Starting phenix.real_space_refine on Sun Sep 13 18:35:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y5o_72515/09_2026/9y5o_72515.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y5o_72515/09_2026/9y5o_72515.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9y5o_72515/09_2026/9y5o_72515.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y5o_72515/09_2026/9y5o_72515.map" model { file = "/net/cci-nas-00/data/ceres_data/9y5o_72515/09_2026/9y5o_72515.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y5o_72515/09_2026/9y5o_72515.cif" } resolution = 3.47 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= 0.036 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 1 5.21 5 S 117 5.16 5 C 15420 2.51 5 N 4174 2.21 5 O 4618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24343 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 4028 Classifications: {'peptide': 516} Link IDs: {'PTRANS': 24, 'TRANS': 491} Chain breaks: 2 Chain: "B" Number of atoms: 4091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4091 Classifications: {'peptide': 526} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 24, 'TRANS': 501} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 4099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4099 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 24, 'TRANS': 502} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 4047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 4047 Classifications: {'peptide': 520} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 24, 'TRANS': 495} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "E" Number of atoms: 4039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 519, 4039 Classifications: {'peptide': 519} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 24, 'TRANS': 494} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 3872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 3872 Classifications: {'peptide': 496} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 23, 'TRANS': 472} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.07, per 1000 atoms: 0.25 Number of scatterers: 24343 At special positions: 0 Unit cell: (121.9, 138, 134.55, 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 117 16.00 P 13 15.00 Mg 1 11.99 O 4618 8.00 N 4174 7.00 C 15420 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.17 Conformation dependent library (CDL) restraints added in 1.1 seconds 6140 Ramachandran restraints generated. 3070 Oldfield, 0 Emsley, 3070 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5778 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 27 sheets defined 53.3% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 417 through 428 removed outlier: 4.356A pdb=" N PHE A 421 " --> pdb=" O ILE A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 448 removed outlier: 4.380A pdb=" N VAL A 437 " --> pdb=" O HIS A 433 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU A 440 " --> pdb=" O ASP A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 467 removed outlier: 3.590A pdb=" N ASN A 456 " --> pdb=" O SER A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 491 Processing helix chain 'A' and resid 494 through 512 Processing helix chain 'A' and resid 528 through 541 Processing helix chain 'A' and resid 555 through 560 Processing helix chain 'A' and resid 571 through 581 removed outlier: 3.572A pdb=" N GLN A 575 " --> pdb=" O GLY A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 612 Processing helix chain 'A' and resid 614 through 619 removed outlier: 3.511A pdb=" N ALA A 617 " --> pdb=" O GLU A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 653 removed outlier: 3.580A pdb=" N MET A 653 " --> pdb=" O LEU A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 683 removed outlier: 3.718A pdb=" N ARG A 672 " --> pdb=" O ALA A 668 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N VAL A 675 " --> pdb=" O GLU A 671 " (cutoff:3.500A) Proline residue: A 676 - end of helix Processing helix chain 'A' and resid 692 through 702 Processing helix chain 'A' and resid 709 through 729 Processing helix chain 'A' and resid 741 through 746 removed outlier: 4.102A pdb=" N PHE A 745 " --> pdb=" O ASN A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 829 Processing helix chain 'A' and resid 833 through 838 Processing helix chain 'A' and resid 853 through 855 No H-bonds generated for 'chain 'A' and resid 853 through 855' Processing helix chain 'A' and resid 856 through 870 Processing helix chain 'A' and resid 894 through 905 Processing helix chain 'A' and resid 916 through 922 Processing helix chain 'A' and resid 938 through 947 removed outlier: 3.971A pdb=" N ILE A 942 " --> pdb=" O HIS A 938 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 428 removed outlier: 4.602A pdb=" N ARG B 424 " --> pdb=" O LYS B 420 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU B 425 " --> pdb=" O PHE B 421 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU B 427 " --> pdb=" O GLU B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 448 Processing helix chain 'B' and resid 452 through 468 Processing helix chain 'B' and resid 479 through 491 removed outlier: 3.593A pdb=" N ASP B 490 " --> pdb=" O VAL B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 511 Processing helix chain 'B' and resid 530 through 541 removed outlier: 3.548A pdb=" N ARG B 534 " --> pdb=" O THR B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 560 Processing helix chain 'B' and resid 571 through 581 Processing helix chain 'B' and resid 592 through 595 Processing helix chain 'B' and resid 603 through 611 removed outlier: 4.397A pdb=" N GLU B 609 " --> pdb=" O SER B 605 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU B 610 " --> pdb=" O ALA B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 619 Processing helix chain 'B' and resid 646 through 653 removed outlier: 3.880A pdb=" N MET B 653 " --> pdb=" O LEU B 649 " (cutoff:3.500A) 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 741 through 747 removed outlier: 3.828A pdb=" N PHE B 745 " --> pdb=" O ASN B 741 " (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 853 through 855 No H-bonds generated for 'chain 'B' and resid 853 through 855' Processing helix chain 'B' and resid 856 through 870 Processing helix chain 'B' and resid 894 through 905 Processing helix chain 'B' and resid 916 through 921 Processing helix chain 'B' and resid 938 through 947 removed outlier: 3.954A pdb=" N ILE B 942 " --> pdb=" O HIS B 938 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 426 Processing helix chain 'C' and resid 431 through 448 removed outlier: 3.736A pdb=" N LEU C 447 " --> pdb=" O SER C 443 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU C 448 " --> pdb=" O LYS C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 468 Processing helix chain 'C' and resid 479 through 491 Processing helix chain 'C' and resid 494 through 512 Processing helix chain 'C' and resid 530 through 541 removed outlier: 3.583A pdb=" N ARG C 534 " --> pdb=" O THR C 530 " (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 591 through 595 Processing helix chain 'C' and resid 602 through 612 Processing helix chain 'C' and resid 614 through 619 removed outlier: 3.532A pdb=" N ALA C 617 " --> pdb=" O GLU C 614 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE C 619 " --> pdb=" O ASN C 616 " (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 704 Processing helix chain 'C' and resid 709 through 729 Processing helix chain 'C' and resid 741 through 747 removed outlier: 4.032A pdb=" N PHE C 745 " --> pdb=" O ASN C 741 " (cutoff:3.500A) Processing helix chain 'C' and resid 807 through 829 Processing helix chain 'C' and resid 833 through 838 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 905 Processing helix chain 'C' and resid 916 through 921 Processing helix chain 'C' and resid 938 through 947 removed outlier: 4.029A pdb=" N ILE C 942 " --> pdb=" O HIS C 938 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 427 removed outlier: 4.120A pdb=" N GLU D 427 " --> pdb=" O GLU D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 448 removed outlier: 3.780A pdb=" N LEU D 448 " --> pdb=" O LYS D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 468 removed outlier: 3.956A pdb=" N ILE D 468 " --> pdb=" O TRP D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 479 through 491 Processing helix chain 'D' and resid 494 through 512 Processing helix chain 'D' and resid 528 through 541 Processing helix chain 'D' and resid 554 through 560 removed outlier: 4.029A pdb=" N ILE D 558 " --> pdb=" O ASP D 554 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 581 removed outlier: 4.286A pdb=" N ILE D 574 " --> pdb=" O PRO D 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 595 Processing helix chain 'D' and resid 604 through 612 removed outlier: 4.118A pdb=" N LEU D 608 " --> pdb=" O SER D 604 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU D 609 " --> pdb=" O SER D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 612 through 617 Processing helix chain 'D' and resid 641 through 645 removed outlier: 4.060A pdb=" N THR D 644 " --> pdb=" O VAL D 641 " (cutoff:3.500A) Processing helix chain 'D' and resid 646 through 653 removed outlier: 3.822A pdb=" N ARG D 652 " --> pdb=" O PRO D 648 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N MET D 653 " --> pdb=" O LEU D 649 " (cutoff:3.500A) 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 730 Processing helix chain 'D' and resid 741 through 747 removed outlier: 3.832A pdb=" N PHE D 745 " --> pdb=" O ASN D 741 " (cutoff:3.500A) Processing helix chain 'D' and resid 807 through 829 Processing helix chain 'D' and resid 833 through 838 Processing helix chain 'D' and resid 853 through 855 No H-bonds generated for 'chain 'D' and resid 853 through 855' Processing helix chain 'D' and resid 856 through 870 Processing helix chain 'D' and resid 894 through 905 Processing helix chain 'D' and resid 916 through 921 Processing helix chain 'D' and resid 924 through 929 removed outlier: 3.597A pdb=" N THR D 928 " --> pdb=" O ALA D 924 " (cutoff:3.500A) Processing helix chain 'D' and resid 938 through 947 removed outlier: 4.033A pdb=" N ILE D 942 " --> pdb=" O HIS D 938 " (cutoff:3.500A) Processing helix chain 'E' and resid 420 through 427 removed outlier: 3.788A pdb=" N GLU E 427 " --> pdb=" O GLU E 423 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 448 Processing helix chain 'E' and resid 452 through 468 removed outlier: 4.102A pdb=" N ILE E 468 " --> pdb=" O TRP E 464 " (cutoff:3.500A) Processing helix chain 'E' and resid 479 through 491 Processing helix chain 'E' and resid 494 through 512 Processing helix chain 'E' and resid 528 through 541 removed outlier: 3.865A pdb=" N ALA E 533 " --> pdb=" O LYS E 529 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG E 534 " --> pdb=" O THR E 530 " (cutoff:3.500A) Processing helix chain 'E' and resid 555 through 560 Processing helix chain 'E' and resid 572 through 581 Processing helix chain 'E' and resid 591 through 595 removed outlier: 3.520A pdb=" N LYS E 594 " --> pdb=" O GLU E 591 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ILE E 595 " --> pdb=" O VAL E 592 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 591 through 595' Processing helix chain 'E' and resid 603 through 611 Processing helix chain 'E' and resid 612 through 617 removed outlier: 4.304A 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: 4.552A 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 702 Processing helix chain 'E' and resid 709 through 729 Processing helix chain 'E' and resid 741 through 747 removed outlier: 3.938A pdb=" N PHE E 745 " --> pdb=" O ASN E 741 " (cutoff:3.500A) Processing helix chain 'E' and resid 807 through 829 Processing helix chain 'E' and resid 833 through 838 removed outlier: 3.524A pdb=" N THR E 837 " --> pdb=" O ASP E 833 " (cutoff:3.500A) Processing helix chain 'E' and resid 856 through 870 Processing helix chain 'E' and resid 894 through 906 Processing helix chain 'E' and resid 916 through 921 removed outlier: 3.540A pdb=" N TYR E 921 " --> pdb=" O LYS E 917 " (cutoff:3.500A) Processing helix chain 'E' and resid 924 through 929 removed outlier: 3.663A pdb=" N THR E 928 " --> pdb=" O ALA E 924 " (cutoff:3.500A) Processing helix chain 'E' and resid 938 through 947 removed outlier: 3.939A pdb=" N ILE E 942 " --> pdb=" O HIS E 938 " (cutoff:3.500A) Processing helix chain 'F' and resid 423 through 428 removed outlier: 4.250A pdb=" N GLU F 427 " --> pdb=" O GLU F 423 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LEU F 428 " --> pdb=" O ARG F 424 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 423 through 428' Processing helix chain 'F' and resid 431 through 448 Processing helix chain 'F' and resid 452 through 468 removed outlier: 3.855A pdb=" N VAL F 457 " --> pdb=" O SER F 453 " (cutoff:3.500A) Processing helix chain 'F' and resid 479 through 491 removed outlier: 3.577A 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 removed outlier: 3.662A pdb=" N ALA F 533 " --> pdb=" O LYS F 529 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG F 534 " --> pdb=" O THR F 530 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 581 Processing helix chain 'F' and resid 591 through 595 removed outlier: 3.541A pdb=" N ILE F 595 " --> pdb=" O VAL F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 603 through 612 Processing helix chain 'F' and resid 612 through 617 removed outlier: 3.836A pdb=" N ALA F 617 " --> pdb=" O PRO F 613 " (cutoff:3.500A) Processing helix chain 'F' and resid 629 through 632 removed outlier: 3.894A pdb=" N LYS F 632 " --> pdb=" O ASP F 629 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 629 through 632' Processing helix chain 'F' and resid 646 through 653 Processing helix chain 'F' and resid 662 through 673 Processing helix chain 'F' and resid 673 through 683 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 747 removed outlier: 4.312A pdb=" N GLN F 743 " --> pdb=" O PRO F 739 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N ASP F 744 " --> pdb=" O GLU F 740 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N PHE F 745 " --> pdb=" O ASN F 741 " (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 853 through 855 No H-bonds generated for 'chain 'F' and resid 853 through 855' Processing helix chain 'F' and resid 856 through 870 Processing helix chain 'F' and resid 894 through 905 Processing helix chain 'F' and resid 916 through 922 removed outlier: 3.531A pdb=" N ASP F 922 " --> pdb=" O LYS F 918 " (cutoff:3.500A) Processing helix chain 'F' and resid 924 through 929 removed outlier: 3.557A pdb=" N THR F 928 " --> pdb=" O ALA F 924 " (cutoff:3.500A) Processing helix chain 'F' and resid 938 through 947 removed outlier: 3.978A pdb=" N ILE F 942 " --> pdb=" O HIS F 938 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 544 through 548 removed outlier: 8.090A pdb=" N ILE A 656 " --> pdb=" O ILE A 518 " (cutoff:3.500A) removed outlier: 6.087A 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 691 removed outlier: 6.870A pdb=" N LYS A 690 " --> pdb=" O VAL A 737 " (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 770 removed outlier: 6.333A pdb=" N SER A 799 " --> pdb=" O ILE A 840 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N LEU A 842 " --> pdb=" O SER A 799 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N GLU A 801 " --> pdb=" O LEU A 842 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 877 through 879 Processing sheet with id=AA5, first strand: chain 'A' and resid 882 through 883 Processing sheet with id=AA6, first strand: chain 'B' and resid 544 through 548 removed outlier: 3.666A pdb=" N ASP B 590 " --> pdb=" O PHE B 547 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE B 518 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N ILE B 656 " --> pdb=" O ILE B 518 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N CYS B 520 " --> pdb=" O ILE B 656 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 689 through 690 removed outlier: 3.542A pdb=" N LYS B 690 " --> pdb=" O VAL B 735 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 799 through 803 removed outlier: 6.043A pdb=" N SER B 799 " --> pdb=" O ILE B 840 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N LEU B 842 " --> pdb=" O SER B 799 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N GLU B 801 " --> pdb=" O LEU B 842 " (cutoff:3.500A) removed outlier: 10.450A pdb=" N VAL B 764 " --> pdb=" O LEU B 877 " (cutoff:3.500A) removed outlier: 10.353A pdb=" N MET B 879 " --> pdb=" O VAL B 764 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N MET B 766 " --> pdb=" O MET B 879 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 882 through 883 removed outlier: 3.618A pdb=" N GLU B 882 " --> pdb=" O LEU B 890 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 544 through 548 removed outlier: 3.933A pdb=" N GLU C 654 " --> pdb=" O ILE C 518 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 764 through 771 removed outlier: 6.070A pdb=" N SER C 799 " --> pdb=" O ILE C 840 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N LEU C 842 " --> pdb=" O SER C 799 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N GLU C 801 " --> pdb=" O LEU C 842 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 877 through 879 removed outlier: 6.936A pdb=" N ALA C 878 " --> pdb=" O VAL C 911 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 882 through 883 removed outlier: 3.838A pdb=" N GLU C 882 " --> pdb=" O LEU C 890 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 544 through 548 removed outlier: 4.065A pdb=" N ASP D 590 " --> pdb=" O PHE D 547 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU D 654 " --> pdb=" O ILE D 518 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 689 through 691 removed outlier: 6.930A pdb=" N LYS D 690 " --> pdb=" O VAL D 737 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'D' and resid 764 through 771 removed outlier: 6.090A pdb=" N SER D 799 " --> pdb=" O ILE D 840 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N LEU D 842 " --> pdb=" O SER D 799 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLU D 801 " --> pdb=" O LEU D 842 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 877 through 879 removed outlier: 6.987A pdb=" N ALA D 878 " --> pdb=" O VAL D 911 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 882 through 883 Processing sheet with id=AC1, first strand: chain 'E' and resid 544 through 548 removed outlier: 6.752A pdb=" N PHE E 545 " --> pdb=" O LEU E 588 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ASP E 590 " --> pdb=" O PHE E 545 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N PHE E 547 " --> pdb=" O ASP E 590 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ILE E 518 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N ILE E 656 " --> pdb=" O ILE E 518 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N CYS E 520 " --> pdb=" O ILE E 656 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 689 through 691 removed outlier: 6.801A pdb=" N LYS E 690 " --> pdb=" O VAL E 737 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'E' and resid 764 through 771 removed outlier: 6.257A pdb=" N SER E 799 " --> pdb=" O ILE E 840 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N LEU E 842 " --> pdb=" O SER E 799 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N GLU E 801 " --> pdb=" O LEU E 842 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 877 through 879 removed outlier: 6.914A pdb=" N ALA E 878 " --> pdb=" O VAL E 911 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 882 through 883 Processing sheet with id=AC6, first strand: chain 'F' and resid 544 through 548 removed outlier: 3.803A pdb=" N ASP F 590 " --> pdb=" O PHE F 547 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE F 635 " --> pdb=" O LYS F 517 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 689 through 691 removed outlier: 6.926A pdb=" N LYS F 690 " --> pdb=" O VAL F 737 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'F' and resid 799 through 803 removed outlier: 6.310A pdb=" N SER F 799 " --> pdb=" O ILE F 840 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N LEU F 842 " --> pdb=" O SER F 799 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLU F 801 " --> pdb=" O LEU F 842 " (cutoff:3.500A) removed outlier: 10.265A pdb=" N VAL F 764 " --> pdb=" O LEU F 877 " (cutoff:3.500A) removed outlier: 10.280A pdb=" N MET F 879 " --> pdb=" O VAL F 764 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N MET F 766 " --> pdb=" O MET F 879 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 882 through 883 1200 hydrogen bonds defined for protein. 3540 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: 5.60 Time building geometry restraints manager: 2.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8014 1.34 - 1.46: 3883 1.46 - 1.58: 12675 1.58 - 1.70: 20 1.70 - 1.82: 192 Bond restraints: 24784 Sorted by residual: bond pdb=" N MET C 756 " pdb=" CA MET C 756 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.20e-02 6.94e+03 6.31e+00 bond pdb=" N TYR C 757 " pdb=" CA TYR C 757 " ideal model delta sigma weight residual 1.459 1.488 -0.028 1.27e-02 6.20e+03 4.96e+00 bond pdb=" N ASP C 758 " pdb=" CA ASP C 758 " ideal model delta sigma weight residual 1.459 1.485 -0.025 1.23e-02 6.61e+03 4.29e+00 bond pdb=" N TYR B 461 " pdb=" CA TYR B 461 " ideal model delta sigma weight residual 1.459 1.483 -0.024 1.19e-02 7.06e+03 4.03e+00 bond pdb=" N LYS F 420 " pdb=" CA LYS F 420 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.20e+00 ... (remaining 24779 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 32910 1.80 - 3.60: 547 3.60 - 5.41: 81 5.41 - 7.21: 26 7.21 - 9.01: 2 Bond angle restraints: 33566 Sorted by residual: angle pdb=" C TYR B 757 " pdb=" CA TYR B 757 " pdb=" CB TYR B 757 " ideal model delta sigma weight residual 109.71 100.70 9.01 1.83e+00 2.99e-01 2.42e+01 angle pdb=" N ASP C 758 " pdb=" CA ASP C 758 " pdb=" C ASP C 758 " ideal model delta sigma weight residual 111.36 106.70 4.66 1.09e+00 8.42e-01 1.83e+01 angle pdb=" C TYR C 757 " pdb=" CA TYR C 757 " pdb=" CB TYR C 757 " ideal model delta sigma weight residual 110.79 104.52 6.27 1.63e+00 3.76e-01 1.48e+01 angle pdb=" N VAL C 549 " pdb=" CA VAL C 549 " pdb=" C VAL C 549 " ideal model delta sigma weight residual 113.47 109.84 3.63 1.01e+00 9.80e-01 1.29e+01 angle pdb=" N VAL F 527 " pdb=" CA VAL F 527 " pdb=" C VAL F 527 " ideal model delta sigma weight residual 113.47 110.02 3.45 1.01e+00 9.80e-01 1.17e+01 ... (remaining 33561 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.59: 14041 20.59 - 41.18: 893 41.18 - 61.77: 139 61.77 - 82.36: 35 82.36 - 102.95: 8 Dihedral angle restraints: 15116 sinusoidal: 6156 harmonic: 8960 Sorted by residual: dihedral pdb=" C5' ADP F1000 " pdb=" O5' ADP F1000 " pdb=" PA ADP F1000 " pdb=" O2A ADP F1000 " ideal model delta sinusoidal sigma weight residual -60.00 -162.95 102.95 1 2.00e+01 2.50e-03 2.94e+01 dihedral pdb=" C TYR B 757 " pdb=" N TYR B 757 " pdb=" CA TYR B 757 " pdb=" CB TYR B 757 " ideal model delta harmonic sigma weight residual -122.60 -109.87 -12.73 0 2.50e+00 1.60e-01 2.59e+01 dihedral pdb=" CA ASN A 475 " pdb=" C ASN A 475 " pdb=" N GLU A 476 " pdb=" CA GLU A 476 " ideal model delta harmonic sigma weight residual 180.00 156.18 23.82 0 5.00e+00 4.00e-02 2.27e+01 ... (remaining 15113 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 3425 0.061 - 0.122: 399 0.122 - 0.183: 37 0.183 - 0.244: 2 0.244 - 0.305: 2 Chirality restraints: 3865 Sorted by residual: chirality pdb=" CA TYR B 757 " pdb=" N TYR B 757 " pdb=" C TYR B 757 " pdb=" CB TYR B 757 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" C2' ATP B1000 " pdb=" C1' ATP B1000 " pdb=" C3' ATP B1000 " pdb=" O2' ATP B1000 " both_signs ideal model delta sigma weight residual False -2.68 -2.98 0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" C3' ATP B1000 " pdb=" C2' ATP B1000 " pdb=" C4' ATP B1000 " pdb=" O3' ATP B1000 " both_signs ideal model delta sigma weight residual False -2.63 -2.88 0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 3862 not shown) Planarity restraints: 4287 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL C 675 " 0.031 5.00e-02 4.00e+02 4.61e-02 3.41e+00 pdb=" N PRO C 676 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO C 676 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 676 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL F 430 " 0.030 5.00e-02 4.00e+02 4.51e-02 3.26e+00 pdb=" N PRO F 431 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO F 431 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO F 431 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 670 " -0.009 2.00e-02 2.50e+03 1.76e-02 3.08e+00 pdb=" C ALA B 670 " 0.030 2.00e-02 2.50e+03 pdb=" O ALA B 670 " -0.011 2.00e-02 2.50e+03 pdb=" N GLU B 671 " -0.010 2.00e-02 2.50e+03 ... (remaining 4284 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 122 2.51 - 3.11: 18969 3.11 - 3.71: 37315 3.71 - 4.30: 52188 4.30 - 4.90: 88220 Nonbonded interactions: 196814 Sorted by model distance: nonbonded pdb=" O3G ATP B1000 " pdb="MG MG B1001 " model vdw 1.915 2.170 nonbonded pdb=" O1G ATP B1000 " pdb="MG MG B1001 " model vdw 2.031 2.170 nonbonded pdb=" N GLU C 897 " pdb=" OE1 GLU C 897 " model vdw 2.194 3.120 nonbonded pdb=" OD2 ASP D 685 " pdb=" NZ LYS D 688 " model vdw 2.201 3.120 nonbonded pdb=" O ASP C 833 " pdb=" OD1 ASP C 833 " model vdw 2.203 3.040 ... (remaining 196809 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 420 and (name N or name CA or name C or name O or name CB \ )) or resid 421 through 550 or resid 572 through 631 or (resid 632 and (name N \ or name CA or name 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 throug \ h 689 or (resid 690 and (name N or name CA or name C or name O or name CB )) or \ resid 691 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 796 through 947)) selection = (chain 'B' and ((resid 420 and (name N or name CA or name C or name O or name CB \ )) or resid 421 through 550 or resid 572 through 593 or resid 603 through 631 o \ r (resid 632 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 33 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 through 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 796 thro \ ugh 947)) selection = (chain 'C' and ((resid 420 and (name N or name CA or name C or name O or name CB \ )) or resid 421 through 550 or resid 572 through 593 or resid 603 through 631 o \ r (resid 632 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 33 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 through 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 796 thro \ ugh 947)) selection = (chain 'D' and ((resid 420 and (name N or name CA or name C or name O or name CB \ )) or resid 421 through 550 or resid 572 through 593 or resid 603 through 631 o \ r (resid 632 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 33 through 685 or (resid 686 and (name N or name CA or name C or name O or name \ CB )) or resid 687 through 947)) selection = (chain 'E' and (resid 420 through 550 or resid 572 through 593 or resid 603 thro \ ugh 631 or (resid 632 and (name N or name CA or name C or name O or name CB )) o \ r resid 633 through 689 or (resid 690 and (name N or name CA or name C or name O \ or name CB )) or resid 691 through 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 796 through 947 \ )) selection = (chain 'F' and ((resid 420 and (name N or name CA or name C or name O or name CB \ )) or resid 421 through 593 or resid 603 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 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 796 through 947)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.890 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: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 24.480 Find NCS groups from input model: 0.740 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:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 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 : 0.003 0.063 24784 Z= 0.143 Angle : 0.612 9.009 33566 Z= 0.334 Chirality : 0.041 0.305 3865 Planarity : 0.004 0.046 4287 Dihedral : 13.939 102.950 9338 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.30 % Allowed : 9.06 % Favored : 90.64 % Cbeta Deviations : 0.03 % 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: 0.81 (0.15), residues: 3070 helix: 1.28 (0.14), residues: 1386 sheet: 1.17 (0.25), residues: 428 loop : -0.46 (0.18), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 546 TYR 0.011 0.001 TYR F 623 PHE 0.026 0.001 PHE A 455 TRP 0.016 0.001 TRP E 470 HIS 0.006 0.001 HIS A 491 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 (24784) covalent geometry : angle 0.61227 / 0.33 (33566) hydrogen bonds : bond 0.14906 / 10.07 ( 1200) hydrogen bonds : angle 6.65898 / 4.71 ( 3540) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6140 Ramachandran restraints generated. 3070 Oldfield, 0 Emsley, 3070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6140 Ramachandran restraints generated. 3070 Oldfield, 0 Emsley, 3070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 223 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 635 PHE cc_start: 0.8358 (m-80) cc_final: 0.8139 (m-80) REVERT: A 651 ASP cc_start: 0.7673 (t0) cc_final: 0.7347 (t0) REVERT: A 653 MET cc_start: 0.7426 (mtt) cc_final: 0.6893 (mtt) REVERT: A 698 LEU cc_start: 0.8854 (mt) cc_final: 0.8631 (mt) REVERT: B 826 MET cc_start: 0.8868 (tmm) cc_final: 0.8543 (tmm) REVERT: C 563 ARG cc_start: 0.8014 (mtp180) cc_final: 0.7708 (mtm-85) REVERT: C 573 ILE cc_start: 0.9323 (mm) cc_final: 0.9108 (mm) REVERT: C 594 LYS cc_start: 0.8653 (mptt) cc_final: 0.8331 (ttmm) REVERT: C 602 ASP cc_start: 0.7684 (t0) cc_final: 0.7347 (t0) REVERT: C 879 MET cc_start: 0.8954 (ptp) cc_final: 0.8619 (ptm) REVERT: D 459 ARG cc_start: 0.7956 (ptp-170) cc_final: 0.7508 (ptp-170) REVERT: D 461 TYR cc_start: 0.8448 (t80) cc_final: 0.7928 (t80) REVERT: D 577 LEU cc_start: 0.8856 (mm) cc_final: 0.8327 (mm) REVERT: E 591 GLU cc_start: 0.8178 (tp30) cc_final: 0.7611 (tp30) REVERT: E 609 GLU cc_start: 0.8416 (tt0) cc_final: 0.8141 (tp30) REVERT: E 655 MET cc_start: 0.8500 (mmm) cc_final: 0.8073 (mmt) REVERT: F 640 ASN cc_start: 0.8472 (t0) cc_final: 0.8060 (t0) outliers start: 8 outliers final: 3 residues processed: 229 average time/residue: 0.1707 time to fit residues: 62.2702 Evaluate side-chains 201 residues out of total 2648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 198 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 618 ASN Chi-restraints excluded: chain E residue 681 LEU Chi-restraints excluded: chain F residue 651 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 40.0000 chunk 248 optimal weight: 0.4980 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 0.8980 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 876 ASN B 460 ASN C 934 HIS D 561 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.110105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.076625 restraints weight = 54270.099| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 3.01 r_work: 0.2948 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 24784 Z= 0.265 Angle : 0.704 9.295 33566 Z= 0.355 Chirality : 0.046 0.311 3865 Planarity : 0.005 0.053 4287 Dihedral : 7.196 104.726 3446 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.25 % Allowed : 9.67 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.72 (0.15), residues: 3070 helix: 1.17 (0.13), residues: 1401 sheet: 1.11 (0.25), residues: 410 loop : -0.46 (0.17), residues: 1259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 546 TYR 0.016 0.002 TYR C 544 PHE 0.020 0.002 PHE F 545 TRP 0.012 0.001 TRP A 470 HIS 0.007 0.001 HIS A 433 Details of bonding type rmsd/Z covalent geometry : bond 0.00635 / 0.26 (24784) covalent geometry : angle 0.70444 / 0.36 (33566) hydrogen bonds : bond 0.04935 / 3.36 ( 1200) hydrogen bonds : angle 5.40351 / 3.82 ( 3540) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6140 Ramachandran restraints generated. 3070 Oldfield, 0 Emsley, 3070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6140 Ramachandran restraints generated. 3070 Oldfield, 0 Emsley, 3070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 211 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 435 MET cc_start: 0.3799 (ppp) cc_final: 0.3264 (mmm) REVERT: A 487 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8365 (mp) REVERT: A 635 PHE cc_start: 0.8693 (m-80) cc_final: 0.8486 (m-80) REVERT: A 651 ASP cc_start: 0.7789 (t0) cc_final: 0.7535 (t0) REVERT: B 651 ASP cc_start: 0.8251 (OUTLIER) cc_final: 0.7990 (p0) REVERT: B 771 THR cc_start: 0.8911 (OUTLIER) cc_final: 0.8691 (p) REVERT: C 494 MET cc_start: 0.8418 (mtm) cc_final: 0.8201 (mtm) REVERT: C 569 MET cc_start: 0.8518 (mmp) cc_final: 0.7565 (mtp) REVERT: C 573 ILE cc_start: 0.9475 (mm) cc_final: 0.9212 (mm) REVERT: C 594 LYS cc_start: 0.8589 (mptt) cc_final: 0.8191 (ttmm) REVERT: C 879 MET cc_start: 0.9222 (ptp) cc_final: 0.8959 (ptm) REVERT: D 424 ARG cc_start: 0.9048 (tpp80) cc_final: 0.8430 (tpt90) REVERT: D 459 ARG cc_start: 0.8088 (ptp-170) cc_final: 0.7688 (ptp-170) REVERT: D 461 TYR cc_start: 0.8285 (t80) cc_final: 0.7947 (t80) REVERT: D 465 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8185 (mt) REVERT: D 577 LEU cc_start: 0.8835 (mm) cc_final: 0.8381 (mm) REVERT: E 591 GLU cc_start: 0.8362 (tp30) cc_final: 0.7754 (tp30) REVERT: E 609 GLU cc_start: 0.8656 (tt0) cc_final: 0.8193 (tp30) REVERT: E 655 MET cc_start: 0.8776 (mmm) cc_final: 0.8429 (mmt) REVERT: F 640 ASN cc_start: 0.8624 (t0) cc_final: 0.8123 (t0) outliers start: 33 outliers final: 14 residues processed: 234 average time/residue: 0.1660 time to fit residues: 62.5188 Evaluate side-chains 208 residues out of total 2648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 190 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 876 ASN Chi-restraints excluded: chain B residue 651 ASP Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain B residue 771 THR Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 625 ASP Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 621 ASP Chi-restraints excluded: chain E residue 440 GLU Chi-restraints excluded: chain E residue 552 MET Chi-restraints excluded: chain E residue 561 HIS Chi-restraints excluded: chain E residue 607 LEU Chi-restraints excluded: chain E residue 611 LEU Chi-restraints excluded: chain E residue 626 VAL Chi-restraints excluded: chain E residue 653 MET Chi-restraints excluded: chain F residue 611 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 257 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 297 optimal weight: 4.9990 chunk 274 optimal weight: 4.9990 chunk 211 optimal weight: 9.9990 chunk 116 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 150 optimal weight: 1.9990 chunk 263 optimal weight: 20.0000 chunk 6 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 876 ASN B 460 ASN D 575 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.112043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.078346 restraints weight = 54067.280| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 3.05 r_work: 0.2979 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24784 Z= 0.144 Angle : 0.607 8.690 33566 Z= 0.303 Chirality : 0.042 0.252 3865 Planarity : 0.005 0.058 4287 Dihedral : 6.818 100.191 3440 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.55 % Allowed : 10.35 % Favored : 88.10 % 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: 0.95 (0.15), residues: 3070 helix: 1.41 (0.14), residues: 1401 sheet: 1.23 (0.25), residues: 409 loop : -0.41 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 650 TYR 0.014 0.001 TYR F 623 PHE 0.015 0.001 PHE D 545 TRP 0.032 0.002 TRP E 464 HIS 0.006 0.001 HIS C 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (24784) covalent geometry : angle 0.60711 / 0.30 (33566) hydrogen bonds : bond 0.04188 / 2.84 ( 1200) hydrogen bonds : angle 5.07216 / 3.59 ( 3540) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6140 Ramachandran restraints generated. 3070 Oldfield, 0 Emsley, 3070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6140 Ramachandran restraints generated. 3070 Oldfield, 0 Emsley, 3070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 211 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 435 MET cc_start: 0.3961 (ppp) cc_final: 0.3583 (mmm) REVERT: A 438 VAL cc_start: 0.6608 (OUTLIER) cc_final: 0.6254 (p) REVERT: A 487 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8277 (mp) REVERT: A 635 PHE cc_start: 0.8682 (m-80) cc_final: 0.8470 (m-80) REVERT: A 651 ASP cc_start: 0.7790 (t0) cc_final: 0.7545 (t0) REVERT: B 425 LEU cc_start: 0.8376 (mt) cc_final: 0.8056 (tt) REVERT: B 428 LEU cc_start: 0.6316 (OUTLIER) cc_final: 0.6103 (mp) REVERT: B 651 ASP cc_start: 0.8280 (OUTLIER) cc_final: 0.7967 (p0) REVERT: B 654 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7903 (tm-30) REVERT: B 771 THR cc_start: 0.8865 (OUTLIER) cc_final: 0.8665 (p) REVERT: B 897 GLU cc_start: 0.8424 (mp0) cc_final: 0.7844 (mp0) REVERT: C 563 ARG cc_start: 0.8145 (mtp180) cc_final: 0.7680 (mtm-85) REVERT: C 569 MET cc_start: 0.8406 (mmp) cc_final: 0.7415 (mtm) REVERT: C 573 ILE cc_start: 0.9438 (mm) cc_final: 0.9191 (mm) REVERT: C 594 LYS cc_start: 0.8520 (mptt) cc_final: 0.8171 (ttmm) REVERT: C 879 MET cc_start: 0.9159 (ptp) cc_final: 0.8887 (ptm) REVERT: C 932 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.6995 (tm-30) REVERT: D 424 ARG cc_start: 0.8995 (tpp80) cc_final: 0.8330 (tpt90) REVERT: D 459 ARG cc_start: 0.8106 (ptp-170) cc_final: 0.7700 (ptp-170) REVERT: D 461 TYR cc_start: 0.8290 (t80) cc_final: 0.7965 (t80) REVERT: D 465 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8108 (mt) REVERT: D 609 GLU cc_start: 0.9009 (OUTLIER) cc_final: 0.8630 (tt0) REVERT: D 625 ASP cc_start: 0.8517 (OUTLIER) cc_final: 0.8232 (m-30) REVERT: E 463 ASP cc_start: 0.8795 (OUTLIER) cc_final: 0.8122 (m-30) REVERT: E 591 GLU cc_start: 0.8321 (tp30) cc_final: 0.7664 (tp30) REVERT: E 609 GLU cc_start: 0.8694 (tt0) cc_final: 0.8165 (tp30) REVERT: E 618 ASN cc_start: 0.8854 (m-40) cc_final: 0.7898 (p0) REVERT: E 655 MET cc_start: 0.8784 (mmm) cc_final: 0.8399 (mmt) REVERT: F 640 ASN cc_start: 0.8665 (t0) cc_final: 0.8140 (t0) outliers start: 41 outliers final: 16 residues processed: 241 average time/residue: 0.1501 time to fit residues: 59.2977 Evaluate side-chains 214 residues out of total 2648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 187 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain B residue 428 LEU Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 651 ASP Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain B residue 771 THR Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 932 GLU Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 609 GLU Chi-restraints excluded: chain D residue 625 ASP Chi-restraints excluded: chain E residue 440 GLU Chi-restraints excluded: chain E residue 463 ASP Chi-restraints excluded: chain E residue 561 HIS Chi-restraints excluded: chain E residue 607 LEU Chi-restraints excluded: chain E residue 611 LEU Chi-restraints excluded: chain E residue 626 VAL Chi-restraints excluded: chain E residue 653 MET Chi-restraints excluded: chain E residue 681 LEU Chi-restraints excluded: chain E residue 884 SER Chi-restraints excluded: chain F residue 527 VAL Chi-restraints excluded: chain F residue 645 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 279 optimal weight: 3.9990 chunk 306 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 236 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 55 optimal weight: 9.9990 chunk 85 optimal weight: 4.9990 chunk 168 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 215 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 541 ASN A 715 GLN A 839 HIS D 615 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.110858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.077333 restraints weight = 53609.765| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 3.00 r_work: 0.2955 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 24784 Z= 0.196 Angle : 0.621 7.662 33566 Z= 0.308 Chirality : 0.043 0.257 3865 Planarity : 0.004 0.056 4287 Dihedral : 6.704 98.613 3440 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.97 % Allowed : 11.37 % Favored : 86.66 % 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: 0.88 (0.15), residues: 3070 helix: 1.38 (0.13), residues: 1404 sheet: 1.16 (0.25), residues: 411 loop : -0.49 (0.17), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 422 TYR 0.015 0.002 TYR F 623 PHE 0.017 0.002 PHE D 820 TRP 0.029 0.002 TRP E 464 HIS 0.021 0.001 HIS A 622 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.20 (24784) covalent geometry : angle 0.62066 / 0.31 (33566) hydrogen bonds : bond 0.04153 / 2.82 ( 1200) hydrogen bonds : angle 4.99950 / 3.55 ( 3540) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6140 Ramachandran restraints generated. 3070 Oldfield, 0 Emsley, 3070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6140 Ramachandran restraints generated. 3070 Oldfield, 0 Emsley, 3070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 203 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 435 MET cc_start: 0.4545 (ppp) cc_final: 0.4136 (mmt) REVERT: A 438 VAL cc_start: 0.6610 (OUTLIER) cc_final: 0.6254 (p) REVERT: A 651 ASP cc_start: 0.7801 (t0) cc_final: 0.7549 (t0) REVERT: B 425 LEU cc_start: 0.8519 (mt) cc_final: 0.8220 (tt) REVERT: B 654 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7931 (tm-30) REVERT: B 897 GLU cc_start: 0.8457 (mp0) cc_final: 0.7793 (mp0) REVERT: C 461 TYR cc_start: 0.8394 (t80) cc_final: 0.8160 (t80) REVERT: C 569 MET cc_start: 0.8541 (mmp) cc_final: 0.7790 (mtm) REVERT: C 573 ILE cc_start: 0.9419 (mm) cc_final: 0.9157 (mm) REVERT: C 594 LYS cc_start: 0.8531 (mptt) cc_final: 0.8192 (ttmm) REVERT: C 879 MET cc_start: 0.9172 (ptp) cc_final: 0.8894 (ptm) REVERT: C 932 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7181 (tm-30) REVERT: D 424 ARG cc_start: 0.9024 (tpp80) cc_final: 0.8492 (tpt170) REVERT: D 459 ARG cc_start: 0.8093 (ptp-170) cc_final: 0.7667 (ptp-170) REVERT: D 461 TYR cc_start: 0.8288 (t80) cc_final: 0.7878 (t80) REVERT: D 465 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8098 (mt) REVERT: D 543 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7772 (mm-30) REVERT: D 573 ILE cc_start: 0.8891 (mp) cc_final: 0.8690 (mp) REVERT: D 577 LEU cc_start: 0.8923 (mm) cc_final: 0.8488 (mm) REVERT: D 609 GLU cc_start: 0.8943 (OUTLIER) cc_final: 0.8550 (tt0) REVERT: D 625 ASP cc_start: 0.8560 (OUTLIER) cc_final: 0.8220 (m-30) REVERT: E 591 GLU cc_start: 0.8384 (tp30) cc_final: 0.7821 (tp30) REVERT: E 609 GLU cc_start: 0.8749 (tt0) cc_final: 0.8202 (tp30) REVERT: E 618 ASN cc_start: 0.8865 (m-40) cc_final: 0.7881 (p0) REVERT: E 655 MET cc_start: 0.8816 (mmm) cc_final: 0.8418 (mmt) REVERT: E 808 GLU cc_start: 0.7790 (tp30) cc_final: 0.7547 (tp30) REVERT: F 640 ASN cc_start: 0.8624 (t0) cc_final: 0.8245 (t0) outliers start: 52 outliers final: 24 residues processed: 243 average time/residue: 0.1600 time to fit residues: 63.5458 Evaluate side-chains 223 residues out of total 2648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 193 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain C residue 932 GLU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 559 LYS Chi-restraints excluded: chain D residue 609 GLU Chi-restraints excluded: chain D residue 625 ASP Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain E residue 440 GLU Chi-restraints excluded: chain E residue 561 HIS Chi-restraints excluded: chain E residue 607 LEU Chi-restraints excluded: chain E residue 611 LEU Chi-restraints excluded: chain E residue 626 VAL Chi-restraints excluded: chain E residue 653 MET Chi-restraints excluded: chain E residue 681 LEU Chi-restraints excluded: chain E residue 859 THR Chi-restraints excluded: chain E residue 884 SER Chi-restraints excluded: chain F residue 470 TRP Chi-restraints excluded: chain F residue 527 VAL Chi-restraints excluded: chain F residue 611 LEU Chi-restraints excluded: chain F residue 645 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 30 optimal weight: 0.4980 chunk 219 optimal weight: 1.9990 chunk 188 optimal weight: 2.9990 chunk 227 optimal weight: 9.9990 chunk 208 optimal weight: 0.9980 chunk 155 optimal weight: 6.9990 chunk 158 optimal weight: 10.0000 chunk 223 optimal weight: 0.9980 chunk 193 optimal weight: 2.9990 chunk 267 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 715 GLN B 615 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.112054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.078370 restraints weight = 53422.904| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 3.01 r_work: 0.2981 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24784 Z= 0.137 Angle : 0.585 7.840 33566 Z= 0.289 Chirality : 0.042 0.248 3865 Planarity : 0.004 0.053 4287 Dihedral : 6.465 96.052 3440 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.97 % Allowed : 12.28 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.15), residues: 3070 helix: 1.50 (0.14), residues: 1409 sheet: 1.20 (0.24), residues: 409 loop : -0.52 (0.17), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 422 TYR 0.015 0.001 TYR C 623 PHE 0.019 0.001 PHE A 635 TRP 0.028 0.001 TRP E 464 HIS 0.017 0.001 HIS A 622 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (24784) covalent geometry : angle 0.58473 / 0.29 (33566) hydrogen bonds : bond 0.03732 / 2.53 ( 1200) hydrogen bonds : angle 4.83912 / 3.44 ( 3540) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6140 Ramachandran restraints generated. 3070 Oldfield, 0 Emsley, 3070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6140 Ramachandran restraints generated. 3070 Oldfield, 0 Emsley, 3070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 216 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 435 MET cc_start: 0.4734 (ppp) cc_final: 0.4139 (mmt) REVERT: A 438 VAL cc_start: 0.6644 (OUTLIER) cc_final: 0.6223 (p) REVERT: A 651 ASP cc_start: 0.7784 (t0) cc_final: 0.7509 (t0) REVERT: B 425 LEU cc_start: 0.8526 (mt) cc_final: 0.8232 (tt) REVERT: B 462 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8877 (mm) REVERT: B 651 ASP cc_start: 0.8261 (OUTLIER) cc_final: 0.7970 (p0) REVERT: B 897 GLU cc_start: 0.8418 (mp0) cc_final: 0.7858 (mp0) REVERT: C 432 LYS cc_start: 0.9285 (tptp) cc_final: 0.9045 (tmtt) REVERT: C 461 TYR cc_start: 0.8416 (t80) cc_final: 0.8116 (t80) REVERT: C 569 MET cc_start: 0.8495 (mmp) cc_final: 0.7917 (mtp) REVERT: C 573 ILE cc_start: 0.9407 (mm) cc_final: 0.9169 (mm) REVERT: C 826 MET cc_start: 0.9256 (tmm) cc_final: 0.8174 (ptm) REVERT: C 879 MET cc_start: 0.9120 (ptp) cc_final: 0.8857 (ptm) REVERT: C 932 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7032 (tm-30) REVERT: D 422 ARG cc_start: 0.9271 (mmm160) cc_final: 0.9057 (mmm160) REVERT: D 459 ARG cc_start: 0.8069 (ptp-170) cc_final: 0.7679 (ptp-170) REVERT: D 461 TYR cc_start: 0.8287 (t80) cc_final: 0.7844 (t80) REVERT: D 465 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8087 (mt) REVERT: D 543 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7804 (mm-30) REVERT: D 557 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7266 (tt0) REVERT: D 609 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.8582 (tt0) REVERT: D 615 GLN cc_start: 0.8831 (pt0) cc_final: 0.8598 (pt0) REVERT: D 625 ASP cc_start: 0.8542 (OUTLIER) cc_final: 0.8174 (m-30) REVERT: E 591 GLU cc_start: 0.8372 (tp30) cc_final: 0.7802 (tp30) REVERT: E 609 GLU cc_start: 0.8765 (tt0) cc_final: 0.8233 (tp30) REVERT: E 618 ASN cc_start: 0.8853 (m-40) cc_final: 0.7947 (p0) REVERT: E 655 MET cc_start: 0.8853 (mmm) cc_final: 0.8444 (mmt) REVERT: E 808 GLU cc_start: 0.7764 (tp30) cc_final: 0.7526 (tp30) REVERT: F 640 ASN cc_start: 0.8593 (t0) cc_final: 0.8233 (t0) outliers start: 52 outliers final: 28 residues processed: 253 average time/residue: 0.1709 time to fit residues: 69.4021 Evaluate side-chains 231 residues out of total 2648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 195 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 651 ASP Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain B residue 827 GLN Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 658 VAL Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 932 GLU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 557 GLU Chi-restraints excluded: chain D residue 559 LYS Chi-restraints excluded: chain D residue 609 GLU Chi-restraints excluded: chain D residue 625 ASP Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 770 TRP Chi-restraints excluded: chain E residue 440 GLU Chi-restraints excluded: chain E residue 489 GLU Chi-restraints excluded: chain E residue 561 HIS Chi-restraints excluded: chain E residue 607 LEU Chi-restraints excluded: chain E residue 626 VAL Chi-restraints excluded: chain E residue 681 LEU Chi-restraints excluded: chain E residue 859 THR Chi-restraints excluded: chain E residue 884 SER Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain F residue 470 TRP Chi-restraints excluded: chain F residue 538 ARG Chi-restraints excluded: chain F residue 628 VAL Chi-restraints excluded: chain F residue 645 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 92 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 218 optimal weight: 2.9990 chunk 247 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 176 optimal weight: 0.8980 chunk 237 optimal weight: 0.9990 chunk 217 optimal weight: 0.8980 chunk 289 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 274 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 715 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.112533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.078838 restraints weight = 53428.652| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 3.02 r_work: 0.2991 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 24784 Z= 0.128 Angle : 0.578 8.585 33566 Z= 0.283 Chirality : 0.041 0.235 3865 Planarity : 0.004 0.053 4287 Dihedral : 6.314 94.123 3440 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.90 % Allowed : 12.74 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.15), residues: 3070 helix: 1.59 (0.14), residues: 1409 sheet: 1.19 (0.24), residues: 412 loop : -0.49 (0.17), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 422 TYR 0.015 0.001 TYR C 623 PHE 0.018 0.001 PHE E 547 TRP 0.036 0.001 TRP E 464 HIS 0.015 0.001 HIS A 622 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (24784) covalent geometry : angle 0.57761 / 0.28 (33566) hydrogen bonds : bond 0.03577 / 2.42 ( 1200) hydrogen bonds : angle 4.75587 / 3.38 ( 3540) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6140 Ramachandran restraints generated. 3070 Oldfield, 0 Emsley, 3070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6140 Ramachandran restraints generated. 3070 Oldfield, 0 Emsley, 3070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 210 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 435 MET cc_start: 0.4904 (ppp) cc_final: 0.4328 (mmm) REVERT: A 438 VAL cc_start: 0.6674 (OUTLIER) cc_final: 0.6306 (p) REVERT: A 651 ASP cc_start: 0.7891 (t0) cc_final: 0.7599 (t0) REVERT: B 425 LEU cc_start: 0.8590 (mt) cc_final: 0.8289 (tp) REVERT: B 462 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8901 (mm) REVERT: B 651 ASP cc_start: 0.8205 (OUTLIER) cc_final: 0.7826 (p0) REVERT: B 654 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7839 (tm-30) REVERT: B 826 MET cc_start: 0.9340 (tmm) cc_final: 0.9109 (tmm) REVERT: B 897 GLU cc_start: 0.8398 (mp0) cc_final: 0.7836 (mp0) REVERT: C 432 LYS cc_start: 0.9277 (tptp) cc_final: 0.9072 (tmtt) REVERT: C 461 TYR cc_start: 0.8477 (t80) cc_final: 0.8262 (t80) REVERT: C 569 MET cc_start: 0.8572 (mmp) cc_final: 0.8092 (mtp) REVERT: C 879 MET cc_start: 0.9135 (ptp) cc_final: 0.8864 (ptm) REVERT: C 932 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7064 (tm-30) REVERT: D 422 ARG cc_start: 0.9303 (mmm160) cc_final: 0.9101 (mmm160) REVERT: D 424 ARG cc_start: 0.9014 (tpp80) cc_final: 0.8465 (tpt170) REVERT: D 459 ARG cc_start: 0.8065 (ptp-170) cc_final: 0.7729 (ptp-170) REVERT: D 461 TYR cc_start: 0.8301 (t80) cc_final: 0.7812 (t80) REVERT: D 465 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8119 (mt) REVERT: D 543 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7798 (mm-30) REVERT: D 609 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.8604 (tt0) REVERT: D 625 ASP cc_start: 0.8512 (OUTLIER) cc_final: 0.8174 (m-30) REVERT: E 609 GLU cc_start: 0.8772 (tt0) cc_final: 0.8316 (tp30) REVERT: E 618 ASN cc_start: 0.8861 (m-40) cc_final: 0.7954 (p0) REVERT: E 655 MET cc_start: 0.8869 (mmm) cc_final: 0.8428 (mmt) REVERT: E 808 GLU cc_start: 0.7873 (tp30) cc_final: 0.7502 (tp30) REVERT: F 591 GLU cc_start: 0.8084 (pm20) cc_final: 0.7750 (pm20) REVERT: F 640 ASN cc_start: 0.8545 (t0) cc_final: 0.8248 (t0) outliers start: 50 outliers final: 30 residues processed: 244 average time/residue: 0.1664 time to fit residues: 65.8825 Evaluate side-chains 235 residues out of total 2648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 197 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 651 ASP Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain B residue 827 GLN Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain C residue 658 VAL Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 932 GLU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 552 MET Chi-restraints excluded: chain D residue 609 GLU Chi-restraints excluded: chain D residue 625 ASP Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 770 TRP Chi-restraints excluded: chain E residue 440 GLU Chi-restraints excluded: chain E residue 489 GLU Chi-restraints excluded: chain E residue 561 HIS Chi-restraints excluded: chain E residue 607 LEU Chi-restraints excluded: chain E residue 626 VAL Chi-restraints excluded: chain E residue 653 MET Chi-restraints excluded: chain E residue 681 LEU Chi-restraints excluded: chain E residue 859 THR Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain F residue 470 TRP Chi-restraints excluded: chain F residue 527 VAL Chi-restraints excluded: chain F residue 645 ILE Chi-restraints excluded: chain F residue 837 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 84 optimal weight: 0.9990 chunk 268 optimal weight: 5.9990 chunk 298 optimal weight: 3.9990 chunk 217 optimal weight: 3.9990 chunk 299 optimal weight: 0.7980 chunk 297 optimal weight: 0.8980 chunk 239 optimal weight: 6.9990 chunk 181 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 280 optimal weight: 0.7980 chunk 150 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.113354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.079599 restraints weight = 53329.641| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 3.02 r_work: 0.3007 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 24784 Z= 0.114 Angle : 0.565 8.421 33566 Z= 0.277 Chirality : 0.041 0.232 3865 Planarity : 0.004 0.053 4287 Dihedral : 6.163 91.842 3440 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.74 % Allowed : 13.23 % Favored : 85.03 % 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: 1.15 (0.15), residues: 3070 helix: 1.68 (0.14), residues: 1410 sheet: 1.34 (0.24), residues: 402 loop : -0.47 (0.17), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 652 TYR 0.016 0.001 TYR C 623 PHE 0.021 0.001 PHE A 635 TRP 0.023 0.001 TRP E 464 HIS 0.013 0.001 HIS A 622 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (24784) covalent geometry : angle 0.56536 / 0.28 (33566) hydrogen bonds : bond 0.03411 / 2.31 ( 1200) hydrogen bonds : angle 4.65897 / 3.31 ( 3540) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6140 Ramachandran restraints generated. 3070 Oldfield, 0 Emsley, 3070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6140 Ramachandran restraints generated. 3070 Oldfield, 0 Emsley, 3070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 213 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 435 MET cc_start: 0.4711 (ppp) cc_final: 0.4128 (mmm) REVERT: A 438 VAL cc_start: 0.6623 (OUTLIER) cc_final: 0.6401 (t) REVERT: B 425 LEU cc_start: 0.8492 (mt) cc_final: 0.8175 (tt) REVERT: B 462 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8932 (mm) REVERT: B 651 ASP cc_start: 0.8083 (OUTLIER) cc_final: 0.7742 (p0) REVERT: B 654 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7834 (tm-30) REVERT: B 826 MET cc_start: 0.9335 (tmm) cc_final: 0.9097 (tmm) REVERT: B 897 GLU cc_start: 0.8427 (mp0) cc_final: 0.7908 (mp0) REVERT: C 461 TYR cc_start: 0.8450 (t80) cc_final: 0.8218 (t80) REVERT: C 569 MET cc_start: 0.8561 (mmp) cc_final: 0.8127 (mtp) REVERT: C 826 MET cc_start: 0.9252 (tmm) cc_final: 0.8236 (ptm) REVERT: C 879 MET cc_start: 0.9122 (ptp) cc_final: 0.8843 (ptm) REVERT: C 932 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7076 (tm-30) REVERT: D 422 ARG cc_start: 0.9305 (mmm160) cc_final: 0.9094 (mmm160) REVERT: D 424 ARG cc_start: 0.8988 (tpp80) cc_final: 0.8482 (tpt90) REVERT: D 440 GLU cc_start: 0.8381 (pt0) cc_final: 0.8057 (tm-30) REVERT: D 459 ARG cc_start: 0.8113 (ptp-170) cc_final: 0.7798 (ptp-170) REVERT: D 461 TYR cc_start: 0.8294 (t80) cc_final: 0.7799 (t80) REVERT: D 462 LEU cc_start: 0.8315 (mm) cc_final: 0.8061 (mm) REVERT: D 465 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8080 (mt) REVERT: D 577 LEU cc_start: 0.8981 (mm) cc_final: 0.8552 (mm) REVERT: D 609 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.8669 (tt0) REVERT: D 625 ASP cc_start: 0.8539 (OUTLIER) cc_final: 0.8155 (m-30) REVERT: E 444 LYS cc_start: 0.6608 (mmpt) cc_final: 0.6196 (mtmm) REVERT: E 591 GLU cc_start: 0.8361 (tp30) cc_final: 0.7885 (tp30) REVERT: E 595 ILE cc_start: 0.7390 (OUTLIER) cc_final: 0.6741 (tp) REVERT: E 609 GLU cc_start: 0.8771 (tt0) cc_final: 0.8310 (tp30) REVERT: E 618 ASN cc_start: 0.8826 (m-40) cc_final: 0.7935 (p0) REVERT: E 655 MET cc_start: 0.8872 (mmm) cc_final: 0.8427 (mmt) REVERT: E 808 GLU cc_start: 0.7901 (tp30) cc_final: 0.7487 (tp30) REVERT: F 435 MET cc_start: 0.7892 (mtp) cc_final: 0.7527 (mmt) REVERT: F 640 ASN cc_start: 0.8536 (t0) cc_final: 0.8256 (t0) outliers start: 46 outliers final: 28 residues processed: 249 average time/residue: 0.1674 time to fit residues: 67.3896 Evaluate side-chains 235 residues out of total 2648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 198 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 651 ASP Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain B residue 827 GLN Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain C residue 658 VAL Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 932 GLU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 609 GLU Chi-restraints excluded: chain D residue 625 ASP Chi-restraints excluded: chain D residue 770 TRP Chi-restraints excluded: chain D residue 858 CYS Chi-restraints excluded: chain E residue 440 GLU Chi-restraints excluded: chain E residue 489 GLU Chi-restraints excluded: chain E residue 561 HIS Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 607 LEU Chi-restraints excluded: chain E residue 626 VAL Chi-restraints excluded: chain E residue 681 LEU Chi-restraints excluded: chain E residue 859 THR Chi-restraints excluded: chain E residue 884 SER Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain F residue 470 TRP Chi-restraints excluded: chain F residue 527 VAL Chi-restraints excluded: chain F residue 628 VAL Chi-restraints excluded: chain F residue 645 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 280 optimal weight: 4.9990 chunk 247 optimal weight: 4.9990 chunk 275 optimal weight: 2.9990 chunk 271 optimal weight: 0.3980 chunk 41 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 163 optimal weight: 1.9990 chunk 162 optimal weight: 0.6980 chunk 252 optimal weight: 4.9990 chunk 284 optimal weight: 0.9990 chunk 193 optimal weight: 0.6980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 615 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.113750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.080006 restraints weight = 53020.475| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 3.02 r_work: 0.3015 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 24784 Z= 0.111 Angle : 0.573 9.903 33566 Z= 0.278 Chirality : 0.041 0.266 3865 Planarity : 0.004 0.054 4287 Dihedral : 6.057 90.311 3440 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.86 % Allowed : 13.23 % Favored : 84.91 % 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: 1.24 (0.15), residues: 3070 helix: 1.77 (0.14), residues: 1411 sheet: 1.48 (0.25), residues: 393 loop : -0.47 (0.17), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 422 TYR 0.022 0.001 TYR F 544 PHE 0.020 0.001 PHE E 547 TRP 0.021 0.001 TRP D 470 HIS 0.011 0.001 HIS A 622 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (24784) covalent geometry : angle 0.57253 / 0.28 (33566) hydrogen bonds : bond 0.03301 / 2.24 ( 1200) hydrogen bonds : angle 4.59747 / 3.26 ( 3540) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6140 Ramachandran restraints generated. 3070 Oldfield, 0 Emsley, 3070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6140 Ramachandran restraints generated. 3070 Oldfield, 0 Emsley, 3070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 218 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 435 MET cc_start: 0.4865 (ppp) cc_final: 0.4224 (mmm) REVERT: A 438 VAL cc_start: 0.6628 (OUTLIER) cc_final: 0.6381 (t) REVERT: A 455 PHE cc_start: 0.5499 (t80) cc_final: 0.5242 (t80) REVERT: B 423 GLU cc_start: 0.9222 (tp30) cc_final: 0.8722 (pp20) REVERT: B 425 LEU cc_start: 0.8487 (mt) cc_final: 0.8242 (tt) REVERT: B 462 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8925 (mm) REVERT: B 503 GLU cc_start: 0.8663 (mt-10) cc_final: 0.8162 (mp0) REVERT: B 608 LEU cc_start: 0.8503 (mt) cc_final: 0.8280 (mt) REVERT: B 651 ASP cc_start: 0.8102 (OUTLIER) cc_final: 0.7791 (p0) REVERT: B 826 MET cc_start: 0.9343 (tmm) cc_final: 0.9101 (tmm) REVERT: B 897 GLU cc_start: 0.8424 (mp0) cc_final: 0.7905 (mp0) REVERT: C 451 HIS cc_start: 0.8142 (OUTLIER) cc_final: 0.7823 (p-80) REVERT: C 461 TYR cc_start: 0.8491 (t80) cc_final: 0.8247 (t80) REVERT: C 569 MET cc_start: 0.8571 (mmp) cc_final: 0.8087 (mtm) REVERT: C 826 MET cc_start: 0.9243 (tmm) cc_final: 0.8221 (ptm) REVERT: C 879 MET cc_start: 0.9129 (ptp) cc_final: 0.8868 (ptm) REVERT: C 932 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7026 (tm-30) REVERT: D 422 ARG cc_start: 0.9298 (mmm160) cc_final: 0.9094 (mmm160) REVERT: D 440 GLU cc_start: 0.8382 (pt0) cc_final: 0.8057 (tm-30) REVERT: D 459 ARG cc_start: 0.8109 (ptp-170) cc_final: 0.7799 (ptp-170) REVERT: D 461 TYR cc_start: 0.8309 (t80) cc_final: 0.7828 (t80) REVERT: D 462 LEU cc_start: 0.8372 (mm) cc_final: 0.8120 (mm) REVERT: D 465 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8013 (mt) REVERT: D 470 TRP cc_start: 0.8812 (m100) cc_final: 0.8486 (m100) REVERT: D 558 ILE cc_start: 0.7792 (OUTLIER) cc_final: 0.7562 (mp) REVERT: D 577 LEU cc_start: 0.8964 (mm) cc_final: 0.8532 (mm) REVERT: D 625 ASP cc_start: 0.8526 (OUTLIER) cc_final: 0.8156 (m-30) REVERT: E 441 GLU cc_start: 0.7342 (mm-30) cc_final: 0.7118 (pt0) REVERT: E 444 LYS cc_start: 0.6611 (mmpt) cc_final: 0.6198 (mtmm) REVERT: E 591 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7750 (mm-30) REVERT: E 595 ILE cc_start: 0.7303 (OUTLIER) cc_final: 0.6659 (tp) REVERT: E 609 GLU cc_start: 0.8775 (tt0) cc_final: 0.8308 (tp30) REVERT: E 618 ASN cc_start: 0.8819 (m-40) cc_final: 0.7931 (p0) REVERT: E 647 GLU cc_start: 0.8140 (tm-30) cc_final: 0.7751 (tp30) REVERT: E 655 MET cc_start: 0.8863 (mmm) cc_final: 0.8426 (mmt) REVERT: E 808 GLU cc_start: 0.7876 (tp30) cc_final: 0.7545 (tp30) REVERT: F 435 MET cc_start: 0.7931 (mtp) cc_final: 0.7555 (mmt) REVERT: F 591 GLU cc_start: 0.7824 (pm20) cc_final: 0.7484 (pm20) REVERT: F 640 ASN cc_start: 0.8530 (t0) cc_final: 0.8271 (t0) outliers start: 49 outliers final: 30 residues processed: 253 average time/residue: 0.1695 time to fit residues: 69.1002 Evaluate side-chains 248 residues out of total 2648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 208 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 651 ASP Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain B residue 827 GLN Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 439 ASP Chi-restraints excluded: chain C residue 451 HIS Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain C residue 658 VAL Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 932 GLU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 558 ILE Chi-restraints excluded: chain D residue 625 ASP Chi-restraints excluded: chain D residue 770 TRP Chi-restraints excluded: chain D residue 858 CYS Chi-restraints excluded: chain E residue 440 GLU Chi-restraints excluded: chain E residue 489 GLU Chi-restraints excluded: chain E residue 561 HIS Chi-restraints excluded: chain E residue 591 GLU Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 607 LEU Chi-restraints excluded: chain E residue 626 VAL Chi-restraints excluded: chain E residue 681 LEU Chi-restraints excluded: chain E residue 884 SER Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain F residue 470 TRP Chi-restraints excluded: chain F residue 527 VAL Chi-restraints excluded: chain F residue 628 VAL Chi-restraints excluded: chain F residue 645 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 26 optimal weight: 0.9990 chunk 211 optimal weight: 2.9990 chunk 246 optimal weight: 0.7980 chunk 302 optimal weight: 0.9990 chunk 206 optimal weight: 0.0040 chunk 109 optimal weight: 2.9990 chunk 299 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 273 optimal weight: 0.6980 chunk 305 optimal weight: 0.0070 overall best weight: 0.5012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 715 GLN ** D 615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 561 HIS E 640 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.114857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.081008 restraints weight = 53311.921| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 3.04 r_work: 0.3032 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 24784 Z= 0.102 Angle : 0.575 9.485 33566 Z= 0.279 Chirality : 0.040 0.231 3865 Planarity : 0.004 0.054 4287 Dihedral : 5.925 88.392 3440 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.67 % Allowed : 13.57 % Favored : 84.76 % 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: 1.32 (0.15), residues: 3070 helix: 1.82 (0.14), residues: 1419 sheet: 1.67 (0.25), residues: 384 loop : -0.46 (0.17), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 422 TYR 0.019 0.001 TYR C 623 PHE 0.023 0.001 PHE E 751 TRP 0.025 0.001 TRP D 464 HIS 0.009 0.000 HIS A 622 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (24784) covalent geometry : angle 0.57505 / 0.28 (33566) hydrogen bonds : bond 0.03174 / 2.15 ( 1200) hydrogen bonds : angle 4.53669 / 3.22 ( 3540) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6140 Ramachandran restraints generated. 3070 Oldfield, 0 Emsley, 3070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6140 Ramachandran restraints generated. 3070 Oldfield, 0 Emsley, 3070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 220 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 435 MET cc_start: 0.4862 (ppp) cc_final: 0.4233 (mmm) REVERT: A 438 VAL cc_start: 0.6621 (OUTLIER) cc_final: 0.6369 (t) REVERT: A 455 PHE cc_start: 0.5817 (t80) cc_final: 0.5604 (t80) REVERT: A 653 MET cc_start: 0.7117 (mtm) cc_final: 0.6643 (mtt) REVERT: A 766 MET cc_start: 0.8900 (ttm) cc_final: 0.8676 (ttt) REVERT: B 423 GLU cc_start: 0.9209 (tp30) cc_final: 0.8736 (pp20) REVERT: B 425 LEU cc_start: 0.8540 (mt) cc_final: 0.8280 (tt) REVERT: B 462 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8918 (mm) REVERT: B 503 GLU cc_start: 0.8649 (mt-10) cc_final: 0.8174 (mp0) REVERT: B 608 LEU cc_start: 0.8492 (mt) cc_final: 0.8241 (mt) REVERT: B 651 ASP cc_start: 0.8047 (OUTLIER) cc_final: 0.7788 (p0) REVERT: B 826 MET cc_start: 0.9318 (tmm) cc_final: 0.9089 (tmm) REVERT: B 897 GLU cc_start: 0.8411 (mp0) cc_final: 0.7891 (mp0) REVERT: C 451 HIS cc_start: 0.8125 (OUTLIER) cc_final: 0.7804 (p-80) REVERT: C 569 MET cc_start: 0.8405 (mmp) cc_final: 0.8067 (mtm) REVERT: C 583 GLU cc_start: 0.8475 (tp30) cc_final: 0.7852 (tp30) REVERT: C 590 ASP cc_start: 0.8189 (p0) cc_final: 0.7887 (p0) REVERT: C 826 MET cc_start: 0.9251 (tmm) cc_final: 0.8228 (ptm) REVERT: C 879 MET cc_start: 0.9087 (ptp) cc_final: 0.8817 (ptm) REVERT: C 932 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7133 (tm-30) REVERT: D 440 GLU cc_start: 0.8382 (pt0) cc_final: 0.8052 (tm-30) REVERT: D 459 ARG cc_start: 0.8067 (ptp-170) cc_final: 0.7728 (ptp-170) REVERT: D 461 TYR cc_start: 0.8318 (t80) cc_final: 0.7773 (t80) REVERT: D 462 LEU cc_start: 0.8426 (mm) cc_final: 0.8200 (mm) REVERT: D 464 TRP cc_start: 0.7906 (m100) cc_final: 0.7661 (m100) REVERT: D 465 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.7957 (mt) REVERT: D 470 TRP cc_start: 0.8811 (m100) cc_final: 0.8471 (m100) REVERT: D 559 LYS cc_start: 0.8511 (mmmt) cc_final: 0.8114 (tppt) REVERT: D 577 LEU cc_start: 0.8977 (mm) cc_final: 0.8546 (mm) REVERT: D 611 LEU cc_start: 0.9539 (OUTLIER) cc_final: 0.9316 (pp) REVERT: D 625 ASP cc_start: 0.8500 (OUTLIER) cc_final: 0.8109 (m-30) REVERT: E 441 GLU cc_start: 0.7311 (mm-30) cc_final: 0.7107 (pt0) REVERT: E 444 LYS cc_start: 0.6610 (mmpt) cc_final: 0.6200 (mtmm) REVERT: E 591 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7731 (tp30) REVERT: E 609 GLU cc_start: 0.8781 (tt0) cc_final: 0.8302 (tp30) REVERT: E 618 ASN cc_start: 0.8834 (m-40) cc_final: 0.7956 (p0) REVERT: E 647 GLU cc_start: 0.8151 (tm-30) cc_final: 0.7759 (tp30) REVERT: E 655 MET cc_start: 0.8930 (mmm) cc_final: 0.8582 (mmt) REVERT: E 808 GLU cc_start: 0.7794 (tp30) cc_final: 0.7472 (tp30) REVERT: F 435 MET cc_start: 0.7929 (mtp) cc_final: 0.7563 (mmt) REVERT: F 640 ASN cc_start: 0.8501 (t0) cc_final: 0.8270 (t0) outliers start: 44 outliers final: 28 residues processed: 254 average time/residue: 0.1656 time to fit residues: 67.8060 Evaluate side-chains 241 residues out of total 2648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 204 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 569 MET Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 651 ASP Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 439 ASP Chi-restraints excluded: chain C residue 451 HIS Chi-restraints excluded: chain C residue 548 SER Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain C residue 658 VAL Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 932 GLU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 625 ASP Chi-restraints excluded: chain D residue 770 TRP Chi-restraints excluded: chain E residue 440 GLU Chi-restraints excluded: chain E residue 489 GLU Chi-restraints excluded: chain E residue 561 HIS Chi-restraints excluded: chain E residue 591 GLU Chi-restraints excluded: chain E residue 607 LEU Chi-restraints excluded: chain E residue 626 VAL Chi-restraints excluded: chain E residue 681 LEU Chi-restraints excluded: chain E residue 859 THR Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain F residue 527 VAL Chi-restraints excluded: chain F residue 628 VAL Chi-restraints excluded: chain F residue 645 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 240 optimal weight: 0.7980 chunk 175 optimal weight: 3.9990 chunk 258 optimal weight: 30.0000 chunk 28 optimal weight: 3.9990 chunk 208 optimal weight: 0.9990 chunk 230 optimal weight: 0.5980 chunk 12 optimal weight: 4.9990 chunk 212 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 166 optimal weight: 3.9990 chunk 193 optimal weight: 2.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 715 GLN E 561 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.114134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.080321 restraints weight = 53097.008| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 3.02 r_work: 0.3016 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 24784 Z= 0.125 Angle : 0.597 13.945 33566 Z= 0.287 Chirality : 0.041 0.235 3865 Planarity : 0.004 0.053 4287 Dihedral : 5.907 88.287 3440 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.44 % Allowed : 13.76 % Favored : 84.80 % 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: 1.32 (0.15), residues: 3070 helix: 1.84 (0.14), residues: 1411 sheet: 1.60 (0.25), residues: 389 loop : -0.46 (0.17), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 422 TYR 0.015 0.001 TYR C 623 PHE 0.021 0.001 PHE E 751 TRP 0.019 0.001 TRP A 464 HIS 0.009 0.001 HIS A 622 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 (24784) covalent geometry : angle 0.59659 / 0.29 (33566) hydrogen bonds : bond 0.03291 / 2.23 ( 1200) hydrogen bonds : angle 4.54546 / 3.22 ( 3540) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6140 Ramachandran restraints generated. 3070 Oldfield, 0 Emsley, 3070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6140 Ramachandran restraints generated. 3070 Oldfield, 0 Emsley, 3070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 208 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 435 MET cc_start: 0.4851 (ppp) cc_final: 0.4222 (mmm) REVERT: A 438 VAL cc_start: 0.6607 (OUTLIER) cc_final: 0.6353 (t) REVERT: A 455 PHE cc_start: 0.5838 (t80) cc_final: 0.5627 (t80) REVERT: A 653 MET cc_start: 0.7210 (mtm) cc_final: 0.6683 (mtt) REVERT: B 423 GLU cc_start: 0.9220 (tp30) cc_final: 0.8749 (pp20) REVERT: B 425 LEU cc_start: 0.8552 (mt) cc_final: 0.8256 (tt) REVERT: B 462 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8931 (mm) REVERT: B 503 GLU cc_start: 0.8664 (mt-10) cc_final: 0.8171 (mp0) REVERT: B 608 LEU cc_start: 0.8339 (mt) cc_final: 0.8120 (mt) REVERT: B 651 ASP cc_start: 0.8068 (OUTLIER) cc_final: 0.7794 (p0) REVERT: B 826 MET cc_start: 0.9326 (tmm) cc_final: 0.9086 (tmm) REVERT: B 897 GLU cc_start: 0.8425 (mp0) cc_final: 0.7904 (mp0) REVERT: C 451 HIS cc_start: 0.8214 (OUTLIER) cc_final: 0.7841 (p-80) REVERT: C 569 MET cc_start: 0.8426 (mmp) cc_final: 0.8048 (mtm) REVERT: C 590 ASP cc_start: 0.8194 (p0) cc_final: 0.7918 (p0) REVERT: C 826 MET cc_start: 0.9245 (tmm) cc_final: 0.8228 (ptm) REVERT: C 879 MET cc_start: 0.9108 (ptp) cc_final: 0.8838 (ptm) REVERT: C 897 GLU cc_start: 0.8677 (mp0) cc_final: 0.8413 (mp0) REVERT: C 932 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7119 (tm-30) REVERT: D 440 GLU cc_start: 0.8371 (pt0) cc_final: 0.8022 (tm-30) REVERT: D 459 ARG cc_start: 0.8067 (ptp-170) cc_final: 0.7753 (ptp-170) REVERT: D 461 TYR cc_start: 0.8327 (t80) cc_final: 0.7789 (t80) REVERT: D 462 LEU cc_start: 0.8390 (mm) cc_final: 0.8144 (mm) REVERT: D 465 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.7987 (mt) REVERT: D 470 TRP cc_start: 0.8824 (m100) cc_final: 0.8516 (m100) REVERT: D 559 LYS cc_start: 0.8619 (mmmt) cc_final: 0.8152 (tppt) REVERT: D 577 LEU cc_start: 0.9028 (mm) cc_final: 0.8607 (mm) REVERT: D 611 LEU cc_start: 0.9562 (OUTLIER) cc_final: 0.9341 (pp) REVERT: D 625 ASP cc_start: 0.8464 (OUTLIER) cc_final: 0.7979 (m-30) REVERT: E 441 GLU cc_start: 0.7327 (mm-30) cc_final: 0.7127 (pt0) REVERT: E 444 LYS cc_start: 0.6623 (mmpt) cc_final: 0.6198 (mtmm) REVERT: E 609 GLU cc_start: 0.8761 (tt0) cc_final: 0.8311 (tp30) REVERT: E 618 ASN cc_start: 0.8843 (m-40) cc_final: 0.7981 (p0) REVERT: E 647 GLU cc_start: 0.8154 (tm-30) cc_final: 0.7754 (tp30) REVERT: E 655 MET cc_start: 0.8910 (mmm) cc_final: 0.8531 (mmt) REVERT: E 808 GLU cc_start: 0.7867 (tp30) cc_final: 0.7545 (tp30) REVERT: F 435 MET cc_start: 0.7943 (mtp) cc_final: 0.7574 (mmt) REVERT: F 640 ASN cc_start: 0.8502 (t0) cc_final: 0.8273 (t0) outliers start: 38 outliers final: 29 residues processed: 236 average time/residue: 0.1642 time to fit residues: 62.5302 Evaluate side-chains 240 residues out of total 2648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 203 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 569 MET Chi-restraints excluded: chain A residue 759 VAL Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 651 ASP Chi-restraints excluded: chain B residue 737 VAL Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 439 ASP Chi-restraints excluded: chain C residue 451 HIS Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain C residue 658 VAL Chi-restraints excluded: chain C residue 709 VAL Chi-restraints excluded: chain C residue 932 GLU Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 625 ASP Chi-restraints excluded: chain D residue 770 TRP Chi-restraints excluded: chain E residue 440 GLU Chi-restraints excluded: chain E residue 489 GLU Chi-restraints excluded: chain E residue 561 HIS Chi-restraints excluded: chain E residue 607 LEU Chi-restraints excluded: chain E residue 626 VAL Chi-restraints excluded: chain E residue 681 LEU Chi-restraints excluded: chain E residue 884 SER Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 430 VAL Chi-restraints excluded: chain F residue 445 LEU Chi-restraints excluded: chain F residue 470 TRP Chi-restraints excluded: chain F residue 527 VAL Chi-restraints excluded: chain F residue 628 VAL Chi-restraints excluded: chain F residue 645 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 47 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 chunk 293 optimal weight: 1.9990 chunk 299 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 270 optimal weight: 3.9990 chunk 255 optimal weight: 2.9990 chunk 245 optimal weight: 1.9990 chunk 200 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 63 optimal weight: 0.0670 overall best weight: 1.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 561 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.113846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.079894 restraints weight = 53334.308| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 3.02 r_work: 0.3011 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 24784 Z= 0.132 Angle : 0.598 12.372 33566 Z= 0.289 Chirality : 0.041 0.235 3865 Planarity : 0.004 0.053 4287 Dihedral : 5.914 88.332 3440 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.71 % Allowed : 13.61 % Favored : 84.69 % 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: 1.29 (0.15), residues: 3070 helix: 1.83 (0.14), residues: 1411 sheet: 1.55 (0.25), residues: 390 loop : -0.48 (0.17), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 562 TYR 0.018 0.001 TYR A 623 PHE 0.022 0.001 PHE E 751 TRP 0.043 0.002 TRP E 464 HIS 0.009 0.001 HIS A 622 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (24784) covalent geometry : angle 0.59840 / 0.29 (33566) hydrogen bonds : bond 0.03333 / 2.26 ( 1200) hydrogen bonds : angle 4.58573 / 3.25 ( 3540) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5299.20 seconds wall clock time: 92 minutes 6.99 seconds (5526.99 seconds total)