Starting phenix.real_space_refine on Mon Sep 14 16:48:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6sko_10230/09_2026/6sko_10230_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6sko_10230/09_2026/6sko_10230.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6sko_10230/09_2026/6sko_10230.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6sko_10230/09_2026/6sko_10230.map" model { file = "/net/cci-nas-00/data/ceres_data/6sko_10230/09_2026/6sko_10230_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6sko_10230/09_2026/6sko_10230_trim.cif" } resolution = 3.4 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= 0.001 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: 7 Type Number sf(0) Gaussians P 31 5.49 5 Mg 5 5.21 5 S 72 5.16 5 C 9799 2.51 5 N 2735 2.21 5 O 3073 1.98 5 H 15838 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 83 residue(s): 0.02s 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: 31553 Number of models: 1 Model: "" Number of chains: 12 Chain: "6" Number of atoms: 5130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 5130 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 9, 'TRANS': 318} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "7" Number of atoms: 5242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 5242 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 14, 'TRANS': 320} Chain breaks: 1 Chain: "2" Number of atoms: 5499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 5499 Classifications: {'peptide': 346} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 334} Chain breaks: 5 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "5" Number of atoms: 4460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 4460 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 8, 'TRANS': 271} Chain breaks: 7 Chain: "3" Number of atoms: 5327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 5327 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 12, 'TRANS': 323} Chain breaks: 2 Chain: "4" Number of atoms: 5223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 5223 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 13, 'TRANS': 316} Chain breaks: 3 Chain: "I" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 512 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "6" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "7" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "2" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "3" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "4" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.09, per 1000 atoms: 0.16 Number of scatterers: 31553 At special positions: 0 Unit cell: (134.272, 137.419, 112.243, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 72 16.00 P 31 15.00 Mg 5 11.99 O 3073 8.00 N 2735 7.00 C 9799 6.00 H 15838 1.00 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: 2.95 Conformation dependent library (CDL) restraints added in 922.2 milliseconds 3806 Ramachandran restraints generated. 1903 Oldfield, 0 Emsley, 1903 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3704 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 28 sheets defined 54.7% 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 '6' and resid 500 through 508 Processing helix chain '6' and resid 509 through 522 removed outlier: 3.616A pdb=" N GLU 6 515 " --> pdb=" O ASP 6 511 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU 6 516 " --> pdb=" O GLU 6 512 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU 6 518 " --> pdb=" O ASN 6 514 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N MET 6 519 " --> pdb=" O GLU 6 515 " (cutoff:3.500A) Processing helix chain '6' and resid 524 through 533 removed outlier: 3.503A pdb=" N ILE 6 533 " --> pdb=" O LEU 6 529 " (cutoff:3.500A) Processing helix chain '6' and resid 540 through 553 Processing helix chain '6' and resid 580 through 590 removed outlier: 3.696A pdb=" N LEU 6 585 " --> pdb=" O LYS 6 581 " (cutoff:3.500A) Processing helix chain '6' and resid 640 through 644 Processing helix chain '6' and resid 645 through 654 removed outlier: 3.900A pdb=" N VAL 6 650 " --> pdb=" O ILE 6 646 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ALA 6 651 " --> pdb=" O SER 6 647 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE 6 652 " --> pdb=" O ASP 6 648 " (cutoff:3.500A) Processing helix chain '6' and resid 694 through 699 Processing helix chain '6' and resid 702 through 708 Processing helix chain '6' and resid 720 through 738 removed outlier: 3.979A pdb=" N GLU 6 726 " --> pdb=" O LYS 6 722 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER 6 729 " --> pdb=" O THR 6 725 " (cutoff:3.500A) Processing helix chain '6' and resid 739 through 741 No H-bonds generated for 'chain '6' and resid 739 through 741' Processing helix chain '6' and resid 747 through 759 removed outlier: 3.937A pdb=" N ARG 6 753 " --> pdb=" O GLU 6 749 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR 6 754 " --> pdb=" O GLN 6 750 " (cutoff:3.500A) Processing helix chain '6' and resid 766 through 783 removed outlier: 4.097A pdb=" N GLU 6 775 " --> pdb=" O SER 6 771 " (cutoff:3.500A) Processing helix chain '6' and resid 797 through 814 removed outlier: 3.516A pdb=" N GLU 6 801 " --> pdb=" O VAL 6 797 " (cutoff:3.500A) Processing helix chain '6' and resid 820 through 835 removed outlier: 3.546A pdb=" N ILE 6 824 " --> pdb=" O THR 6 820 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU 6 830 " --> pdb=" O GLU 6 826 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE 6 835 " --> pdb=" O LEU 6 831 " (cutoff:3.500A) Processing helix chain '7' and resid 395 through 408 removed outlier: 4.564A pdb=" N GLU 7 403 " --> pdb=" O GLU 7 399 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU 7 404 " --> pdb=" O ARG 7 400 " (cutoff:3.500A) Processing helix chain '7' and resid 409 through 418 Processing helix chain '7' and resid 425 through 438 removed outlier: 4.338A pdb=" N LEU 7 434 " --> pdb=" O LYS 7 430 " (cutoff:3.500A) Processing helix chain '7' and resid 466 through 477 removed outlier: 3.659A pdb=" N ALA 7 472 " --> pdb=" O GLN 7 468 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS 7 475 " --> pdb=" O LYS 7 471 " (cutoff:3.500A) Processing helix chain '7' and resid 489 through 494 Processing helix chain '7' and resid 511 through 516 Processing helix chain '7' and resid 525 through 529 removed outlier: 3.715A pdb=" N MET 7 529 " --> pdb=" O PHE 7 526 " (cutoff:3.500A) Processing helix chain '7' and resid 530 through 535 Processing helix chain '7' and resid 537 through 542 removed outlier: 3.984A pdb=" N GLU 7 542 " --> pdb=" O HIS 7 538 " (cutoff:3.500A) Processing helix chain '7' and resid 579 through 585 Processing helix chain '7' and resid 587 through 592 Processing helix chain '7' and resid 605 through 622 removed outlier: 3.842A pdb=" N GLU 7 610 " --> pdb=" O ARG 7 606 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TYR 7 618 " --> pdb=" O GLU 7 614 " (cutoff:3.500A) Processing helix chain '7' and resid 634 through 646 removed outlier: 3.858A pdb=" N TYR 7 644 " --> pdb=" O GLU 7 640 " (cutoff:3.500A) Processing helix chain '7' and resid 653 through 674 removed outlier: 3.802A pdb=" N TYR 7 659 " --> pdb=" O ALA 7 655 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLN 7 662 " --> pdb=" O ASP 7 658 " (cutoff:3.500A) Processing helix chain '7' and resid 676 through 680 Processing helix chain '7' and resid 685 through 703 Processing helix chain '7' and resid 709 through 729 removed outlier: 3.618A pdb=" N VAL 7 713 " --> pdb=" O ASP 7 709 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU 7 715 " --> pdb=" O ASP 7 711 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL 7 720 " --> pdb=" O ALA 7 716 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS 7 724 " --> pdb=" O VAL 7 720 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N LEU 7 727 " --> pdb=" O SER 7 723 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR 7 728 " --> pdb=" O LYS 7 724 " (cutoff:3.500A) Processing helix chain '2' and resid 477 through 488 removed outlier: 3.911A pdb=" N ARG 2 482 " --> pdb=" O GLU 2 478 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG 2 485 " --> pdb=" O GLU 2 481 " (cutoff:3.500A) Processing helix chain '2' and resid 492 through 501 Processing helix chain '2' and resid 508 through 521 Processing helix chain '2' and resid 548 through 558 removed outlier: 3.712A pdb=" N LEU 2 553 " --> pdb=" O LYS 2 549 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS 2 554 " --> pdb=" O SER 2 550 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYS 2 558 " --> pdb=" O LYS 2 554 " (cutoff:3.500A) Processing helix chain '2' and resid 572 through 577 Processing helix chain '2' and resid 615 through 624 removed outlier: 3.618A pdb=" N ILE 2 620 " --> pdb=" O ASP 2 616 " (cutoff:3.500A) Processing helix chain '2' and resid 632 through 636 Processing helix chain '2' and resid 662 through 667 removed outlier: 3.680A pdb=" N ASN 2 666 " --> pdb=" O PRO 2 662 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N VAL 2 667 " --> pdb=" O LEU 2 663 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 662 through 667' Processing helix chain '2' and resid 670 through 677 removed outlier: 3.661A pdb=" N LEU 2 674 " --> pdb=" O THR 2 670 " (cutoff:3.500A) Processing helix chain '2' and resid 688 through 706 removed outlier: 3.713A pdb=" N ARG 2 694 " --> pdb=" O GLU 2 690 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N PHE 2 698 " --> pdb=" O ARG 2 694 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP 2 701 " --> pdb=" O THR 2 697 " (cutoff:3.500A) Processing helix chain '2' and resid 746 through 752 removed outlier: 4.070A pdb=" N LYS 2 750 " --> pdb=" O GLN 2 746 " (cutoff:3.500A) Processing helix chain '2' and resid 759 through 774 removed outlier: 3.702A pdb=" N LEU 2 763 " --> pdb=" O PRO 2 759 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N MET 2 764 " --> pdb=" O GLN 2 760 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N LYS 2 765 " --> pdb=" O GLU 2 761 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N HIS 2 768 " --> pdb=" O MET 2 764 " (cutoff:3.500A) Processing helix chain '2' and resid 779 through 800 removed outlier: 3.858A pdb=" N MET 2 783 " --> pdb=" O HIS 2 779 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ASP 2 784 " --> pdb=" O GLN 2 780 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N LYS 2 785 " --> pdb=" O MET 2 781 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL 2 786 " --> pdb=" O ASP 2 782 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR 2 800 " --> pdb=" O GLU 2 796 " (cutoff:3.500A) Processing helix chain '2' and resid 806 through 824 removed outlier: 3.718A pdb=" N ILE 2 813 " --> pdb=" O HIS 2 809 " (cutoff:3.500A) Processing helix chain '2' and resid 830 through 847 removed outlier: 3.563A pdb=" N LEU 2 834 " --> pdb=" O SER 2 830 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASP 2 843 " --> pdb=" O LYS 2 839 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N SER 2 844 " --> pdb=" O VAL 2 840 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N PHE 2 845 " --> pdb=" O VAL 2 841 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL 2 846 " --> pdb=" O VAL 2 842 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP 2 847 " --> pdb=" O ASP 2 843 " (cutoff:3.500A) Processing helix chain '2' and resid 849 through 866 removed outlier: 5.880A pdb=" N ARG 2 855 " --> pdb=" O VAL 2 851 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N GLN 2 856 " --> pdb=" O SER 2 852 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ILE 2 863 " --> pdb=" O ARG 2 859 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N TYR 2 864 " --> pdb=" O SER 2 860 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR 2 865 " --> pdb=" O PHE 2 861 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LEU 2 866 " --> pdb=" O ALA 2 862 " (cutoff:3.500A) Processing helix chain '5' and resid 350 through 363 removed outlier: 4.203A pdb=" N GLU 5 355 " --> pdb=" O GLU 5 351 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N GLU 5 356 " --> pdb=" O GLU 5 352 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N PHE 5 357 " --> pdb=" O GLU 5 353 " (cutoff:3.500A) Processing helix chain '5' and resid 365 through 372 Processing helix chain '5' and resid 381 through 394 Processing helix chain '5' and resid 422 through 433 removed outlier: 3.868A pdb=" N LEU 5 426 " --> pdb=" O LYS 5 422 " (cutoff:3.500A) Processing helix chain '5' and resid 467 through 472 Processing helix chain '5' and resid 490 through 500 removed outlier: 4.077A pdb=" N GLU 5 495 " --> pdb=" O VAL 5 491 " (cutoff:3.500A) Processing helix chain '5' and resid 544 through 548 removed outlier: 3.883A pdb=" N LEU 5 547 " --> pdb=" O THR 5 544 " (cutoff:3.500A) Processing helix chain '5' and resid 562 through 577 removed outlier: 3.823A pdb=" N ILE 5 566 " --> pdb=" O GLU 5 562 " (cutoff:3.500A) Processing helix chain '5' and resid 595 through 610 removed outlier: 4.519A pdb=" N ARG 5 601 " --> pdb=" O GLU 5 597 " (cutoff:3.500A) Processing helix chain '5' and resid 615 through 636 Processing helix chain '5' and resid 649 through 666 removed outlier: 3.629A pdb=" N ALA 5 655 " --> pdb=" O ARG 5 651 " (cutoff:3.500A) Processing helix chain '5' and resid 673 through 686 removed outlier: 3.761A pdb=" N GLU 5 679 " --> pdb=" O ARG 5 675 " (cutoff:3.500A) Processing helix chain '3' and resid 343 through 355 removed outlier: 3.597A pdb=" N ARG 3 348 " --> pdb=" O ASP 3 344 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS 3 355 " --> pdb=" O ASN 3 351 " (cutoff:3.500A) Processing helix chain '3' and resid 358 through 367 Processing helix chain '3' and resid 374 through 387 Processing helix chain '3' and resid 414 through 423 removed outlier: 3.735A pdb=" N LEU 3 419 " --> pdb=" O LYS 3 415 " (cutoff:3.500A) Processing helix chain '3' and resid 438 through 443 Processing helix chain '3' and resid 474 through 478 Processing helix chain '3' and resid 479 through 493 removed outlier: 4.881A pdb=" N ALA 3 485 " --> pdb=" O VAL 3 481 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ILE 3 486 " --> pdb=" O ASP 3 482 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N HIS 3 487 " --> pdb=" O ARG 3 483 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLU 3 488 " --> pdb=" O VAL 3 484 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL 3 489 " --> pdb=" O ALA 3 485 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLU 3 491 " --> pdb=" O HIS 3 487 " (cutoff:3.500A) Processing helix chain '3' and resid 528 through 533 Processing helix chain '3' and resid 536 through 541 Processing helix chain '3' and resid 554 through 569 Processing helix chain '3' and resid 652 through 667 removed outlier: 3.651A pdb=" N VAL 3 667 " --> pdb=" O ALA 3 663 " (cutoff:3.500A) Processing helix chain '3' and resid 672 through 689 removed outlier: 3.960A pdb=" N VAL 3 678 " --> pdb=" O GLU 3 674 " (cutoff:3.500A) Processing helix chain '3' and resid 698 through 716 removed outlier: 4.115A pdb=" N LEU 3 702 " --> pdb=" O THR 3 698 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLU 3 703 " --> pdb=" O ALA 3 699 " (cutoff:3.500A) Processing helix chain '3' and resid 722 through 738 Processing helix chain '4' and resid 502 through 514 removed outlier: 3.686A pdb=" N ALA 4 514 " --> pdb=" O ARG 4 510 " (cutoff:3.500A) Processing helix chain '4' and resid 517 through 527 removed outlier: 4.303A pdb=" N ALA 4 527 " --> pdb=" O ALA 4 523 " (cutoff:3.500A) Processing helix chain '4' and resid 533 through 546 removed outlier: 3.956A pdb=" N LEU 4 542 " --> pdb=" O LYS 4 538 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE 4 545 " --> pdb=" O LEU 4 541 " (cutoff:3.500A) Processing helix chain '4' and resid 573 through 585 Processing helix chain '4' and resid 597 through 602 Processing helix chain '4' and resid 621 through 625 removed outlier: 4.120A pdb=" N ASP 4 625 " --> pdb=" O VAL 4 622 " (cutoff:3.500A) Processing helix chain '4' and resid 633 through 637 Processing helix chain '4' and resid 638 through 643 Processing helix chain '4' and resid 644 through 651 removed outlier: 4.321A pdb=" N VAL 4 648 " --> pdb=" O VAL 4 644 " (cutoff:3.500A) Processing helix chain '4' and resid 687 through 693 Processing helix chain '4' and resid 695 through 700 Processing helix chain '4' and resid 713 through 725 removed outlier: 4.648A pdb=" N GLU 4 719 " --> pdb=" O LYS 4 715 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS 4 722 " --> pdb=" O ARG 4 718 " (cutoff:3.500A) Processing helix chain '4' and resid 726 through 730 removed outlier: 3.545A pdb=" N LEU 4 729 " --> pdb=" O ASN 4 726 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU 4 730 " --> pdb=" O LEU 4 727 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 726 through 730' Processing helix chain '4' and resid 743 through 758 removed outlier: 3.731A pdb=" N MET 4 749 " --> pdb=" O GLU 4 745 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU 4 756 " --> pdb=" O SER 4 752 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE 4 758 " --> pdb=" O ALA 4 754 " (cutoff:3.500A) Processing helix chain '4' and resid 763 through 779 removed outlier: 3.627A pdb=" N THR 4 768 " --> pdb=" O GLU 4 764 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLU 4 769 " --> pdb=" O ALA 4 765 " (cutoff:3.500A) Processing helix chain '4' and resid 795 through 812 removed outlier: 3.565A pdb=" N GLU 4 799 " --> pdb=" O THR 4 795 " (cutoff:3.500A) Processing helix chain '4' and resid 818 through 833 removed outlier: 3.790A pdb=" N GLU 4 824 " --> pdb=" O GLU 4 820 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE 4 833 " --> pdb=" O ILE 4 829 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '6' and resid 557 through 558 Processing sheet with id=AA2, first strand: chain '6' and resid 635 through 638 removed outlier: 6.737A pdb=" N CYS 6 636 " --> pdb=" O LEU 6 679 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N ALA 6 681 " --> pdb=" O CYS 6 636 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE 6 638 " --> pdb=" O ALA 6 681 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE 6 571 " --> pdb=" O ALA 6 680 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ALA 6 682 " --> pdb=" O ILE 6 571 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL 6 573 " --> pdb=" O ALA 6 682 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '6' and resid 610 through 614 Processing sheet with id=AA4, first strand: chain '6' and resid 661 through 663 Processing sheet with id=AA5, first strand: chain '6' and resid 764 through 765 removed outlier: 6.936A pdb=" N ILE 6 764 " --> pdb=" O ILE 6 819 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain '7' and resid 442 through 443 Processing sheet with id=AA7, first strand: chain '7' and resid 481 through 484 removed outlier: 6.873A pdb=" N VAL 7 481 " --> pdb=" O CYS 7 522 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ASP 7 524 " --> pdb=" O VAL 7 481 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N THR 7 483 " --> pdb=" O ASP 7 524 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU 7 458 " --> pdb=" O ALA 7 565 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '7' and resid 495 through 498 Processing sheet with id=AA9, first strand: chain '7' and resid 546 through 550 Processing sheet with id=AB1, first strand: chain '2' and resid 563 through 566 removed outlier: 6.034A pdb=" N VAL 2 564 " --> pdb=" O LEU 2 605 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N ASP 2 607 " --> pdb=" O VAL 2 564 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N ALA 2 566 " --> pdb=" O ASP 2 607 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N CYS 2 604 " --> pdb=" O ILE 2 647 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N ALA 2 649 " --> pdb=" O CYS 2 604 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N ILE 2 606 " --> pdb=" O ALA 2 649 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL 2 539 " --> pdb=" O ALA 2 648 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N ALA 2 650 " --> pdb=" O VAL 2 539 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LEU 2 541 " --> pdb=" O ALA 2 650 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '2' and resid 578 through 581 Processing sheet with id=AB3, first strand: chain '2' and resid 628 through 631 Processing sheet with id=AB4, first strand: chain '2' and resid 777 through 778 removed outlier: 6.829A pdb=" N LYS 2 777 " --> pdb=" O VAL 2 829 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain '5' and resid 398 through 399 removed outlier: 3.545A pdb=" N LYS 5 398 " --> pdb=" O LEU 5 406 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain '5' and resid 436 through 438 removed outlier: 6.581A pdb=" N VAL 5 437 " --> pdb=" O CYS 5 478 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N GLY 5 475 " --> pdb=" O SER 5 518 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N LEU 5 520 " --> pdb=" O GLY 5 475 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL 5 477 " --> pdb=" O LEU 5 520 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N ALA 5 522 " --> pdb=" O VAL 5 477 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE 5 479 " --> pdb=" O ALA 5 522 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL 5 412 " --> pdb=" O ALA 5 521 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ASN 5 411 " --> pdb=" O MET 5 552 " (cutoff:3.500A) removed outlier: 8.710A pdb=" N PHE 5 554 " --> pdb=" O ASN 5 411 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LEU 5 413 " --> pdb=" O PHE 5 554 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain '5' and resid 451 through 454 Processing sheet with id=AB8, first strand: chain '5' and resid 501 through 506 removed outlier: 3.582A pdb=" N THR 5 511 " --> pdb=" O ILE 5 504 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain '5' and resid 613 through 614 removed outlier: 6.674A pdb=" N ARG 5 613 " --> pdb=" O ALA 5 672 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain '3' and resid 391 through 392 Processing sheet with id=AC2, first strand: chain '3' and resid 429 through 433 removed outlier: 6.797A pdb=" N ILE 3 430 " --> pdb=" O CYS 3 471 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N ASP 3 473 " --> pdb=" O ILE 3 430 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N THR 3 432 " --> pdb=" O ASP 3 473 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE 3 405 " --> pdb=" O ALA 3 514 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N ALA 3 516 " --> pdb=" O ILE 3 405 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N MET 3 407 " --> pdb=" O ALA 3 516 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N LEU 3 406 " --> pdb=" O PHE 3 547 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N VAL 3 549 " --> pdb=" O LEU 3 406 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N VAL 3 408 " --> pdb=" O VAL 3 549 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain '3' and resid 444 through 447 Processing sheet with id=AC4, first strand: chain '3' and resid 494 through 499 Processing sheet with id=AC5, first strand: chain '3' and resid 670 through 671 removed outlier: 6.652A pdb=" N GLN 3 670 " --> pdb=" O VAL 3 721 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain '4' and resid 550 through 551 Processing sheet with id=AC7, first strand: chain '4' and resid 588 through 592 removed outlier: 6.326A pdb=" N VAL 4 589 " --> pdb=" O CYS 4 630 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N ASP 4 632 " --> pdb=" O VAL 4 589 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N THR 4 591 " --> pdb=" O ASP 4 632 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LEU 4 565 " --> pdb=" O TYR 4 706 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N VAL 4 708 " --> pdb=" O LEU 4 565 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N CYS 4 567 " --> pdb=" O VAL 4 708 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain '4' and resid 603 through 606 Processing sheet with id=AC9, first strand: chain '4' and resid 653 through 657 Processing sheet with id=AD1, first strand: chain '4' and resid 761 through 762 removed outlier: 6.753A pdb=" N ILE 4 761 " --> pdb=" O VAL 4 817 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 700 hydrogen bonds defined for protein. 2007 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: 7.25 Time building geometry restraints manager: 4.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.93 - 1.11: 15816 1.11 - 1.28: 2658 1.28 - 1.46: 4864 1.46 - 1.64: 8321 1.64 - 1.82: 122 Bond restraints: 31781 Sorted by residual: bond pdb=" O3A ANP 21500 " pdb=" PB ANP 21500 " ideal model delta sigma weight residual 1.700 1.425 0.275 2.00e-02 2.50e+03 1.89e+02 bond pdb=" N3B ANP 21500 " pdb=" PG ANP 21500 " ideal model delta sigma weight residual 1.795 1.540 0.255 2.00e-02 2.50e+03 1.63e+02 bond pdb=" N3B ANP 41500 " pdb=" PG ANP 41500 " ideal model delta sigma weight residual 1.795 1.557 0.238 2.00e-02 2.50e+03 1.42e+02 bond pdb=" N3B ANP 31500 " pdb=" PG ANP 31500 " ideal model delta sigma weight residual 1.795 1.563 0.232 2.00e-02 2.50e+03 1.35e+02 bond pdb=" N3B ANP 71500 " pdb=" PG ANP 71500 " ideal model delta sigma weight residual 1.795 1.572 0.223 2.00e-02 2.50e+03 1.25e+02 ... (remaining 31776 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.96: 56986 6.96 - 13.92: 603 13.92 - 20.88: 17 20.88 - 27.84: 1 27.84 - 34.80: 1 Bond angle restraints: 57608 Sorted by residual: angle pdb=" O5' DT I 10 " pdb=" C5' DT I 10 " pdb=" C4' DT I 10 " ideal model delta sigma weight residual 109.40 118.92 -9.52 8.00e-01 1.56e+00 1.42e+02 angle pdb="HH21 ARG 6 798 " pdb=" NH2 ARG 6 798 " pdb="HH22 ARG 6 798 " ideal model delta sigma weight residual 120.00 85.20 34.80 3.00e+00 1.11e-01 1.35e+02 angle pdb=" O4' DT I 16 " pdb=" C1' DT I 16 " pdb=" N1 DT I 16 " ideal model delta sigma weight residual 108.00 115.13 -7.13 7.00e-01 2.04e+00 1.04e+02 angle pdb=" O5' DT I 2 " pdb=" C5' DT I 2 " pdb=" C4' DT I 2 " ideal model delta sigma weight residual 109.40 117.51 -8.11 8.00e-01 1.56e+00 1.03e+02 angle pdb=" O2 DT I 3 " pdb=" C2 DT I 3 " pdb=" N3 DT I 3 " ideal model delta sigma weight residual 122.30 116.64 5.66 6.00e-01 2.78e+00 8.91e+01 ... (remaining 57603 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.92: 13910 31.92 - 63.85: 712 63.85 - 95.77: 130 95.77 - 127.69: 2 127.69 - 159.61: 2 Dihedral angle restraints: 14756 sinusoidal: 8452 harmonic: 6304 Sorted by residual: dihedral pdb=" C GLN 2 849 " pdb=" N GLN 2 849 " pdb=" CA GLN 2 849 " pdb=" CB GLN 2 849 " ideal model delta harmonic sigma weight residual -122.60 -140.26 17.66 0 2.50e+00 1.60e-01 4.99e+01 dihedral pdb=" N GLN 2 849 " pdb=" C GLN 2 849 " pdb=" CA GLN 2 849 " pdb=" CB GLN 2 849 " ideal model delta harmonic sigma weight residual 122.80 139.55 -16.75 0 2.50e+00 1.60e-01 4.49e+01 dihedral pdb=" CA HIS 2 561 " pdb=" C HIS 2 561 " pdb=" N ARG 2 562 " pdb=" CA ARG 2 562 " ideal model delta harmonic sigma weight residual 180.00 150.44 29.56 0 5.00e+00 4.00e-02 3.50e+01 ... (remaining 14753 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.139: 2068 0.139 - 0.277: 418 0.277 - 0.416: 57 0.416 - 0.555: 9 0.555 - 0.693: 1 Chirality restraints: 2553 Sorted by residual: chirality pdb=" CA GLN 2 849 " pdb=" N GLN 2 849 " pdb=" C GLN 2 849 " pdb=" CB GLN 2 849 " both_signs ideal model delta sigma weight residual False 2.51 1.82 0.69 2.00e-01 2.50e+01 1.20e+01 chirality pdb=" CA SER 4 573 " pdb=" N SER 4 573 " pdb=" C SER 4 573 " pdb=" CB SER 4 573 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.44e+00 chirality pdb=" CA THR 2 618 " pdb=" N THR 2 618 " pdb=" C THR 2 618 " pdb=" CB THR 2 618 " both_signs ideal model delta sigma weight residual False 2.53 2.05 0.47 2.00e-01 2.50e+01 5.58e+00 ... (remaining 2550 not shown) Planarity restraints: 4543 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG 6 798 " 0.357 9.50e-02 1.11e+02 4.15e-01 3.57e+03 pdb=" NE ARG 6 798 " 0.080 2.00e-02 2.50e+03 pdb=" CZ ARG 6 798 " 0.124 2.00e-02 2.50e+03 pdb=" NH1 ARG 6 798 " 0.285 2.00e-02 2.50e+03 pdb=" NH2 ARG 6 798 " 0.027 2.00e-02 2.50e+03 pdb="HH11 ARG 6 798 " -0.538 2.00e-02 2.50e+03 pdb="HH12 ARG 6 798 " 0.323 2.00e-02 2.50e+03 pdb="HH21 ARG 6 798 " -0.820 2.00e-02 2.50e+03 pdb="HH22 ARG 6 798 " 0.503 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG 6 708 " -0.504 9.50e-02 1.11e+02 2.23e-01 5.10e+02 pdb=" NE ARG 6 708 " -0.093 2.00e-02 2.50e+03 pdb=" CZ ARG 6 708 " -0.093 2.00e-02 2.50e+03 pdb=" NH1 ARG 6 708 " -0.159 2.00e-02 2.50e+03 pdb=" NH2 ARG 6 708 " -0.000 2.00e-02 2.50e+03 pdb="HH11 ARG 6 708 " 0.326 2.00e-02 2.50e+03 pdb="HH12 ARG 6 708 " -0.114 2.00e-02 2.50e+03 pdb="HH21 ARG 6 708 " 0.175 2.00e-02 2.50e+03 pdb="HH22 ARG 6 708 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN 2 551 " -0.136 2.00e-02 2.50e+03 1.70e-01 4.34e+02 pdb=" CD GLN 2 551 " 0.037 2.00e-02 2.50e+03 pdb=" OE1 GLN 2 551 " 0.051 2.00e-02 2.50e+03 pdb=" NE2 GLN 2 551 " 0.264 2.00e-02 2.50e+03 pdb="HE21 GLN 2 551 " 0.062 2.00e-02 2.50e+03 pdb="HE22 GLN 2 551 " -0.279 2.00e-02 2.50e+03 ... (remaining 4540 not shown) Histogram of nonbonded interaction distances: 1.41 - 2.05: 1100 2.05 - 2.69: 43784 2.69 - 3.32: 95631 3.32 - 3.96: 121593 3.96 - 4.60: 183287 Nonbonded interactions: 445395 Sorted by model distance: nonbonded pdb=" HG1 THR 2 590 " pdb=" H LEU 2 591 " model vdw 1.412 2.100 nonbonded pdb=" O VAL 2 699 " pdb=" HG SER 2 702 " model vdw 1.589 2.450 nonbonded pdb="HG11 VAL 6 816 " pdb=" H GLU 6 818 " model vdw 1.601 2.270 nonbonded pdb=" O THR 6 579 " pdb=" HG SER 6 580 " model vdw 1.602 2.450 nonbonded pdb=" OD1 ASP 7 530 " pdb=" HG SER 7 532 " model vdw 1.613 2.450 ... (remaining 445390 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 3.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.210 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 28.940 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6863 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 : 0.014 0.275 15943 Z= 0.883 Angle : 2.111 18.692 21605 Z= 1.396 Chirality : 0.114 0.693 2553 Planarity : 0.020 0.224 2678 Dihedral : 16.939 159.613 6182 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 1.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 0.24 % Allowed : 3.75 % Favored : 96.01 % Cbeta Deviations : 1.13 % 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: -3.05 (0.16), residues: 1903 helix: -2.38 (0.12), residues: 950 sheet: -1.43 (0.32), residues: 225 loop : -1.38 (0.21), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.002 ARG 2 617 TYR 0.154 0.023 TYR 6 828 PHE 0.135 0.018 PHE 7 598 TRP 0.094 0.024 TRP 2 476 HIS 0.015 0.004 HIS 5 676 Details of bonding type rmsd/Z covalent geometry : bond 0.01389 / 0.88 (15943) covalent geometry : angle 2.11145 / 1.40 (21605) hydrogen bonds : bond 0.20360 / 13.99 ( 700) hydrogen bonds : angle 8.32436 / 5.91 ( 2007) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3806 Ramachandran restraints generated. 1903 Oldfield, 0 Emsley, 1903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3806 Ramachandran restraints generated. 1903 Oldfield, 0 Emsley, 1903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 705 is missing expected H atoms. Skipping. Residue MET 706 is missing expected H atoms. Skipping. Residue SER 797 is missing expected H atoms. Skipping. Evaluate side-chains 321 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 317 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 650 VAL cc_start: 0.8168 (p) cc_final: 0.7840 (m) REVERT: 6 660 THR cc_start: 0.7770 (m) cc_final: 0.7376 (m) REVERT: 7 443 ARG cc_start: 0.8679 (ttp-110) cc_final: 0.8368 (mmm160) REVERT: 7 479 ARG cc_start: 0.8709 (mtp85) cc_final: 0.8315 (mtt90) REVERT: 7 728 TYR cc_start: 0.7398 (t80) cc_final: 0.7099 (t80) REVERT: 2 764 MET cc_start: 0.8176 (mtm) cc_final: 0.7764 (mtm) REVERT: 2 810 LEU cc_start: 0.7984 (tp) cc_final: 0.7757 (tt) REVERT: 5 409 ASP cc_start: 0.6864 (m-30) cc_final: 0.6470 (m-30) REVERT: 5 572 VAL cc_start: 0.7728 (t) cc_final: 0.7455 (t) REVERT: 3 673 GLN cc_start: 0.9289 (tt0) cc_final: 0.9020 (tp-100) outliers start: 4 outliers final: 0 residues processed: 320 average time/residue: 0.3263 time to fit residues: 150.9525 Evaluate side-chains 170 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 6 690 ASN 6 700 ASN 7 543 GLN 7 657 ASN 7 683 GLN 2 508 HIS 3 417 GLN 3 517 ASN 4 685 ASN 4 797 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.099886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.078023 restraints weight = 134123.046| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 3.80 r_work: 0.3252 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 15943 Z= 0.189 Angle : 0.752 8.049 21605 Z= 0.413 Chirality : 0.045 0.185 2553 Planarity : 0.006 0.089 2678 Dihedral : 15.416 165.782 2432 Min Nonbonded Distance : 1.715 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.73 % Favored : 96.22 % Rotamer: Outliers : 1.13 % Allowed : 7.80 % Favored : 91.07 % 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: -1.66 (0.18), residues: 1903 helix: -0.76 (0.15), residues: 957 sheet: -1.45 (0.31), residues: 240 loop : -1.20 (0.21), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG 7 534 TYR 0.018 0.002 TYR 6 828 PHE 0.026 0.002 PHE 7 526 TRP 0.006 0.002 TRP 2 476 HIS 0.007 0.002 HIS 2 621 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.19 (15943) covalent geometry : angle 0.75205 / 0.41 (21605) hydrogen bonds : bond 0.05867 / 4.04 ( 700) hydrogen bonds : angle 5.72680 / 4.09 ( 2007) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3806 Ramachandran restraints generated. 1903 Oldfield, 0 Emsley, 1903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3806 Ramachandran restraints generated. 1903 Oldfield, 0 Emsley, 1903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 705 is missing expected H atoms. Skipping. Residue MET 706 is missing expected H atoms. Skipping. Residue SER 797 is missing expected H atoms. Skipping. Evaluate side-chains 208 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 189 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 564 LYS cc_start: 0.8902 (mttt) cc_final: 0.8665 (ptmt) REVERT: 6 780 LEU cc_start: 0.9157 (mt) cc_final: 0.8936 (mt) REVERT: 2 810 LEU cc_start: 0.7452 (tp) cc_final: 0.7198 (tt) REVERT: 5 661 GLU cc_start: 0.8801 (mt-10) cc_final: 0.8598 (tt0) REVERT: 3 462 MET cc_start: 0.8993 (mmm) cc_final: 0.8769 (mmm) REVERT: 4 561 ASP cc_start: 0.8007 (m-30) cc_final: 0.7759 (m-30) outliers start: 19 outliers final: 12 residues processed: 204 average time/residue: 0.2944 time to fit residues: 90.8710 Evaluate side-chains 157 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 145 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 675 ARG Chi-restraints excluded: chain 7 residue 397 VAL Chi-restraints excluded: chain 7 residue 555 THR Chi-restraints excluded: chain 2 residue 494 ILE Chi-restraints excluded: chain 5 residue 360 LEU Chi-restraints excluded: chain 5 residue 429 VAL Chi-restraints excluded: chain 5 residue 433 SER Chi-restraints excluded: chain 5 residue 464 LEU Chi-restraints excluded: chain 5 residue 476 VAL Chi-restraints excluded: chain 5 residue 648 ILE Chi-restraints excluded: chain 3 residue 430 ILE Chi-restraints excluded: chain 3 residue 737 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 15 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 chunk 167 optimal weight: 0.6980 chunk 181 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 83 optimal weight: 6.9990 chunk 178 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 129 optimal weight: 0.5980 chunk 61 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 6 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 508 HIS 2 768 HIS 4 651 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.098967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.077286 restraints weight = 133751.910| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 3.80 r_work: 0.3237 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15943 Z= 0.131 Angle : 0.615 6.196 21605 Z= 0.336 Chirality : 0.043 0.170 2553 Planarity : 0.004 0.058 2678 Dihedral : 14.080 162.727 2432 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.25 % Allowed : 9.47 % Favored : 89.28 % 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 (0.18), residues: 1903 helix: -0.09 (0.16), residues: 977 sheet: -1.36 (0.33), residues: 221 loop : -1.13 (0.22), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG 2 643 TYR 0.023 0.002 TYR 6 597 PHE 0.014 0.001 PHE 2 698 TRP 0.003 0.001 TRP 2 589 HIS 0.015 0.001 HIS 2 621 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 (15943) covalent geometry : angle 0.61547 / 0.34 (21605) hydrogen bonds : bond 0.04550 / 3.14 ( 700) hydrogen bonds : angle 5.13986 / 3.66 ( 2007) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3806 Ramachandran restraints generated. 1903 Oldfield, 0 Emsley, 1903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3806 Ramachandran restraints generated. 1903 Oldfield, 0 Emsley, 1903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 705 is missing expected H atoms. Skipping. Residue MET 706 is missing expected H atoms. Skipping. Residue SER 797 is missing expected H atoms. Skipping. Evaluate side-chains 189 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 168 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 564 LYS cc_start: 0.8970 (mttt) cc_final: 0.8723 (ptmt) REVERT: 6 649 GLN cc_start: 0.7332 (mt0) cc_final: 0.6466 (tt0) REVERT: 5 354 GLU cc_start: 0.8670 (pp20) cc_final: 0.8282 (pp20) REVERT: 5 482 PHE cc_start: 0.7996 (OUTLIER) cc_final: 0.7582 (m-80) REVERT: 5 572 VAL cc_start: 0.8166 (t) cc_final: 0.7962 (p) REVERT: 3 462 MET cc_start: 0.8917 (mmm) cc_final: 0.8648 (mmm) REVERT: 4 561 ASP cc_start: 0.8000 (m-30) cc_final: 0.7741 (m-30) outliers start: 21 outliers final: 10 residues processed: 186 average time/residue: 0.2519 time to fit residues: 75.1927 Evaluate side-chains 163 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 152 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 675 ARG Chi-restraints excluded: chain 7 residue 397 VAL Chi-restraints excluded: chain 7 residue 555 THR Chi-restraints excluded: chain 2 residue 494 ILE Chi-restraints excluded: chain 2 residue 695 LEU Chi-restraints excluded: chain 5 residue 429 VAL Chi-restraints excluded: chain 5 residue 433 SER Chi-restraints excluded: chain 5 residue 476 VAL Chi-restraints excluded: chain 5 residue 481 GLU Chi-restraints excluded: chain 5 residue 482 PHE Chi-restraints excluded: chain 3 residue 737 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 19 optimal weight: 5.9990 chunk 184 optimal weight: 0.0970 chunk 34 optimal weight: 2.9990 chunk 114 optimal weight: 6.9990 chunk 59 optimal weight: 0.7980 chunk 116 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 6 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 508 HIS 5 632 GLN 5 636 ASN 4 582 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.096192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.074410 restraints weight = 135166.846| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 3.79 r_work: 0.3172 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.4406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 15943 Z= 0.195 Angle : 0.602 8.572 21605 Z= 0.325 Chirality : 0.042 0.201 2553 Planarity : 0.004 0.051 2678 Dihedral : 13.281 164.490 2432 Min Nonbonded Distance : 1.724 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.31 % Allowed : 10.01 % Favored : 88.68 % 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: -0.76 (0.19), residues: 1903 helix: 0.18 (0.16), residues: 990 sheet: -1.31 (0.33), residues: 221 loop : -1.05 (0.22), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 2 705 TYR 0.016 0.001 TYR 2 769 PHE 0.015 0.001 PHE 2 520 TRP 0.002 0.001 TRP 2 589 HIS 0.006 0.001 HIS 2 707 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.20 (15943) covalent geometry : angle 0.60241 / 0.33 (21605) hydrogen bonds : bond 0.03904 / 2.68 ( 700) hydrogen bonds : angle 4.98330 / 3.58 ( 2007) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3806 Ramachandran restraints generated. 1903 Oldfield, 0 Emsley, 1903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3806 Ramachandran restraints generated. 1903 Oldfield, 0 Emsley, 1903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 705 is missing expected H atoms. Skipping. Residue MET 706 is missing expected H atoms. Skipping. Residue SER 797 is missing expected H atoms. Skipping. Evaluate side-chains 176 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 154 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 583 GLN cc_start: 0.8684 (mm110) cc_final: 0.8441 (mt0) REVERT: 6 649 GLN cc_start: 0.7590 (mt0) cc_final: 0.6343 (tm-30) REVERT: 6 780 LEU cc_start: 0.9124 (mt) cc_final: 0.8899 (mt) REVERT: 5 404 MET cc_start: 0.8459 (tpp) cc_final: 0.8154 (tpp) REVERT: 5 500 GLN cc_start: 0.8246 (mm-40) cc_final: 0.7488 (tm-30) REVERT: 5 572 VAL cc_start: 0.8406 (t) cc_final: 0.8167 (p) REVERT: 3 417 GLN cc_start: 0.9178 (tp40) cc_final: 0.8840 (tp-100) REVERT: 3 462 MET cc_start: 0.8862 (mmm) cc_final: 0.8501 (mmm) REVERT: 4 561 ASP cc_start: 0.8082 (m-30) cc_final: 0.7781 (m-30) outliers start: 22 outliers final: 15 residues processed: 172 average time/residue: 0.2567 time to fit residues: 70.2973 Evaluate side-chains 151 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 675 ARG Chi-restraints excluded: chain 7 residue 483 THR Chi-restraints excluded: chain 7 residue 555 THR Chi-restraints excluded: chain 7 residue 561 THR Chi-restraints excluded: chain 7 residue 598 PHE Chi-restraints excluded: chain 2 residue 511 ILE Chi-restraints excluded: chain 2 residue 552 ILE Chi-restraints excluded: chain 2 residue 695 LEU Chi-restraints excluded: chain 5 residue 429 VAL Chi-restraints excluded: chain 5 residue 433 SER Chi-restraints excluded: chain 5 residue 464 LEU Chi-restraints excluded: chain 5 residue 476 VAL Chi-restraints excluded: chain 3 residue 363 LEU Chi-restraints excluded: chain 3 residue 737 LEU Chi-restraints excluded: chain 4 residue 749 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 148 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 160 optimal weight: 2.9990 chunk 129 optimal weight: 0.8980 chunk 144 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 167 optimal weight: 0.6980 chunk 77 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 508 HIS ** 2 621 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 632 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.096436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.074820 restraints weight = 133593.012| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 3.77 r_work: 0.3185 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.4681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15943 Z= 0.126 Angle : 0.537 7.299 21605 Z= 0.292 Chirality : 0.041 0.159 2553 Planarity : 0.003 0.032 2678 Dihedral : 12.752 163.461 2432 Min Nonbonded Distance : 1.754 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.07 % Allowed : 11.26 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.19), residues: 1903 helix: 0.51 (0.17), residues: 994 sheet: -1.22 (0.32), residues: 231 loop : -0.83 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 5 675 TYR 0.009 0.001 TYR 4 750 PHE 0.011 0.001 PHE 2 520 TRP 0.002 0.001 TRP 2 589 HIS 0.006 0.001 HIS 5 494 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.13 (15943) covalent geometry : angle 0.53688 / 0.29 (21605) hydrogen bonds : bond 0.03510 / 2.42 ( 700) hydrogen bonds : angle 4.67550 / 3.33 ( 2007) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3806 Ramachandran restraints generated. 1903 Oldfield, 0 Emsley, 1903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3806 Ramachandran restraints generated. 1903 Oldfield, 0 Emsley, 1903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 705 is missing expected H atoms. Skipping. Residue MET 706 is missing expected H atoms. Skipping. Residue SER 797 is missing expected H atoms. Skipping. Evaluate side-chains 165 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 147 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 649 GLN cc_start: 0.7720 (mt0) cc_final: 0.7440 (tm-30) REVERT: 6 780 LEU cc_start: 0.9117 (mt) cc_final: 0.8875 (mt) REVERT: 7 459 MET cc_start: 0.9217 (mmm) cc_final: 0.8736 (tpt) REVERT: 5 482 PHE cc_start: 0.8270 (OUTLIER) cc_final: 0.8039 (m-80) REVERT: 3 417 GLN cc_start: 0.9193 (tp40) cc_final: 0.8919 (tp-100) REVERT: 3 462 MET cc_start: 0.8827 (mmm) cc_final: 0.8408 (mmm) REVERT: 4 561 ASP cc_start: 0.8048 (m-30) cc_final: 0.7748 (m-30) outliers start: 18 outliers final: 12 residues processed: 162 average time/residue: 0.2694 time to fit residues: 69.2661 Evaluate side-chains 148 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 135 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 675 ARG Chi-restraints excluded: chain 6 residue 701 MET Chi-restraints excluded: chain 7 residue 561 THR Chi-restraints excluded: chain 7 residue 598 PHE Chi-restraints excluded: chain 2 residue 515 VAL Chi-restraints excluded: chain 2 residue 695 LEU Chi-restraints excluded: chain 5 residue 433 SER Chi-restraints excluded: chain 5 residue 464 LEU Chi-restraints excluded: chain 5 residue 476 VAL Chi-restraints excluded: chain 5 residue 482 PHE Chi-restraints excluded: chain 3 residue 546 LEU Chi-restraints excluded: chain 3 residue 737 LEU Chi-restraints excluded: chain 4 residue 749 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 35 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 8 optimal weight: 0.0980 chunk 158 optimal weight: 3.9990 chunk 167 optimal weight: 1.9990 chunk 70 optimal weight: 0.3980 chunk 172 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 128 optimal weight: 2.9990 chunk 78 optimal weight: 7.9990 chunk 123 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 6 583 GLN 2 508 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.095778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.074197 restraints weight = 133487.815| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 3.74 r_work: 0.3175 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.4903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15943 Z= 0.130 Angle : 0.523 6.880 21605 Z= 0.284 Chirality : 0.040 0.160 2553 Planarity : 0.003 0.056 2678 Dihedral : 12.422 163.744 2432 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.83 % Allowed : 11.79 % Favored : 87.37 % 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: -0.16 (0.19), residues: 1903 helix: 0.72 (0.17), residues: 981 sheet: -1.11 (0.32), residues: 233 loop : -0.82 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 7 673 TYR 0.010 0.001 TYR 6 597 PHE 0.009 0.001 PHE 5 554 TRP 0.001 0.001 TRP 2 589 HIS 0.006 0.001 HIS 5 494 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (15943) covalent geometry : angle 0.52304 / 0.28 (21605) hydrogen bonds : bond 0.03303 / 2.27 ( 700) hydrogen bonds : angle 4.56034 / 3.24 ( 2007) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3806 Ramachandran restraints generated. 1903 Oldfield, 0 Emsley, 1903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3806 Ramachandran restraints generated. 1903 Oldfield, 0 Emsley, 1903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 705 is missing expected H atoms. Skipping. Residue MET 706 is missing expected H atoms. Skipping. Residue SER 797 is missing expected H atoms. Skipping. Evaluate side-chains 151 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 137 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 649 GLN cc_start: 0.7710 (mt0) cc_final: 0.7373 (tm-30) REVERT: 6 780 LEU cc_start: 0.9111 (mt) cc_final: 0.8859 (mt) REVERT: 5 500 GLN cc_start: 0.8179 (mm-40) cc_final: 0.7468 (tm-30) REVERT: 3 488 GLU cc_start: 0.8668 (tp30) cc_final: 0.8466 (tp30) REVERT: 4 561 ASP cc_start: 0.8076 (m-30) cc_final: 0.7785 (m-30) outliers start: 14 outliers final: 11 residues processed: 148 average time/residue: 0.2602 time to fit residues: 61.6344 Evaluate side-chains 146 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 135 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 675 ARG Chi-restraints excluded: chain 7 residue 561 THR Chi-restraints excluded: chain 7 residue 598 PHE Chi-restraints excluded: chain 2 residue 515 VAL Chi-restraints excluded: chain 2 residue 695 LEU Chi-restraints excluded: chain 5 residue 433 SER Chi-restraints excluded: chain 5 residue 464 LEU Chi-restraints excluded: chain 5 residue 476 VAL Chi-restraints excluded: chain 3 residue 737 LEU Chi-restraints excluded: chain 4 residue 572 THR Chi-restraints excluded: chain 4 residue 749 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 110 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 151 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 180 optimal weight: 0.8980 chunk 166 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 129 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 7 615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 508 HIS 2 651 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.095761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.074441 restraints weight = 134966.928| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 3.72 r_work: 0.3179 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.5118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15943 Z= 0.114 Angle : 0.510 8.257 21605 Z= 0.274 Chirality : 0.040 0.159 2553 Planarity : 0.003 0.072 2678 Dihedral : 12.100 162.292 2432 Min Nonbonded Distance : 1.747 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.07 % Allowed : 11.79 % Favored : 87.14 % 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: 0.14 (0.20), residues: 1903 helix: 0.97 (0.17), residues: 983 sheet: -0.93 (0.31), residues: 252 loop : -0.69 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 7 673 TYR 0.009 0.001 TYR 2 790 PHE 0.010 0.001 PHE 5 554 TRP 0.001 0.001 TRP 2 589 HIS 0.007 0.001 HIS 5 494 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (15943) covalent geometry : angle 0.50959 / 0.27 (21605) hydrogen bonds : bond 0.03109 / 2.13 ( 700) hydrogen bonds : angle 4.39158 / 3.13 ( 2007) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3806 Ramachandran restraints generated. 1903 Oldfield, 0 Emsley, 1903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3806 Ramachandran restraints generated. 1903 Oldfield, 0 Emsley, 1903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 705 is missing expected H atoms. Skipping. Residue MET 706 is missing expected H atoms. Skipping. Residue SER 797 is missing expected H atoms. Skipping. Evaluate side-chains 162 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 649 GLN cc_start: 0.7749 (mt0) cc_final: 0.7266 (tm-30) REVERT: 6 780 LEU cc_start: 0.9117 (mt) cc_final: 0.8866 (mt) REVERT: 2 695 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8583 (tp) REVERT: 5 500 GLN cc_start: 0.8190 (mm-40) cc_final: 0.7493 (tm-30) REVERT: 3 417 GLN cc_start: 0.9059 (tp40) cc_final: 0.8838 (tp-100) REVERT: 4 561 ASP cc_start: 0.8086 (m-30) cc_final: 0.7787 (m-30) outliers start: 18 outliers final: 14 residues processed: 159 average time/residue: 0.2641 time to fit residues: 66.6284 Evaluate side-chains 150 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 135 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 589 VAL Chi-restraints excluded: chain 6 residue 701 MET Chi-restraints excluded: chain 7 residue 483 THR Chi-restraints excluded: chain 7 residue 561 THR Chi-restraints excluded: chain 7 residue 598 PHE Chi-restraints excluded: chain 2 residue 515 VAL Chi-restraints excluded: chain 2 residue 552 ILE Chi-restraints excluded: chain 2 residue 695 LEU Chi-restraints excluded: chain 5 residue 433 SER Chi-restraints excluded: chain 5 residue 464 LEU Chi-restraints excluded: chain 5 residue 476 VAL Chi-restraints excluded: chain 5 residue 577 THR Chi-restraints excluded: chain 3 residue 737 LEU Chi-restraints excluded: chain 4 residue 572 THR Chi-restraints excluded: chain 4 residue 749 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 47 optimal weight: 3.9990 chunk 148 optimal weight: 0.0970 chunk 192 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 chunk 151 optimal weight: 0.5980 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 6 583 GLN 2 508 HIS 2 651 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.094433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.072951 restraints weight = 134917.223| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 3.69 r_work: 0.3149 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.5290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15943 Z= 0.153 Angle : 0.520 7.132 21605 Z= 0.282 Chirality : 0.040 0.162 2553 Planarity : 0.003 0.032 2678 Dihedral : 11.924 163.335 2432 Min Nonbonded Distance : 1.726 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.43 % Allowed : 11.55 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.19), residues: 1903 helix: 1.00 (0.17), residues: 983 sheet: -0.93 (0.32), residues: 254 loop : -0.71 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 3 455 TYR 0.008 0.001 TYR 5 438 PHE 0.011 0.001 PHE 5 554 TRP 0.001 0.000 TRP 2 589 HIS 0.005 0.001 HIS 2 508 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (15943) covalent geometry : angle 0.51998 / 0.28 (21605) hydrogen bonds : bond 0.03142 / 2.14 ( 700) hydrogen bonds : angle 4.42500 / 3.16 ( 2007) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3806 Ramachandran restraints generated. 1903 Oldfield, 0 Emsley, 1903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3806 Ramachandran restraints generated. 1903 Oldfield, 0 Emsley, 1903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 705 is missing expected H atoms. Skipping. Residue MET 706 is missing expected H atoms. Skipping. Residue SER 797 is missing expected H atoms. Skipping. Evaluate side-chains 158 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 134 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 649 GLN cc_start: 0.7813 (mt0) cc_final: 0.7272 (tm-30) REVERT: 6 780 LEU cc_start: 0.9122 (mt) cc_final: 0.8869 (mt) REVERT: 2 695 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8680 (tp) REVERT: 5 500 GLN cc_start: 0.8179 (mm-40) cc_final: 0.7372 (tm-30) REVERT: 3 417 GLN cc_start: 0.9137 (tp40) cc_final: 0.8886 (tp-100) REVERT: 4 561 ASP cc_start: 0.8216 (m-30) cc_final: 0.7742 (m-30) outliers start: 24 outliers final: 18 residues processed: 153 average time/residue: 0.2654 time to fit residues: 64.4831 Evaluate side-chains 148 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 589 VAL Chi-restraints excluded: chain 6 residue 675 ARG Chi-restraints excluded: chain 6 residue 701 MET Chi-restraints excluded: chain 7 residue 481 VAL Chi-restraints excluded: chain 7 residue 483 THR Chi-restraints excluded: chain 7 residue 561 THR Chi-restraints excluded: chain 7 residue 598 PHE Chi-restraints excluded: chain 2 residue 511 ILE Chi-restraints excluded: chain 2 residue 515 VAL Chi-restraints excluded: chain 2 residue 538 ASN Chi-restraints excluded: chain 2 residue 552 ILE Chi-restraints excluded: chain 2 residue 695 LEU Chi-restraints excluded: chain 5 residue 433 SER Chi-restraints excluded: chain 5 residue 464 LEU Chi-restraints excluded: chain 5 residue 476 VAL Chi-restraints excluded: chain 5 residue 577 THR Chi-restraints excluded: chain 3 residue 363 LEU Chi-restraints excluded: chain 4 residue 572 THR Chi-restraints excluded: chain 4 residue 749 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 82 optimal weight: 0.3980 chunk 120 optimal weight: 0.0980 chunk 132 optimal weight: 0.9990 chunk 167 optimal weight: 0.8980 chunk 88 optimal weight: 0.7980 chunk 148 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 7 615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 508 HIS 2 651 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.095211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.073802 restraints weight = 133173.737| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 3.75 r_work: 0.3172 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.5427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 15943 Z= 0.098 Angle : 0.490 8.724 21605 Z= 0.264 Chirality : 0.040 0.155 2553 Planarity : 0.003 0.058 2678 Dihedral : 11.740 161.697 2432 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.89 % Allowed : 11.91 % Favored : 87.19 % 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: 0.41 (0.20), residues: 1903 helix: 1.23 (0.17), residues: 981 sheet: -0.92 (0.31), residues: 264 loop : -0.54 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG 4 559 TYR 0.008 0.001 TYR 4 750 PHE 0.016 0.001 PHE 5 684 TRP 0.001 0.000 TRP 2 589 HIS 0.008 0.001 HIS 7 622 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.10 (15943) covalent geometry : angle 0.49001 / 0.26 (21605) hydrogen bonds : bond 0.02917 / 1.99 ( 700) hydrogen bonds : angle 4.21609 / 3.00 ( 2007) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3806 Ramachandran restraints generated. 1903 Oldfield, 0 Emsley, 1903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3806 Ramachandran restraints generated. 1903 Oldfield, 0 Emsley, 1903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 705 is missing expected H atoms. Skipping. Residue MET 706 is missing expected H atoms. Skipping. Residue SER 797 is missing expected H atoms. Skipping. Evaluate side-chains 154 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 139 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 649 GLN cc_start: 0.7812 (mt0) cc_final: 0.7304 (tm-30) REVERT: 6 660 THR cc_start: 0.7690 (m) cc_final: 0.7457 (p) REVERT: 6 780 LEU cc_start: 0.9120 (mt) cc_final: 0.8859 (mt) REVERT: 2 695 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8666 (tp) REVERT: 5 393 MET cc_start: 0.8250 (mmm) cc_final: 0.8031 (mmm) REVERT: 5 500 GLN cc_start: 0.7690 (mm-40) cc_final: 0.7440 (tm-30) REVERT: 3 417 GLN cc_start: 0.9090 (tp40) cc_final: 0.8842 (tp-100) REVERT: 4 561 ASP cc_start: 0.8113 (m-30) cc_final: 0.7768 (m-30) REVERT: 4 847 MET cc_start: 0.8653 (mmp) cc_final: 0.8307 (mmp) outliers start: 15 outliers final: 13 residues processed: 151 average time/residue: 0.2603 time to fit residues: 62.6149 Evaluate side-chains 145 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 589 VAL Chi-restraints excluded: chain 6 residue 675 ARG Chi-restraints excluded: chain 6 residue 701 MET Chi-restraints excluded: chain 7 residue 483 THR Chi-restraints excluded: chain 7 residue 598 PHE Chi-restraints excluded: chain 2 residue 515 VAL Chi-restraints excluded: chain 2 residue 552 ILE Chi-restraints excluded: chain 2 residue 695 LEU Chi-restraints excluded: chain 5 residue 433 SER Chi-restraints excluded: chain 5 residue 476 VAL Chi-restraints excluded: chain 5 residue 577 THR Chi-restraints excluded: chain 3 residue 363 LEU Chi-restraints excluded: chain 4 residue 572 THR Chi-restraints excluded: chain 4 residue 749 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 79 optimal weight: 8.9990 chunk 141 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 99 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 142 optimal weight: 0.8980 chunk 192 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 185 optimal weight: 0.7980 chunk 129 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 6 583 GLN 2 508 HIS 2 651 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.094904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.073410 restraints weight = 134266.735| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 3.73 r_work: 0.3162 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.5538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15943 Z= 0.117 Angle : 0.499 8.868 21605 Z= 0.269 Chirality : 0.040 0.160 2553 Planarity : 0.003 0.036 2678 Dihedral : 11.642 162.624 2432 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.01 % Allowed : 11.97 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.20), residues: 1903 helix: 1.24 (0.17), residues: 982 sheet: -0.89 (0.32), residues: 255 loop : -0.55 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG 4 559 TYR 0.007 0.001 TYR 4 750 PHE 0.013 0.001 PHE 5 684 TRP 0.004 0.001 TRP 2 476 HIS 0.008 0.001 HIS 5 494 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (15943) covalent geometry : angle 0.49912 / 0.27 (21605) hydrogen bonds : bond 0.02941 / 1.99 ( 700) hydrogen bonds : angle 4.23803 / 3.02 ( 2007) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3806 Ramachandran restraints generated. 1903 Oldfield, 0 Emsley, 1903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3806 Ramachandran restraints generated. 1903 Oldfield, 0 Emsley, 1903 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 581 is missing expected H atoms. Skipping. Residue ILE 705 is missing expected H atoms. Skipping. Residue MET 706 is missing expected H atoms. Skipping. Residue SER 797 is missing expected H atoms. Skipping. Evaluate side-chains 154 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 137 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 6 649 GLN cc_start: 0.7824 (mt0) cc_final: 0.7396 (tm-30) REVERT: 6 660 THR cc_start: 0.7812 (m) cc_final: 0.7592 (p) REVERT: 6 780 LEU cc_start: 0.9111 (mt) cc_final: 0.8858 (mt) REVERT: 2 695 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8700 (tp) REVERT: 5 500 GLN cc_start: 0.8021 (mm-40) cc_final: 0.7333 (tm-30) REVERT: 3 417 GLN cc_start: 0.9090 (tp40) cc_final: 0.8835 (tp-100) REVERT: 3 435 ARG cc_start: 0.8290 (tmt170) cc_final: 0.7881 (ttt180) REVERT: 4 561 ASP cc_start: 0.8148 (m-30) cc_final: 0.7804 (m-30) REVERT: 4 847 MET cc_start: 0.8668 (mmp) cc_final: 0.8333 (mmp) outliers start: 17 outliers final: 13 residues processed: 150 average time/residue: 0.2477 time to fit residues: 59.2831 Evaluate side-chains 148 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 589 VAL Chi-restraints excluded: chain 6 residue 701 MET Chi-restraints excluded: chain 7 residue 483 THR Chi-restraints excluded: chain 7 residue 598 PHE Chi-restraints excluded: chain 2 residue 511 ILE Chi-restraints excluded: chain 2 residue 515 VAL Chi-restraints excluded: chain 2 residue 552 ILE Chi-restraints excluded: chain 2 residue 695 LEU Chi-restraints excluded: chain 5 residue 433 SER Chi-restraints excluded: chain 5 residue 476 VAL Chi-restraints excluded: chain 5 residue 577 THR Chi-restraints excluded: chain 3 residue 363 LEU Chi-restraints excluded: chain 4 residue 572 THR Chi-restraints excluded: chain 4 residue 749 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 150 optimal weight: 0.9980 chunk 120 optimal weight: 0.0870 chunk 186 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 142 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 162 optimal weight: 0.4980 chunk 7 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 508 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.095288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.073735 restraints weight = 133263.573| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 3.82 r_work: 0.3172 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.5662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15943 Z= 0.097 Angle : 0.481 7.239 21605 Z= 0.259 Chirality : 0.040 0.159 2553 Planarity : 0.003 0.044 2678 Dihedral : 11.532 161.386 2432 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.89 % Allowed : 12.21 % Favored : 86.90 % 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: 0.58 (0.20), residues: 1903 helix: 1.35 (0.17), residues: 987 sheet: -0.88 (0.31), residues: 262 loop : -0.44 (0.25), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG 4 559 TYR 0.008 0.001 TYR 3 659 PHE 0.012 0.001 PHE 5 684 TRP 0.001 0.000 TRP 2 589 HIS 0.007 0.001 HIS 7 622 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.10 (15943) covalent geometry : angle 0.48092 / 0.26 (21605) hydrogen bonds : bond 0.02805 / 1.90 ( 700) hydrogen bonds : angle 4.14949 / 2.95 ( 2007) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6555.58 seconds wall clock time: 112 minutes 4.89 seconds (6724.89 seconds total)