid 446 through 462 removed outlier: 4.802A pdb=" N GLU F 452 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG F 457 " --> pdb=" O GLU F 453 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N MET F 459 " --> pdb=" O LEU F 455 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE F 460 " --> pdb=" O LEU F 456 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LYS F 461 " --> pdb=" O ARG F 457 " (cutoff:3.500A) Processing helix chain 'F' and resid 474 through 479 removed outlier: 3.838A pdb=" N GLY F 478 " --> pdb=" O ALA F 474 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ARG F 479 " --> pdb=" O ALA F 475 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 474 through 479' Processing helix chain 'F' and resid 479 through 494 removed outlier: 3.860A pdb=" N ALA F 484 " --> pdb=" O ILE F 480 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N PHE F 485 " --> pdb=" O THR F 481 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL F 489 " --> pdb=" O PHE F 485 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL F 490 " --> pdb=" O THR F 486 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS F 491 " --> pdb=" O GLU F 487 " (cutoff:3.500A) Processing helix chain 'F' and resid 508 through 522 removed outlier: 3.679A pdb=" N LEU F 516 " --> pdb=" O GLN F 512 " (cutoff:3.500A) Processing helix chain 'F' and resid 525 through 534 removed outlier: 3.567A pdb=" N LEU F 531 " --> pdb=" O VAL F 527 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU F 534 " --> pdb=" O LEU F 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 543 through 551 removed outlier: 3.690A pdb=" N GLN F 547 " --> pdb=" O PHE F 543 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL F 549 " --> pdb=" O SER F 545 " (cutoff:3.500A) Processing helix chain 'F' and resid 555 through 571 Processing helix chain 'F' and resid 612 through 616 Processing helix chain 'F' and resid 642 through 659 Processing helix chain 'F' and resid 695 through 717 removed outlier: 3.529A pdb=" N ARG F 712 " --> pdb=" O LEU F 708 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU F 715 " --> pdb=" O LYS F 711 " (cutoff:3.500A) Processing helix chain 'G' and resid 446 through 462 removed outlier: 4.802A pdb=" N GLU G 452 " --> pdb=" O ASN G 448 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG G 457 " --> pdb=" O GLU G 453 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N MET G 459 " --> pdb=" O LEU G 455 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE G 460 " --> pdb=" O LEU G 456 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LYS G 461 " --> pdb=" O ARG G 457 " (cutoff:3.500A) Processing helix chain 'G' and resid 474 through 479 removed outlier: 3.838A pdb=" N GLY G 478 " --> pdb=" O ALA G 474 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ARG G 479 " --> pdb=" O ALA G 475 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 474 through 479' Processing helix chain 'G' and resid 479 through 494 removed outlier: 3.860A pdb=" N ALA G 484 " --> pdb=" O ILE G 480 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N PHE G 485 " --> pdb=" O THR G 481 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL G 489 " --> pdb=" O PHE G 485 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL G 490 " --> pdb=" O THR G 486 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS G 491 " --> pdb=" O GLU G 487 " (cutoff:3.500A) Processing helix chain 'G' and resid 508 through 522 removed outlier: 3.678A pdb=" N LEU G 516 " --> pdb=" O GLN G 512 " (cutoff:3.500A) Processing helix chain 'G' and resid 525 through 534 removed outlier: 3.566A pdb=" N LEU G 531 " --> pdb=" O VAL G 527 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU G 534 " --> pdb=" O LEU G 530 " (cutoff:3.500A) Processing helix chain 'G' and resid 543 through 551 removed outlier: 3.690A pdb=" N GLN G 547 " --> pdb=" O PHE G 543 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL G 549 " --> pdb=" O SER G 545 " (cutoff:3.500A) Processing helix chain 'G' and resid 555 through 571 Processing helix chain 'G' and resid 612 through 616 Processing helix chain 'G' and resid 642 through 659 Processing helix chain 'G' and resid 695 through 717 removed outlier: 3.530A pdb=" N ARG G 712 " --> pdb=" O LEU G 708 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU G 715 " --> pdb=" O LYS G 711 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 580 through 582 removed outlier: 6.515A pdb=" N VAL A 599 " --> pdb=" O GLU A 591 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N MET A 593 " --> pdb=" O THR A 597 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N THR A 597 " --> pdb=" O MET A 593 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LYS A 607 " --> pdb=" O ASN F 622 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL F 599 " --> pdb=" O GLU F 591 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N MET F 593 " --> pdb=" O THR F 597 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N THR F 597 " --> pdb=" O MET F 593 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LYS F 607 " --> pdb=" O ASN E 622 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL E 599 " --> pdb=" O GLU E 591 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N MET E 593 " --> pdb=" O THR E 597 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N THR E 597 " --> pdb=" O MET E 593 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LYS E 607 " --> pdb=" O ASN D 622 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL D 599 " --> pdb=" O GLU D 591 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N MET D 593 " --> pdb=" O THR D 597 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N THR D 597 " --> pdb=" O MET D 593 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LYS D 607 " --> pdb=" O ASN C 622 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL C 599 " --> pdb=" O GLU C 591 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N MET C 593 " --> pdb=" O THR C 597 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N THR C 597 " --> pdb=" O MET C 593 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N LYS C 607 " --> pdb=" O ASN G 622 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL G 599 " --> pdb=" O GLU G 591 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N MET G 593 " --> pdb=" O THR G 597 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N THR G 597 " --> pdb=" O MET G 593 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LYS G 607 " --> pdb=" O ASN B 622 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL B 599 " --> pdb=" O GLU B 591 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N MET B 593 " --> pdb=" O THR B 597 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N THR B 597 " --> pdb=" O MET B 593 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LYS B 607 " --> pdb=" O ASN A 622 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 630 through 638 removed outlier: 6.685A pdb=" N LYS A 680 " --> pdb=" O ILE A 675 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ILE A 675 " --> pdb=" O LYS A 680 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LYS A 682 " --> pdb=" O LYS A 673 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 726 through 731 removed outlier: 3.942A pdb=" N LEU B 730 " --> pdb=" O THR A 731 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU G 730 " --> pdb=" O THR B 731 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLN C 726 " --> pdb=" O ASN G 729 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N THR G 731 " --> pdb=" O GLN C 726 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE C 728 " --> pdb=" O THR G 731 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU D 730 " --> pdb=" O THR C 731 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU E 730 " --> pdb=" O THR D 731 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU F 730 " --> pdb=" O THR E 731 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLN A 726 " --> pdb=" O ASN F 729 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N THR F 731 " --> pdb=" O GLN A 726 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ILE A 728 " --> pdb=" O THR F 731 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 630 through 638 removed outlier: 6.685A pdb=" N LYS B 680 " --> pdb=" O ILE B 675 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ILE B 675 " --> pdb=" O LYS B 680 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LYS B 682 " --> pdb=" O LYS B 673 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 630 through 638 removed outlier: 6.685A pdb=" N LYS C 680 " --> pdb=" O ILE C 675 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ILE C 675 " --> pdb=" O LYS C 680 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LYS C 682 " --> pdb=" O LYS C 673 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 630 through 638 removed outlier: 6.685A pdb=" N LYS D 680 " --> pdb=" O ILE D 675 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ILE D 675 " --> pdb=" O LYS D 680 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LYS D 682 " --> pdb=" O LYS D 673 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 630 through 638 removed outlier: 6.685A pdb=" N LYS E 680 " --> pdb=" O ILE E 675 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ILE E 675 " --> pdb=" O LYS E 680 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LYS E 682 " --> pdb=" O LYS E 673 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 630 through 638 removed outlier: 6.686A pdb=" N LYS F 680 " --> pdb=" O ILE F 675 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ILE F 675 " --> pdb=" O LYS F 680 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LYS F 682 " --> pdb=" O LYS F 673 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 630 through 638 removed outlier: 6.686A pdb=" N LYS G 680 " --> pdb=" O ILE G 675 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ILE G 675 " --> pdb=" O LYS G 680 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LYS G 682 " --> pdb=" O LYS G 673 " (cutoff:3.500A) 748 hydrogen bonds defined for protein. 2187 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: 2.45 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 2608 1.27 - 1.40: 3986 1.40 - 1.53: 7724 1.53 - 1.66: 669 1.66 - 1.79: 126 Bond restraints: 15113 Sorted by residual: bond pdb=" CG GLU C 591 " pdb=" CD GLU C 591 " ideal model delta sigma weight residual 1.516 1.334 0.182 2.50e-02 1.60e+03 5.30e+01 bond pdb=" CG GLU A 591 " pdb=" CD GLU A 591 " ideal model delta sigma weight residual 1.516 1.334 0.182 2.50e-02 1.60e+03 5.30e+01 bond pdb=" CG GLU B 591 " pdb=" CD GLU B 591 " ideal model delta sigma weight residual 1.516 1.334 0.182 2.50e-02 1.60e+03 5.29e+01 bond pdb=" CG GLU G 591 " pdb=" CD GLU G 591 " ideal model delta sigma weight residual 1.516 1.335 0.181 2.50e-02 1.60e+03 5.27e+01 bond pdb=" CG GLU E 591 " pdb=" CD GLU E 591 " ideal model delta sigma weight residual 1.516 1.335 0.181 2.50e-02 1.60e+03 5.25e+01 ... (remaining 15108 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.02: 18117 3.02 - 6.03: 2009 6.03 - 9.05: 356 9.05 - 12.06: 105 12.06 - 15.08: 7 Bond angle restraints: 20594 Sorted by residual: angle pdb=" N PRO D 445 " pdb=" CA PRO D 445 " pdb=" CB PRO D 445 " ideal model delta sigma weight residual 103.25 111.16 -7.91 1.05e+00 9.07e-01 5.67e+01 angle pdb=" N PRO B 445 " pdb=" CA PRO B 445 " pdb=" CB PRO B 445 " ideal model delta sigma weight residual 103.25 111.15 -7.90 1.05e+00 9.07e-01 5.66e+01 angle pdb=" N PRO F 445 " pdb=" CA PRO F 445 " pdb=" CB PRO F 445 " ideal model delta sigma weight residual 103.25 111.14 -7.89 1.05e+00 9.07e-01 5.65e+01 angle pdb=" N PRO C 445 " pdb=" CA PRO C 445 " pdb=" CB PRO C 445 " ideal model delta sigma weight residual 103.25 111.13 -7.88 1.05e+00 9.07e-01 5.64e+01 angle pdb=" N PRO A 445 " pdb=" CA PRO A 445 " pdb=" CB PRO A 445 " ideal model delta sigma weight residual 103.25 111.12 -7.87 1.05e+00 9.07e-01 5.62e+01 ... (remaining 20589 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.58: 8015 14.58 - 29.16: 882 29.16 - 43.74: 154 43.74 - 58.32: 35 58.32 - 72.90: 21 Dihedral angle restraints: 9107 sinusoidal: 3255 harmonic: 5852 Sorted by residual: dihedral pdb=" CA ALA F 552 " pdb=" C ALA F 552 " pdb=" N PHE F 553 " pdb=" CA PHE F 553 " ideal model delta harmonic sigma weight residual 180.00 151.65 28.35 0 5.00e+00 4.00e-02 3.22e+01 dihedral pdb=" CA ALA D 552 " pdb=" C ALA D 552 " pdb=" N PHE D 553 " pdb=" CA PHE D 553 " ideal model delta harmonic sigma weight residual 180.00 151.67 28.33 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA ALA B 552 " pdb=" C ALA B 552 " pdb=" N PHE B 553 " pdb=" CA PHE B 553 " ideal model delta harmonic sigma weight residual 180.00 151.68 28.32 0 5.00e+00 4.00e-02 3.21e+01 ... (remaining 9104 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 1344 0.095 - 0.191: 769 0.191 - 0.286: 271 0.286 - 0.382: 157 0.382 - 0.477: 28 Chirality restraints: 2569 Sorted by residual: chirality pdb=" CG LEU B 685 " pdb=" CB LEU B 685 " pdb=" CD1 LEU B 685 " pdb=" CD2 LEU B 685 " both_signs ideal model delta sigma weight residual False -2.59 -2.11 -0.48 2.00e-01 2.50e+01 5.69e+00 chirality pdb=" CG LEU A 685 " pdb=" CB LEU A 685 " pdb=" CD1 LEU A 685 " pdb=" CD2 LEU A 685 " both_signs ideal model delta sigma weight residual False -2.59 -2.11 -0.48 2.00e-01 2.50e+01 5.67e+00 chirality pdb=" CG LEU E 685 " pdb=" CB LEU E 685 " pdb=" CD1 LEU E 685 " pdb=" CD2 LEU E 685 " both_signs ideal model delta sigma weight residual False -2.59 -2.11 -0.48 2.00e-01 2.50e+01 5.67e+00 ... (remaining 2566 not shown) Planarity restraints: 2562 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 679 " -0.017 2.00e-02 2.50e+03 3.41e-02 1.16e+01 pdb=" CG ASN E 679 " 0.059 2.00e-02 2.50e+03 pdb=" OD1 ASN E 679 " -0.022 2.00e-02 2.50e+03 pdb=" ND2 ASN E 679 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 679 " -0.017 2.00e-02 2.50e+03 3.41e-02 1.16e+01 pdb=" CG ASN D 679 " 0.059 2.00e-02 2.50e+03 pdb=" OD1 ASN D 679 " -0.022 2.00e-02 2.50e+03 pdb=" ND2 ASN D 679 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN G 679 " 0.017 2.00e-02 2.50e+03 3.40e-02 1.16e+01 pdb=" CG ASN G 679 " -0.059 2.00e-02 2.50e+03 pdb=" OD1 ASN G 679 " 0.022 2.00e-02 2.50e+03 pdb=" ND2 ASN G 679 " 0.020 2.00e-02 2.50e+03 ... (remaining 2559 not shown) Histogram of nonbonded interaction distances: 1.32 - 2.04: 7 2.04 - 2.75: 2852 2.75 - 3.47: 18293 3.47 - 4.18: 35513 4.18 - 4.90: 61181 Nonbonded interactions: 117846 Sorted by model distance: nonbonded pdb=" CE2 TYR G 610 " pdb=" CG LEU G 615 " model vdw 1.322 3.770 nonbonded pdb=" CE2 TYR F 610 " pdb=" CG LEU F 615 " model vdw 1.324 3.770 nonbonded pdb=" CE2 TYR B 610 " pdb=" CG LEU B 615 " model vdw 1.325 3.770 nonbonded pdb=" CE2 TYR E 610 " pdb=" CG LEU E 615 " model vdw 1.325 3.770 nonbonded pdb=" CE2 TYR A 610 " pdb=" CG LEU A 615 " model vdw 1.326 3.770 ... (remaining 117841 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: 0.06 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.940 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 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 : 0.046 0.250 15113 Z= 1.874 Angle : 2.122 15.076 20594 Z= 1.134 Chirality : 0.148 0.477 2569 Planarity : 0.011 0.060 2562 Dihedral : 13.175 72.895 5257 Min Nonbonded Distance : 1.322 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.18 % Favored : 93.45 % Rotamer: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.49 (0.17), residues: 1925 helix: -4.29 (0.11), residues: 931 sheet: -0.61 (0.25), residues: 350 loop : -1.79 (0.26), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.003 ARG A 699 TYR 0.043 0.009 TYR E 721 PHE 0.041 0.009 PHE F 600 TRP 0.052 0.010 TRP G 488 HIS 0.027 0.008 HIS G 573 Details of bonding type rmsd covalent geometry : bond 0.04555 (15113) covalent geometry : angle 2.12241 (20594) hydrogen bonds : bond 0.30431 ( 748) hydrogen bonds : angle 11.15771 ( 2187) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 0.566 Fit side-chains REVERT: A 515 LYS cc_start: 0.8261 (mtmt) cc_final: 0.7947 (mtmt) REVERT: A 522 MET cc_start: 0.6424 (mmt) cc_final: 0.5373 (ptt) REVERT: A 676 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7961 (mt-10) REVERT: B 515 LYS cc_start: 0.8135 (mtmt) cc_final: 0.7895 (mtpt) REVERT: B 522 MET cc_start: 0.6625 (mmt) cc_final: 0.6253 (mmm) REVERT: B 652 ARG cc_start: 0.7751 (ttm-80) cc_final: 0.7545 (mtp85) REVERT: B 676 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7806 (mt-10) REVERT: C 515 LYS cc_start: 0.8319 (mtmt) cc_final: 0.8075 (mtpt) REVERT: C 522 MET cc_start: 0.6989 (mmt) cc_final: 0.6684 (mmm) REVERT: C 629 MET cc_start: 0.9405 (mtp) cc_final: 0.9181 (mtm) REVERT: C 652 ARG cc_start: 0.7872 (ttm-80) cc_final: 0.7459 (mtp85) REVERT: C 659 GLN cc_start: 0.8513 (pt0) cc_final: 0.8283 (pt0) REVERT: C 720 ASP cc_start: 0.8524 (p0) cc_final: 0.8323 (p0) REVERT: D 522 MET cc_start: 0.6524 (mmt) cc_final: 0.6315 (mmm) REVERT: D 593 MET cc_start: 0.9121 (mtp) cc_final: 0.8761 (mtp) REVERT: D 712 ARG cc_start: 0.8119 (ttp80) cc_final: 0.7903 (ttp-170) REVERT: D 720 ASP cc_start: 0.8511 (p0) cc_final: 0.8180 (p0) REVERT: E 512 GLN cc_start: 0.6846 (tt0) cc_final: 0.6642 (tt0) REVERT: E 515 LYS cc_start: 0.8367 (mtmt) cc_final: 0.8150 (mtpt) REVERT: E 522 MET cc_start: 0.6596 (mmt) cc_final: 0.5608 (ptt) REVERT: E 629 MET cc_start: 0.9379 (mtp) cc_final: 0.9077 (mtm) REVERT: E 655 GLU cc_start: 0.7988 (tt0) cc_final: 0.7737 (tt0) REVERT: E 720 ASP cc_start: 0.8505 (p0) cc_final: 0.8127 (p0) REVERT: E 729 ASN cc_start: 0.8626 (m-40) cc_final: 0.8394 (m-40) REVERT: F 515 LYS cc_start: 0.8056 (mtmt) cc_final: 0.7805 (mtmt) REVERT: F 522 MET cc_start: 0.6600 (mmt) cc_final: 0.6251 (mmm) REVERT: F 572 MET cc_start: 0.8551 (mtt) cc_final: 0.8254 (mtt) REVERT: F 629 MET cc_start: 0.9390 (mtp) cc_final: 0.9067 (mtm) REVERT: F 652 ARG cc_start: 0.7720 (ttm-80) cc_final: 0.7460 (mtp85) REVERT: F 655 GLU cc_start: 0.7986 (tt0) cc_final: 0.7743 (tt0) REVERT: F 676 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7933 (mt-10) REVERT: F 720 ASP cc_start: 0.8635 (p0) cc_final: 0.8398 (p0) REVERT: G 515 LYS cc_start: 0.8287 (mtmt) cc_final: 0.8083 (mtmt) REVERT: G 522 MET cc_start: 0.6527 (mmt) cc_final: 0.5455 (ptt) REVERT: G 652 ARG cc_start: 0.7837 (ttm-80) cc_final: 0.7604 (mtt180) REVERT: G 676 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7856 (mt-10) REVERT: G 713 MET cc_start: 0.8732 (mtt) cc_final: 0.8307 (mtt) outliers start: 0 outliers final: 0 residues processed: 264 average time/residue: 0.7216 time to fit residues: 204.9634 Evaluate side-chains 212 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 561 ASN A 612 ASN A 663 HIS A 677 ASN A 694 GLN A 726 GLN B 561 ASN B 612 ASN B 659 GLN B 663 HIS B 677 ASN B 679 ASN B 694 GLN B 726 GLN C 561 ASN C 612 ASN C 663 HIS C 677 ASN C 679 ASN C 694 GLN C 726 GLN D 561 ASN D 612 ASN D 659 GLN D 663 HIS D 677 ASN D 694 GLN D 726 GLN E 561 ASN E 612 ASN E 659 GLN E 663 HIS E 677 ASN E 679 ASN E 694 GLN E 726 GLN F 512 GLN F 561 ASN F 612 ASN F 659 GLN F 663 HIS F 677 ASN F 679 ASN F 694 GLN F 726 GLN G 561 ASN G 612 ASN G 663 HIS G 677 ASN G 694 GLN G 726 GLN Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.163732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.099457 restraints weight = 15109.221| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 1.59 r_work: 0.2705 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2584 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15113 Z= 0.147 Angle : 0.659 7.937 20594 Z= 0.356 Chirality : 0.046 0.152 2569 Planarity : 0.005 0.031 2562 Dihedral : 6.354 19.195 2058 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.10 % Allowed : 8.78 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.16 (0.18), residues: 1925 helix: -2.65 (0.14), residues: 945 sheet: -0.02 (0.27), residues: 336 loop : -2.03 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 703 TYR 0.009 0.002 TYR D 721 PHE 0.015 0.002 PHE D 639 TRP 0.014 0.002 TRP G 488 HIS 0.005 0.001 HIS E 689 Details of bonding type rmsd covalent geometry : bond 0.00332 (15113) covalent geometry : angle 0.65913 (20594) hydrogen bonds : bond 0.05030 ( 748) hydrogen bonds : angle 5.63604 ( 2187) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 243 time to evaluate : 0.481 Fit side-chains REVERT: A 515 LYS cc_start: 0.7799 (mtmt) cc_final: 0.7480 (mtmt) REVERT: A 522 MET cc_start: 0.6518 (mmt) cc_final: 0.5288 (ptt) REVERT: A 558 THR cc_start: 0.8133 (OUTLIER) cc_final: 0.7744 (p) REVERT: A 572 MET cc_start: 0.8943 (mtt) cc_final: 0.8720 (mtt) REVERT: A 651 GLU cc_start: 0.8411 (tt0) cc_final: 0.8124 (mt-10) REVERT: A 655 GLU cc_start: 0.8602 (tt0) cc_final: 0.8374 (tm-30) REVERT: A 676 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8522 (mm-30) REVERT: A 705 GLU cc_start: 0.8807 (tt0) cc_final: 0.8586 (tp30) REVERT: B 515 LYS cc_start: 0.7750 (mtmt) cc_final: 0.7490 (mtpt) REVERT: B 522 MET cc_start: 0.6734 (mmt) cc_final: 0.6243 (mmm) REVERT: B 651 GLU cc_start: 0.8490 (tt0) cc_final: 0.8137 (mt-10) REVERT: B 655 GLU cc_start: 0.8656 (tt0) cc_final: 0.8435 (tm-30) REVERT: B 729 ASN cc_start: 0.8617 (m-40) cc_final: 0.8404 (m110) REVERT: C 515 LYS cc_start: 0.7661 (mtmt) cc_final: 0.7355 (mtmt) REVERT: C 522 MET cc_start: 0.6910 (mmt) cc_final: 0.5623 (ptt) REVERT: C 558 THR cc_start: 0.7971 (OUTLIER) cc_final: 0.7671 (p) REVERT: C 651 GLU cc_start: 0.8523 (tt0) cc_final: 0.8165 (mt-10) REVERT: C 699 ARG cc_start: 0.8994 (OUTLIER) cc_final: 0.8690 (ttt180) REVERT: C 705 GLU cc_start: 0.8845 (tt0) cc_final: 0.8596 (tp30) REVERT: C 720 ASP cc_start: 0.8667 (p0) cc_final: 0.8453 (p0) REVERT: D 522 MET cc_start: 0.6660 (mmt) cc_final: 0.5658 (ptt) REVERT: D 593 MET cc_start: 0.9318 (mtp) cc_final: 0.8901 (mtp) REVERT: D 651 GLU cc_start: 0.8579 (tt0) cc_final: 0.8201 (mt-10) REVERT: D 705 GLU cc_start: 0.8820 (tt0) cc_final: 0.8397 (tp30) REVERT: D 720 ASP cc_start: 0.8802 (p0) cc_final: 0.8519 (p0) REVERT: E 515 LYS cc_start: 0.7903 (mtmt) cc_final: 0.7535 (mtmt) REVERT: E 522 MET cc_start: 0.6869 (mmt) cc_final: 0.5618 (ptt) REVERT: E 576 ASP cc_start: 0.8751 (m-30) cc_final: 0.8441 (m-30) REVERT: E 579 ASP cc_start: 0.8942 (p0) cc_final: 0.8603 (p0) REVERT: E 629 MET cc_start: 0.9441 (mtp) cc_final: 0.9129 (mtm) REVERT: E 651 GLU cc_start: 0.8310 (tt0) cc_final: 0.8039 (mt-10) REVERT: E 655 GLU cc_start: 0.8642 (tt0) cc_final: 0.8353 (tm-30) REVERT: E 705 GLU cc_start: 0.8743 (tt0) cc_final: 0.8400 (tp30) REVERT: F 515 LYS cc_start: 0.7795 (mtmt) cc_final: 0.7539 (mtmt) REVERT: F 522 MET cc_start: 0.6847 (mmt) cc_final: 0.6374 (mmm) REVERT: F 558 THR cc_start: 0.8106 (OUTLIER) cc_final: 0.7776 (p) REVERT: F 572 MET cc_start: 0.9000 (mtt) cc_final: 0.8731 (mtp) REVERT: F 651 GLU cc_start: 0.8519 (tt0) cc_final: 0.8079 (mt-10) REVERT: F 655 GLU cc_start: 0.8563 (tt0) cc_final: 0.8190 (tm-30) REVERT: F 713 MET cc_start: 0.9031 (mtt) cc_final: 0.8708 (mtt) REVERT: F 720 ASP cc_start: 0.8763 (p0) cc_final: 0.8496 (p0) REVERT: G 515 LYS cc_start: 0.7726 (mtmt) cc_final: 0.7439 (mtmt) REVERT: G 522 MET cc_start: 0.6456 (mmt) cc_final: 0.5243 (ptt) REVERT: G 651 GLU cc_start: 0.8533 (tt0) cc_final: 0.8219 (mt-10) outliers start: 32 outliers final: 4 residues processed: 264 average time/residue: 0.5829 time to fit residues: 167.4257 Evaluate side-chains 226 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 217 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 705 GLU Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 699 ARG Chi-restraints excluded: chain F residue 558 THR Chi-restraints excluded: chain F residue 643 VAL Chi-restraints excluded: chain F residue 688 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 195 optimal weight: 6.9990 chunk 125 optimal weight: 0.0000 chunk 59 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 168 optimal weight: 50.0000 chunk 101 optimal weight: 2.9990 chunk 23 optimal weight: 7.9990 chunk 147 optimal weight: 9.9990 chunk 158 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 overall best weight: 1.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 561 ASN A 659 GLN B 561 ASN B 659 GLN C 561 ASN C 659 GLN D 561 ASN D 659 GLN E 561 ASN E 659 GLN E 668 HIS F 561 ASN F 659 GLN G 561 ASN G 659 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.161228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.109723 restraints weight = 15138.453| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.74 r_work: 0.2656 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2528 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15113 Z= 0.176 Angle : 0.634 7.524 20594 Z= 0.339 Chirality : 0.046 0.166 2569 Planarity : 0.004 0.034 2562 Dihedral : 5.958 16.764 2058 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.70 % Allowed : 11.21 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.05 (0.19), residues: 1925 helix: -1.31 (0.17), residues: 917 sheet: 0.01 (0.27), residues: 336 loop : -1.94 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 703 TYR 0.012 0.002 TYR B 721 PHE 0.020 0.002 PHE D 639 TRP 0.012 0.002 TRP G 488 HIS 0.005 0.001 HIS C 689 Details of bonding type rmsd covalent geometry : bond 0.00421 (15113) covalent geometry : angle 0.63444 (20594) hydrogen bonds : bond 0.05193 ( 748) hydrogen bonds : angle 5.20163 ( 2187) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 239 time to evaluate : 0.514 Fit side-chains REVERT: A 515 LYS cc_start: 0.7658 (mtmt) cc_final: 0.7372 (mtmt) REVERT: A 522 MET cc_start: 0.6469 (mmt) cc_final: 0.5198 (ptt) REVERT: A 705 GLU cc_start: 0.8856 (tt0) cc_final: 0.8629 (tp30) REVERT: B 515 LYS cc_start: 0.7689 (mtmt) cc_final: 0.7478 (mtpt) REVERT: B 522 MET cc_start: 0.6689 (mmt) cc_final: 0.6227 (mmm) REVERT: B 651 GLU cc_start: 0.8668 (tt0) cc_final: 0.8418 (mt-10) REVERT: C 515 LYS cc_start: 0.7594 (mtmt) cc_final: 0.7270 (mtmt) REVERT: C 522 MET cc_start: 0.6785 (mmt) cc_final: 0.6376 (mmm) REVERT: C 651 GLU cc_start: 0.8505 (tt0) cc_final: 0.8214 (mt-10) REVERT: C 699 ARG cc_start: 0.9061 (OUTLIER) cc_final: 0.8752 (ttt180) REVERT: C 720 ASP cc_start: 0.8802 (p0) cc_final: 0.8576 (p0) REVERT: D 522 MET cc_start: 0.6821 (mmt) cc_final: 0.5752 (ptt) REVERT: D 593 MET cc_start: 0.9300 (mtp) cc_final: 0.8905 (mtp) REVERT: D 651 GLU cc_start: 0.8598 (tt0) cc_final: 0.8309 (mt-10) REVERT: D 658 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7671 (mt-10) REVERT: D 705 GLU cc_start: 0.8921 (tt0) cc_final: 0.8512 (tp30) REVERT: D 720 ASP cc_start: 0.8844 (p0) cc_final: 0.8603 (p0) REVERT: E 515 LYS cc_start: 0.7803 (mtmt) cc_final: 0.7598 (mtpt) REVERT: E 522 MET cc_start: 0.6785 (mmt) cc_final: 0.5420 (ptt) REVERT: E 579 ASP cc_start: 0.9029 (p0) cc_final: 0.8732 (p0) REVERT: E 655 GLU cc_start: 0.8676 (tt0) cc_final: 0.8405 (tm-30) REVERT: E 720 ASP cc_start: 0.8929 (p0) cc_final: 0.8492 (p0) REVERT: F 515 LYS cc_start: 0.7707 (mtmt) cc_final: 0.7468 (mtmt) REVERT: F 522 MET cc_start: 0.6736 (mmt) cc_final: 0.6293 (mmm) REVERT: F 558 THR cc_start: 0.8152 (p) cc_final: 0.7790 (m) REVERT: F 651 GLU cc_start: 0.8637 (tt0) cc_final: 0.8365 (mt-10) REVERT: F 655 GLU cc_start: 0.8754 (tt0) cc_final: 0.8396 (tm-30) REVERT: F 720 ASP cc_start: 0.8767 (p0) cc_final: 0.8511 (p0) REVERT: G 515 LYS cc_start: 0.7614 (mtmt) cc_final: 0.7312 (mtmt) REVERT: G 522 MET cc_start: 0.6502 (mmt) cc_final: 0.5364 (ptt) REVERT: G 651 GLU cc_start: 0.8653 (tt0) cc_final: 0.8362 (mt-10) REVERT: G 655 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8449 (tm-30) REVERT: G 676 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8341 (mt-10) outliers start: 26 outliers final: 14 residues processed: 247 average time/residue: 0.7115 time to fit residues: 189.6586 Evaluate side-chains 240 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 222 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain B residue 591 GLU Chi-restraints excluded: chain B residue 643 VAL Chi-restraints excluded: chain B residue 705 GLU Chi-restraints excluded: chain C residue 643 VAL Chi-restraints excluded: chain C residue 688 ASP Chi-restraints excluded: chain C residue 699 ARG Chi-restraints excluded: chain D residue 511 LYS Chi-restraints excluded: chain D residue 591 GLU Chi-restraints excluded: chain D residue 643 VAL Chi-restraints excluded: chain D residue 658 GLU Chi-restraints excluded: chain E residue 591 GLU Chi-restraints excluded: chain E residue 643 VAL Chi-restraints excluded: chain F residue 643 VAL Chi-restraints excluded: chain G residue 643 VAL Chi-restraints excluded: chain G residue 655 GLU Chi-restraints excluded: chain G residue 676 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 143 optimal weight: 0.1980 chunk 91 optimal weight: 9.9990 chunk 108 optimal weight: 0.9990 chunk 131 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 169 optimal weight: 50.0000 chunk 101 optimal weight: 0.9990 chunk 194 optimal weight: 0.0980 chunk 95 optimal weight: 0.7980 chunk 56 optimal weight: 50.0000 chunk 118 optimal weight: 3.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 561 ASN A 659 GLN B 561 ASN B 659 GLN C 659 GLN D 659 GLN E 659 GLN G 561 ASN G 659 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.166644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.114120 restraints weight = 15109.126| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 2.24 r_work: 0.2780 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 15113 Z= 0.095 Angle : 0.508 8.190 20594 Z= 0.271 Chirality : 0.043 0.138 2569 Planarity : 0.003 0.031 2562 Dihedral : 5.100 14.949 2058 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.70 % Allowed : 12.19 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.30 (0.20), residues: 1925 helix: -0.62 (0.18), residues: 966 sheet: 0.28 (0.27), residues: 336 loop : -1.69 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 703 TYR 0.005 0.001 TYR B 623 PHE 0.010 0.001 PHE A 600 TRP 0.006 0.001 TRP G 488 HIS 0.005 0.001 HIS G 689 Details of bonding type rmsd covalent geometry : bond 0.00202 (15113) covalent geometry : angle 0.50776 (20594) hydrogen bonds : bond 0.03350 ( 748) hydrogen bonds : angle 4.52733 ( 2187) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 234 time to evaluate : 0.600 Fit side-chains REVERT: A 515 LYS cc_start: 0.7623 (mtmt) cc_final: 0.7389 (mtmt) REVERT: A 522 MET cc_start: 0.6599 (mmt) cc_final: 0.5264 (ptt) REVERT: A 676 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8131 (mm-30) REVERT: B 515 LYS cc_start: 0.7722 (mtmt) cc_final: 0.7516 (mtpt) REVERT: B 522 MET cc_start: 0.6632 (mmt) cc_final: 0.6099 (mmm) REVERT: C 515 LYS cc_start: 0.7592 (mtmt) cc_final: 0.7337 (mtmt) REVERT: C 522 MET cc_start: 0.6693 (mmt) cc_final: 0.5424 (ptt) REVERT: C 699 ARG cc_start: 0.8937 (OUTLIER) cc_final: 0.8529 (ttt180) REVERT: D 522 MET cc_start: 0.6605 (mmt) cc_final: 0.5623 (ptt) REVERT: D 591 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8277 (pp20) REVERT: D 658 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7386 (mt-10) REVERT: D 705 GLU cc_start: 0.8758 (tt0) cc_final: 0.8390 (tp30) REVERT: D 720 ASP cc_start: 0.8705 (p0) cc_final: 0.8440 (p0) REVERT: E 515 LYS cc_start: 0.7808 (mtmt) cc_final: 0.7582 (mtpt) REVERT: E 522 MET cc_start: 0.6662 (mmt) cc_final: 0.5401 (ptt) REVERT: E 576 ASP cc_start: 0.8637 (m-30) cc_final: 0.8385 (m-30) REVERT: E 655 GLU cc_start: 0.8528 (tt0) cc_final: 0.8252 (tm-30) REVERT: F 522 MET cc_start: 0.6603 (mmt) cc_final: 0.6111 (mmm) REVERT: F 655 GLU cc_start: 0.8509 (tt0) cc_final: 0.8123 (tm-30) REVERT: F 676 GLU cc_start: 0.8666 (mt-10) cc_final: 0.8383 (mm-30) REVERT: F 720 ASP cc_start: 0.8626 (p0) cc_final: 0.8361 (p0) REVERT: G 515 LYS cc_start: 0.7649 (mtmt) cc_final: 0.7374 (mtmt) REVERT: G 522 MET cc_start: 0.6449 (mmt) cc_final: 0.5301 (ptt) REVERT: G 676 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8118 (mt-10) outliers start: 26 outliers final: 5 residues processed: 251 average time/residue: 0.6714 time to fit residues: 182.1679 Evaluate side-chains 238 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 228 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain B residue 591 GLU Chi-restraints excluded: chain B residue 705 GLU Chi-restraints excluded: chain C residue 591 GLU Chi-restraints excluded: chain C residue 699 ARG Chi-restraints excluded: chain D residue 591 GLU Chi-restraints excluded: chain D residue 658 GLU Chi-restraints excluded: chain E residue 591 GLU Chi-restraints excluded: chain F residue 688 ASP Chi-restraints excluded: chain G residue 676 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 19 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 177 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 182 optimal weight: 0.9990 chunk 186 optimal weight: 2.9990 chunk 137 optimal weight: 0.6980 chunk 38 optimal weight: 10.0000 chunk 16 optimal weight: 0.5980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 659 GLN B 512 GLN C 659 GLN D 659 GLN F 659 GLN G 659 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.164285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.111883 restraints weight = 15154.229| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 2.88 r_work: 0.2646 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2514 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15113 Z= 0.127 Angle : 0.538 7.782 20594 Z= 0.287 Chirality : 0.044 0.140 2569 Planarity : 0.003 0.031 2562 Dihedral : 5.185 16.162 2058 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.29 % Allowed : 13.96 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.99 (0.20), residues: 1925 helix: -0.28 (0.18), residues: 966 sheet: 0.37 (0.27), residues: 336 loop : -1.66 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 703 TYR 0.008 0.001 TYR B 721 PHE 0.015 0.002 PHE D 639 TRP 0.007 0.001 TRP G 488 HIS 0.004 0.001 HIS D 689 Details of bonding type rmsd covalent geometry : bond 0.00292 (15113) covalent geometry : angle 0.53844 (20594) hydrogen bonds : bond 0.04115 ( 748) hydrogen bonds : angle 4.58728 ( 2187) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 220 time to evaluate : 0.537 Fit side-chains REVERT: A 515 LYS cc_start: 0.7352 (mtmt) cc_final: 0.7112 (mtmt) REVERT: A 522 MET cc_start: 0.6456 (mmt) cc_final: 0.5210 (ptt) REVERT: A 676 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.8202 (mm-30) REVERT: B 515 LYS cc_start: 0.7497 (mtmt) cc_final: 0.7245 (mtpt) REVERT: B 522 MET cc_start: 0.6662 (mmt) cc_final: 0.6107 (mmm) REVERT: B 595 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8645 (mp) REVERT: B 676 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.7958 (mm-30) REVERT: B 712 ARG cc_start: 0.8420 (ttp-170) cc_final: 0.8015 (ttp80) REVERT: C 515 LYS cc_start: 0.7394 (mtmt) cc_final: 0.7141 (mtmt) REVERT: C 522 MET cc_start: 0.6724 (mmt) cc_final: 0.5294 (ptm) REVERT: D 522 MET cc_start: 0.6665 (mmt) cc_final: 0.5610 (ptt) REVERT: D 558 THR cc_start: 0.7920 (p) cc_final: 0.7612 (m) REVERT: D 658 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7480 (mt-10) REVERT: D 705 GLU cc_start: 0.8868 (tt0) cc_final: 0.8389 (tp30) REVERT: D 720 ASP cc_start: 0.8740 (p0) cc_final: 0.8453 (p0) REVERT: E 515 LYS cc_start: 0.7627 (mtmt) cc_final: 0.7404 (mtpt) REVERT: E 522 MET cc_start: 0.6601 (mmt) cc_final: 0.5302 (ptt) REVERT: E 655 GLU cc_start: 0.8654 (tt0) cc_final: 0.8372 (tt0) REVERT: F 522 MET cc_start: 0.6581 (mmt) cc_final: 0.6069 (mmm) REVERT: F 655 GLU cc_start: 0.8620 (tt0) cc_final: 0.8375 (tm-30) REVERT: F 720 ASP cc_start: 0.8732 (p0) cc_final: 0.8458 (p0) REVERT: G 515 LYS cc_start: 0.7377 (mtmt) cc_final: 0.7110 (mtmt) REVERT: G 522 MET cc_start: 0.6500 (mmt) cc_final: 0.5233 (ptt) REVERT: G 676 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8181 (mt-10) outliers start: 35 outliers final: 16 residues processed: 232 average time/residue: 0.6884 time to fit residues: 172.9957 Evaluate side-chains 235 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 214 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain B residue 591 GLU Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 643 VAL Chi-restraints excluded: chain B residue 676 GLU Chi-restraints excluded: chain B residue 705 GLU Chi-restraints excluded: chain C residue 591 GLU Chi-restraints excluded: chain C residue 643 VAL Chi-restraints excluded: chain C residue 655 GLU Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain D residue 511 LYS Chi-restraints excluded: chain D residue 591 GLU Chi-restraints excluded: chain D residue 643 VAL Chi-restraints excluded: chain D residue 658 GLU Chi-restraints excluded: chain E residue 591 GLU Chi-restraints excluded: chain E residue 643 VAL Chi-restraints excluded: chain F residue 643 VAL Chi-restraints excluded: chain F residue 688 ASP Chi-restraints excluded: chain G residue 643 VAL Chi-restraints excluded: chain G residue 676 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 39 optimal weight: 1.9990 chunk 57 optimal weight: 50.0000 chunk 81 optimal weight: 0.5980 chunk 166 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 146 optimal weight: 1.9990 chunk 157 optimal weight: 0.9990 chunk 89 optimal weight: 0.0570 chunk 11 optimal weight: 0.7980 chunk 109 optimal weight: 0.7980 chunk 65 optimal weight: 8.9990 overall best weight: 0.6500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 659 GLN C 659 GLN D 659 GLN D 660 ASN E 514 ASN F 659 GLN G 659 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.166457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.114485 restraints weight = 15047.525| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 1.58 r_work: 0.2762 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 15113 Z= 0.091 Angle : 0.485 7.434 20594 Z= 0.257 Chirality : 0.042 0.136 2569 Planarity : 0.003 0.030 2562 Dihedral : 4.721 14.688 2058 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.57 % Allowed : 14.68 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.20), residues: 1925 helix: 0.26 (0.18), residues: 952 sheet: 0.43 (0.28), residues: 336 loop : -1.56 (0.25), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 703 TYR 0.004 0.001 TYR B 721 PHE 0.010 0.001 PHE A 600 TRP 0.005 0.001 TRP E 488 HIS 0.003 0.001 HIS B 689 Details of bonding type rmsd covalent geometry : bond 0.00199 (15113) covalent geometry : angle 0.48452 (20594) hydrogen bonds : bond 0.03165 ( 748) hydrogen bonds : angle 4.24609 ( 2187) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 223 time to evaluate : 0.372 Fit side-chains REVERT: A 515 LYS cc_start: 0.7587 (mtmt) cc_final: 0.7343 (mtmt) REVERT: A 522 MET cc_start: 0.6471 (mmt) cc_final: 0.5286 (ptt) REVERT: A 676 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8275 (mm-30) REVERT: A 705 GLU cc_start: 0.8859 (tt0) cc_final: 0.8461 (tp30) REVERT: B 515 LYS cc_start: 0.7740 (mtmt) cc_final: 0.7525 (mtmt) REVERT: B 522 MET cc_start: 0.6686 (mmt) cc_final: 0.6140 (mmm) REVERT: B 676 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.7875 (mm-30) REVERT: B 712 ARG cc_start: 0.8479 (ttp-170) cc_final: 0.8075 (ttp80) REVERT: C 515 LYS cc_start: 0.7713 (mtmt) cc_final: 0.7443 (mtmt) REVERT: C 522 MET cc_start: 0.6853 (mmt) cc_final: 0.5447 (ptm) REVERT: D 522 MET cc_start: 0.6498 (mmt) cc_final: 0.5554 (ptt) REVERT: D 593 MET cc_start: 0.9230 (mtp) cc_final: 0.8831 (mtp) REVERT: D 658 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7373 (mt-10) REVERT: D 705 GLU cc_start: 0.8831 (tt0) cc_final: 0.8485 (tp30) REVERT: D 720 ASP cc_start: 0.8734 (p0) cc_final: 0.8470 (p0) REVERT: E 515 LYS cc_start: 0.7771 (mtmt) cc_final: 0.7568 (mtpt) REVERT: E 522 MET cc_start: 0.6709 (mmt) cc_final: 0.5343 (ptt) REVERT: E 655 GLU cc_start: 0.8637 (tt0) cc_final: 0.8362 (tm-30) REVERT: F 522 MET cc_start: 0.6735 (mmt) cc_final: 0.6207 (mmm) REVERT: F 655 GLU cc_start: 0.8640 (tt0) cc_final: 0.8256 (tm-30) REVERT: F 720 ASP cc_start: 0.8663 (p0) cc_final: 0.8392 (p0) REVERT: G 515 LYS cc_start: 0.7619 (mtmt) cc_final: 0.7336 (mtmt) REVERT: G 522 MET cc_start: 0.6566 (mmt) cc_final: 0.5258 (ptt) REVERT: G 560 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.8143 (tttm) REVERT: G 676 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8139 (mt-10) REVERT: G 705 GLU cc_start: 0.8666 (tp30) cc_final: 0.8418 (tp30) outliers start: 24 outliers final: 12 residues processed: 228 average time/residue: 0.6814 time to fit residues: 167.6892 Evaluate side-chains 234 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 217 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain B residue 591 GLU Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 643 VAL Chi-restraints excluded: chain B residue 676 GLU Chi-restraints excluded: chain C residue 591 GLU Chi-restraints excluded: chain C residue 643 VAL Chi-restraints excluded: chain C residue 655 GLU Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain D residue 643 VAL Chi-restraints excluded: chain D residue 658 GLU Chi-restraints excluded: chain E residue 591 GLU Chi-restraints excluded: chain E residue 643 VAL Chi-restraints excluded: chain F residue 688 ASP Chi-restraints excluded: chain G residue 560 LYS Chi-restraints excluded: chain G residue 643 VAL Chi-restraints excluded: chain G residue 676 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 122 optimal weight: 10.0000 chunk 145 optimal weight: 20.0000 chunk 15 optimal weight: 1.9990 chunk 0 optimal weight: 50.0000 chunk 190 optimal weight: 0.6980 chunk 83 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 60 optimal weight: 7.9990 chunk 35 optimal weight: 20.0000 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 659 GLN C 659 GLN D 659 GLN E 514 ASN F 659 GLN G 659 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.165080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.111964 restraints weight = 14958.797| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.34 r_work: 0.2733 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2614 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15113 Z= 0.115 Angle : 0.514 7.400 20594 Z= 0.273 Chirality : 0.043 0.139 2569 Planarity : 0.003 0.031 2562 Dihedral : 4.896 15.814 2058 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.70 % Allowed : 14.81 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.20), residues: 1925 helix: 0.53 (0.18), residues: 952 sheet: 0.43 (0.28), residues: 336 loop : -1.57 (0.24), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 625 TYR 0.007 0.001 TYR B 721 PHE 0.014 0.002 PHE D 639 TRP 0.006 0.001 TRP G 488 HIS 0.004 0.001 HIS F 689 Details of bonding type rmsd covalent geometry : bond 0.00263 (15113) covalent geometry : angle 0.51374 (20594) hydrogen bonds : bond 0.03821 ( 748) hydrogen bonds : angle 4.37115 ( 2187) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 230 time to evaluate : 0.470 Fit side-chains REVERT: A 515 LYS cc_start: 0.7504 (mtmt) cc_final: 0.7256 (mtmt) REVERT: A 522 MET cc_start: 0.6475 (mmt) cc_final: 0.5259 (ptt) REVERT: A 676 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8273 (mm-30) REVERT: B 515 LYS cc_start: 0.7612 (mtmt) cc_final: 0.7373 (mtmt) REVERT: B 522 MET cc_start: 0.6664 (mmt) cc_final: 0.6114 (mmm) REVERT: B 595 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8622 (mp) REVERT: B 676 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.7840 (mm-30) REVERT: B 712 ARG cc_start: 0.8462 (ttp-170) cc_final: 0.8109 (ttp80) REVERT: C 515 LYS cc_start: 0.7631 (mtmt) cc_final: 0.7364 (mtmt) REVERT: C 522 MET cc_start: 0.6760 (mmt) cc_final: 0.5306 (ptm) REVERT: D 522 MET cc_start: 0.6595 (mmt) cc_final: 0.5496 (ptt) REVERT: D 593 MET cc_start: 0.9212 (mtp) cc_final: 0.8869 (mtp) REVERT: D 658 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7459 (mt-10) REVERT: D 705 GLU cc_start: 0.8812 (tt0) cc_final: 0.8435 (tp30) REVERT: D 720 ASP cc_start: 0.8748 (p0) cc_final: 0.8509 (p0) REVERT: E 522 MET cc_start: 0.6572 (mmt) cc_final: 0.5163 (ptm) REVERT: E 655 GLU cc_start: 0.8602 (tt0) cc_final: 0.8338 (tt0) REVERT: F 522 MET cc_start: 0.6876 (mmt) cc_final: 0.6341 (mmm) REVERT: G 515 LYS cc_start: 0.7542 (mtmt) cc_final: 0.7256 (mtmt) REVERT: G 522 MET cc_start: 0.6562 (mmt) cc_final: 0.5162 (ptt) REVERT: G 560 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.8149 (tttm) REVERT: G 676 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8132 (mt-10) REVERT: G 705 GLU cc_start: 0.8617 (tp30) cc_final: 0.8350 (tp30) outliers start: 26 outliers final: 14 residues processed: 234 average time/residue: 0.7300 time to fit residues: 184.2808 Evaluate side-chains 240 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 220 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain B residue 591 GLU Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 643 VAL Chi-restraints excluded: chain B residue 676 GLU Chi-restraints excluded: chain C residue 591 GLU Chi-restraints excluded: chain C residue 643 VAL Chi-restraints excluded: chain C residue 655 GLU Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain D residue 643 VAL Chi-restraints excluded: chain D residue 658 GLU Chi-restraints excluded: chain E residue 591 GLU Chi-restraints excluded: chain E residue 643 VAL Chi-restraints excluded: chain F residue 643 VAL Chi-restraints excluded: chain F residue 688 ASP Chi-restraints excluded: chain G residue 560 LYS Chi-restraints excluded: chain G residue 643 VAL Chi-restraints excluded: chain G residue 676 GLU Chi-restraints excluded: chain G residue 695 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 172 optimal weight: 4.9990 chunk 145 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 115 optimal weight: 50.0000 chunk 35 optimal weight: 0.0010 chunk 10 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 149 optimal weight: 1.9990 chunk 180 optimal weight: 0.6980 chunk 187 optimal weight: 0.0980 chunk 165 optimal weight: 0.7980 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 659 GLN C 659 GLN E 514 ASN F 659 GLN G 659 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.169397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.116408 restraints weight = 15118.506| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.12 r_work: 0.2813 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 15113 Z= 0.082 Angle : 0.459 6.696 20594 Z= 0.244 Chirality : 0.041 0.135 2569 Planarity : 0.003 0.029 2562 Dihedral : 4.450 13.987 2058 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.38 % Allowed : 15.53 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.20), residues: 1925 helix: 0.95 (0.18), residues: 952 sheet: 0.52 (0.28), residues: 336 loop : -1.53 (0.24), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 703 TYR 0.005 0.001 TYR B 623 PHE 0.009 0.001 PHE F 600 TRP 0.004 0.001 TRP E 488 HIS 0.003 0.001 HIS B 689 Details of bonding type rmsd covalent geometry : bond 0.00175 (15113) covalent geometry : angle 0.45870 (20594) hydrogen bonds : bond 0.02867 ( 748) hydrogen bonds : angle 4.06478 ( 2187) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 223 time to evaluate : 0.408 Fit side-chains REVERT: A 515 LYS cc_start: 0.7321 (mtmt) cc_final: 0.7093 (mtmt) REVERT: A 522 MET cc_start: 0.6545 (mmt) cc_final: 0.5245 (ptt) REVERT: A 676 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8155 (mm-30) REVERT: A 705 GLU cc_start: 0.8718 (tt0) cc_final: 0.8257 (tp30) REVERT: B 515 LYS cc_start: 0.7446 (mtmt) cc_final: 0.7124 (mtmt) REVERT: B 522 MET cc_start: 0.6861 (mmt) cc_final: 0.6258 (mmm) REVERT: B 676 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.7733 (mm-30) REVERT: B 712 ARG cc_start: 0.8290 (ttp-170) cc_final: 0.7959 (ttp80) REVERT: C 515 LYS cc_start: 0.7430 (mtmt) cc_final: 0.7133 (mtmt) REVERT: C 522 MET cc_start: 0.6691 (mmt) cc_final: 0.5284 (ptm) REVERT: C 676 GLU cc_start: 0.8336 (mt-10) cc_final: 0.8012 (mm-30) REVERT: D 522 MET cc_start: 0.6549 (mmt) cc_final: 0.5446 (ptt) REVERT: D 676 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8200 (mm-30) REVERT: D 705 GLU cc_start: 0.8674 (tt0) cc_final: 0.8272 (tp30) REVERT: D 720 ASP cc_start: 0.8650 (p0) cc_final: 0.8410 (p0) REVERT: E 522 MET cc_start: 0.6974 (mmt) cc_final: 0.5404 (ptm) REVERT: E 655 GLU cc_start: 0.8509 (tt0) cc_final: 0.8204 (tm-30) REVERT: F 522 MET cc_start: 0.6804 (mmt) cc_final: 0.6269 (mmm) REVERT: F 655 GLU cc_start: 0.8397 (tm-30) cc_final: 0.8026 (tm-30) REVERT: F 730 LEU cc_start: 0.8821 (tp) cc_final: 0.8566 (mt) REVERT: G 515 LYS cc_start: 0.7410 (mtmt) cc_final: 0.7147 (mtmt) REVERT: G 522 MET cc_start: 0.6531 (mmt) cc_final: 0.5163 (ptt) REVERT: G 560 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.8012 (tttm) REVERT: G 676 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8031 (mt-10) REVERT: G 705 GLU cc_start: 0.8545 (tp30) cc_final: 0.8264 (tp30) outliers start: 21 outliers final: 12 residues processed: 229 average time/residue: 0.6061 time to fit residues: 149.6936 Evaluate side-chains 236 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 220 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 655 GLU Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain B residue 591 GLU Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 643 VAL Chi-restraints excluded: chain B residue 676 GLU Chi-restraints excluded: chain C residue 591 GLU Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain D residue 643 VAL Chi-restraints excluded: chain E residue 591 GLU Chi-restraints excluded: chain E residue 643 VAL Chi-restraints excluded: chain F residue 688 ASP Chi-restraints excluded: chain G residue 560 LYS Chi-restraints excluded: chain G residue 643 VAL Chi-restraints excluded: chain G residue 676 GLU Chi-restraints excluded: chain G residue 695 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 1.9990 chunk 119 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 185 optimal weight: 0.8980 chunk 91 optimal weight: 7.9990 chunk 174 optimal weight: 0.9990 chunk 136 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 164 optimal weight: 0.9990 chunk 182 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 659 GLN C 659 GLN C 668 HIS E 514 ASN F 659 GLN G 659 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.166248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.110998 restraints weight = 15067.914| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 2.17 r_work: 0.2729 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2609 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15113 Z= 0.118 Angle : 0.511 6.546 20594 Z= 0.273 Chirality : 0.043 0.140 2569 Planarity : 0.003 0.031 2562 Dihedral : 4.791 15.935 2058 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.83 % Allowed : 15.33 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.20), residues: 1925 helix: 1.00 (0.18), residues: 952 sheet: 0.53 (0.28), residues: 336 loop : -1.54 (0.24), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 625 TYR 0.008 0.001 TYR B 721 PHE 0.014 0.002 PHE D 639 TRP 0.005 0.001 TRP E 488 HIS 0.004 0.001 HIS F 689 Details of bonding type rmsd covalent geometry : bond 0.00272 (15113) covalent geometry : angle 0.51108 (20594) hydrogen bonds : bond 0.03845 ( 748) hydrogen bonds : angle 4.30116 ( 2187) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 223 time to evaluate : 0.365 Fit side-chains REVERT: A 515 LYS cc_start: 0.7356 (mtmt) cc_final: 0.7101 (mtmt) REVERT: A 522 MET cc_start: 0.6429 (mmt) cc_final: 0.5163 (ptt) REVERT: A 676 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8153 (mm-30) REVERT: A 678 MET cc_start: 0.8989 (mtp) cc_final: 0.8772 (mtm) REVERT: B 515 LYS cc_start: 0.7431 (mtmt) cc_final: 0.7159 (mtmt) REVERT: B 522 MET cc_start: 0.6879 (mmt) cc_final: 0.6270 (mmm) REVERT: B 595 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8611 (mp) REVERT: B 676 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.7749 (mm-30) REVERT: B 712 ARG cc_start: 0.8298 (ttp-170) cc_final: 0.7986 (ttp80) REVERT: C 515 LYS cc_start: 0.7517 (mtmt) cc_final: 0.7261 (mtmt) REVERT: C 522 MET cc_start: 0.6744 (mmt) cc_final: 0.6314 (mmm) REVERT: D 522 MET cc_start: 0.6568 (mmt) cc_final: 0.5406 (ptt) REVERT: D 705 GLU cc_start: 0.8717 (tt0) cc_final: 0.8289 (tp30) REVERT: D 720 ASP cc_start: 0.8678 (p0) cc_final: 0.8458 (p0) REVERT: D 730 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8542 (mt) REVERT: E 522 MET cc_start: 0.6830 (mmt) cc_final: 0.5223 (ptm) REVERT: E 655 GLU cc_start: 0.8534 (tt0) cc_final: 0.8224 (tm-30) REVERT: E 720 ASP cc_start: 0.8741 (p0) cc_final: 0.8380 (p0) REVERT: F 522 MET cc_start: 0.6804 (mmt) cc_final: 0.6252 (mmm) REVERT: F 730 LEU cc_start: 0.8774 (tp) cc_final: 0.8541 (mt) REVERT: G 515 LYS cc_start: 0.7404 (mtmt) cc_final: 0.7135 (mtmt) REVERT: G 522 MET cc_start: 0.6541 (mmt) cc_final: 0.5166 (ptt) REVERT: G 560 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.8014 (tttm) REVERT: G 676 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8075 (mt-10) REVERT: G 705 GLU cc_start: 0.8551 (tp30) cc_final: 0.8245 (tp30) outliers start: 28 outliers final: 13 residues processed: 231 average time/residue: 0.5866 time to fit residues: 146.6906 Evaluate side-chains 239 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 220 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain B residue 591 GLU Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 643 VAL Chi-restraints excluded: chain B residue 676 GLU Chi-restraints excluded: chain C residue 591 GLU Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain D residue 643 VAL Chi-restraints excluded: chain D residue 730 LEU Chi-restraints excluded: chain E residue 591 GLU Chi-restraints excluded: chain E residue 643 VAL Chi-restraints excluded: chain F residue 643 VAL Chi-restraints excluded: chain F residue 688 ASP Chi-restraints excluded: chain G residue 560 LYS Chi-restraints excluded: chain G residue 632 THR Chi-restraints excluded: chain G residue 643 VAL Chi-restraints excluded: chain G residue 676 GLU Chi-restraints excluded: chain G residue 695 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 0.7980 chunk 174 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 109 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 161 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 659 GLN C 660 ASN E 514 ASN F 659 GLN G 659 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.166713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.112626 restraints weight = 15075.952| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.19 r_work: 0.2774 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 15113 Z= 0.103 Angle : 0.490 6.436 20594 Z= 0.262 Chirality : 0.042 0.138 2569 Planarity : 0.003 0.030 2562 Dihedral : 4.653 15.501 2058 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.51 % Allowed : 15.79 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.20), residues: 1925 helix: 1.07 (0.18), residues: 959 sheet: 0.55 (0.28), residues: 336 loop : -1.46 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 703 TYR 0.006 0.001 TYR B 721 PHE 0.012 0.002 PHE D 639 TRP 0.005 0.001 TRP E 488 HIS 0.003 0.001 HIS B 689 Details of bonding type rmsd covalent geometry : bond 0.00231 (15113) covalent geometry : angle 0.49047 (20594) hydrogen bonds : bond 0.03474 ( 748) hydrogen bonds : angle 4.20609 ( 2187) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3850 Ramachandran restraints generated. 1925 Oldfield, 0 Emsley, 1925 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 220 time to evaluate : 0.395 Fit side-chains REVERT: A 515 LYS cc_start: 0.7430 (mtmt) cc_final: 0.7155 (mtmt) REVERT: A 522 MET cc_start: 0.6539 (mmt) cc_final: 0.6179 (mmm) REVERT: A 676 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8286 (mm-30) REVERT: A 678 MET cc_start: 0.8894 (mtp) cc_final: 0.8677 (mtm) REVERT: B 515 LYS cc_start: 0.7441 (mtmt) cc_final: 0.7183 (mtmt) REVERT: B 522 MET cc_start: 0.6820 (mmt) cc_final: 0.6179 (mmm) REVERT: B 676 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.7679 (mm-30) REVERT: C 515 LYS cc_start: 0.7572 (mtmt) cc_final: 0.7317 (mtmt) REVERT: C 522 MET cc_start: 0.6721 (mmt) cc_final: 0.5286 (ptm) REVERT: C 652 ARG cc_start: 0.8382 (mmm-85) cc_final: 0.8159 (mmm160) REVERT: D 522 MET cc_start: 0.6529 (mmt) cc_final: 0.5367 (ptt) REVERT: D 705 GLU cc_start: 0.8685 (tt0) cc_final: 0.8285 (tp30) REVERT: D 720 ASP cc_start: 0.8680 (p0) cc_final: 0.8437 (p0) REVERT: D 730 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8557 (mt) REVERT: E 522 MET cc_start: 0.6758 (mmt) cc_final: 0.5201 (ptm) REVERT: E 655 GLU cc_start: 0.8520 (tt0) cc_final: 0.8210 (tm-30) REVERT: E 720 ASP cc_start: 0.8698 (p0) cc_final: 0.8331 (p0) REVERT: F 522 MET cc_start: 0.6721 (mmt) cc_final: 0.6147 (mmm) REVERT: F 655 GLU cc_start: 0.8359 (tm-30) cc_final: 0.8037 (tm-30) REVERT: F 730 LEU cc_start: 0.8815 (tp) cc_final: 0.8577 (mt) REVERT: G 515 LYS cc_start: 0.7464 (mtmt) cc_final: 0.7191 (mtmt) REVERT: G 522 MET cc_start: 0.6546 (mmt) cc_final: 0.5966 (mmm) REVERT: G 560 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.8015 (tttm) REVERT: G 676 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8041 (mt-10) REVERT: G 705 GLU cc_start: 0.8503 (tp30) cc_final: 0.8209 (tp30) outliers start: 23 outliers final: 15 residues processed: 227 average time/residue: 0.5874 time to fit residues: 144.3515 Evaluate side-chains 239 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 219 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain B residue 591 GLU Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 643 VAL Chi-restraints excluded: chain B residue 676 GLU Chi-restraints excluded: chain C residue 591 GLU Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain D residue 511 LYS Chi-restraints excluded: chain D residue 643 VAL Chi-restraints excluded: chain D residue 730 LEU Chi-restraints excluded: chain E residue 591 GLU Chi-restraints excluded: chain E residue 643 VAL Chi-restraints excluded: chain F residue 595 LEU Chi-restraints excluded: chain F residue 643 VAL Chi-restraints excluded: chain F residue 688 ASP Chi-restraints excluded: chain G residue 560 LYS Chi-restraints excluded: chain G residue 632 THR Chi-restraints excluded: chain G residue 643 VAL Chi-restraints excluded: chain G residue 676 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 24 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 33 optimal weight: 20.0000 chunk 112 optimal weight: 50.0000 chunk 123 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 63 optimal weight: 0.1980 chunk 49 optimal weight: 0.9990 chunk 184 optimal weight: 0.6980 chunk 81 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 659 GLN E 514 ASN F 659 GLN G 659 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.168858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.114155 restraints weight = 15039.626| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 2.11 r_work: 0.2749 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2625 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 15113 Z= 0.089 Angle : 0.466 6.396 20594 Z= 0.250 Chirality : 0.042 0.136 2569 Planarity : 0.003 0.029 2562 Dihedral : 4.469 14.410 2058 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.51 % Allowed : 15.73 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.20), residues: 1925 helix: 1.25 (0.19), residues: 959 sheet: 0.59 (0.28), residues: 336 loop : -1.41 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 703 TYR 0.004 0.001 TYR C 623 PHE 0.010 0.001 PHE F 600 TRP 0.004 0.001 TRP E 488 HIS 0.003 0.001 HIS B 689 Details of bonding type rmsd covalent geometry : bond 0.00194 (15113) covalent geometry : angle 0.46624 (20594) hydrogen bonds : bond 0.03070 ( 748) hydrogen bonds : angle 4.07658 ( 2187) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5965.89 seconds wall clock time: 102 minutes 0.27 seconds (6120.27 seconds total)