Starting phenix.real_space_refine on Tue Dec 31 04:58:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jwe_36680/12_2024/8jwe_36680.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jwe_36680/12_2024/8jwe_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_36680/12_2024/8jwe_36680.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jwe_36680/12_2024/8jwe_36680.map" model { file = "/net/cci-nas-00/data/ceres_data/8jwe_36680/12_2024/8jwe_36680.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jwe_36680/12_2024/8jwe_36680.cif" } resolution = 2.74 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 5, 'GLU:plan': 7, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 114 Restraints were copied for chains: C, B, E, D, G, F Time building chain proxies: 5.75, per 1000 atoms: 0.39 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: 3.40 Conformation dependent library (CDL) restraints added in 2.7 seconds 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: 1.80 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: 4.79 Time building geometry restraints manager: 4.00 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: 0.00 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: 2.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.600 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 32.640 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.780 ------------------------------------------------------------------------------- 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= 2.964 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.052 0.010 TRP G 488 HIS 0.027 0.008 HIS G 573 PHE 0.041 0.009 PHE F 600 TYR 0.043 0.009 TYR E 721 ARG 0.023 0.003 ARG A 699 *********************** 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 : 1.696 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: 1.6479 time to fit residues: 469.7705 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 : 1.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 0.9980 chunk 148 optimal weight: 7.9990 chunk 82 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 114 optimal weight: 40.0000 chunk 177 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 694 GLN B 726 GLN C 561 ASN C 612 ASN C 663 HIS C 677 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 694 GLN E 726 GLN F 512 GLN F 561 ASN F 612 ASN F 659 GLN F 663 HIS F 677 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: 47 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 15113 Z= 0.314 Angle : 0.723 8.101 20594 Z= 0.389 Chirality : 0.048 0.167 2569 Planarity : 0.006 0.034 2562 Dihedral : 6.604 19.515 2058 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.56 % Allowed : 8.98 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.22 (0.18), residues: 1925 helix: -2.73 (0.14), residues: 945 sheet: -0.04 (0.27), residues: 336 loop : -2.00 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 488 HIS 0.006 0.002 HIS C 689 PHE 0.021 0.002 PHE D 639 TYR 0.013 0.002 TYR B 721 ARG 0.007 0.001 ARG G 625 *********************** 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 282 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 243 time to evaluate : 1.780 Fit side-chains REVERT: A 515 LYS cc_start: 0.7805 (mtmt) cc_final: 0.7492 (mtmt) REVERT: A 522 MET cc_start: 0.6504 (mmt) cc_final: 0.5478 (ptt) REVERT: A 558 THR cc_start: 0.7965 (OUTLIER) cc_final: 0.7580 (p) REVERT: A 572 MET cc_start: 0.8603 (mtt) cc_final: 0.8349 (mtt) REVERT: A 676 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7603 (mm-30) REVERT: B 515 LYS cc_start: 0.7792 (mtmt) cc_final: 0.7549 (mtpt) REVERT: B 522 MET cc_start: 0.6497 (mmt) cc_final: 0.6128 (mmm) REVERT: B 527 VAL cc_start: 0.7329 (OUTLIER) cc_final: 0.7129 (p) REVERT: B 676 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7582 (mm-30) REVERT: B 720 ASP cc_start: 0.8357 (p0) cc_final: 0.8116 (p0) REVERT: B 729 ASN cc_start: 0.8293 (m-40) cc_final: 0.8075 (m-40) REVERT: C 515 LYS cc_start: 0.7797 (mtmt) cc_final: 0.7508 (mtmt) REVERT: C 522 MET cc_start: 0.6746 (mmt) cc_final: 0.5698 (ptm) REVERT: C 527 VAL cc_start: 0.7403 (OUTLIER) cc_final: 0.7202 (p) REVERT: C 558 THR cc_start: 0.7902 (OUTLIER) cc_final: 0.7574 (p) REVERT: C 576 ASP cc_start: 0.8598 (m-30) cc_final: 0.8375 (m-30) REVERT: C 699 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.8476 (ttt180) REVERT: D 522 MET cc_start: 0.6618 (mmt) cc_final: 0.5836 (ptt) REVERT: D 593 MET cc_start: 0.9047 (mtp) cc_final: 0.8772 (mtp) REVERT: D 658 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.6743 (mt-10) REVERT: D 712 ARG cc_start: 0.8021 (ttp80) cc_final: 0.7597 (ttp-170) REVERT: D 720 ASP cc_start: 0.8297 (p0) cc_final: 0.7953 (p0) REVERT: E 515 LYS cc_start: 0.7929 (mtmt) cc_final: 0.7592 (mtmt) REVERT: E 522 MET cc_start: 0.6571 (mmt) cc_final: 0.5563 (ptt) REVERT: E 655 GLU cc_start: 0.7850 (tt0) cc_final: 0.7493 (tm-30) REVERT: E 720 ASP cc_start: 0.8366 (p0) cc_final: 0.7918 (p0) REVERT: E 729 ASN cc_start: 0.8446 (m-40) cc_final: 0.8221 (m-40) REVERT: F 510 VAL cc_start: 0.8251 (OUTLIER) cc_final: 0.8018 (t) REVERT: F 522 MET cc_start: 0.6589 (mmt) cc_final: 0.6136 (mmm) REVERT: F 558 THR cc_start: 0.7924 (OUTLIER) cc_final: 0.7566 (p) REVERT: F 572 MET cc_start: 0.8607 (mtt) cc_final: 0.8346 (mtt) REVERT: F 651 GLU cc_start: 0.7704 (tt0) cc_final: 0.7362 (mt-10) REVERT: F 655 GLU cc_start: 0.7742 (tt0) cc_final: 0.7358 (tm-30) REVERT: F 705 GLU cc_start: 0.7653 (tt0) cc_final: 0.7451 (tt0) REVERT: F 720 ASP cc_start: 0.8282 (p0) cc_final: 0.7985 (p0) REVERT: G 515 LYS cc_start: 0.7793 (mtmt) cc_final: 0.7555 (mtmt) REVERT: G 522 MET cc_start: 0.6411 (mmt) cc_final: 0.5504 (ptt) REVERT: G 527 VAL cc_start: 0.7447 (OUTLIER) cc_final: 0.7237 (p) REVERT: G 558 THR cc_start: 0.7804 (OUTLIER) cc_final: 0.7467 (p) outliers start: 39 outliers final: 11 residues processed: 267 average time/residue: 1.4628 time to fit residues: 425.4389 Evaluate side-chains 236 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 213 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain A residue 643 VAL Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain B residue 527 VAL Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 676 GLU Chi-restraints excluded: chain B residue 705 GLU Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain C residue 643 VAL Chi-restraints excluded: chain C residue 699 ARG Chi-restraints excluded: chain D residue 511 LYS Chi-restraints excluded: chain D residue 558 THR Chi-restraints excluded: chain D residue 658 GLU Chi-restraints excluded: chain E residue 521 LEU Chi-restraints excluded: chain E residue 643 VAL Chi-restraints excluded: chain F residue 510 VAL Chi-restraints excluded: chain F residue 558 THR Chi-restraints excluded: chain F residue 643 VAL Chi-restraints excluded: chain F residue 688 ASP Chi-restraints excluded: chain G residue 527 VAL Chi-restraints excluded: chain G residue 558 THR Chi-restraints excluded: chain G residue 643 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 1.9990 chunk 55 optimal weight: 0.2980 chunk 148 optimal weight: 0.0170 chunk 121 optimal weight: 8.9990 chunk 49 optimal weight: 0.0670 chunk 178 optimal weight: 0.9980 chunk 192 optimal weight: 3.9990 chunk 158 optimal weight: 4.9990 chunk 176 optimal weight: 20.0000 chunk 60 optimal weight: 7.9990 chunk 143 optimal weight: 9.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- 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 B 679 ASN C 561 ASN C 679 ASN D 561 ASN D 659 GLN E 512 GLN E 561 ASN E 659 GLN F 561 ASN F 679 ASN G 561 ASN G 659 GLN G 663 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2986 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= 0.142 Angle : 0.531 7.036 20594 Z= 0.285 Chirality : 0.043 0.152 2569 Planarity : 0.004 0.031 2562 Dihedral : 5.408 16.114 2058 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.25 % Allowed : 11.47 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.19), residues: 1925 helix: -1.22 (0.17), residues: 966 sheet: 0.16 (0.27), residues: 336 loop : -1.72 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 488 HIS 0.005 0.001 HIS G 689 PHE 0.010 0.001 PHE A 600 TYR 0.007 0.001 TYR F 686 ARG 0.002 0.000 ARG F 703 *********************** 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 251 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 232 time to evaluate : 1.792 Fit side-chains REVERT: A 515 LYS cc_start: 0.7735 (mtmt) cc_final: 0.7485 (mtmt) REVERT: A 522 MET cc_start: 0.6508 (mmt) cc_final: 0.5510 (ptt) REVERT: B 515 LYS cc_start: 0.7756 (mtmt) cc_final: 0.7527 (mtpt) REVERT: B 522 MET cc_start: 0.6546 (mmt) cc_final: 0.6128 (mmm) REVERT: C 515 LYS cc_start: 0.7733 (mtmt) cc_final: 0.7419 (mtmt) REVERT: C 522 MET cc_start: 0.6814 (mmt) cc_final: 0.5744 (ptm) REVERT: C 699 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.8343 (ttt180) REVERT: D 522 MET cc_start: 0.6660 (mmt) cc_final: 0.5966 (ptt) REVERT: D 593 MET cc_start: 0.8991 (mtp) cc_final: 0.8636 (mtp) REVERT: D 720 ASP cc_start: 0.8272 (p0) cc_final: 0.7972 (p0) REVERT: E 522 MET cc_start: 0.6624 (mmt) cc_final: 0.5538 (ptt) REVERT: E 576 ASP cc_start: 0.8300 (m-30) cc_final: 0.8094 (m-30) REVERT: E 655 GLU cc_start: 0.7714 (tt0) cc_final: 0.7363 (tm-30) REVERT: E 676 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7321 (mm-30) REVERT: F 522 MET cc_start: 0.6603 (mmt) cc_final: 0.6154 (mmm) REVERT: F 572 MET cc_start: 0.8567 (mtt) cc_final: 0.8302 (mtt) REVERT: F 588 MET cc_start: 0.8916 (mtt) cc_final: 0.8681 (mtm) REVERT: F 655 GLU cc_start: 0.7690 (tt0) cc_final: 0.7267 (tm-30) REVERT: F 705 GLU cc_start: 0.7664 (tt0) cc_final: 0.7353 (tt0) REVERT: G 515 LYS cc_start: 0.7707 (mtmt) cc_final: 0.7394 (mtmt) REVERT: G 522 MET cc_start: 0.6488 (mmt) cc_final: 0.5629 (ptt) REVERT: G 527 VAL cc_start: 0.7490 (OUTLIER) cc_final: 0.7288 (p) REVERT: G 655 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7458 (tm-30) REVERT: G 662 GLN cc_start: 0.8902 (pm20) cc_final: 0.8660 (pm20) REVERT: G 676 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7458 (mt-10) REVERT: G 678 MET cc_start: 0.8809 (mtp) cc_final: 0.8553 (mtm) outliers start: 19 outliers final: 5 residues processed: 243 average time/residue: 1.7904 time to fit residues: 471.0976 Evaluate side-chains 229 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 220 time to evaluate : 1.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain B residue 705 GLU Chi-restraints excluded: chain C residue 688 ASP Chi-restraints excluded: chain C residue 699 ARG Chi-restraints excluded: chain E residue 591 GLU Chi-restraints excluded: chain F residue 688 ASP Chi-restraints excluded: chain G residue 527 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 176 optimal weight: 1.9990 chunk 134 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 85 optimal weight: 50.0000 chunk 119 optimal weight: 8.9990 chunk 178 optimal weight: 8.9990 chunk 189 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 169 optimal weight: 50.0000 chunk 51 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 A 668 HIS B 561 ASN B 659 GLN C 659 GLN C 668 HIS D 561 ASN D 659 GLN E 561 ASN E 668 HIS G 561 ASN G 659 GLN G 663 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 15113 Z= 0.344 Angle : 0.660 8.351 20594 Z= 0.350 Chirality : 0.048 0.177 2569 Planarity : 0.004 0.033 2562 Dihedral : 5.846 17.831 2058 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.21 % Allowed : 12.71 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.19), residues: 1925 helix: -0.81 (0.17), residues: 945 sheet: 0.07 (0.26), residues: 336 loop : -1.83 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP G 488 HIS 0.006 0.002 HIS G 663 PHE 0.026 0.003 PHE D 639 TYR 0.014 0.002 TYR B 721 ARG 0.004 0.001 ARG G 625 *********************** 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 272 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 223 time to evaluate : 1.864 Fit side-chains REVERT: A 515 LYS cc_start: 0.7787 (mtmt) cc_final: 0.7537 (mtmt) REVERT: A 522 MET cc_start: 0.6475 (mmt) cc_final: 0.5446 (ptt) REVERT: A 676 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7343 (mm-30) REVERT: B 515 LYS cc_start: 0.7781 (mtmt) cc_final: 0.7559 (mtpt) REVERT: B 522 MET cc_start: 0.6608 (mmt) cc_final: 0.6154 (mmm) REVERT: B 712 ARG cc_start: 0.8049 (ttp-170) cc_final: 0.7674 (ttp80) REVERT: C 515 LYS cc_start: 0.7784 (mtmt) cc_final: 0.7486 (mtmt) REVERT: C 522 MET cc_start: 0.6613 (mmt) cc_final: 0.6347 (mmm) REVERT: C 652 ARG cc_start: 0.7909 (mtp180) cc_final: 0.7630 (mmm-85) REVERT: D 522 MET cc_start: 0.6679 (mmt) cc_final: 0.5800 (ptt) REVERT: D 593 MET cc_start: 0.8984 (mtp) cc_final: 0.8532 (mtp) REVERT: D 658 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.6955 (mt-10) REVERT: D 720 ASP cc_start: 0.8355 (p0) cc_final: 0.8004 (p0) REVERT: E 521 LEU cc_start: 0.7238 (OUTLIER) cc_final: 0.6996 (mt) REVERT: E 522 MET cc_start: 0.6594 (mmt) cc_final: 0.5504 (ptt) REVERT: E 655 GLU cc_start: 0.7821 (tt0) cc_final: 0.7492 (tm-30) REVERT: E 720 ASP cc_start: 0.8455 (p0) cc_final: 0.8009 (p0) REVERT: F 522 MET cc_start: 0.6572 (mmt) cc_final: 0.6115 (mmm) REVERT: F 558 THR cc_start: 0.7831 (p) cc_final: 0.7559 (m) REVERT: F 572 MET cc_start: 0.8532 (mtt) cc_final: 0.8255 (mtt) REVERT: F 655 GLU cc_start: 0.7750 (tt0) cc_final: 0.7342 (tm-30) REVERT: F 720 ASP cc_start: 0.8332 (p0) cc_final: 0.8050 (p0) REVERT: G 515 LYS cc_start: 0.7695 (mtmt) cc_final: 0.7407 (mtmt) REVERT: G 522 MET cc_start: 0.6506 (mmt) cc_final: 0.5594 (ptt) REVERT: G 591 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7753 (pp20) REVERT: G 652 ARG cc_start: 0.8059 (mmm-85) cc_final: 0.7721 (mmm-85) REVERT: G 655 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7435 (tm-30) REVERT: G 676 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7525 (mt-10) outliers start: 49 outliers final: 13 residues processed: 251 average time/residue: 1.5101 time to fit residues: 411.7045 Evaluate side-chains 247 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 228 time to evaluate : 1.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 591 GLU 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 643 VAL Chi-restraints excluded: chain B residue 705 GLU Chi-restraints excluded: chain C residue 643 VAL Chi-restraints excluded: chain C residue 655 GLU Chi-restraints excluded: chain C residue 688 ASP Chi-restraints excluded: chain D residue 643 VAL Chi-restraints excluded: chain D residue 658 GLU Chi-restraints excluded: chain E residue 521 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 G residue 591 GLU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 2 optimal weight: 40.0000 chunk 141 optimal weight: 50.0000 chunk 78 optimal weight: 0.9990 chunk 161 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 chunk 0 optimal weight: 50.0000 chunk 96 optimal weight: 3.9990 chunk 170 optimal weight: 30.0000 chunk 47 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 659 GLN B 512 GLN B 659 GLN C 659 GLN D 659 GLN G 659 GLN G 660 ASN G 663 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 15113 Z= 0.320 Angle : 0.634 8.098 20594 Z= 0.336 Chirality : 0.047 0.173 2569 Planarity : 0.004 0.034 2562 Dihedral : 5.667 18.300 2058 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.49 % Allowed : 14.42 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.19), residues: 1925 helix: -0.58 (0.17), residues: 952 sheet: 0.19 (0.27), residues: 336 loop : -1.80 (0.24), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP G 488 HIS 0.006 0.001 HIS G 663 PHE 0.024 0.003 PHE D 639 TYR 0.013 0.002 TYR B 721 ARG 0.004 0.001 ARG G 625 *********************** 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 261 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 223 time to evaluate : 1.727 Fit side-chains REVERT: A 515 LYS cc_start: 0.7817 (mtmt) cc_final: 0.7540 (mtmt) REVERT: A 522 MET cc_start: 0.6450 (mmt) cc_final: 0.5423 (ptt) REVERT: A 676 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7483 (mm-30) REVERT: B 515 LYS cc_start: 0.7775 (mtmt) cc_final: 0.7551 (mtpt) REVERT: B 522 MET cc_start: 0.6605 (mmt) cc_final: 0.6128 (mmm) REVERT: B 655 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7356 (tm-30) REVERT: B 676 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.6888 (mm-30) REVERT: B 712 ARG cc_start: 0.8005 (ttp-170) cc_final: 0.7617 (ttp80) REVERT: C 515 LYS cc_start: 0.7841 (mtmt) cc_final: 0.7528 (mtmt) REVERT: C 522 MET cc_start: 0.6476 (mmt) cc_final: 0.6156 (mmm) REVERT: C 528 ILE cc_start: 0.6282 (OUTLIER) cc_final: 0.6065 (tt) REVERT: C 652 ARG cc_start: 0.7919 (mtp180) cc_final: 0.7653 (mmm-85) REVERT: C 699 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.8514 (ttt180) REVERT: D 511 LYS cc_start: 0.7738 (OUTLIER) cc_final: 0.6833 (ptpt) REVERT: D 522 MET cc_start: 0.6677 (mmt) cc_final: 0.5809 (ptt) REVERT: D 658 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.6854 (mt-10) REVERT: D 720 ASP cc_start: 0.8367 (p0) cc_final: 0.8041 (p0) REVERT: D 730 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8345 (mp) REVERT: E 522 MET cc_start: 0.6470 (mmt) cc_final: 0.5332 (ptm) REVERT: E 551 LEU cc_start: 0.7066 (pp) cc_final: 0.6847 (tt) REVERT: E 655 GLU cc_start: 0.7740 (tt0) cc_final: 0.7364 (tm-30) REVERT: E 720 ASP cc_start: 0.8444 (p0) cc_final: 0.8012 (p0) REVERT: F 522 MET cc_start: 0.6543 (mmt) cc_final: 0.6063 (mmm) REVERT: F 558 THR cc_start: 0.7817 (p) cc_final: 0.7542 (m) REVERT: F 572 MET cc_start: 0.8551 (mtt) cc_final: 0.8310 (mtt) REVERT: F 655 GLU cc_start: 0.7838 (tt0) cc_final: 0.7394 (tm-30) REVERT: F 720 ASP cc_start: 0.8317 (p0) cc_final: 0.8050 (p0) REVERT: G 522 MET cc_start: 0.6463 (mmt) cc_final: 0.5509 (ptt) REVERT: G 591 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7714 (pp20) REVERT: G 655 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7507 (tm-30) REVERT: G 676 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7307 (mt-10) REVERT: G 705 GLU cc_start: 0.7465 (tp30) cc_final: 0.7155 (tp30) outliers start: 38 outliers final: 16 residues processed: 235 average time/residue: 1.5268 time to fit residues: 389.5412 Evaluate side-chains 247 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 220 time to evaluate : 1.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 591 GLU 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 643 VAL Chi-restraints excluded: chain B residue 655 GLU Chi-restraints excluded: chain B residue 676 GLU Chi-restraints excluded: chain B residue 705 GLU Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 643 VAL Chi-restraints excluded: chain C residue 655 GLU 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 643 VAL Chi-restraints excluded: chain D residue 658 GLU 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 511 LYS 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 591 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 0.6980 chunk 170 optimal weight: 50.0000 chunk 37 optimal weight: 5.9990 chunk 111 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 189 optimal weight: 0.7980 chunk 157 optimal weight: 2.9990 chunk 87 optimal weight: 50.0000 chunk 15 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 659 GLN F 659 GLN G 659 GLN G 663 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3158 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= 0.198 Angle : 0.548 7.732 20594 Z= 0.292 Chirality : 0.044 0.153 2569 Planarity : 0.003 0.033 2562 Dihedral : 5.233 16.666 2058 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.97 % Allowed : 15.73 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.19), residues: 1925 helix: -0.09 (0.18), residues: 952 sheet: 0.33 (0.27), residues: 336 loop : -1.71 (0.24), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 488 HIS 0.006 0.001 HIS G 663 PHE 0.015 0.002 PHE D 639 TYR 0.008 0.001 TYR B 721 ARG 0.003 0.000 ARG G 703 *********************** 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 251 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 221 time to evaluate : 1.676 Fit side-chains REVERT: A 515 LYS cc_start: 0.7760 (mtmt) cc_final: 0.7509 (mtmt) REVERT: A 522 MET cc_start: 0.6400 (mmt) cc_final: 0.5417 (ptt) REVERT: A 676 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7474 (mm-30) REVERT: B 515 LYS cc_start: 0.7776 (mtmt) cc_final: 0.7554 (mtpt) REVERT: B 522 MET cc_start: 0.6574 (mmt) cc_final: 0.6133 (mmm) REVERT: B 655 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7657 (tm-30) REVERT: B 676 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.6890 (mm-30) REVERT: B 712 ARG cc_start: 0.7969 (ttp-170) cc_final: 0.7573 (ttp80) REVERT: C 515 LYS cc_start: 0.7880 (mtmt) cc_final: 0.7613 (mtmt) REVERT: C 522 MET cc_start: 0.6648 (mmt) cc_final: 0.6303 (mmm) REVERT: C 652 ARG cc_start: 0.7890 (mtp180) cc_final: 0.7647 (mmm-85) REVERT: C 699 ARG cc_start: 0.8726 (OUTLIER) cc_final: 0.8495 (ttt180) REVERT: D 522 MET cc_start: 0.6574 (mmt) cc_final: 0.5778 (ptt) REVERT: D 593 MET cc_start: 0.8942 (mtp) cc_final: 0.8538 (mtp) REVERT: D 658 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.6844 (mt-10) REVERT: D 720 ASP cc_start: 0.8323 (p0) cc_final: 0.8101 (p0) REVERT: D 730 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8566 (mt) REVERT: E 522 MET cc_start: 0.6430 (mmt) cc_final: 0.5414 (ptm) REVERT: E 655 GLU cc_start: 0.7738 (tt0) cc_final: 0.7390 (tm-30) REVERT: F 522 MET cc_start: 0.6608 (mmt) cc_final: 0.6137 (mmm) REVERT: F 572 MET cc_start: 0.8533 (mtt) cc_final: 0.8262 (mtp) REVERT: F 655 GLU cc_start: 0.7744 (tt0) cc_final: 0.7281 (tm-30) REVERT: F 720 ASP cc_start: 0.8295 (p0) cc_final: 0.8014 (p0) REVERT: F 730 LEU cc_start: 0.8866 (tp) cc_final: 0.8653 (mt) REVERT: G 522 MET cc_start: 0.6312 (mmt) cc_final: 0.5353 (ptt) REVERT: G 591 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7652 (pp20) REVERT: G 676 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7336 (mt-10) REVERT: G 705 GLU cc_start: 0.7386 (tp30) cc_final: 0.7175 (tp30) outliers start: 30 outliers final: 14 residues processed: 230 average time/residue: 1.6388 time to fit residues: 413.5472 Evaluate side-chains 238 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 216 time to evaluate : 1.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 643 VAL 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 643 VAL Chi-restraints excluded: chain B residue 655 GLU Chi-restraints excluded: chain B residue 676 GLU 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 C residue 705 GLU Chi-restraints excluded: chain D residue 643 VAL Chi-restraints excluded: chain D residue 658 GLU 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 G residue 591 GLU 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 182 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 108 optimal weight: 0.3980 chunk 138 optimal weight: 0.9980 chunk 107 optimal weight: 0.6980 chunk 159 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 188 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 chunk 115 optimal weight: 50.0000 chunk 87 optimal weight: 50.0000 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 G 663 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3413 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= 0.145 Angle : 0.498 7.588 20594 Z= 0.266 Chirality : 0.043 0.139 2569 Planarity : 0.003 0.031 2562 Dihedral : 4.869 15.553 2058 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.38 % Allowed : 16.64 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.20), residues: 1925 helix: 0.48 (0.18), residues: 945 sheet: 0.41 (0.28), residues: 336 loop : -1.56 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 488 HIS 0.006 0.001 HIS G 663 PHE 0.011 0.001 PHE B 600 TYR 0.005 0.001 TYR B 721 ARG 0.002 0.000 ARG A 703 *********************** 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 244 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 223 time to evaluate : 1.726 Fit side-chains REVERT: A 515 LYS cc_start: 0.7686 (mtmt) cc_final: 0.7449 (mtmt) REVERT: A 522 MET cc_start: 0.6441 (mmt) cc_final: 0.5472 (ptt) REVERT: A 676 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7570 (mm-30) REVERT: B 515 LYS cc_start: 0.7796 (mtmt) cc_final: 0.7578 (mtpt) REVERT: B 522 MET cc_start: 0.6622 (mmt) cc_final: 0.6166 (mmm) REVERT: B 655 GLU cc_start: 0.7872 (tt0) cc_final: 0.7625 (tm-30) REVERT: B 676 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.6944 (mm-30) REVERT: B 712 ARG cc_start: 0.7934 (ttp-170) cc_final: 0.7559 (ttp80) REVERT: C 515 LYS cc_start: 0.7794 (mtmt) cc_final: 0.7525 (mtmt) REVERT: C 522 MET cc_start: 0.6640 (mmt) cc_final: 0.5482 (ptm) REVERT: D 511 LYS cc_start: 0.7622 (OUTLIER) cc_final: 0.6713 (ptpt) REVERT: D 522 MET cc_start: 0.6491 (mmt) cc_final: 0.5702 (ptt) REVERT: D 593 MET cc_start: 0.8949 (mtp) cc_final: 0.8523 (mtp) REVERT: D 720 ASP cc_start: 0.8346 (p0) cc_final: 0.8120 (p0) REVERT: D 730 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8542 (mt) REVERT: E 522 MET cc_start: 0.6522 (mmt) cc_final: 0.5444 (ptm) REVERT: E 655 GLU cc_start: 0.7745 (tt0) cc_final: 0.7407 (tm-30) REVERT: F 522 MET cc_start: 0.6671 (mmt) cc_final: 0.6169 (mmm) REVERT: F 572 MET cc_start: 0.8534 (mtt) cc_final: 0.8299 (mtt) REVERT: F 655 GLU cc_start: 0.7741 (tt0) cc_final: 0.7279 (tm-30) REVERT: G 522 MET cc_start: 0.6350 (mmt) cc_final: 0.5350 (ptt) REVERT: G 676 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7327 (mt-10) REVERT: G 705 GLU cc_start: 0.7378 (tp30) cc_final: 0.7162 (tp30) outliers start: 21 outliers final: 7 residues processed: 229 average time/residue: 1.6041 time to fit residues: 397.6764 Evaluate side-chains 228 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 216 time to evaluate : 1.647 ------------------------------------------------------------------------------- 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 676 GLU Chi-restraints excluded: chain B residue 705 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 688 ASP Chi-restraints excluded: chain G residue 676 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 chunk 112 optimal weight: 50.0000 chunk 56 optimal weight: 50.0000 chunk 37 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 120 optimal weight: 0.9990 chunk 128 optimal weight: 2.9990 chunk 93 optimal weight: 0.4980 chunk 17 optimal weight: 0.6980 chunk 148 optimal weight: 0.7980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 659 GLN A 660 ASN E 514 ASN F 659 GLN G 659 GLN G 663 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3425 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= 0.167 Angle : 0.513 7.250 20594 Z= 0.274 Chirality : 0.043 0.147 2569 Planarity : 0.003 0.032 2562 Dihedral : 4.909 16.108 2058 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.25 % Allowed : 17.23 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.20), residues: 1925 helix: 0.72 (0.18), residues: 952 sheet: 0.44 (0.28), residues: 336 loop : -1.57 (0.24), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 488 HIS 0.007 0.001 HIS G 663 PHE 0.012 0.002 PHE D 639 TYR 0.006 0.001 TYR B 721 ARG 0.002 0.000 ARG E 703 *********************** 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 238 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 219 time to evaluate : 1.683 Fit side-chains REVERT: A 515 LYS cc_start: 0.7659 (mtmt) cc_final: 0.7406 (mtmt) REVERT: A 522 MET cc_start: 0.6462 (mmt) cc_final: 0.5456 (ptt) REVERT: A 676 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7504 (mm-30) REVERT: B 515 LYS cc_start: 0.7791 (mtmt) cc_final: 0.7585 (mtmt) REVERT: B 522 MET cc_start: 0.6624 (mmt) cc_final: 0.6150 (mmm) REVERT: B 655 GLU cc_start: 0.7901 (tt0) cc_final: 0.7646 (tm-30) REVERT: B 676 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.6941 (mm-30) REVERT: B 712 ARG cc_start: 0.8015 (ttp-170) cc_final: 0.7603 (ttp80) REVERT: C 515 LYS cc_start: 0.7785 (mtmt) cc_final: 0.7516 (mtmt) REVERT: C 522 MET cc_start: 0.6664 (mmt) cc_final: 0.5525 (ptm) REVERT: C 528 ILE cc_start: 0.6000 (OUTLIER) cc_final: 0.5474 (tt) REVERT: D 522 MET cc_start: 0.6566 (mmt) cc_final: 0.5710 (ptt) REVERT: D 593 MET cc_start: 0.8948 (mtp) cc_final: 0.8512 (mtp) REVERT: D 720 ASP cc_start: 0.8357 (p0) cc_final: 0.8133 (p0) REVERT: D 730 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8551 (mt) REVERT: E 522 MET cc_start: 0.6726 (mmt) cc_final: 0.5542 (ptm) REVERT: E 655 GLU cc_start: 0.7759 (tt0) cc_final: 0.7416 (tm-30) REVERT: F 522 MET cc_start: 0.6599 (mmt) cc_final: 0.6090 (mmm) REVERT: F 572 MET cc_start: 0.8529 (mtt) cc_final: 0.8290 (mtt) REVERT: G 522 MET cc_start: 0.6335 (mmt) cc_final: 0.5345 (ptt) REVERT: G 676 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7326 (mt-10) REVERT: G 705 GLU cc_start: 0.7388 (tp30) cc_final: 0.7167 (tp30) outliers start: 19 outliers final: 10 residues processed: 224 average time/residue: 1.5547 time to fit residues: 377.2249 Evaluate side-chains 232 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 217 time to evaluate : 1.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 643 VAL 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 676 GLU Chi-restraints excluded: chain B residue 705 GLU Chi-restraints excluded: chain C residue 528 ILE 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 10.0000 chunk 180 optimal weight: 1.9990 chunk 165 optimal weight: 0.9980 chunk 176 optimal weight: 2.9990 chunk 105 optimal weight: 0.5980 chunk 76 optimal weight: 4.9990 chunk 138 optimal weight: 0.3980 chunk 54 optimal weight: 0.9980 chunk 159 optimal weight: 7.9990 chunk 166 optimal weight: 5.9990 chunk 175 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 G 663 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3491 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= 0.166 Angle : 0.507 7.117 20594 Z= 0.272 Chirality : 0.043 0.147 2569 Planarity : 0.003 0.032 2562 Dihedral : 4.841 16.030 2058 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.64 % Allowed : 16.84 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.20), residues: 1925 helix: 0.91 (0.18), residues: 952 sheet: 0.47 (0.28), residues: 336 loop : -1.54 (0.24), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 488 HIS 0.007 0.001 HIS G 663 PHE 0.012 0.002 PHE D 639 TYR 0.006 0.001 TYR B 721 ARG 0.002 0.000 ARG A 703 *********************** 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 245 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 220 time to evaluate : 1.690 Fit side-chains REVERT: A 515 LYS cc_start: 0.7657 (mtmt) cc_final: 0.7400 (mtmt) REVERT: A 522 MET cc_start: 0.6418 (mmt) cc_final: 0.5432 (ptt) REVERT: A 528 ILE cc_start: 0.5854 (OUTLIER) cc_final: 0.5322 (tt) REVERT: A 591 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7417 (pp20) REVERT: A 676 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7499 (mm-30) REVERT: B 515 LYS cc_start: 0.7743 (mtmt) cc_final: 0.7538 (mtmt) REVERT: B 522 MET cc_start: 0.6813 (mmt) cc_final: 0.6301 (mmm) REVERT: B 655 GLU cc_start: 0.7892 (tt0) cc_final: 0.7633 (tm-30) REVERT: B 676 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.6943 (mm-30) REVERT: B 712 ARG cc_start: 0.7974 (ttp-170) cc_final: 0.7576 (ttp80) REVERT: C 515 LYS cc_start: 0.7756 (mtmt) cc_final: 0.7491 (mtmt) REVERT: C 522 MET cc_start: 0.6657 (mmt) cc_final: 0.5525 (ptm) REVERT: C 528 ILE cc_start: 0.6009 (OUTLIER) cc_final: 0.5451 (tt) REVERT: D 522 MET cc_start: 0.6537 (mmt) cc_final: 0.5629 (ptt) REVERT: D 593 MET cc_start: 0.8947 (mtp) cc_final: 0.8518 (mtp) REVERT: D 720 ASP cc_start: 0.8353 (p0) cc_final: 0.8129 (p0) REVERT: D 730 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8538 (mt) REVERT: E 522 MET cc_start: 0.6736 (mmt) cc_final: 0.5511 (ptm) REVERT: E 528 ILE cc_start: 0.6115 (OUTLIER) cc_final: 0.5631 (tt) REVERT: E 652 ARG cc_start: 0.7984 (mmm-85) cc_final: 0.7779 (mmm-85) REVERT: E 655 GLU cc_start: 0.7720 (tt0) cc_final: 0.7367 (tm-30) REVERT: E 720 ASP cc_start: 0.8436 (p0) cc_final: 0.8024 (p0) REVERT: F 522 MET cc_start: 0.6664 (mmt) cc_final: 0.6159 (mmm) REVERT: F 572 MET cc_start: 0.8526 (mtt) cc_final: 0.8270 (mtt) REVERT: F 655 GLU cc_start: 0.7734 (tm-30) cc_final: 0.7364 (tm-30) REVERT: G 522 MET cc_start: 0.6316 (mmt) cc_final: 0.5341 (ptt) REVERT: G 676 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7326 (mt-10) REVERT: G 705 GLU cc_start: 0.7384 (tp30) cc_final: 0.7163 (tp30) outliers start: 25 outliers final: 14 residues processed: 226 average time/residue: 1.5871 time to fit residues: 388.5220 Evaluate side-chains 236 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 214 time to evaluate : 1.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 643 VAL 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 643 VAL Chi-restraints excluded: chain B residue 676 GLU Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 643 VAL Chi-restraints excluded: chain C residue 655 GLU Chi-restraints excluded: chain C residue 688 ASP 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 528 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 50.0000 chunk 186 optimal weight: 0.6980 chunk 113 optimal weight: 50.0000 chunk 88 optimal weight: 0.9990 chunk 129 optimal weight: 3.9990 chunk 195 optimal weight: 3.9990 chunk 179 optimal weight: 0.6980 chunk 155 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 120 optimal weight: 6.9990 chunk 95 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 G 659 GLN G 663 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.3460 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= 0.193 Angle : 0.529 7.008 20594 Z= 0.283 Chirality : 0.044 0.151 2569 Planarity : 0.003 0.032 2562 Dihedral : 4.945 16.568 2058 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.64 % Allowed : 17.10 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.20), residues: 1925 helix: 0.90 (0.18), residues: 959 sheet: 0.48 (0.28), residues: 336 loop : -1.46 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 488 HIS 0.007 0.001 HIS G 663 PHE 0.015 0.002 PHE D 639 TYR 0.007 0.001 TYR B 721 ARG 0.002 0.000 ARG E 703 ********************** 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 246 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 221 time to evaluate : 2.081 Fit side-chains REVERT: A 515 LYS cc_start: 0.7681 (mtmt) cc_final: 0.7422 (mtmt) REVERT: A 522 MET cc_start: 0.6453 (mmt) cc_final: 0.6078 (mmm) REVERT: A 528 ILE cc_start: 0.5867 (OUTLIER) cc_final: 0.5324 (tt) REVERT: A 591 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7522 (pp20) REVERT: A 676 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7479 (mm-30) REVERT: B 515 LYS cc_start: 0.7749 (mtmt) cc_final: 0.7542 (mtmt) REVERT: B 522 MET cc_start: 0.6802 (mmt) cc_final: 0.6284 (mmm) REVERT: B 655 GLU cc_start: 0.7900 (tt0) cc_final: 0.7648 (tm-30) REVERT: B 674 GLU cc_start: 0.8216 (mm-30) cc_final: 0.8008 (mm-30) REVERT: B 676 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.6982 (mm-30) REVERT: B 712 ARG cc_start: 0.7981 (ttp-170) cc_final: 0.7668 (ttp80) REVERT: C 515 LYS cc_start: 0.7780 (mtmt) cc_final: 0.7511 (mtmt) REVERT: C 522 MET cc_start: 0.6653 (mmt) cc_final: 0.6274 (mmm) REVERT: C 528 ILE cc_start: 0.6079 (OUTLIER) cc_final: 0.5524 (tt) REVERT: D 522 MET cc_start: 0.6523 (mmt) cc_final: 0.5634 (ptt) REVERT: D 593 MET cc_start: 0.8940 (mtp) cc_final: 0.8504 (mtp) REVERT: D 720 ASP cc_start: 0.8313 (p0) cc_final: 0.8083 (p0) REVERT: D 730 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8561 (mt) REVERT: E 522 MET cc_start: 0.6712 (mmt) cc_final: 0.5454 (ptm) REVERT: E 528 ILE cc_start: 0.5997 (OUTLIER) cc_final: 0.5544 (tt) REVERT: E 655 GLU cc_start: 0.7708 (tt0) cc_final: 0.7348 (tm-30) REVERT: E 720 ASP cc_start: 0.8445 (p0) cc_final: 0.8052 (p0) REVERT: F 522 MET cc_start: 0.6450 (mmt) cc_final: 0.6087 (mmm) REVERT: F 572 MET cc_start: 0.8521 (mtt) cc_final: 0.8241 (mtp) REVERT: F 655 GLU cc_start: 0.7721 (tm-30) cc_final: 0.7356 (tm-30) REVERT: G 522 MET cc_start: 0.6309 (mmt) cc_final: 0.5326 (ptt) REVERT: G 676 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7333 (mt-10) REVERT: G 705 GLU cc_start: 0.7392 (tp30) cc_final: 0.7172 (tp30) outliers start: 25 outliers final: 14 residues processed: 229 average time/residue: 1.5270 time to fit residues: 379.5906 Evaluate side-chains 239 residues out of total 1799 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 217 time to evaluate : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 ILE Chi-restraints excluded: chain A residue 591 GLU Chi-restraints excluded: chain A residue 643 VAL 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 643 VAL Chi-restraints excluded: chain B residue 676 GLU Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 643 VAL Chi-restraints excluded: chain C residue 688 ASP 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 528 ILE 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 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 123 optimal weight: 0.7980 chunk 165 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 143 optimal weight: 40.0000 chunk 22 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 155 optimal weight: 0.9980 chunk 65 optimal weight: 8.9990 chunk 159 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 28 optimal weight: 50.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 G 663 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.166783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.115973 restraints weight = 15081.284| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.25 r_work: 0.2758 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2646 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.3601 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= 0.153 Angle : 0.495 6.903 20594 Z= 0.265 Chirality : 0.043 0.139 2569 Planarity : 0.003 0.032 2562 Dihedral : 4.732 15.820 2058 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.70 % Allowed : 17.04 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.20), residues: 1925 helix: 1.06 (0.18), residues: 959 sheet: 0.54 (0.28), residues: 336 loop : -1.42 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 488 HIS 0.008 0.001 HIS G 663 PHE 0.012 0.001 PHE G 600 TYR 0.005 0.001 TYR B 721 ARG 0.002 0.000 ARG E 703 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6026.58 seconds wall clock time: 110 minutes 17.81 seconds (6617.81 seconds total)