Starting phenix.real_space_refine on Sun Jul 5 10:34:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/22ib_68281/07_2026/22ib_68281.cif Found real_map, /net/cci-nas-00/data/ceres_data/22ib_68281/07_2026/22ib_68281.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/22ib_68281/07_2026/22ib_68281.cif" } default_model = "/net/cci-nas-00/data/ceres_data/22ib_68281/07_2026/22ib_68281.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/22ib_68281/07_2026/22ib_68281.map" default_real_map = "/net/cci-nas-00/data/ceres_data/22ib_68281/07_2026/22ib_68281.map" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.017 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: 6 Type Number sf(0) Gaussians P 13 5.49 5 Mg 2 5.21 5 S 122 5.16 5 C 16801 2.51 5 N 4565 2.21 5 O 5066 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26569 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4479 Classifications: {'peptide': 573} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 25, 'TRANS': 547} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 4310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 4310 Classifications: {'peptide': 553} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 25, 'TRANS': 527} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "C" Number of atoms: 4459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4459 Classifications: {'peptide': 570} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 25, 'TRANS': 544} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "D" Number of atoms: 4292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 4292 Classifications: {'peptide': 553} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 25, 'TRANS': 527} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 4439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4439 Classifications: {'peptide': 569} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 25, 'TRANS': 543} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "F" Number of atoms: 4301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 4301 Classifications: {'peptide': 553} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 25, 'TRANS': 527} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ASP:plan': 3} Unresolved non-hydrogen planarities: 9 Chain: "G" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 140 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'TRANS': 27} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'UNK:plan-1': 28} Unresolved non-hydrogen planarities: 28 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.66, per 1000 atoms: 0.25 Number of scatterers: 26569 At special positions: 0 Unit cell: (135.3, 129.56, 155.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 122 16.00 P 13 15.00 Mg 2 11.99 O 5066 8.00 N 4565 7.00 C 16801 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS D 520 " - pdb=" SG CYS D 637 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.53 Conformation dependent library (CDL) restraints added in 1.0 seconds 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6314 Finding SS restraints... Secondary structure from input PDB file: 140 helices and 30 sheets defined 51.6% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 378 through 401 removed outlier: 3.582A pdb=" N GLU A 382 " --> pdb=" O ARG A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 412 removed outlier: 3.551A pdb=" N GLU A 406 " --> pdb=" O ILE A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 419 Processing helix chain 'A' and resid 419 through 425 Processing helix chain 'A' and resid 431 through 447 Processing helix chain 'A' and resid 452 through 467 Processing helix chain 'A' and resid 479 through 491 Processing helix chain 'A' and resid 494 through 512 removed outlier: 4.123A pdb=" N LYS A 498 " --> pdb=" O MET A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 540 removed outlier: 3.700A pdb=" N ARG A 534 " --> pdb=" O THR A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 560 removed outlier: 3.660A pdb=" N LYS A 559 " --> pdb=" O VAL A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 581 Processing helix chain 'A' and resid 603 through 612 removed outlier: 3.609A pdb=" N LEU A 607 " --> pdb=" O PRO A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 653 Processing helix chain 'A' and resid 662 through 673 Processing helix chain 'A' and resid 673 through 683 Processing helix chain 'A' and resid 692 through 703 Processing helix chain 'A' and resid 709 through 729 Processing helix chain 'A' and resid 738 through 747 Processing helix chain 'A' and resid 807 through 829 Processing helix chain 'A' and resid 833 through 838 Processing helix chain 'A' and resid 856 through 870 Processing helix chain 'A' and resid 894 through 906 Processing helix chain 'A' and resid 916 through 923 removed outlier: 3.845A pdb=" N LEU A 923 " --> pdb=" O ASP A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 947 removed outlier: 3.894A pdb=" N ILE A 942 " --> pdb=" O HIS A 938 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 407 removed outlier: 3.839A pdb=" N ILE B 402 " --> pdb=" O GLU B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 411 Processing helix chain 'B' and resid 412 through 427 removed outlier: 3.709A pdb=" N GLU B 427 " --> pdb=" O GLU B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 446 removed outlier: 3.886A pdb=" N VAL B 437 " --> pdb=" O HIS B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 468 Processing helix chain 'B' and resid 479 through 491 Processing helix chain 'B' and resid 494 through 512 Processing helix chain 'B' and resid 530 through 541 removed outlier: 3.713A pdb=" N ARG B 534 " --> pdb=" O THR B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 581 removed outlier: 4.267A pdb=" N ILE B 574 " --> pdb=" O PRO B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 611 removed outlier: 4.169A pdb=" N ALA B 606 " --> pdb=" O ASP B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 646 through 653 Processing helix chain 'B' and resid 662 through 673 Processing helix chain 'B' and resid 673 through 683 Processing helix chain 'B' and resid 692 through 703 Processing helix chain 'B' and resid 709 through 729 Processing helix chain 'B' and resid 738 through 746 removed outlier: 4.565A pdb=" N GLN B 743 " --> pdb=" O PRO B 739 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ASP B 744 " --> pdb=" O GLU B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 829 Processing helix chain 'B' and resid 833 through 838 Processing helix chain 'B' and resid 856 through 870 Processing helix chain 'B' and resid 894 through 906 removed outlier: 3.741A pdb=" N LYS B 898 " --> pdb=" O GLY B 894 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 923 Processing helix chain 'B' and resid 938 through 947 removed outlier: 3.994A pdb=" N ILE B 942 " --> pdb=" O HIS B 938 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 401 removed outlier: 3.569A pdb=" N ARG C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 425 Processing helix chain 'C' and resid 431 through 448 Processing helix chain 'C' and resid 452 through 468 removed outlier: 3.590A pdb=" N VAL C 457 " --> pdb=" O SER C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 491 removed outlier: 3.811A pdb=" N ASP C 490 " --> pdb=" O VAL C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 512 Processing helix chain 'C' and resid 530 through 541 removed outlier: 4.068A pdb=" N ARG C 534 " --> pdb=" O THR C 530 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER C 535 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 560 Processing helix chain 'C' and resid 571 through 581 Processing helix chain 'C' and resid 602 through 611 removed outlier: 3.859A pdb=" N ALA C 606 " --> pdb=" O ASP C 602 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU C 608 " --> pdb=" O SER C 604 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLU C 609 " --> pdb=" O SER C 605 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU C 610 " --> pdb=" O ALA C 606 " (cutoff:3.500A) Processing helix chain 'C' and resid 646 through 653 Processing helix chain 'C' and resid 662 through 673 Processing helix chain 'C' and resid 673 through 683 Processing helix chain 'C' and resid 692 through 703 Processing helix chain 'C' and resid 709 through 729 Processing helix chain 'C' and resid 741 through 746 Processing helix chain 'C' and resid 807 through 829 Processing helix chain 'C' and resid 833 through 838 removed outlier: 3.662A pdb=" N THR C 837 " --> pdb=" O ASP C 833 " (cutoff:3.500A) Processing helix chain 'C' and resid 853 through 855 No H-bonds generated for 'chain 'C' and resid 853 through 855' Processing helix chain 'C' and resid 856 through 870 Processing helix chain 'C' and resid 894 through 906 removed outlier: 3.722A pdb=" N LYS C 898 " --> pdb=" O GLY C 894 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 922 Processing helix chain 'C' and resid 938 through 947 removed outlier: 3.856A pdb=" N ILE C 942 " --> pdb=" O HIS C 938 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP C 944 " --> pdb=" O ARG C 940 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 406 removed outlier: 3.855A pdb=" N ILE D 403 " --> pdb=" O GLN D 399 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS D 404 " --> pdb=" O LEU D 400 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU D 406 " --> pdb=" O ILE D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 427 removed outlier: 3.987A pdb=" N GLU D 427 " --> pdb=" O GLU D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 448 Processing helix chain 'D' and resid 452 through 467 Processing helix chain 'D' and resid 479 through 491 Processing helix chain 'D' and resid 494 through 512 Processing helix chain 'D' and resid 530 through 541 removed outlier: 3.704A pdb=" N ARG D 534 " --> pdb=" O THR D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 554 through 558 removed outlier: 3.582A pdb=" N GLU D 557 " --> pdb=" O ASP D 554 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 581 Processing helix chain 'D' and resid 591 through 595 removed outlier: 3.553A pdb=" N ILE D 595 " --> pdb=" O VAL D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 602 through 612 removed outlier: 3.792A pdb=" N ALA D 606 " --> pdb=" O ASP D 602 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU D 609 " --> pdb=" O SER D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 612 through 617 removed outlier: 4.642A pdb=" N ALA D 617 " --> pdb=" O PRO D 613 " (cutoff:3.500A) Processing helix chain 'D' and resid 646 through 653 Processing helix chain 'D' and resid 662 through 673 Processing helix chain 'D' and resid 673 through 683 Processing helix chain 'D' and resid 692 through 703 Processing helix chain 'D' and resid 709 through 729 Processing helix chain 'D' and resid 738 through 746 removed outlier: 4.071A pdb=" N GLN D 743 " --> pdb=" O PRO D 739 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ASP D 744 " --> pdb=" O GLU D 740 " (cutoff:3.500A) Processing helix chain 'D' and resid 807 through 829 Processing helix chain 'D' and resid 857 through 870 Processing helix chain 'D' and resid 894 through 906 Processing helix chain 'D' and resid 916 through 922 Processing helix chain 'D' and resid 938 through 947 removed outlier: 4.026A pdb=" N ILE D 942 " --> pdb=" O HIS D 938 " (cutoff:3.500A) Processing helix chain 'E' and resid 382 through 406 removed outlier: 3.891A pdb=" N GLU E 406 " --> pdb=" O ILE E 402 " (cutoff:3.500A) Processing helix chain 'E' and resid 415 through 428 removed outlier: 3.624A pdb=" N LEU E 428 " --> pdb=" O ARG E 424 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 448 Processing helix chain 'E' and resid 452 through 467 Processing helix chain 'E' and resid 479 through 491 Processing helix chain 'E' and resid 494 through 512 removed outlier: 3.567A pdb=" N LYS E 498 " --> pdb=" O MET E 494 " (cutoff:3.500A) Processing helix chain 'E' and resid 530 through 540 Processing helix chain 'E' and resid 555 through 560 Processing helix chain 'E' and resid 572 through 581 removed outlier: 3.666A pdb=" N LYS E 581 " --> pdb=" O LEU E 577 " (cutoff:3.500A) Processing helix chain 'E' and resid 602 through 612 removed outlier: 3.613A pdb=" N ALA E 606 " --> pdb=" O ASP E 602 " (cutoff:3.500A) Processing helix chain 'E' and resid 612 through 617 removed outlier: 4.550A pdb=" N ALA E 617 " --> pdb=" O PRO E 613 " (cutoff:3.500A) Processing helix chain 'E' and resid 646 through 653 Processing helix chain 'E' and resid 662 through 683 removed outlier: 4.865A pdb=" N VAL E 675 " --> pdb=" O GLU E 671 " (cutoff:3.500A) Proline residue: E 676 - end of helix Processing helix chain 'E' and resid 692 through 703 Processing helix chain 'E' and resid 709 through 730 Processing helix chain 'E' and resid 738 through 742 Processing helix chain 'E' and resid 807 through 829 Processing helix chain 'E' and resid 833 through 838 Processing helix chain 'E' and resid 858 through 870 Processing helix chain 'E' and resid 894 through 906 Processing helix chain 'E' and resid 916 through 922 Processing helix chain 'E' and resid 924 through 929 Processing helix chain 'E' and resid 938 through 947 removed outlier: 3.918A pdb=" N ILE E 942 " --> pdb=" O HIS E 938 " (cutoff:3.500A) Processing helix chain 'F' and resid 398 through 406 Processing helix chain 'F' and resid 409 through 413 Processing helix chain 'F' and resid 415 through 427 Processing helix chain 'F' and resid 431 through 448 Processing helix chain 'F' and resid 452 through 468 Processing helix chain 'F' and resid 479 through 491 removed outlier: 3.516A pdb=" N HIS F 491 " --> pdb=" O LEU F 487 " (cutoff:3.500A) Processing helix chain 'F' and resid 494 through 512 Processing helix chain 'F' and resid 528 through 540 Processing helix chain 'F' and resid 555 through 560 Processing helix chain 'F' and resid 571 through 581 removed outlier: 3.534A pdb=" N GLN F 575 " --> pdb=" O GLY F 571 " (cutoff:3.500A) Processing helix chain 'F' and resid 591 through 595 removed outlier: 3.526A pdb=" N LYS F 594 " --> pdb=" O GLU F 591 " (cutoff:3.500A) Processing helix chain 'F' and resid 603 through 612 removed outlier: 4.010A pdb=" N LEU F 607 " --> pdb=" O PRO F 603 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LEU F 610 " --> pdb=" O ALA F 606 " (cutoff:3.500A) Processing helix chain 'F' and resid 612 through 619 removed outlier: 3.643A pdb=" N ASN F 618 " --> pdb=" O GLU F 614 " (cutoff:3.500A) Processing helix chain 'F' and resid 646 through 652 Processing helix chain 'F' and resid 662 through 683 removed outlier: 5.646A pdb=" N VAL F 675 " --> pdb=" O GLU F 671 " (cutoff:3.500A) Proline residue: F 676 - end of helix Processing helix chain 'F' and resid 692 through 703 Processing helix chain 'F' and resid 709 through 730 Processing helix chain 'F' and resid 738 through 746 removed outlier: 3.915A pdb=" N GLN F 743 " --> pdb=" O PRO F 739 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASP F 744 " --> pdb=" O GLU F 740 " (cutoff:3.500A) Processing helix chain 'F' and resid 807 through 829 Processing helix chain 'F' and resid 833 through 838 Processing helix chain 'F' and resid 857 through 870 Processing helix chain 'F' and resid 894 through 906 removed outlier: 3.596A pdb=" N LYS F 898 " --> pdb=" O GLY F 894 " (cutoff:3.500A) Processing helix chain 'F' and resid 916 through 922 Processing helix chain 'F' and resid 938 through 947 removed outlier: 4.110A pdb=" N ILE F 942 " --> pdb=" O HIS F 938 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 15 Processing sheet with id=AA1, first strand: chain 'A' and resid 544 through 548 removed outlier: 6.840A pdb=" N PHE A 545 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ASP A 590 " --> pdb=" O PHE A 545 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N PHE A 547 " --> pdb=" O ASP A 590 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N THR A 638 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE A 589 " --> pdb=" O THR A 638 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N CYS A 520 " --> pdb=" O ILE A 656 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 689 through 690 removed outlier: 3.807A pdb=" N LYS A 690 " --> pdb=" O VAL A 735 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 764 through 769 Processing sheet with id=AA4, first strand: chain 'A' and resid 784 through 786 removed outlier: 7.424A pdb=" N HIS A 839 " --> pdb=" O ARG A 785 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 877 through 879 removed outlier: 6.504A pdb=" N ILE A 910 " --> pdb=" O HIS A 934 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N VAL A 936 " --> pdb=" O ILE A 910 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU A 912 " --> pdb=" O VAL A 936 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 882 through 883 removed outlier: 3.585A pdb=" N GLU A 882 " --> pdb=" O LEU A 890 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 519 through 522 removed outlier: 6.055A pdb=" N CYS B 520 " --> pdb=" O ILE B 656 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 544 through 546 removed outlier: 6.838A pdb=" N PHE B 545 " --> pdb=" O LEU B 588 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 775 through 779 removed outlier: 6.634A pdb=" N MET B 766 " --> pdb=" O MET B 879 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ALA B 878 " --> pdb=" O VAL B 911 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 781 through 786 removed outlier: 7.545A pdb=" N HIS B 839 " --> pdb=" O ARG B 785 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N GLU B 801 " --> pdb=" O LEU B 842 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 882 through 883 Processing sheet with id=AB3, first strand: chain 'C' and resid 635 through 638 removed outlier: 7.235A pdb=" N ILE C 518 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ILE C 656 " --> pdb=" O ILE C 518 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N CYS C 520 " --> pdb=" O ILE C 656 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 544 through 548 Processing sheet with id=AB5, first strand: chain 'C' and resid 619 through 620 removed outlier: 3.644A pdb=" N PHE C 619 " --> pdb=" O VAL C 628 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 765 through 770 removed outlier: 3.563A pdb=" N VAL C 765 " --> pdb=" O VAL C 780 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER C 783 " --> pdb=" O HIS C 841 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 911 through 913 removed outlier: 6.580A pdb=" N LEU C 912 " --> pdb=" O VAL C 936 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D' and resid 519 through 522 removed outlier: 5.718A pdb=" N CYS D 520 " --> pdb=" O ILE D 656 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'D' and resid 544 through 547 removed outlier: 6.708A pdb=" N PHE D 545 " --> pdb=" O LEU D 588 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'D' and resid 689 through 691 removed outlier: 6.906A pdb=" N LYS D 690 " --> pdb=" O VAL D 737 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'D' and resid 800 through 803 removed outlier: 6.205A pdb=" N GLU D 801 " --> pdb=" O LEU D 842 " (cutoff:3.500A) removed outlier: 10.074A pdb=" N VAL D 764 " --> pdb=" O LEU D 877 " (cutoff:3.500A) removed outlier: 9.616A pdb=" N MET D 879 " --> pdb=" O VAL D 764 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N MET D 766 " --> pdb=" O MET D 879 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE D 910 " --> pdb=" O HIS D 934 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N VAL D 936 " --> pdb=" O ILE D 910 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N LEU D 912 " --> pdb=" O VAL D 936 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 769 through 771 Processing sheet with id=AC4, first strand: chain 'E' and resid 519 through 522 removed outlier: 5.690A pdb=" N CYS E 520 " --> pdb=" O ILE E 656 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'E' and resid 544 through 548 removed outlier: 5.679A pdb=" N ILE E 587 " --> pdb=" O ILE E 636 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N THR E 638 " --> pdb=" O ILE E 587 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE E 589 " --> pdb=" O THR E 638 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 690 through 691 removed outlier: 6.670A pdb=" N LYS E 690 " --> pdb=" O VAL E 737 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'E' and resid 800 through 803 removed outlier: 6.178A pdb=" N GLU E 801 " --> pdb=" O LEU E 842 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N HIS E 839 " --> pdb=" O ARG E 785 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N MET E 766 " --> pdb=" O MET E 879 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ILE E 910 " --> pdb=" O HIS E 934 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N VAL E 936 " --> pdb=" O ILE E 910 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N LEU E 912 " --> pdb=" O VAL E 936 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 544 through 547 removed outlier: 6.326A pdb=" N PHE F 545 " --> pdb=" O LEU F 588 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N LEU F 519 " --> pdb=" O PHE F 635 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N CYS F 637 " --> pdb=" O LEU F 519 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA F 639 " --> pdb=" O PHE F 521 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 689 through 690 Processing sheet with id=AD1, first strand: chain 'F' and resid 775 through 777 removed outlier: 6.694A pdb=" N MET F 766 " --> pdb=" O MET F 879 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA F 878 " --> pdb=" O VAL F 911 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 781 through 786 removed outlier: 3.590A pdb=" N SER F 783 " --> pdb=" O HIS F 841 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N HIS F 839 " --> pdb=" O ARG F 785 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 882 through 883 removed outlier: 3.733A pdb=" N GLU F 882 " --> pdb=" O LEU F 890 " (cutoff:3.500A) 1219 hydrogen bonds defined for protein. 3609 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: 5.12 Time building geometry restraints manager: 3.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 8967 1.37 - 1.51: 6996 1.51 - 1.66: 10876 1.66 - 1.80: 140 1.80 - 1.95: 59 Bond restraints: 27038 Sorted by residual: bond pdb=" C4 ADP E1001 " pdb=" C5 ADP E1001 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.06e+01 bond pdb=" O2G AGS C1001 " pdb=" PG AGS C1001 " ideal model delta sigma weight residual 1.604 1.500 0.104 2.00e-02 2.50e+03 2.71e+01 bond pdb=" O2G AGS A1001 " pdb=" PG AGS A1001 " ideal model delta sigma weight residual 1.604 1.503 0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" O2G AGS B1001 " pdb=" PG AGS B1001 " ideal model delta sigma weight residual 1.604 1.508 0.096 2.00e-02 2.50e+03 2.29e+01 bond pdb=" C5 ADP E1001 " pdb=" C6 ADP E1001 " ideal model delta sigma weight residual 1.490 1.406 0.084 2.00e-02 2.50e+03 1.76e+01 ... (remaining 27033 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 35818 2.53 - 5.05: 740 5.05 - 7.58: 30 7.58 - 10.11: 4 10.11 - 12.64: 1 Bond angle restraints: 36593 Sorted by residual: angle pdb=" CA PRO A 646 " pdb=" C PRO A 646 " pdb=" O PRO A 646 " ideal model delta sigma weight residual 122.31 115.29 7.02 1.41e+00 5.03e-01 2.48e+01 angle pdb=" N ASN D 618 " pdb=" CA ASN D 618 " pdb=" C ASN D 618 " ideal model delta sigma weight residual 113.23 107.18 6.05 1.22e+00 6.72e-01 2.46e+01 angle pdb=" CA GLY A 804 " pdb=" C GLY A 804 " pdb=" O GLY A 804 " ideal model delta sigma weight residual 122.29 118.32 3.97 8.10e-01 1.52e+00 2.41e+01 angle pdb=" C ASN D 618 " pdb=" CA ASN D 618 " pdb=" CB ASN D 618 " ideal model delta sigma weight residual 111.26 119.31 -8.05 1.67e+00 3.59e-01 2.32e+01 angle pdb=" N VAL C 592 " pdb=" CA VAL C 592 " pdb=" C VAL C 592 " ideal model delta sigma weight residual 113.07 106.82 6.25 1.36e+00 5.41e-01 2.11e+01 ... (remaining 36588 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.53: 15174 18.53 - 37.06: 1102 37.06 - 55.58: 189 55.58 - 74.11: 115 74.11 - 92.64: 32 Dihedral angle restraints: 16612 sinusoidal: 6801 harmonic: 9811 Sorted by residual: dihedral pdb=" CA GLN A 377 " pdb=" C GLN A 377 " pdb=" N ARG A 378 " pdb=" CA ARG A 378 " ideal model delta harmonic sigma weight residual 180.00 161.62 18.38 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA CYS D 520 " pdb=" CB CYS D 520 " pdb=" SG CYS D 520 " pdb=" SG CYS D 637 " ideal model delta sinusoidal sigma weight residual 79.00 16.79 62.21 1 2.00e+01 2.50e-03 1.28e+01 dihedral pdb=" C ASN D 618 " pdb=" N ASN D 618 " pdb=" CA ASN D 618 " pdb=" CB ASN D 618 " ideal model delta harmonic sigma weight residual -122.60 -131.51 8.91 0 2.50e+00 1.60e-01 1.27e+01 ... (remaining 16609 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 3551 0.067 - 0.134: 510 0.134 - 0.200: 96 0.200 - 0.267: 22 0.267 - 0.334: 3 Chirality restraints: 4182 Sorted by residual: chirality pdb=" C3' AGS B1001 " pdb=" C2' AGS B1001 " pdb=" C4' AGS B1001 " pdb=" O3' AGS B1001 " both_signs ideal model delta sigma weight residual False -2.37 -2.70 0.33 2.00e-01 2.50e+01 2.79e+00 chirality pdb=" C3' AGS C1001 " pdb=" C2' AGS C1001 " pdb=" C4' AGS C1001 " pdb=" O3' AGS C1001 " both_signs ideal model delta sigma weight residual False -2.37 -2.66 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" C3' AGS A1001 " pdb=" C2' AGS A1001 " pdb=" C4' AGS A1001 " pdb=" O3' AGS A1001 " both_signs ideal model delta sigma weight residual False -2.37 -2.64 0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 4179 not shown) Planarity restraints: 4707 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 546 " 0.455 9.50e-02 1.11e+02 2.04e-01 2.56e+01 pdb=" NE ARG C 546 " -0.029 2.00e-02 2.50e+03 pdb=" CZ ARG C 546 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG C 546 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG C 546 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 652 " -0.385 9.50e-02 1.11e+02 1.73e-01 1.83e+01 pdb=" NE ARG D 652 " 0.024 2.00e-02 2.50e+03 pdb=" CZ ARG D 652 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG D 652 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG D 652 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 652 " -0.381 9.50e-02 1.11e+02 1.71e-01 1.79e+01 pdb=" NE ARG C 652 " 0.023 2.00e-02 2.50e+03 pdb=" CZ ARG C 652 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG C 652 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 652 " -0.013 2.00e-02 2.50e+03 ... (remaining 4704 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 385 2.65 - 3.21: 26556 3.21 - 3.77: 43322 3.77 - 4.34: 59640 4.34 - 4.90: 96495 Nonbonded interactions: 226398 Sorted by model distance: nonbonded pdb=" O ALA D 617 " pdb=" OD1 ASN D 618 " model vdw 2.085 3.040 nonbonded pdb=" O PRO A 762 " pdb=" OG SER A 866 " model vdw 2.178 3.040 nonbonded pdb=" OG1 THR C 738 " pdb=" ND2 ASN C 741 " model vdw 2.202 3.120 nonbonded pdb=" OG1 THR F 803 " pdb=" NE2 HIS F 841 " model vdw 2.203 3.120 nonbonded pdb=" OE1 GLU A 781 " pdb=" OG SER B 884 " model vdw 2.231 3.040 ... (remaining 226393 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' and (resid 397 through 410 or (resid 411 and (name N or name CA or na \ me C or name O or name CB )) or resid 412 through 413 or (resid 414 and (name N \ or name CA or name C or name O or name CB )) or resid 415 through 448 or (resid \ 449 and (name N or name CA or name C or name O or name CB )) or resid 450 throug \ h 601 or (resid 602 and (name N or name CA or name C or name O or name CB )) or \ resid 603 through 631 or (resid 632 and (name N or name CA or name C or name O o \ r name CB )) or resid 633 through 685 or (resid 686 and (name N or name CA or na \ me C or name O or name CB )) or resid 687 through 689 or (resid 690 and (name N \ or name CA or name C or name O or name CB )) or resid 691 through 720 or (resid \ 721 and (name N or name CA or name C or name O or name CB )) or resid 722 throug \ h 772 or (resid 773 and (name N or name CA or name C or name O or name CB )) or \ resid 774 through 789 or (resid 790 and (name N or name CA or name C or name O o \ r name CB )) or resid 791 through 836 or (resid 837 and (name N or name CA or na \ me C or name O or name CB )) or resid 838 through 948 or (resid 949 and (name N \ or name CA or name C or name O or name CB )))) selection = (chain 'B' and (resid 397 through 410 or (resid 411 and (name N or name CA or na \ me C or name O or name CB )) or resid 412 through 448 or (resid 449 and (name N \ or name CA or name C or name O or name CB )) or resid 450 through 596 or (resid \ 597 and (name N or name CA or name C or name O or name CB )) or resid 598 throug \ h 601 or (resid 602 and (name N or name CA or name C or name O or name CB )) or \ resid 603 through 631 or (resid 632 and (name N or name CA or name C or name O o \ r name CB )) or resid 633 through 685 or (resid 686 and (name N or name CA or na \ me C or name O or name CB )) or resid 687 through 689 or (resid 690 and (name N \ or name CA or name C or name O or name CB )) or resid 691 through 720 or (resid \ 721 and (name N or name CA or name C or name O or name CB )) or resid 722 throug \ h 772 or (resid 773 and (name N or name CA or name C or name O or name CB )) or \ resid 774 through 788 or (resid 789 through 790 and (name N or name CA or name C \ or name O or name CB )) or resid 791 through 796 or (resid 797 and (name N or n \ ame CA or name C or name O or name CB )) or resid 798 through 836 or (resid 837 \ and (name N or name CA or name C or name O or name CB )) or resid 838 through 94 \ 8 or (resid 949 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'C' and (resid 397 through 410 or (resid 411 and (name N or name CA or na \ me C or name O or name CB )) or resid 412 through 413 or (resid 414 and (name N \ or name CA or name C or name O or name CB )) or resid 415 through 448 or (resid \ 449 and (name N or name CA or name C or name O or name CB )) or resid 450 throug \ h 596 or (resid 597 and (name N or name CA or name C or name O or name CB )) or \ resid 598 through 601 or (resid 602 and (name N or name CA or name C or name O o \ r name CB )) or resid 603 through 631 or (resid 632 and (name N or name CA or na \ me C or name O or name CB )) or resid 633 through 685 or (resid 686 and (name N \ or name CA or name C or name O or name CB )) or resid 687 through 689 or (resid \ 690 and (name N or name CA or name C or name O or name CB )) or resid 691 throug \ h 720 or (resid 721 and (name N or name CA or name C or name O or name CB )) or \ resid 722 through 772 or (resid 773 and (name N or name CA or name C or name O o \ r name CB )) or resid 774 through 788 or (resid 789 through 790 and (name N or n \ ame CA or name C or name O or name CB )) or resid 791 through 796 or (resid 797 \ and (name N or name CA or name C or name O or name CB )) or resid 798 through 83 \ 6 or (resid 837 and (name N or name CA or name C or name O or name CB )) or resi \ d 838 through 948 or (resid 949 and (name N or name CA or name C or name O or na \ me CB )))) selection = (chain 'D' and (resid 397 through 410 or (resid 411 and (name N or name CA or na \ me C or name O or name CB )) or resid 412 through 448 or (resid 449 and (name N \ or name CA or name C or name O or name CB )) or resid 450 through 596 or (resid \ 597 and (name N or name CA or name C or name O or name CB )) or resid 598 throug \ h 601 or (resid 602 and (name N or name CA or name C or name O or name CB )) or \ resid 603 through 631 or (resid 632 and (name N or name CA or name C or name O o \ r name CB )) or resid 633 through 685 or (resid 686 and (name N or name CA or na \ me C or name O or name CB )) or resid 687 through 789 or (resid 790 and (name N \ or name CA or name C or name O or name CB )) or resid 791 through 796 or (resid \ 797 and (name N or name CA or name C or name O or name CB )) or resid 798 throug \ h 948 or (resid 949 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'E' and (resid 397 through 413 or (resid 414 and (name N or name CA or na \ me C or name O or name CB )) or resid 415 through 448 or (resid 449 and (name N \ or name CA or name C or name O or name CB )) or resid 450 through 601 or (resid \ 602 and (name N or name CA or name C or name O or name CB )) or resid 603 throug \ h 631 or (resid 632 and (name N or name CA or name C or name O or name CB )) or \ resid 633 through 689 or (resid 690 and (name N or name CA or name C or name O o \ r name CB )) or resid 691 through 720 or (resid 721 and (name N or name CA or na \ me C or name O or name CB )) or resid 722 through 772 or (resid 773 and (name N \ or name CA or name C or name O or name CB )) or resid 774 through 789 or (resid \ 790 and (name N or name CA or name C or name O or name CB )) or resid 791 throug \ h 796 or (resid 797 and (name N or name CA or name C or name O or name CB )) or \ resid 798 through 836 or (resid 837 and (name N or name CA or name C or name O o \ r name CB )) or resid 838 through 949)) selection = (chain 'F' and (resid 397 through 410 or (resid 411 and (name N or name CA or na \ me C or name O or name CB )) or resid 412 through 413 or (resid 414 and (name N \ or name CA or name C or name O or name CB )) or resid 415 through 596 or (resid \ 597 and (name N or name CA or name C or name O or name CB )) or resid 598 throug \ h 685 or (resid 686 and (name N or name CA or name C or name O or name CB )) or \ resid 687 through 689 or (resid 690 and (name N or name CA or name C or name O o \ r name CB )) or resid 691 through 720 or (resid 721 and (name N or name CA or na \ me C or name O or name CB )) or resid 722 through 772 or (resid 773 and (name N \ or name CA or name C or name O or name CB )) or resid 774 through 789 or (resid \ 790 and (name N or name CA or name C or name O or name CB )) or resid 791 throug \ h 796 or (resid 797 and (name N or name CA or name C or name O or name CB )) or \ resid 798 through 836 or (resid 837 and (name N or name CA or name C or name O o \ r name CB )) or resid 838 through 948 or (resid 949 and (name N or name CA or na \ me C or name O or name CB )))) } 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: 4.550 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: 0.040 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 25.930 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.060 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6596 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 : 0.006 0.111 27039 Z= 0.404 Angle : 0.763 12.636 36595 Z= 0.514 Chirality : 0.052 0.334 4182 Planarity : 0.008 0.204 4707 Dihedral : 14.678 92.638 10295 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.04 % Allowed : 1.30 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.14), residues: 3359 helix: 0.95 (0.13), residues: 1572 sheet: -1.90 (0.26), residues: 371 loop : -1.05 (0.15), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 652 TYR 0.014 0.001 TYR B 939 PHE 0.013 0.001 PHE D 619 TRP 0.010 0.001 TRP A 470 HIS 0.004 0.001 HIS A 841 Details of bonding type rmsd/Z covalent geometry : bond 0.00601 / 0.40 (27038) covalent geometry : angle 0.76312 / 0.51 (36593) SS BOND : bond 0.00145 / 0.08 ( 1) SS BOND : angle 0.38250 / 0.21 ( 2) hydrogen bonds : bond 0.15394 / 10.12 ( 1219) hydrogen bonds : angle 6.73287 / 4.74 ( 3609) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 635 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 541 ASN cc_start: 0.7321 (m110) cc_final: 0.7007 (m110) REVERT: B 609 GLU cc_start: 0.6842 (tm-30) cc_final: 0.6526 (tm-30) REVERT: C 486 VAL cc_start: 0.8352 (p) cc_final: 0.7936 (m) REVERT: C 518 ILE cc_start: 0.7347 (mm) cc_final: 0.7092 (mm) REVERT: C 593 ASP cc_start: 0.6298 (t70) cc_final: 0.5986 (t0) REVERT: C 700 ILE cc_start: 0.7150 (mt) cc_final: 0.6638 (mt) REVERT: C 882 GLU cc_start: 0.7172 (tp30) cc_final: 0.6882 (tt0) REVERT: C 895 ILE cc_start: 0.5748 (tp) cc_final: 0.5444 (mm) REVERT: C 935 PHE cc_start: 0.7705 (m-80) cc_final: 0.7501 (m-80) REVERT: E 514 THR cc_start: 0.7894 (t) cc_final: 0.7662 (t) REVERT: E 661 TYR cc_start: 0.6968 (m-80) cc_final: 0.6376 (m-80) REVERT: E 801 GLU cc_start: 0.6824 (tt0) cc_final: 0.6556 (tt0) REVERT: F 426 LYS cc_start: 0.6727 (tttt) cc_final: 0.6027 (mttt) REVERT: F 482 ARG cc_start: 0.6250 (tpt90) cc_final: 0.5302 (mmm160) REVERT: F 579 LYS cc_start: 0.7512 (ttmm) cc_final: 0.6939 (pttt) REVERT: F 686 GLU cc_start: 0.5827 (mm-30) cc_final: 0.5615 (mm-30) REVERT: F 803 THR cc_start: 0.7254 (p) cc_final: 0.6872 (p) outliers start: 1 outliers final: 0 residues processed: 636 average time/residue: 0.1954 time to fit residues: 191.8868 Evaluate side-chains 367 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 367 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 0.1980 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.0970 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 4.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 456 ASN A 484 GLN A 561 HIS A 622 HIS B 515 GLN B 561 HIS B 788 GLN D 456 ASN ** D 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 399 GLN E 456 ASN E 484 GLN ** E 843 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 934 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.209948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.155077 restraints weight = 30828.859| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 2.71 r_work: 0.3732 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27039 Z= 0.146 Angle : 0.624 12.003 36595 Z= 0.314 Chirality : 0.042 0.206 4182 Planarity : 0.005 0.060 4707 Dihedral : 7.307 59.927 3811 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.65 % Allowed : 9.33 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.14), residues: 3359 helix: 1.13 (0.13), residues: 1614 sheet: -1.68 (0.24), residues: 389 loop : -0.98 (0.16), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 511 TYR 0.019 0.001 TYR E 757 PHE 0.031 0.002 PHE D 547 TRP 0.026 0.002 TRP A 770 HIS 0.007 0.001 HIS E 843 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (27038) covalent geometry : angle 0.62433 / 0.31 (36593) SS BOND : bond 0.00448 / 0.24 ( 1) SS BOND : angle 0.59065 / 0.34 ( 2) hydrogen bonds : bond 0.04193 / 2.76 ( 1219) hydrogen bonds : angle 5.19585 / 3.71 ( 3609) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 430 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 430 VAL cc_start: 0.6706 (OUTLIER) cc_final: 0.6328 (p) REVERT: A 435 MET cc_start: 0.7312 (mmm) cc_final: 0.6331 (mtm) REVERT: A 456 ASN cc_start: 0.6753 (OUTLIER) cc_final: 0.6476 (p0) REVERT: A 459 ARG cc_start: 0.6810 (tpt90) cc_final: 0.6587 (tmm160) REVERT: A 503 GLU cc_start: 0.7258 (mm-30) cc_final: 0.6219 (mt-10) REVERT: A 541 ASN cc_start: 0.7399 (m110) cc_final: 0.6991 (m110) REVERT: A 820 PHE cc_start: 0.7714 (t80) cc_final: 0.7387 (t80) REVERT: B 609 GLU cc_start: 0.6801 (tm-30) cc_final: 0.6488 (tm-30) REVERT: B 652 ARG cc_start: 0.7514 (mtt90) cc_final: 0.7305 (mtt90) REVERT: B 754 GLU cc_start: 0.5869 (mm-30) cc_final: 0.5574 (mm-30) REVERT: B 773 MET cc_start: 0.5848 (tmm) cc_final: 0.5274 (mmm) REVERT: B 882 GLU cc_start: 0.7927 (tm-30) cc_final: 0.6839 (mt-10) REVERT: C 486 VAL cc_start: 0.8241 (p) cc_final: 0.7762 (m) REVERT: C 661 TYR cc_start: 0.7819 (m-80) cc_final: 0.7437 (m-80) REVERT: C 700 ILE cc_start: 0.7438 (mt) cc_final: 0.6882 (mt) REVERT: C 808 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7039 (mt-10) REVERT: C 882 GLU cc_start: 0.7721 (tp30) cc_final: 0.7416 (tt0) REVERT: D 435 MET cc_start: 0.7369 (mmm) cc_final: 0.7159 (mmm) REVERT: D 557 GLU cc_start: 0.6470 (mm-30) cc_final: 0.6127 (mm-30) REVERT: E 484 GLN cc_start: 0.7798 (OUTLIER) cc_final: 0.7108 (tp-100) REVERT: E 582 THR cc_start: 0.6742 (t) cc_final: 0.6281 (m) REVERT: E 652 ARG cc_start: 0.6923 (ttm-80) cc_final: 0.6623 (ttm-80) REVERT: E 661 TYR cc_start: 0.7257 (m-80) cc_final: 0.6783 (m-80) REVERT: F 426 LYS cc_start: 0.6563 (tttt) cc_final: 0.5850 (mtmt) REVERT: F 543 GLU cc_start: 0.7270 (mp0) cc_final: 0.6934 (mp0) REVERT: F 579 LYS cc_start: 0.7554 (ttmm) cc_final: 0.6918 (pttt) REVERT: F 686 GLU cc_start: 0.6129 (mm-30) cc_final: 0.5918 (mm-30) REVERT: F 715 GLN cc_start: 0.6457 (OUTLIER) cc_final: 0.5612 (mp10) REVERT: F 803 THR cc_start: 0.5901 (p) cc_final: 0.5275 (t) outliers start: 47 outliers final: 24 residues processed: 459 average time/residue: 0.1684 time to fit residues: 126.6148 Evaluate side-chains 381 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 353 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 456 ASN Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 520 CYS Chi-restraints excluded: chain A residue 655 MET Chi-restraints excluded: chain B residue 631 SER Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 723 SER Chi-restraints excluded: chain C residue 771 THR Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 489 GLU Chi-restraints excluded: chain D residue 707 SER Chi-restraints excluded: chain D residue 764 VAL Chi-restraints excluded: chain D residue 771 THR Chi-restraints excluded: chain D residue 809 VAL Chi-restraints excluded: chain E residue 484 GLN Chi-restraints excluded: chain E residue 492 TYR Chi-restraints excluded: chain E residue 693 SER Chi-restraints excluded: chain E residue 764 VAL Chi-restraints excluded: chain E residue 879 MET Chi-restraints excluded: chain F residue 508 SER Chi-restraints excluded: chain F residue 715 GLN Chi-restraints excluded: chain F residue 833 ASP Chi-restraints excluded: chain F residue 859 THR Chi-restraints excluded: chain F residue 927 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 65 optimal weight: 0.9990 chunk 190 optimal weight: 0.9980 chunk 300 optimal weight: 8.9990 chunk 35 optimal weight: 0.0070 chunk 155 optimal weight: 2.9990 chunk 283 optimal weight: 0.0050 chunk 81 optimal weight: 0.9980 chunk 247 optimal weight: 10.0000 chunk 318 optimal weight: 2.9990 chunk 201 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 overall best weight: 0.6012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 843 HIS B 477 ASN ** B 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 841 HIS C 391 HIS ** D 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 843 HIS F 702 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.207325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.155942 restraints weight = 30993.463| |-----------------------------------------------------------------------------| r_work (start): 0.3927 rms_B_bonded: 2.90 r_work: 0.3696 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 27039 Z= 0.140 Angle : 0.559 9.887 36595 Z= 0.282 Chirality : 0.040 0.209 4182 Planarity : 0.004 0.049 4707 Dihedral : 6.179 59.256 3811 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.68 % Allowed : 11.50 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.14), residues: 3359 helix: 1.20 (0.13), residues: 1628 sheet: -1.47 (0.25), residues: 386 loop : -0.96 (0.16), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 652 TYR 0.017 0.001 TYR F 522 PHE 0.025 0.002 PHE B 824 TRP 0.023 0.001 TRP A 770 HIS 0.004 0.001 HIS F 843 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (27038) covalent geometry : angle 0.55859 / 0.28 (36593) SS BOND : bond 0.00274 / 0.14 ( 1) SS BOND : angle 0.56345 / 0.33 ( 2) hydrogen bonds : bond 0.03876 / 2.55 ( 1219) hydrogen bonds : angle 4.90072 / 3.52 ( 3609) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 398 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 457 VAL cc_start: 0.4960 (OUTLIER) cc_final: 0.4714 (p) REVERT: A 459 ARG cc_start: 0.6811 (tpt90) cc_final: 0.6564 (tmm160) REVERT: A 460 ASN cc_start: 0.8035 (OUTLIER) cc_final: 0.7807 (m-40) REVERT: A 503 GLU cc_start: 0.7106 (mm-30) cc_final: 0.6130 (mt-10) REVERT: A 541 ASN cc_start: 0.7403 (m110) cc_final: 0.6974 (m110) REVERT: A 629 ASP cc_start: 0.7372 (t0) cc_final: 0.6885 (t0) REVERT: A 820 PHE cc_start: 0.7814 (t80) cc_final: 0.7528 (t80) REVERT: B 609 GLU cc_start: 0.7118 (tm-30) cc_final: 0.6517 (tm-30) REVERT: B 754 GLU cc_start: 0.6020 (mm-30) cc_final: 0.5754 (mm-30) REVERT: B 773 MET cc_start: 0.6142 (tmm) cc_final: 0.5543 (mmm) REVERT: B 882 GLU cc_start: 0.8029 (tm-30) cc_final: 0.7037 (mt-10) REVERT: C 486 VAL cc_start: 0.8178 (p) cc_final: 0.7720 (m) REVERT: C 661 TYR cc_start: 0.8178 (m-80) cc_final: 0.7848 (m-80) REVERT: C 808 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7200 (mt-10) REVERT: C 871 ARG cc_start: 0.8290 (mtm-85) cc_final: 0.8052 (mtm180) REVERT: C 882 GLU cc_start: 0.7935 (tp30) cc_final: 0.7609 (tt0) REVERT: D 557 GLU cc_start: 0.6788 (mm-30) cc_final: 0.6416 (mm-30) REVERT: D 700 ILE cc_start: 0.8027 (mt) cc_final: 0.7785 (mt) REVERT: D 701 LYS cc_start: 0.7586 (ttpp) cc_final: 0.7339 (tttp) REVERT: E 582 THR cc_start: 0.6684 (t) cc_final: 0.6285 (m) REVERT: F 426 LYS cc_start: 0.6542 (tttt) cc_final: 0.5857 (mtmt) REVERT: F 510 LEU cc_start: 0.6713 (OUTLIER) cc_final: 0.6363 (tt) REVERT: F 543 GLU cc_start: 0.7266 (mp0) cc_final: 0.6902 (mp0) REVERT: F 579 LYS cc_start: 0.7449 (ttmm) cc_final: 0.6844 (pttt) REVERT: F 686 GLU cc_start: 0.6278 (mm-30) cc_final: 0.6066 (mm-30) REVERT: F 715 GLN cc_start: 0.6352 (OUTLIER) cc_final: 0.5522 (mp10) outliers start: 48 outliers final: 23 residues processed: 430 average time/residue: 0.1741 time to fit residues: 121.6873 Evaluate side-chains 383 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 356 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 520 CYS Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 771 THR Chi-restraints excluded: chain C residue 569 MET Chi-restraints excluded: chain C residue 771 THR Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain D residue 489 GLU Chi-restraints excluded: chain D residue 566 VAL Chi-restraints excluded: chain D residue 707 SER Chi-restraints excluded: chain D residue 764 VAL Chi-restraints excluded: chain D residue 771 THR Chi-restraints excluded: chain E residue 693 SER Chi-restraints excluded: chain E residue 764 VAL Chi-restraints excluded: chain E residue 859 THR Chi-restraints excluded: chain E residue 879 MET Chi-restraints excluded: chain F residue 508 SER Chi-restraints excluded: chain F residue 510 LEU Chi-restraints excluded: chain F residue 715 GLN Chi-restraints excluded: chain F residue 771 THR Chi-restraints excluded: chain F residue 809 VAL Chi-restraints excluded: chain F residue 859 THR Chi-restraints excluded: chain F residue 927 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 111 optimal weight: 0.9980 chunk 53 optimal weight: 0.0020 chunk 326 optimal weight: 0.5980 chunk 28 optimal weight: 5.9990 chunk 323 optimal weight: 0.8980 chunk 35 optimal weight: 7.9990 chunk 265 optimal weight: 3.9990 chunk 80 optimal weight: 0.0870 chunk 291 optimal weight: 9.9990 chunk 294 optimal weight: 6.9990 chunk 304 optimal weight: 0.9980 overall best weight: 0.5166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 615 GLN B 477 ASN B 515 GLN D 584 ASN D 916 ASN ** E 843 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.207531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.156442 restraints weight = 31145.516| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 2.74 r_work: 0.3700 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27039 Z= 0.121 Angle : 0.550 9.396 36595 Z= 0.278 Chirality : 0.041 0.191 4182 Planarity : 0.004 0.056 4707 Dihedral : 5.464 59.894 3811 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.10 % Allowed : 12.63 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.14), residues: 3359 helix: 1.28 (0.13), residues: 1629 sheet: -1.33 (0.25), residues: 378 loop : -0.97 (0.16), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 785 TYR 0.022 0.001 TYR F 522 PHE 0.037 0.002 PHE F 926 TRP 0.031 0.001 TRP A 770 HIS 0.011 0.001 HIS E 843 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (27038) covalent geometry : angle 0.54999 / 0.28 (36593) SS BOND : bond 0.00132 / 0.07 ( 1) SS BOND : angle 0.49441 / 0.28 ( 2) hydrogen bonds : bond 0.03427 / 2.26 ( 1219) hydrogen bonds : angle 4.60942 / 3.31 ( 3609) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 394 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 435 MET cc_start: 0.7187 (mmm) cc_final: 0.5940 (mtm) REVERT: A 459 ARG cc_start: 0.6730 (tpt90) cc_final: 0.6459 (tmm160) REVERT: A 503 GLU cc_start: 0.7163 (mm-30) cc_final: 0.6177 (mt-10) REVERT: A 541 ASN cc_start: 0.7407 (m110) cc_final: 0.6946 (m110) REVERT: A 629 ASP cc_start: 0.7312 (t0) cc_final: 0.5782 (p0) REVERT: A 667 LEU cc_start: 0.6530 (OUTLIER) cc_final: 0.6209 (tp) REVERT: A 820 PHE cc_start: 0.8066 (t80) cc_final: 0.7792 (t80) REVERT: B 609 GLU cc_start: 0.7169 (tm-30) cc_final: 0.6660 (tm-30) REVERT: B 773 MET cc_start: 0.6267 (tmm) cc_final: 0.5750 (mmm) REVERT: B 882 GLU cc_start: 0.8024 (tm-30) cc_final: 0.7035 (mt-10) REVERT: B 935 PHE cc_start: 0.7942 (m-80) cc_final: 0.7680 (m-80) REVERT: C 488 GLU cc_start: 0.7137 (tt0) cc_final: 0.6853 (mt-10) REVERT: C 661 TYR cc_start: 0.8457 (m-80) cc_final: 0.8232 (m-80) REVERT: C 808 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7394 (mt-10) REVERT: C 882 GLU cc_start: 0.7937 (tp30) cc_final: 0.7697 (tt0) REVERT: D 418 GLU cc_start: 0.7268 (tm-30) cc_final: 0.6769 (tm-30) REVERT: D 557 GLU cc_start: 0.6976 (mm-30) cc_final: 0.6615 (mm-30) REVERT: D 808 GLU cc_start: 0.7967 (tp30) cc_final: 0.7637 (mt-10) REVERT: D 826 MET cc_start: 0.7536 (tmm) cc_final: 0.7151 (ttm) REVERT: D 912 LEU cc_start: 0.7502 (mt) cc_final: 0.6991 (mp) REVERT: E 786 ARG cc_start: 0.8447 (ttt90) cc_final: 0.8137 (ptm160) REVERT: F 426 LYS cc_start: 0.6589 (tttt) cc_final: 0.5888 (mtmt) REVERT: F 543 GLU cc_start: 0.7260 (mp0) cc_final: 0.7007 (mp0) REVERT: F 686 GLU cc_start: 0.6341 (mm-30) cc_final: 0.6117 (mm-30) REVERT: F 715 GLN cc_start: 0.6349 (OUTLIER) cc_final: 0.5440 (mp10) outliers start: 60 outliers final: 23 residues processed: 441 average time/residue: 0.1622 time to fit residues: 118.0841 Evaluate side-chains 358 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 333 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 520 CYS Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 866 SER Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 771 THR Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain C residue 771 THR Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain D residue 489 GLU Chi-restraints excluded: chain D residue 566 VAL Chi-restraints excluded: chain D residue 707 SER Chi-restraints excluded: chain D residue 764 VAL Chi-restraints excluded: chain D residue 771 THR Chi-restraints excluded: chain E residue 492 TYR Chi-restraints excluded: chain E residue 693 SER Chi-restraints excluded: chain E residue 764 VAL Chi-restraints excluded: chain E residue 879 MET Chi-restraints excluded: chain F residue 510 LEU Chi-restraints excluded: chain F residue 715 GLN Chi-restraints excluded: chain F residue 771 THR Chi-restraints excluded: chain F residue 809 VAL Chi-restraints excluded: chain F residue 859 THR Chi-restraints excluded: chain F residue 927 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 134 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 301 optimal weight: 10.0000 chunk 257 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 163 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 95 optimal weight: 0.6980 chunk 108 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 320 optimal weight: 6.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 ASN B 711 ASN C 584 ASN ** D 841 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 640 ASN ** E 843 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 805 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.213281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.158223 restraints weight = 31245.783| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 3.17 r_work: 0.3658 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.4662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 27039 Z= 0.149 Angle : 0.578 13.589 36595 Z= 0.289 Chirality : 0.041 0.184 4182 Planarity : 0.005 0.060 4707 Dihedral : 5.286 58.296 3811 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.21 % Allowed : 14.03 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.14), residues: 3359 helix: 1.30 (0.13), residues: 1630 sheet: -1.50 (0.24), residues: 400 loop : -0.91 (0.16), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 652 TYR 0.028 0.002 TYR B 757 PHE 0.021 0.002 PHE F 935 TRP 0.029 0.001 TRP A 770 HIS 0.006 0.001 HIS F 934 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 (27038) covalent geometry : angle 0.57820 / 0.29 (36593) SS BOND : bond 0.00389 / 0.20 ( 1) SS BOND : angle 0.44947 / 0.26 ( 2) hydrogen bonds : bond 0.03498 / 2.32 ( 1219) hydrogen bonds : angle 4.57338 / 3.32 ( 3609) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 379 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 456 ASN cc_start: 0.6874 (OUTLIER) cc_final: 0.6486 (p0) REVERT: A 459 ARG cc_start: 0.6745 (tpt90) cc_final: 0.6517 (tmm160) REVERT: A 503 GLU cc_start: 0.7335 (mm-30) cc_final: 0.6280 (mt-10) REVERT: A 541 ASN cc_start: 0.7427 (m110) cc_final: 0.6925 (m110) REVERT: A 629 ASP cc_start: 0.7224 (t0) cc_final: 0.5678 (p0) REVERT: A 667 LEU cc_start: 0.6910 (OUTLIER) cc_final: 0.6683 (tp) REVERT: A 808 GLU cc_start: 0.8182 (tp30) cc_final: 0.7725 (tt0) REVERT: B 609 GLU cc_start: 0.7379 (tm-30) cc_final: 0.6915 (tm-30) REVERT: B 773 MET cc_start: 0.6484 (tmm) cc_final: 0.6107 (mmm) REVERT: B 882 GLU cc_start: 0.8404 (tm-30) cc_final: 0.7528 (mt-10) REVERT: C 488 GLU cc_start: 0.7432 (tt0) cc_final: 0.7141 (mt-10) REVERT: C 661 TYR cc_start: 0.8839 (m-80) cc_final: 0.8508 (m-80) REVERT: C 672 ARG cc_start: 0.7696 (mtt-85) cc_final: 0.7471 (mtm180) REVERT: C 801 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7483 (tt0) REVERT: C 808 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7502 (mt-10) REVERT: C 882 GLU cc_start: 0.8242 (tp30) cc_final: 0.8027 (tt0) REVERT: C 889 ILE cc_start: 0.8824 (mm) cc_final: 0.8262 (mm) REVERT: D 418 GLU cc_start: 0.7306 (tm-30) cc_final: 0.6727 (tm-30) REVERT: D 701 LYS cc_start: 0.7983 (ttpp) cc_final: 0.7515 (tttp) REVERT: D 826 MET cc_start: 0.7966 (tmm) cc_final: 0.7719 (ttm) REVERT: D 912 LEU cc_start: 0.8025 (mt) cc_final: 0.7532 (mp) REVERT: E 786 ARG cc_start: 0.8618 (ttt90) cc_final: 0.8405 (ptm-80) REVERT: F 426 LYS cc_start: 0.6559 (tttt) cc_final: 0.5875 (mtmt) REVERT: F 503 GLU cc_start: 0.8759 (mm-30) cc_final: 0.7928 (mm-30) REVERT: F 543 GLU cc_start: 0.7299 (mp0) cc_final: 0.7023 (mp0) REVERT: F 579 LYS cc_start: 0.7360 (ttmm) cc_final: 0.6643 (pttt) REVERT: F 801 GLU cc_start: 0.7323 (tt0) cc_final: 0.7095 (tt0) REVERT: F 838 SER cc_start: 0.8661 (m) cc_final: 0.8399 (p) outliers start: 63 outliers final: 35 residues processed: 419 average time/residue: 0.1744 time to fit residues: 118.2578 Evaluate side-chains 367 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 329 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 456 ASN Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 520 CYS Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 707 SER Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 685 ASP Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 771 THR Chi-restraints excluded: chain B residue 873 VAL Chi-restraints excluded: chain B residue 909 CYS Chi-restraints excluded: chain C residue 569 MET Chi-restraints excluded: chain C residue 633 VAL Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain C residue 771 THR Chi-restraints excluded: chain C residue 801 GLU Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 448 LEU Chi-restraints excluded: chain D residue 489 GLU Chi-restraints excluded: chain D residue 510 LEU Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 566 VAL Chi-restraints excluded: chain D residue 707 SER Chi-restraints excluded: chain D residue 764 VAL Chi-restraints excluded: chain D residue 771 THR Chi-restraints excluded: chain E residue 634 LEU Chi-restraints excluded: chain E residue 693 SER Chi-restraints excluded: chain E residue 764 VAL Chi-restraints excluded: chain F residue 508 SER Chi-restraints excluded: chain F residue 510 LEU Chi-restraints excluded: chain F residue 555 VAL Chi-restraints excluded: chain F residue 771 THR Chi-restraints excluded: chain F residue 809 VAL Chi-restraints excluded: chain F residue 859 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 43 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 217 optimal weight: 3.9990 chunk 289 optimal weight: 2.9990 chunk 112 optimal weight: 7.9990 chunk 121 optimal weight: 7.9990 chunk 176 optimal weight: 6.9990 chunk 265 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 177 optimal weight: 5.9990 chunk 157 optimal weight: 0.9980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 477 ASN C 491 HIS D 584 ASN D 934 HIS ** E 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 433 HIS ** E 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 711 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.196971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.146741 restraints weight = 31278.872| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 2.47 r_work: 0.3566 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3411 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.6755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 27039 Z= 0.251 Angle : 0.738 12.335 36595 Z= 0.371 Chirality : 0.047 0.262 4182 Planarity : 0.005 0.061 4707 Dihedral : 5.658 56.760 3811 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.98 % Allowed : 14.63 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.14), residues: 3359 helix: 0.97 (0.13), residues: 1611 sheet: -1.48 (0.25), residues: 394 loop : -1.14 (0.15), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 652 TYR 0.038 0.002 TYR B 461 PHE 0.030 0.003 PHE A 820 TRP 0.031 0.002 TRP D 464 HIS 0.013 0.002 HIS B 561 Details of bonding type rmsd/Z covalent geometry : bond 0.00615 / 0.25 (27038) covalent geometry : angle 0.73815 / 0.37 (36593) SS BOND : bond 0.01072 / 0.56 ( 1) SS BOND : angle 0.53125 / 0.30 ( 2) hydrogen bonds : bond 0.04027 / 2.68 ( 1219) hydrogen bonds : angle 4.95728 / 3.61 ( 3609) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 384 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 424 ARG cc_start: 0.5832 (ttm170) cc_final: 0.5616 (ttm170) REVERT: A 435 MET cc_start: 0.7063 (mmm) cc_final: 0.5607 (mtm) REVERT: A 459 ARG cc_start: 0.6960 (tpt90) cc_final: 0.6633 (tmm160) REVERT: A 503 GLU cc_start: 0.7640 (mm-30) cc_final: 0.6630 (mt-10) REVERT: A 541 ASN cc_start: 0.7567 (m110) cc_final: 0.7195 (m110) REVERT: A 588 LEU cc_start: 0.8175 (tp) cc_final: 0.7947 (tp) REVERT: A 629 ASP cc_start: 0.7428 (t0) cc_final: 0.5788 (p0) REVERT: A 667 LEU cc_start: 0.7629 (OUTLIER) cc_final: 0.7323 (tp) REVERT: A 808 GLU cc_start: 0.8523 (tp30) cc_final: 0.8262 (tt0) REVERT: B 484 GLN cc_start: 0.7591 (tp40) cc_final: 0.7347 (tp-100) REVERT: B 488 GLU cc_start: 0.8342 (tt0) cc_final: 0.7788 (mm-30) REVERT: B 563 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7971 (mtp180) REVERT: B 609 GLU cc_start: 0.7851 (tm-30) cc_final: 0.7393 (tm-30) REVERT: B 706 GLU cc_start: 0.7124 (OUTLIER) cc_final: 0.6765 (mm-30) REVERT: B 713 GLN cc_start: 0.7950 (tt0) cc_final: 0.7696 (tt0) REVERT: B 731 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7383 (mt-10) REVERT: B 754 GLU cc_start: 0.6935 (mm-30) cc_final: 0.6698 (mm-30) REVERT: B 826 MET cc_start: 0.8858 (OUTLIER) cc_final: 0.8581 (ttt) REVERT: B 869 MET cc_start: 0.9078 (mtp) cc_final: 0.8849 (mtp) REVERT: C 439 ASP cc_start: 0.8441 (m-30) cc_final: 0.7904 (m-30) REVERT: C 488 GLU cc_start: 0.8106 (tt0) cc_final: 0.7829 (mt-10) REVERT: C 618 ASN cc_start: 0.8050 (m-40) cc_final: 0.7451 (p0) REVERT: C 834 TYR cc_start: 0.8374 (t80) cc_final: 0.8143 (t80) REVERT: C 882 GLU cc_start: 0.8669 (tp30) cc_final: 0.8303 (tt0) REVERT: D 552 MET cc_start: 0.7650 (mmt) cc_final: 0.7196 (mmp) REVERT: D 701 LYS cc_start: 0.8239 (ttpp) cc_final: 0.7762 (tttp) REVERT: E 546 ARG cc_start: 0.8554 (ttt90) cc_final: 0.8073 (tpt-90) REVERT: E 582 THR cc_start: 0.7414 (t) cc_final: 0.7124 (m) REVERT: E 672 ARG cc_start: 0.7965 (mtp-110) cc_final: 0.7531 (mtm110) REVERT: E 897 GLU cc_start: 0.8413 (mp0) cc_final: 0.8097 (mt-10) REVERT: F 426 LYS cc_start: 0.6620 (tttt) cc_final: 0.5893 (mttt) REVERT: F 579 LYS cc_start: 0.7482 (ttmm) cc_final: 0.6481 (pttt) REVERT: F 810 MET cc_start: 0.8773 (tpp) cc_final: 0.8447 (ttt) REVERT: F 834 TYR cc_start: 0.8224 (t80) cc_final: 0.7962 (t80) REVERT: F 840 ILE cc_start: 0.8936 (OUTLIER) cc_final: 0.8696 (mm) outliers start: 85 outliers final: 55 residues processed: 436 average time/residue: 0.1719 time to fit residues: 121.6442 Evaluate side-chains 363 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 303 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 520 CYS Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 694 ASP Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 563 ARG Chi-restraints excluded: chain B residue 645 ILE Chi-restraints excluded: chain B residue 685 ASP Chi-restraints excluded: chain B residue 706 GLU Chi-restraints excluded: chain B residue 753 VAL Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 771 THR Chi-restraints excluded: chain B residue 826 MET Chi-restraints excluded: chain B residue 873 VAL Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 909 CYS Chi-restraints excluded: chain B residue 945 ILE Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain C residue 771 THR Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 895 ILE Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 489 GLU Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 566 VAL Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 707 SER Chi-restraints excluded: chain D residue 764 VAL Chi-restraints excluded: chain D residue 771 THR Chi-restraints excluded: chain D residue 776 SER Chi-restraints excluded: chain D residue 827 GLN Chi-restraints excluded: chain D residue 889 ILE Chi-restraints excluded: chain D residue 910 ILE Chi-restraints excluded: chain D residue 911 VAL Chi-restraints excluded: chain E residue 693 SER Chi-restraints excluded: chain E residue 704 CYS Chi-restraints excluded: chain E residue 764 VAL Chi-restraints excluded: chain E residue 879 MET Chi-restraints excluded: chain E residue 900 ILE Chi-restraints excluded: chain F residue 407 LEU Chi-restraints excluded: chain F residue 508 SER Chi-restraints excluded: chain F residue 510 LEU Chi-restraints excluded: chain F residue 555 VAL Chi-restraints excluded: chain F residue 743 GLN Chi-restraints excluded: chain F residue 771 THR Chi-restraints excluded: chain F residue 808 GLU Chi-restraints excluded: chain F residue 809 VAL Chi-restraints excluded: chain F residue 840 ILE Chi-restraints excluded: chain F residue 859 THR Chi-restraints excluded: chain F residue 927 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 50 optimal weight: 0.6980 chunk 62 optimal weight: 9.9990 chunk 19 optimal weight: 2.9990 chunk 18 optimal weight: 8.9990 chunk 288 optimal weight: 10.0000 chunk 90 optimal weight: 1.9990 chunk 213 optimal weight: 0.7980 chunk 267 optimal weight: 0.6980 chunk 183 optimal weight: 2.9990 chunk 214 optimal weight: 0.8980 chunk 191 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 ASN ** B 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 743 GLN E 391 HIS E 541 ASN E 615 GLN F 491 HIS F 711 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.196325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.146460 restraints weight = 31146.444| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 2.61 r_work: 0.3533 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.6959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 27039 Z= 0.147 Angle : 0.584 8.963 36595 Z= 0.294 Chirality : 0.041 0.190 4182 Planarity : 0.004 0.066 4707 Dihedral : 5.313 57.727 3811 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.31 % Allowed : 16.20 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.14), residues: 3359 helix: 1.26 (0.13), residues: 1604 sheet: -1.57 (0.25), residues: 411 loop : -0.98 (0.16), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 652 TYR 0.018 0.001 TYR B 461 PHE 0.028 0.002 PHE B 455 TRP 0.016 0.001 TRP A 770 HIS 0.005 0.001 HIS A 843 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 (27038) covalent geometry : angle 0.58434 / 0.29 (36593) SS BOND : bond 0.00609 / 0.32 ( 1) SS BOND : angle 0.29970 / 0.18 ( 2) hydrogen bonds : bond 0.03491 / 2.31 ( 1219) hydrogen bonds : angle 4.69500 / 3.41 ( 3609) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 348 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 424 ARG cc_start: 0.5839 (ttm170) cc_final: 0.5622 (ttm170) REVERT: A 456 ASN cc_start: 0.6816 (p0) cc_final: 0.6536 (p0) REVERT: A 459 ARG cc_start: 0.6838 (tpt90) cc_final: 0.6532 (tmm160) REVERT: A 503 GLU cc_start: 0.7597 (mm-30) cc_final: 0.6541 (mt-10) REVERT: A 541 ASN cc_start: 0.7461 (m110) cc_final: 0.7007 (m110) REVERT: A 629 ASP cc_start: 0.7369 (t0) cc_final: 0.5775 (p0) REVERT: A 667 LEU cc_start: 0.7471 (OUTLIER) cc_final: 0.7205 (tp) REVERT: B 541 ASN cc_start: 0.8230 (t0) cc_final: 0.7989 (t0) REVERT: B 609 GLU cc_start: 0.7773 (tm-30) cc_final: 0.7310 (tm-30) REVERT: B 731 GLU cc_start: 0.7577 (mt-10) cc_final: 0.7214 (mt-10) REVERT: B 754 GLU cc_start: 0.6902 (mm-30) cc_final: 0.6691 (mm-30) REVERT: B 826 MET cc_start: 0.8606 (OUTLIER) cc_final: 0.8363 (ttt) REVERT: B 869 MET cc_start: 0.8924 (mtp) cc_final: 0.8717 (mtp) REVERT: B 882 GLU cc_start: 0.8420 (tm-30) cc_final: 0.7894 (mt-10) REVERT: C 439 ASP cc_start: 0.8302 (m-30) cc_final: 0.7831 (m-30) REVERT: C 503 GLU cc_start: 0.8319 (mt-10) cc_final: 0.7993 (mt-10) REVERT: C 801 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7666 (tt0) REVERT: C 882 GLU cc_start: 0.8364 (tp30) cc_final: 0.8008 (tt0) REVERT: D 545 PHE cc_start: 0.8619 (t80) cc_final: 0.8287 (t80) REVERT: D 701 LYS cc_start: 0.8206 (ttpp) cc_final: 0.7679 (tttp) REVERT: D 884 SER cc_start: 0.8724 (p) cc_final: 0.8483 (p) REVERT: D 922 ASP cc_start: 0.8002 (m-30) cc_final: 0.7735 (m-30) REVERT: D 940 ARG cc_start: 0.8009 (ttp-110) cc_final: 0.7641 (mtm110) REVERT: E 582 THR cc_start: 0.7268 (t) cc_final: 0.7010 (m) REVERT: E 697 THR cc_start: 0.7782 (OUTLIER) cc_final: 0.7502 (m) REVERT: E 885 LEU cc_start: 0.8683 (tp) cc_final: 0.8099 (tp) REVERT: F 426 LYS cc_start: 0.6562 (tttt) cc_final: 0.5874 (mttt) REVERT: F 503 GLU cc_start: 0.8668 (mm-30) cc_final: 0.7986 (mm-30) REVERT: F 579 LYS cc_start: 0.7422 (ttmm) cc_final: 0.6529 (pttt) REVERT: F 810 MET cc_start: 0.8593 (tpp) cc_final: 0.8291 (ttt) outliers start: 66 outliers final: 41 residues processed: 394 average time/residue: 0.1663 time to fit residues: 108.5769 Evaluate side-chains 360 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 315 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 520 CYS Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 634 LEU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 645 ILE Chi-restraints excluded: chain B residue 756 MET Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 826 MET Chi-restraints excluded: chain B residue 873 VAL Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 909 CYS Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 771 THR Chi-restraints excluded: chain C residue 801 GLU Chi-restraints excluded: chain C residue 806 LEU Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 566 VAL Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 707 SER Chi-restraints excluded: chain D residue 764 VAL Chi-restraints excluded: chain D residue 771 THR Chi-restraints excluded: chain D residue 776 SER Chi-restraints excluded: chain D residue 889 ILE Chi-restraints excluded: chain D residue 911 VAL Chi-restraints excluded: chain E residue 693 SER Chi-restraints excluded: chain E residue 697 THR Chi-restraints excluded: chain E residue 764 VAL Chi-restraints excluded: chain E residue 879 MET Chi-restraints excluded: chain F residue 407 LEU Chi-restraints excluded: chain F residue 508 SER Chi-restraints excluded: chain F residue 510 LEU Chi-restraints excluded: chain F residue 555 VAL Chi-restraints excluded: chain F residue 743 GLN Chi-restraints excluded: chain F residue 771 THR Chi-restraints excluded: chain F residue 809 VAL Chi-restraints excluded: chain F residue 859 THR Chi-restraints excluded: chain F residue 927 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 20 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 238 optimal weight: 0.0370 chunk 128 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 192 optimal weight: 2.9990 chunk 296 optimal weight: 0.9990 chunk 277 optimal weight: 0.8980 chunk 191 optimal weight: 6.9990 chunk 245 optimal weight: 5.9990 chunk 221 optimal weight: 3.9990 overall best weight: 0.7660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 934 HIS B 477 ASN B 484 GLN B 509 GLN C 451 HIS ** C 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 843 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.196926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.145536 restraints weight = 31173.669| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 2.66 r_work: 0.3581 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.7112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27039 Z= 0.129 Angle : 0.560 8.724 36595 Z= 0.280 Chirality : 0.041 0.166 4182 Planarity : 0.004 0.062 4707 Dihedral : 5.164 59.884 3811 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.89 % Allowed : 17.64 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.14), residues: 3359 helix: 1.36 (0.13), residues: 1608 sheet: -1.43 (0.25), residues: 406 loop : -0.95 (0.16), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 652 TYR 0.018 0.001 TYR B 461 PHE 0.024 0.002 PHE E 547 TRP 0.015 0.001 TRP A 770 HIS 0.003 0.001 HIS D 433 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (27038) covalent geometry : angle 0.56044 / 0.28 (36593) SS BOND : bond 0.00424 / 0.22 ( 1) SS BOND : angle 0.27929 / 0.16 ( 2) hydrogen bonds : bond 0.03337 / 2.21 ( 1219) hydrogen bonds : angle 4.58036 / 3.32 ( 3609) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 340 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 424 ARG cc_start: 0.5910 (ttm170) cc_final: 0.5577 (ttm170) REVERT: A 456 ASN cc_start: 0.6846 (p0) cc_final: 0.6399 (p0) REVERT: A 459 ARG cc_start: 0.6895 (tpt90) cc_final: 0.6569 (tmm160) REVERT: A 503 GLU cc_start: 0.7672 (mm-30) cc_final: 0.6616 (mt-10) REVERT: A 541 ASN cc_start: 0.7428 (m110) cc_final: 0.6966 (m110) REVERT: A 629 ASP cc_start: 0.7383 (t0) cc_final: 0.5780 (p0) REVERT: A 667 LEU cc_start: 0.7517 (OUTLIER) cc_final: 0.7266 (tp) REVERT: B 541 ASN cc_start: 0.8269 (t0) cc_final: 0.8034 (t0) REVERT: B 552 MET cc_start: 0.8267 (ptp) cc_final: 0.7970 (ppp) REVERT: B 583 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7516 (tp30) REVERT: B 609 GLU cc_start: 0.7803 (tm-30) cc_final: 0.7331 (tm-30) REVERT: B 615 GLN cc_start: 0.8038 (mm-40) cc_final: 0.7640 (mp10) REVERT: B 754 GLU cc_start: 0.7029 (mm-30) cc_final: 0.6815 (mm-30) REVERT: B 826 MET cc_start: 0.8781 (OUTLIER) cc_final: 0.8518 (ttt) REVERT: B 869 MET cc_start: 0.9033 (mtp) cc_final: 0.8805 (mtp) REVERT: C 673 TYR cc_start: 0.8804 (m-80) cc_final: 0.8587 (m-80) REVERT: C 801 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7928 (tt0) REVERT: C 882 GLU cc_start: 0.8465 (tp30) cc_final: 0.8149 (tt0) REVERT: C 937 GLU cc_start: 0.8564 (pt0) cc_final: 0.8174 (mt-10) REVERT: D 515 GLN cc_start: 0.8611 (pp30) cc_final: 0.8287 (pm20) REVERT: D 701 LYS cc_start: 0.8189 (ttpp) cc_final: 0.7663 (tttp) REVERT: D 707 SER cc_start: 0.8295 (OUTLIER) cc_final: 0.8064 (p) REVERT: D 884 SER cc_start: 0.8733 (p) cc_final: 0.8478 (p) REVERT: D 922 ASP cc_start: 0.8188 (m-30) cc_final: 0.7905 (m-30) REVERT: E 538 ARG cc_start: 0.7705 (ptp90) cc_final: 0.7083 (ptt90) REVERT: E 582 THR cc_start: 0.7252 (t) cc_final: 0.6962 (m) REVERT: E 697 THR cc_start: 0.7806 (OUTLIER) cc_final: 0.7521 (m) REVERT: E 885 LEU cc_start: 0.8718 (tp) cc_final: 0.8138 (tp) REVERT: F 426 LYS cc_start: 0.6618 (tttt) cc_final: 0.5897 (mttt) REVERT: F 579 LYS cc_start: 0.7406 (ttmm) cc_final: 0.6443 (pttt) REVERT: F 656 ILE cc_start: 0.7234 (mm) cc_final: 0.6831 (mp) REVERT: F 808 GLU cc_start: 0.7713 (pt0) cc_final: 0.7425 (mm-30) REVERT: F 810 MET cc_start: 0.8597 (tpp) cc_final: 0.8345 (ttm) REVERT: F 885 LEU cc_start: 0.8566 (tp) cc_final: 0.8320 (tt) outliers start: 54 outliers final: 40 residues processed: 376 average time/residue: 0.1547 time to fit residues: 96.6678 Evaluate side-chains 363 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 317 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 520 CYS Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 645 ILE Chi-restraints excluded: chain B residue 685 ASP Chi-restraints excluded: chain B residue 756 MET Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 826 MET Chi-restraints excluded: chain B residue 873 VAL Chi-restraints excluded: chain B residue 909 CYS Chi-restraints excluded: chain C residue 625 ASP Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 771 THR Chi-restraints excluded: chain C residue 797 ASP Chi-restraints excluded: chain C residue 801 GLU Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 435 MET Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 566 VAL Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 707 SER Chi-restraints excluded: chain D residue 752 THR Chi-restraints excluded: chain D residue 764 VAL Chi-restraints excluded: chain D residue 771 THR Chi-restraints excluded: chain D residue 776 SER Chi-restraints excluded: chain D residue 827 GLN Chi-restraints excluded: chain D residue 889 ILE Chi-restraints excluded: chain D residue 911 VAL Chi-restraints excluded: chain E residue 693 SER Chi-restraints excluded: chain E residue 697 THR Chi-restraints excluded: chain E residue 764 VAL Chi-restraints excluded: chain E residue 879 MET Chi-restraints excluded: chain E residue 929 GLU Chi-restraints excluded: chain F residue 407 LEU Chi-restraints excluded: chain F residue 508 SER Chi-restraints excluded: chain F residue 510 LEU Chi-restraints excluded: chain F residue 555 VAL Chi-restraints excluded: chain F residue 743 GLN Chi-restraints excluded: chain F residue 771 THR Chi-restraints excluded: chain F residue 809 VAL Chi-restraints excluded: chain F residue 859 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 83 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 106 optimal weight: 0.0970 chunk 78 optimal weight: 4.9990 chunk 5 optimal weight: 7.9990 chunk 240 optimal weight: 10.0000 chunk 239 optimal weight: 0.9990 chunk 164 optimal weight: 0.9990 chunk 275 optimal weight: 0.9990 chunk 198 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 ASN ** B 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 451 HIS ** C 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 843 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 491 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.201541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.151768 restraints weight = 30969.440| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 2.75 r_work: 0.3645 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3489 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.7283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27039 Z= 0.130 Angle : 0.559 8.921 36595 Z= 0.278 Chirality : 0.041 0.189 4182 Planarity : 0.004 0.063 4707 Dihedral : 5.061 58.971 3811 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.96 % Allowed : 18.10 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.14), residues: 3359 helix: 1.39 (0.13), residues: 1612 sheet: -1.27 (0.26), residues: 391 loop : -0.92 (0.16), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG B 652 TYR 0.017 0.001 TYR B 461 PHE 0.023 0.002 PHE E 547 TRP 0.015 0.001 TRP A 770 HIS 0.003 0.001 HIS A 843 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (27038) covalent geometry : angle 0.55930 / 0.28 (36593) SS BOND : bond 0.00420 / 0.22 ( 1) SS BOND : angle 0.25964 / 0.15 ( 2) hydrogen bonds : bond 0.03264 / 2.16 ( 1219) hydrogen bonds : angle 4.56316 / 3.31 ( 3609) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 337 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 424 ARG cc_start: 0.5947 (ttm170) cc_final: 0.5268 (ttm170) REVERT: A 435 MET cc_start: 0.7124 (mmm) cc_final: 0.5486 (mtm) REVERT: A 456 ASN cc_start: 0.6832 (p0) cc_final: 0.6356 (p0) REVERT: A 459 ARG cc_start: 0.6941 (tpt90) cc_final: 0.6568 (tmm160) REVERT: A 503 GLU cc_start: 0.7750 (mm-30) cc_final: 0.6733 (mt-10) REVERT: A 541 ASN cc_start: 0.7413 (m110) cc_final: 0.6928 (m110) REVERT: A 629 ASP cc_start: 0.7278 (t0) cc_final: 0.5714 (p0) REVERT: B 541 ASN cc_start: 0.8313 (t0) cc_final: 0.8068 (t0) REVERT: B 583 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7476 (tp30) REVERT: B 609 GLU cc_start: 0.7815 (tm-30) cc_final: 0.7395 (tm-30) REVERT: B 731 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7513 (mt-10) REVERT: B 754 GLU cc_start: 0.7008 (mm-30) cc_final: 0.6799 (mm-30) REVERT: B 826 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8502 (ttt) REVERT: B 869 MET cc_start: 0.9023 (mtp) cc_final: 0.8806 (mtp) REVERT: C 773 MET cc_start: 0.7897 (OUTLIER) cc_final: 0.7383 (mtm) REVERT: C 801 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7909 (tt0) REVERT: C 882 GLU cc_start: 0.8422 (tp30) cc_final: 0.8151 (tt0) REVERT: C 937 GLU cc_start: 0.8491 (pt0) cc_final: 0.8148 (mt-10) REVERT: D 515 GLN cc_start: 0.8560 (pp30) cc_final: 0.8295 (pm20) REVERT: D 701 LYS cc_start: 0.8198 (ttpp) cc_final: 0.7692 (tttp) REVERT: D 707 SER cc_start: 0.8327 (OUTLIER) cc_final: 0.8111 (p) REVERT: D 743 GLN cc_start: 0.7673 (mt0) cc_final: 0.7216 (mm-40) REVERT: D 922 ASP cc_start: 0.8182 (m-30) cc_final: 0.7890 (m-30) REVERT: E 505 ILE cc_start: 0.8515 (mt) cc_final: 0.8310 (mp) REVERT: E 538 ARG cc_start: 0.7653 (ptp90) cc_final: 0.7046 (ptt90) REVERT: E 582 THR cc_start: 0.7237 (t) cc_final: 0.6991 (m) REVERT: E 697 THR cc_start: 0.7835 (OUTLIER) cc_final: 0.7548 (m) REVERT: E 885 LEU cc_start: 0.8683 (tp) cc_final: 0.8073 (tp) REVERT: F 426 LYS cc_start: 0.6567 (tttt) cc_final: 0.5816 (mtmt) REVERT: F 579 LYS cc_start: 0.7397 (ttmm) cc_final: 0.6411 (pttt) REVERT: F 656 ILE cc_start: 0.7289 (mm) cc_final: 0.6901 (mp) REVERT: F 810 MET cc_start: 0.8574 (tpp) cc_final: 0.8313 (ttm) REVERT: F 885 LEU cc_start: 0.8540 (tp) cc_final: 0.8299 (tt) outliers start: 56 outliers final: 42 residues processed: 373 average time/residue: 0.1650 time to fit residues: 102.1415 Evaluate side-chains 371 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 323 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 520 CYS Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 645 ILE Chi-restraints excluded: chain B residue 756 MET Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 826 MET Chi-restraints excluded: chain B residue 873 VAL Chi-restraints excluded: chain B residue 909 CYS Chi-restraints excluded: chain C residue 576 CYS Chi-restraints excluded: chain C residue 625 ASP Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain C residue 771 THR Chi-restraints excluded: chain C residue 773 MET Chi-restraints excluded: chain C residue 777 THR Chi-restraints excluded: chain C residue 797 ASP Chi-restraints excluded: chain C residue 801 GLU Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 435 MET Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 566 VAL Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 707 SER Chi-restraints excluded: chain D residue 752 THR Chi-restraints excluded: chain D residue 764 VAL Chi-restraints excluded: chain D residue 771 THR Chi-restraints excluded: chain D residue 776 SER Chi-restraints excluded: chain D residue 827 GLN Chi-restraints excluded: chain D residue 889 ILE Chi-restraints excluded: chain E residue 693 SER Chi-restraints excluded: chain E residue 697 THR Chi-restraints excluded: chain E residue 764 VAL Chi-restraints excluded: chain E residue 879 MET Chi-restraints excluded: chain E residue 929 GLU Chi-restraints excluded: chain F residue 407 LEU Chi-restraints excluded: chain F residue 508 SER Chi-restraints excluded: chain F residue 510 LEU Chi-restraints excluded: chain F residue 555 VAL Chi-restraints excluded: chain F residue 743 GLN Chi-restraints excluded: chain F residue 771 THR Chi-restraints excluded: chain F residue 809 VAL Chi-restraints excluded: chain F residue 859 THR Chi-restraints excluded: chain F residue 927 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 254 optimal weight: 0.3980 chunk 22 optimal weight: 20.0000 chunk 269 optimal weight: 3.9990 chunk 147 optimal weight: 0.0980 chunk 309 optimal weight: 9.9990 chunk 190 optimal weight: 0.9980 chunk 186 optimal weight: 0.1980 chunk 41 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 145 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 ASN B 832 ASN C 451 HIS ** C 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 843 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.203040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.153368 restraints weight = 30874.746| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 2.89 r_work: 0.3647 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3499 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.7397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 27039 Z= 0.112 Angle : 0.553 9.175 36595 Z= 0.274 Chirality : 0.040 0.206 4182 Planarity : 0.004 0.061 4707 Dihedral : 4.946 57.715 3811 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.75 % Allowed : 18.55 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.14), residues: 3359 helix: 1.47 (0.13), residues: 1614 sheet: -1.14 (0.25), residues: 401 loop : -0.89 (0.16), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 652 TYR 0.019 0.001 TYR B 461 PHE 0.024 0.002 PHE E 545 TRP 0.014 0.001 TRP A 770 HIS 0.003 0.001 HIS E 433 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (27038) covalent geometry : angle 0.55311 / 0.27 (36593) SS BOND : bond 0.00291 / 0.15 ( 1) SS BOND : angle 0.35712 / 0.20 ( 2) hydrogen bonds : bond 0.03159 / 2.09 ( 1219) hydrogen bonds : angle 4.50051 / 3.27 ( 3609) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6718 Ramachandran restraints generated. 3359 Oldfield, 0 Emsley, 3359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 352 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 424 ARG cc_start: 0.5758 (ttm170) cc_final: 0.5461 (ttm170) REVERT: A 435 MET cc_start: 0.7052 (mmm) cc_final: 0.5463 (mtm) REVERT: A 456 ASN cc_start: 0.6812 (p0) cc_final: 0.6335 (p0) REVERT: A 459 ARG cc_start: 0.6932 (tpt90) cc_final: 0.6572 (tmm160) REVERT: A 503 GLU cc_start: 0.7724 (mm-30) cc_final: 0.6728 (mt-10) REVERT: A 541 ASN cc_start: 0.7452 (m110) cc_final: 0.7030 (m110) REVERT: A 629 ASP cc_start: 0.7132 (t0) cc_final: 0.5641 (p0) REVERT: B 488 GLU cc_start: 0.8152 (tt0) cc_final: 0.7817 (mt-10) REVERT: B 489 GLU cc_start: 0.8949 (tm-30) cc_final: 0.8345 (tm-30) REVERT: B 541 ASN cc_start: 0.8318 (t0) cc_final: 0.8066 (t0) REVERT: B 583 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7483 (tp30) REVERT: B 609 GLU cc_start: 0.7779 (tm-30) cc_final: 0.7425 (tm-30) REVERT: B 731 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7577 (mt-10) REVERT: B 826 MET cc_start: 0.8716 (OUTLIER) cc_final: 0.8482 (ttt) REVERT: B 837 THR cc_start: 0.8654 (m) cc_final: 0.8445 (p) REVERT: B 869 MET cc_start: 0.9015 (mtp) cc_final: 0.8790 (mtp) REVERT: B 885 LEU cc_start: 0.8762 (tp) cc_final: 0.8560 (tp) REVERT: C 801 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7904 (tt0) REVERT: C 882 GLU cc_start: 0.8378 (tp30) cc_final: 0.8131 (tt0) REVERT: C 915 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7387 (tp30) REVERT: C 937 GLU cc_start: 0.8527 (pt0) cc_final: 0.8193 (mt-10) REVERT: D 515 GLN cc_start: 0.8488 (pp30) cc_final: 0.8279 (pm20) REVERT: D 701 LYS cc_start: 0.8210 (ttpp) cc_final: 0.7441 (tttp) REVERT: D 705 ARG cc_start: 0.7237 (ttp80) cc_final: 0.6712 (mmm160) REVERT: D 743 GLN cc_start: 0.7656 (mt0) cc_final: 0.7251 (mm-40) REVERT: D 922 ASP cc_start: 0.8286 (m-30) cc_final: 0.7827 (t0) REVERT: E 505 ILE cc_start: 0.8570 (mt) cc_final: 0.8317 (mp) REVERT: E 538 ARG cc_start: 0.7674 (ptp90) cc_final: 0.7077 (ptt90) REVERT: E 582 THR cc_start: 0.7193 (t) cc_final: 0.6915 (m) REVERT: E 697 THR cc_start: 0.7846 (OUTLIER) cc_final: 0.7553 (m) REVERT: E 885 LEU cc_start: 0.8627 (tp) cc_final: 0.7998 (tp) REVERT: F 426 LYS cc_start: 0.6478 (tttt) cc_final: 0.5754 (mtmt) REVERT: F 656 ILE cc_start: 0.7321 (mm) cc_final: 0.6927 (mp) REVERT: F 885 LEU cc_start: 0.8466 (tp) cc_final: 0.8240 (tt) outliers start: 50 outliers final: 36 residues processed: 382 average time/residue: 0.1638 time to fit residues: 102.6001 Evaluate side-chains 367 residues out of total 2877 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 327 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 ASN Chi-restraints excluded: chain A residue 520 CYS Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 515 GLN Chi-restraints excluded: chain B residue 583 GLU Chi-restraints excluded: chain B residue 756 MET Chi-restraints excluded: chain B residue 764 VAL Chi-restraints excluded: chain B residue 826 MET Chi-restraints excluded: chain B residue 832 ASN Chi-restraints excluded: chain B residue 873 VAL Chi-restraints excluded: chain B residue 909 CYS Chi-restraints excluded: chain C residue 576 CYS Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain C residue 771 THR Chi-restraints excluded: chain C residue 777 THR Chi-restraints excluded: chain C residue 797 ASP Chi-restraints excluded: chain C residue 801 GLU Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 435 MET Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 566 VAL Chi-restraints excluded: chain D residue 764 VAL Chi-restraints excluded: chain D residue 771 THR Chi-restraints excluded: chain D residue 776 SER Chi-restraints excluded: chain D residue 827 GLN Chi-restraints excluded: chain E residue 693 SER Chi-restraints excluded: chain E residue 697 THR Chi-restraints excluded: chain E residue 764 VAL Chi-restraints excluded: chain E residue 879 MET Chi-restraints excluded: chain F residue 407 LEU Chi-restraints excluded: chain F residue 508 SER Chi-restraints excluded: chain F residue 510 LEU Chi-restraints excluded: chain F residue 555 VAL Chi-restraints excluded: chain F residue 743 GLN Chi-restraints excluded: chain F residue 771 THR Chi-restraints excluded: chain F residue 809 VAL Chi-restraints excluded: chain F residue 859 THR Chi-restraints excluded: chain F residue 927 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 337 random chunks: chunk 138 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 315 optimal weight: 6.9990 chunk 290 optimal weight: 4.9990 chunk 307 optimal weight: 8.9990 chunk 39 optimal weight: 4.9990 chunk 223 optimal weight: 0.9990 chunk 256 optimal weight: 0.4980 chunk 22 optimal weight: 20.0000 chunk 156 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 477 ASN B 832 ASN C 451 HIS ** C 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 843 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.192206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.141568 restraints weight = 31242.190| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 2.55 r_work: 0.3491 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.7724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 27039 Z= 0.229 Angle : 0.643 12.915 36595 Z= 0.320 Chirality : 0.044 0.207 4182 Planarity : 0.005 0.064 4707 Dihedral : 5.258 59.105 3811 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.96 % Allowed : 18.63 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.14), residues: 3359 helix: 1.31 (0.13), residues: 1600 sheet: -1.23 (0.25), residues: 408 loop : -0.97 (0.16), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 652 TYR 0.019 0.002 TYR C 757 PHE 0.036 0.002 PHE E 521 TRP 0.015 0.001 TRP A 770 HIS 0.009 0.001 HIS A 843 Details of bonding type rmsd/Z covalent geometry : bond 0.00570 / 0.23 (27038) covalent geometry : angle 0.64343 / 0.32 (36593) SS BOND : bond 0.00860 / 0.45 ( 1) SS BOND : angle 0.26941 / 0.14 ( 2) hydrogen bonds : bond 0.03568 / 2.37 ( 1219) hydrogen bonds : angle 4.65546 / 3.36 ( 3609) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7205.21 seconds wall clock time: 124 minutes 31.91 seconds (7471.91 seconds total)