Starting phenix.real_space_refine on Sun Aug 11 09:24:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sko_10230/08_2024/6sko_10230_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sko_10230/08_2024/6sko_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sko_10230/08_2024/6sko_10230.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sko_10230/08_2024/6sko_10230.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sko_10230/08_2024/6sko_10230_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sko_10230/08_2024/6sko_10230_trim.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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 Residue "6 GLU 502": "OE1" <-> "OE2" Residue "6 GLU 515": "OE1" <-> "OE2" Residue "6 GLU 523": "OE1" <-> "OE2" Residue "6 ARG 531": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "6 GLU 541": "OE1" <-> "OE2" Residue "6 ARG 566": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "6 ARG 614": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "6 GLU 654": "OE1" <-> "OE2" Residue "6 GLU 726": "OE1" <-> "OE2" Residue "6 ARG 738": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "6 GLU 740": "OE1" <-> "OE2" Residue "6 TYR 772": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "6 ARG 781": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "6 ARG 798": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "6 GLU 801": "OE1" <-> "OE2" Residue "6 GLU 826": "OE1" <-> "OE2" Residue "7 GLU 399": "OE1" <-> "OE2" Residue "7 ARG 400": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "7 ARG 451": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "7 ARG 479": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "7 GLU 509": "OE1" <-> "OE2" Residue "7 ARG 560": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "7 ARG 573": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "7 GLU 634": "OE1" <-> "OE2" Residue "7 GLU 654": "OE1" <-> "OE2" Residue "7 ARG 694": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "7 ARG 703": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "7 ARG 718": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "7 GLU 730": "OE1" <-> "OE2" Residue "2 GLU 480": "OE1" <-> "OE2" Residue "2 ARG 482": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "2 GLU 483": "OE1" <-> "OE2" Residue "2 ARG 485": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "2 ARG 491": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "2 ARG 509": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "2 ARG 534": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "2 GLU 557": "OE1" <-> "OE2" Residue "2 GLU 588": "OE1" <-> "OE2" Residue "2 GLU 592": "OE1" <-> "OE2" Residue "2 GLU 689": "OE1" <-> "OE2" Residue "2 GLU 693": "OE1" <-> "OE2" Residue "2 ARG 705": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "2 ARG 749": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "2 GLU 753": "OE1" <-> "OE2" Residue "2 ARG 808": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "2 ARG 824": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "2 GLU 827": "OE1" <-> "OE2" Residue "2 ARG 855": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "5 GLU 352": "OE1" <-> "OE2" Residue "5 GLU 354": "OE1" <-> "OE2" Residue "5 ARG 407": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "5 ARG 455": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "5 ARG 486": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "5 ARG 490": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "5 GLU 498": "OE1" <-> "OE2" Residue "5 ARG 549": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "5 GLU 562": "OE1" <-> "OE2" Residue "5 GLU 563": "OE1" <-> "OE2" Residue "5 ARG 651": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "3 ARG 420": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "3 ARG 435": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "3 ARG 455": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "3 ARG 483": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "3 GLU 488": "OE1" <-> "OE2" Residue "3 GLU 555": "OE1" <-> "OE2" Residue "3 GLU 563": "OE1" <-> "OE2" Residue "3 ARG 657": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "3 ARG 700": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "3 GLU 703": "OE1" <-> "OE2" Residue "3 ARG 734": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "4 GLU 511": "OE1" <-> "OE2" Residue "4 GLU 532": "OE1" <-> "OE2" Residue "4 GLU 534": "OE1" <-> "OE2" Residue "4 ARG 557": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "4 ARG 559": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "4 GLU 617": "OE1" <-> "OE2" Residue "4 GLU 647": "OE1" <-> "OE2" Residue "4 ARG 681": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "4 GLU 690": "OE1" <-> "OE2" Residue "4 GLU 745": "OE1" <-> "OE2" Residue "4 GLU 756": "OE1" <-> "OE2" Residue "4 GLU 806": "OE1" <-> "OE2" Residue "4 ARG 827": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/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: 13.98, per 1000 atoms: 0.44 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 - 3.50 Amino acid : False - 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: 25.83 Conformation dependent library (CDL) restraints added in 3.2 seconds 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: 2.86 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: 12.21 Time building geometry restraints manager: 27.04 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: 85.20 - 95.07: 8 95.07 - 104.95: 503 104.95 - 114.82: 39048 114.82 - 124.69: 17029 124.69 - 134.56: 1020 Bond angle restraints: 57608 Sorted by residual: 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="HH11 ARG 6 798 " pdb=" NH1 ARG 6 798 " pdb="HH12 ARG 6 798 " ideal model delta sigma weight residual 120.00 92.50 27.50 3.00e+00 1.11e-01 8.40e+01 angle pdb=" C PRO 7 501 " pdb=" N VAL 7 502 " pdb=" CA VAL 7 502 " ideal model delta sigma weight residual 121.97 130.71 -8.74 1.00e+00 1.00e+00 7.63e+01 angle pdb=" C TYR 2 864 " pdb=" N THR 2 865 " pdb=" CA THR 2 865 " ideal model delta sigma weight residual 120.38 132.00 -11.62 1.37e+00 5.33e-01 7.19e+01 angle pdb=" C HIS 2 561 " pdb=" N ARG 2 562 " pdb=" CA ARG 2 562 " ideal model delta sigma weight residual 122.65 134.19 -11.54 1.49e+00 4.50e-01 6.00e+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: 2070 0.139 - 0.277: 417 0.277 - 0.416: 56 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: 2.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.430 Extract box with map and model: 1.050 Check model and map are aligned: 0.200 Set scattering table: 0.270 Process input model: 98.440 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 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= 0.907 Angle : 2.112 18.692 21605 Z= 1.357 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 : 1.04 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.05 (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 TRP 0.094 0.024 TRP 2 476 HIS 0.015 0.004 HIS 5 676 PHE 0.135 0.018 PHE 7 598 TYR 0.154 0.023 TYR 6 828 ARG 0.029 0.002 ARG 2 617 *********************** 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 fitting. rotamer outliers: 4 poor density : 317 time to evaluate : 2.452 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: 6 650 VAL cc_start: 0.8168 (p) cc_final: 0.7842 (m) REVERT: 6 660 THR cc_start: 0.7770 (m) cc_final: 0.7372 (m) REVERT: 7 443 ARG cc_start: 0.8679 (ttp-110) cc_final: 0.8367 (mmm160) REVERT: 7 728 TYR cc_start: 0.7398 (t80) cc_final: 0.7097 (t80) REVERT: 2 764 MET cc_start: 0.8176 (mtm) cc_final: 0.7763 (mtm) REVERT: 2 810 LEU cc_start: 0.7984 (tp) cc_final: 0.7756 (tt) REVERT: 5 409 ASP cc_start: 0.6864 (m-30) cc_final: 0.6501 (m-30) REVERT: 5 572 VAL cc_start: 0.7728 (t) cc_final: 0.7458 (t) REVERT: 3 673 GLN cc_start: 0.9289 (tt0) cc_final: 0.9021 (tp-100) outliers start: 4 outliers final: 0 residues processed: 320 average time/residue: 0.6912 time to fit residues: 315.1730 Evaluate side-chains 165 residues out of total 1685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 2.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 0.7980 chunk 147 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 99 optimal weight: 0.8980 chunk 78 optimal weight: 5.9990 chunk 152 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 chunk 113 optimal weight: 5.9990 chunk 176 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 690 ASN 6 700 ASN 7 543 GLN 7 657 ASN 7 683 GLN 2 508 HIS ** 3 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 685 ASN 4 797 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15943 Z= 0.253 Angle : 0.746 7.960 21605 Z= 0.411 Chirality : 0.045 0.161 2553 Planarity : 0.006 0.096 2678 Dihedral : 15.409 164.893 2432 Min Nonbonded Distance : 1.714 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.68 % Favored : 96.27 % Rotamer: Outliers : 1.31 % Allowed : 7.98 % Favored : 90.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.18), residues: 1903 helix: -0.80 (0.15), residues: 956 sheet: -1.41 (0.31), residues: 251 loop : -1.17 (0.22), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP 2 589 HIS 0.006 0.002 HIS 2 621 PHE 0.029 0.002 PHE 7 526 TYR 0.019 0.002 TYR 6 828 ARG 0.040 0.001 ARG 6 798 *********************** 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 205 residues out of total 1685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 183 time to evaluate : 2.817 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: 0.8824 (mttt) cc_final: 0.8606 (ptmt) REVERT: 7 443 ARG cc_start: 0.8490 (ttp-110) cc_final: 0.8227 (mmm160) REVERT: 2 624 MET cc_start: -0.1292 (ptm) cc_final: -0.1875 (ptp) REVERT: 5 424 GLN cc_start: 0.7283 (tp40) cc_final: 0.6757 (tt0) REVERT: 5 463 TYR cc_start: 0.7088 (p90) cc_final: 0.6849 (p90) REVERT: 3 462 MET cc_start: 0.9161 (mmm) cc_final: 0.8885 (mmm) outliers start: 22 outliers final: 14 residues processed: 199 average time/residue: 0.5945 time to fit residues: 179.4229 Evaluate side-chains 162 residues out of total 1685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 148 time to evaluate : 2.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 675 ARG Chi-restraints excluded: chain 6 residue 700 ASN 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 542 LEU 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 97 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 146 optimal weight: 0.0970 chunk 119 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 176 optimal weight: 1.9990 chunk 190 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 175 optimal weight: 0.0270 chunk 60 optimal weight: 0.9990 chunk 141 optimal weight: 0.9990 overall best weight: 0.5640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: