Starting phenix.real_space_refine on Wed Feb 21 19:04:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sko_10230/02_2024/6sko_10230_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sko_10230/02_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_10230/02_2024/6sko_10230.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sko_10230/02_2024/6sko_10230.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sko_10230/02_2024/6sko_10230_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sko_10230/02_2024/6sko_10230_trim_updated.pdb" } 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 13.68, per 1000 atoms: 0.43 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: 24.86 Conformation dependent library (CDL) restraints added in 3.0 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... running ksdssp... Secondary structure from input PDB file: 87 helices and 18 sheets defined 47.5% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.15 Creating SS restraints... Processing helix chain '6' and resid 501 through 507 Processing helix chain '6' and resid 510 through 521 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 532 removed outlier: 3.541A pdb=" N LEU 6 529 " --> pdb=" O TYR 6 526 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL 6 530 " --> pdb=" O ASP 6 527 " (cutoff:3.500A) Processing helix chain '6' and resid 541 through 552 Processing helix chain '6' and resid 581 through 589 removed outlier: 3.696A pdb=" N LEU 6 585 " --> pdb=" O LYS 6 581 " (cutoff:3.500A) Processing helix chain '6' and resid 641 through 643 No H-bonds generated for 'chain '6' and resid 641 through 643' Processing helix chain '6' and resid 646 through 655 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) removed outlier: 4.390A pdb=" N ALA 6 655 " --> pdb=" O ALA 6 651 " (cutoff:3.500A) Processing helix chain '6' and resid 695 through 698 No H-bonds generated for 'chain '6' and resid 695 through 698' Processing helix chain '6' and resid 703 through 707 Processing helix chain '6' and resid 721 through 740 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) removed outlier: 8.116A pdb=" N ASP 6 739 " --> pdb=" O HIS 6 735 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N GLU 6 740 " --> pdb=" O MET 6 736 " (cutoff:3.500A) Processing helix chain '6' and resid 748 through 760 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) removed outlier: 3.964A pdb=" N THR 6 760 " --> pdb=" O LYS 6 756 " (cutoff:3.500A) Processing helix chain '6' and resid 767 through 784 removed outlier: 4.097A pdb=" N GLU 6 775 " --> pdb=" O SER 6 771 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP 6 784 " --> pdb=" O LEU 6 780 " (cutoff:3.500A) Processing helix chain '6' and resid 797 through 813 removed outlier: 3.777A pdb=" N SER 6 802 " --> pdb=" O GLN 6 799 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU 6 806 " --> pdb=" O MET 6 803 " (cutoff:3.500A) Processing helix chain '6' and resid 821 through 835 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 407 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 410 through 417 Processing helix chain '7' and resid 426 through 437 removed outlier: 4.338A pdb=" N LEU 7 434 " --> pdb=" O LYS 7 430 " (cutoff:3.500A) Processing helix chain '7' and resid 467 through 476 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 490 through 494 Processing helix chain '7' and resid 512 through 515 No H-bonds generated for 'chain '7' and resid 512 through 515' Processing helix chain '7' and resid 531 through 536 removed outlier: 3.970A pdb=" N ALA 7 536 " --> pdb=" O SER 7 532 " (cutoff:3.500A) Processing helix chain '7' and resid 538 through 541 No H-bonds generated for 'chain '7' and resid 538 through 541' Processing helix chain '7' and resid 580 through 584 Processing helix chain '7' and resid 588 through 593 removed outlier: 3.839A pdb=" N ARG 7 593 " --> pdb=" O ALA 7 589 " (cutoff:3.500A) Processing helix chain '7' and resid 606 through 621 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 635 through 647 removed outlier: 3.858A pdb=" N TYR 7 644 " --> pdb=" O GLU 7 640 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N THR 7 647 " --> pdb=" O ALA 7 643 " (cutoff:3.500A) Processing helix chain '7' and resid 654 through 673 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 677 through 679 No H-bonds generated for 'chain '7' and resid 677 through 679' Processing helix chain '7' and resid 686 through 702 Processing helix chain '7' and resid 710 through 728 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 478 through 487 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 493 through 500 Processing helix chain '2' and resid 509 through 520 Processing helix chain '2' and resid 549 through 557 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) Processing helix chain '2' and resid 573 through 577 Processing helix chain '2' and resid 615 through 623 removed outlier: 3.618A pdb=" N ILE 2 620 " --> pdb=" O ASP 2 616 " (cutoff:3.500A) Processing helix chain '2' and resid 633 through 635 No H-bonds generated for 'chain '2' and resid 633 through 635' Processing helix chain '2' and resid 663 through 666 No H-bonds generated for 'chain '2' and resid 663 through 666' Processing helix chain '2' and resid 671 through 676 Processing helix chain '2' and resid 689 through 705 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: 3.664A pdb=" N GLU 2 752 " --> pdb=" O ARG 2 749 " (cutoff:3.500A) Processing helix chain '2' and resid 760 through 773 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 780 through 799 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) Processing helix chain '2' and resid 807 through 823 removed outlier: 3.718A pdb=" N ILE 2 813 " --> pdb=" O HIS 2 809 " (cutoff:3.500A) Processing helix chain '2' and resid 831 through 846 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) Processing helix chain '2' and resid 850 through 865 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) Processing helix chain '5' and resid 351 through 362 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 366 through 373 Processing helix chain '5' and resid 382 through 393 Processing helix chain '5' and resid 422 through 432 removed outlier: 3.572A pdb=" N LYS 5 427 " --> pdb=" O GLN 5 424 " (cutoff:3.500A) Processing helix chain '5' and resid 468 through 471 No H-bonds generated for 'chain '5' and resid 468 through 471' Processing helix chain '5' and resid 490 through 499 removed outlier: 3.615A pdb=" N HIS 5 494 " --> pdb=" O VAL 5 491 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU 5 495 " --> pdb=" O ALA 5 492 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N MET 5 497 " --> pdb=" O HIS 5 494 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU 5 498 " --> pdb=" O GLU 5 495 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLN 5 499 " --> pdb=" O ALA 5 496 " (cutoff:3.500A) Processing helix chain '5' and resid 545 through 548 Processing helix chain '5' and resid 563 through 576 Processing helix chain '5' and resid 596 through 609 removed outlier: 4.519A pdb=" N ARG 5 601 " --> pdb=" O GLU 5 597 " (cutoff:3.500A) Processing helix chain '5' and resid 616 through 635 Processing helix chain '5' and resid 650 through 667 removed outlier: 3.629A pdb=" N ALA 5 655 " --> pdb=" O ARG 5 651 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N GLU 5 667 " --> pdb=" O LEU 5 663 " (cutoff:3.500A) Processing helix chain '5' and resid 674 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 344 through 354 removed outlier: 3.597A pdb=" N ARG 3 348 " --> pdb=" O ASP 3 344 " (cutoff:3.500A) Processing helix chain '3' and resid 359 through 366 Processing helix chain '3' and resid 375 through 386 Processing helix chain '3' and resid 415 through 425 removed outlier: 3.735A pdb=" N LEU 3 419 " --> pdb=" O LYS 3 415 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ASN 3 424 " --> pdb=" O ARG 3 420 " (cutoff:3.500A) Processing helix chain '3' and resid 439 through 442 No H-bonds generated for 'chain '3' and resid 439 through 442' Processing helix chain '3' and resid 475 through 477 No H-bonds generated for 'chain '3' and resid 475 through 477' Processing helix chain '3' and resid 480 through 492 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 529 through 532 No H-bonds generated for 'chain '3' and resid 529 through 532' Processing helix chain '3' and resid 537 through 540 No H-bonds generated for 'chain '3' and resid 537 through 540' Processing helix chain '3' and resid 555 through 570 Processing helix chain '3' and resid 653 through 666 Processing helix chain '3' and resid 673 through 688 removed outlier: 3.960A pdb=" N VAL 3 678 " --> pdb=" O GLU 3 674 " (cutoff:3.500A) Processing helix chain '3' and resid 699 through 715 removed outlier: 4.127A pdb=" N GLU 3 703 " --> pdb=" O ALA 3 699 " (cutoff:3.500A) Processing helix chain '3' and resid 723 through 737 Processing helix chain '4' and resid 503 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 518 through 526 Processing helix chain '4' and resid 534 through 545 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 574 through 584 Processing helix chain '4' and resid 598 through 601 No H-bonds generated for 'chain '4' and resid 598 through 601' Processing helix chain '4' and resid 622 through 624 No H-bonds generated for 'chain '4' and resid 622 through 624' Processing helix chain '4' and resid 634 through 636 No H-bonds generated for 'chain '4' and resid 634 through 636' Processing helix chain '4' and resid 639 through 650 removed outlier: 3.668A pdb=" N VAL 4 644 " --> pdb=" O SER 4 640 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU 4 645 " --> pdb=" O THR 4 641 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N HIS 4 646 " --> pdb=" O ARG 4 642 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N GLU 4 647 " --> pdb=" O SER 4 643 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N VAL 4 648 " --> pdb=" O VAL 4 644 " (cutoff:3.500A) Processing helix chain '4' and resid 688 through 692 Processing helix chain '4' and resid 696 through 701 removed outlier: 4.242A pdb=" N ARG 4 701 " --> pdb=" O PRO 4 697 " (cutoff:3.500A) Processing helix chain '4' and resid 714 through 729 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) removed outlier: 4.170A pdb=" N ASN 4 726 " --> pdb=" O LYS 4 722 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU 4 727 " --> pdb=" O HIS 4 723 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N TYR 4 728 " --> pdb=" O LEU 4 724 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LEU 4 729 " --> pdb=" O THR 4 725 " (cutoff:3.500A) Processing helix chain '4' and resid 744 through 757 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) Processing helix chain '4' and resid 764 through 778 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 811 removed outlier: 3.565A pdb=" N GLU 4 799 " --> pdb=" O THR 4 795 " (cutoff:3.500A) Processing helix chain '4' and resid 819 through 832 removed outlier: 3.790A pdb=" N GLU 4 824 " --> pdb=" O GLU 4 820 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain '6' and resid 711 through 715 Processing sheet with id= B, first strand: chain '6' and resid 610 through 614 Processing sheet with id= C, first strand: chain '6' and resid 661 through 663 Processing sheet with id= D, first strand: chain '7' and resid 596 through 600 removed outlier: 3.522A pdb=" N LEU 7 458 " --> pdb=" O ALA 7 565 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLY 7 519 " --> pdb=" O SER 7 562 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N LEU 7 564 " --> pdb=" O GLY 7 519 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N CYS 7 521 " --> pdb=" O LEU 7 564 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N ALA 7 566 " --> pdb=" O CYS 7 521 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ILE 7 523 " --> pdb=" O ALA 7 566 " (cutoff:3.500A) 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) Processing sheet with id= E, first strand: chain '7' and resid 495 through 498 Processing sheet with id= F, first strand: chain '7' and resid 546 through 550 Processing sheet with id= G, first strand: chain '2' and resid 679 through 683 removed outlier: 4.003A pdb=" N ASP 2 607 " --> pdb=" O ALA 2 566 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain '2' and resid 578 through 581 Processing sheet with id= I, first strand: chain '2' and resid 628 through 631 Processing sheet with id= J, first strand: chain '5' and resid 552 through 555 removed outlier: 9.176A pdb=" N VAL 5 412 " --> pdb=" O THR 5 517 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL 5 519 " --> pdb=" O VAL 5 412 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N LEU 5 414 " --> pdb=" O VAL 5 519 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ALA 5 521 " --> pdb=" O LEU 5 414 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N GLY 5 474 " --> pdb=" O SER 5 518 " (cutoff:3.500A) removed outlier: 9.598A pdb=" N LEU 5 520 " --> pdb=" O GLY 5 474 " (cutoff:3.500A) removed outlier: 9.592A pdb=" N VAL 5 476 " --> pdb=" O LEU 5 520 " (cutoff:3.500A) removed outlier: 12.825A pdb=" N ALA 5 522 " --> pdb=" O VAL 5 476 " (cutoff:3.500A) removed outlier: 10.089A pdb=" N CYS 5 478 " --> pdb=" O ALA 5 522 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain '5' and resid 451 through 454 Processing sheet with id= L, 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= M, first strand: chain '3' and resid 545 through 549 Processing sheet with id= N, first strand: chain '3' and resid 444 through 447 Processing sheet with id= O, first strand: chain '3' and resid 494 through 499 Processing sheet with id= P, first strand: chain '4' and resid 704 through 708 removed outlier: 3.598A pdb=" N VAL 4 589 " --> pdb=" O VAL 4 628 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain '4' and resid 603 through 606 Processing sheet with id= R, first strand: chain '4' and resid 653 through 657 610 hydrogen bonds defined for protein. 1689 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: 11.27 Time building geometry restraints manager: 25.88 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: 1147 2.05 - 2.69: 43838 2.69 - 3.32: 95704 3.32 - 3.96: 121692 3.96 - 4.60: 183464 Nonbonded interactions: 445845 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 1.850 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 1.850 nonbonded pdb=" OD1 ASP 7 530 " pdb=" HG SER 7 532 " model vdw 1.613 1.850 ... (remaining 445840 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.250 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: 0.450 Extract box with map and model: 11.420 Check model and map are aligned: 0.410 Set scattering table: 0.240 Process input model: 96.010 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.080 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 114.240 ------------------------------------------------------------------------------- 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= 0.915 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 : 2.696 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: 0.7266 time to fit residues: 333.3102 Evaluate side-chains 165 residues out of total 1685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 2.787 ------------------------------------------------------------------------------- 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: 0.6980 chunk 147 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 chunk 152 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 113 optimal weight: 5.9990 chunk 176 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- 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 7 657 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15943 Z= 0.256 Angle : 0.722 8.422 21605 Z= 0.395 Chirality : 0.044 0.151 2553 Planarity : 0.006 0.070 2678 Dihedral : 15.301 155.736 2432 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.31 % Favored : 96.64 % Rotamer: Outliers : 1.49 % Allowed : 7.92 % Favored : 90.59 % 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: -1.73 (0.18), residues: 1903 helix: -0.93 (0.15), residues: 958 sheet: -1.24 (0.30), residues: 251 loop : -1.13 (0.21), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP 2 589 HIS 0.007 0.002 HIS 2 621 PHE 0.028 0.002 PHE 7 526 TYR 0.018 0.002 TYR 6 828 ARG 0.026 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 207 residues out of total 1685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 182 time to evaluate : 2.507 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: 7 443 ARG cc_start: 0.8640 (ttp-110) cc_final: 0.8342 (mmm160) REVERT: 2 624 MET cc_start: -0.1254 (ptm) cc_final: -0.1773 (ptp) REVERT: 5 463 TYR cc_start: 0.7106 (p90) cc_final: 0.6866 (p90) REVERT: 3 462 MET cc_start: 0.9149 (mmm) cc_final: 0.8883 (mmm) outliers start: 25 outliers final: 15 residues processed: 199 average time/residue: 0.5992 time to fit residues: 180.4215 Evaluate side-chains 160 residues out of total 1685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 145 time to evaluate : 2.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 568 ASP 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 526 ASN Chi-restraints excluded: chain 2 residue 542 LEU Chi-restraints excluded: chain 2 residue 622 GLU 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 518 SER 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: 0.9990 chunk 54 optimal weight: 0.0870 chunk 146 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 176 optimal weight: 2.9990 chunk 190 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 175 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 141 optimal weight: 0.7980 overall best weight: 1.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 6 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 508 HIS 2 768 HIS ** 3 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 582 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 15943 Z= 0.210 Angle : 0.607 8.281 21605 Z= 0.328 Chirality : 0.042 0.187 2553 Planarity : 0.004 0.046 2678 Dihedral : 13.831 153.934 2432 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.73 % Allowed : 9.41 % Favored : 88.86 % 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: -1.12 (0.18), residues: 1903 helix: -0.30 (0.16), residues: 968 sheet: -1.21 (0.30), residues: 250 loop : -0.96 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP 2 589 HIS 0.010 0.001 HIS 2 621 PHE 0.014 0.001 PHE 5 550 TYR 0.030 0.002 TYR 6 597 ARG 0.009 0.001 ARG 6 798 *********************** 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 191 residues out of total 1685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 162 time to evaluate : 2.369 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: 6 649 GLN cc_start: 0.7608 (mt0) cc_final: 0.6506 (tm-30) REVERT: 7 443 ARG cc_start: 0.8627 (ttp-110) cc_final: 0.8338 (mmm160) REVERT: 5 354 GLU cc_start: 0.9054 (pp20) cc_final: 0.8818 (pp20) REVERT: 5 463 TYR cc_start: 0.7306 (p90) cc_final: 0.7087 (p90) REVERT: 5 572 VAL cc_start: 0.7763 (t) cc_final: 0.7457 (p) outliers start: 29 outliers final: 15 residues processed: 185 average time/residue: 0.5889 time to fit residues: 171.2742 Evaluate side-chains 155 residues out of total 1685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 140 time to evaluate : 2.680 ------------------------------------------------------------------------------- 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 483 THR Chi-restraints excluded: chain 7 residue 555 THR Chi-restraints excluded: chain 7 residue 561 THR Chi-restraints excluded: chain 2 residue 622 GLU 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 410 ASP Chi-restraints excluded: chain 3 residue 737 LEU Chi-restraints excluded: chain 4 residue 643 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 174 optimal weight: 1.9990 chunk 132 optimal weight: 0.6980 chunk 91 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 177 optimal weight: 0.5980 chunk 187 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 167 optimal weight: 0.8980 chunk 50 optimal weight: 0.0980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 508 HIS ** 3 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.4187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 15943 Z= 0.157 Angle : 0.538 7.299 21605 Z= 0.289 Chirality : 0.040 0.164 2553 Planarity : 0.003 0.053 2678 Dihedral : 13.080 154.530 2432 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.43 % Allowed : 10.01 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.19), residues: 1903 helix: 0.10 (0.17), residues: 971 sheet: -1.04 (0.30), residues: 257 loop : -0.64 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP 2 589 HIS 0.009 0.001 HIS 2 621 PHE 0.009 0.001 PHE 2 520 TYR 0.010 0.001 TYR 2 769 ARG 0.006 0.000 ARG 4 559 *********************** 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 fitting. rotamer outliers: 24 poor density : 152 time to evaluate : 2.708 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: 6 649 GLN cc_start: 0.8019 (mt0) cc_final: 0.7390 (tm-30) REVERT: 5 463 TYR cc_start: 0.7435 (p90) cc_final: 0.7226 (p90) REVERT: 3 462 MET cc_start: 0.9102 (mmm) cc_final: 0.8783 (mmm) outliers start: 24 outliers final: 18 residues processed: 172 average time/residue: 0.5512 time to fit residues: 150.0757 Evaluate side-chains 152 residues out of total 1685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 134 time to evaluate : 2.673 ------------------------------------------------------------------------------- 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 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 7 residue 696 SER Chi-restraints excluded: chain 2 residue 622 GLU 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 5 residue 518 SER Chi-restraints excluded: chain 3 residue 410 ASP Chi-restraints excluded: chain 3 residue 737 LEU Chi-restraints excluded: chain 4 residue 643 SER 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 156 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 160 optimal weight: 0.3980 chunk 129 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 168 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 508 HIS ** 3 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.4569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 15943 Z= 0.243 Angle : 0.557 6.678 21605 Z= 0.300 Chirality : 0.040 0.167 2553 Planarity : 0.003 0.062 2678 Dihedral : 12.709 157.535 2432 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.43 % Allowed : 11.61 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.19), residues: 1903 helix: 0.18 (0.17), residues: 962 sheet: -0.95 (0.30), residues: 257 loop : -0.74 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.001 TRP 2 589 HIS 0.007 0.001 HIS 2 621 PHE 0.014 0.001 PHE 2 677 TYR 0.010 0.001 TYR 6 828 ARG 0.004 0.000 ARG 6 832 *********************** 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 158 residues out of total 1685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 134 time to evaluate : 2.729 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: 6 649 GLN cc_start: 0.8026 (mt0) cc_final: 0.7123 (tm-30) REVERT: 3 462 MET cc_start: 0.9142 (mmm) cc_final: 0.8798 (mmm) outliers start: 24 outliers final: 19 residues processed: 155 average time/residue: 0.5417 time to fit residues: 136.7142 Evaluate side-chains 151 residues out of total 1685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 132 time to evaluate : 2.671 ------------------------------------------------------------------------------- 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 561 THR Chi-restraints excluded: chain 7 residue 598 PHE Chi-restraints excluded: chain 7 residue 696 SER 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 482 PHE Chi-restraints excluded: chain 5 residue 518 SER Chi-restraints excluded: chain 5 residue 606 CYS Chi-restraints excluded: chain 3 residue 410 ASP Chi-restraints excluded: chain 3 residue 737 LEU Chi-restraints excluded: chain 4 residue 572 THR Chi-restraints excluded: chain 4 residue 643 SER Chi-restraints excluded: chain 4 residue 707 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 63 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 110 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 187 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 508 HIS ** 3 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.4798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15943 Z= 0.209 Angle : 0.521 6.363 21605 Z= 0.282 Chirality : 0.040 0.162 2553 Planarity : 0.003 0.026 2678 Dihedral : 12.454 158.597 2432 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.25 % Allowed : 12.51 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.19), residues: 1903 helix: 0.33 (0.17), residues: 957 sheet: -0.80 (0.31), residues: 244 loop : -0.69 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP 2 589 HIS 0.006 0.001 HIS 7 615 PHE 0.011 0.001 PHE 5 482 TYR 0.009 0.001 TYR 2 790 ARG 0.003 0.000 ARG 6 832 *********************** 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 154 residues out of total 1685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 133 time to evaluate : 2.692 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: 6 649 GLN cc_start: 0.8060 (mt0) cc_final: 0.7187 (tm-30) REVERT: 3 462 MET cc_start: 0.9144 (mmm) cc_final: 0.8925 (mmm) outliers start: 21 outliers final: 16 residues processed: 151 average time/residue: 0.4948 time to fit residues: 122.5809 Evaluate side-chains 143 residues out of total 1685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 127 time to evaluate : 2.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 7 residue 622 HIS Chi-restraints excluded: chain 7 residue 696 SER Chi-restraints excluded: chain 2 residue 763 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 517 THR Chi-restraints excluded: chain 3 residue 410 ASP Chi-restraints excluded: chain 3 residue 737 LEU Chi-restraints excluded: chain 4 residue 572 THR Chi-restraints excluded: chain 4 residue 643 SER Chi-restraints excluded: chain 4 residue 707 LEU 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 180 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 137 optimal weight: 0.9980 chunk 158 optimal weight: 2.9990 chunk 104 optimal weight: 0.0060 chunk 186 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 overall best weight: 1.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 6 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 508 HIS ** 3 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.5055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15943 Z= 0.273 Angle : 0.547 6.517 21605 Z= 0.296 Chirality : 0.040 0.177 2553 Planarity : 0.003 0.028 2678 Dihedral : 12.252 160.450 2432 Min Nonbonded Distance : 1.758 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.55 % Allowed : 12.63 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.19), residues: 1903 helix: 0.29 (0.17), residues: 962 sheet: -0.89 (0.30), residues: 262 loop : -0.67 (0.24), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP 2 589 HIS 0.005 0.001 HIS 7 615 PHE 0.010 0.001 PHE 5 554 TYR 0.009 0.001 TYR 3 576 ARG 0.007 0.001 ARG 5 675 *********************** 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 157 residues out of total 1685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 131 time to evaluate : 2.703 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: 6 649 GLN cc_start: 0.8152 (mt0) cc_final: 0.7238 (tm-30) REVERT: 6 660 THR cc_start: 0.7851 (m) cc_final: 0.7647 (p) REVERT: 2 827 GLU cc_start: 0.7119 (tp30) cc_final: 0.6777 (pm20) REVERT: 3 462 MET cc_start: 0.9159 (mmm) cc_final: 0.8909 (mmm) outliers start: 26 outliers final: 23 residues processed: 150 average time/residue: 0.5744 time to fit residues: 136.7815 Evaluate side-chains 148 residues out of total 1685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 125 time to evaluate : 2.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 483 THR Chi-restraints excluded: chain 7 residue 533 ASP Chi-restraints excluded: chain 7 residue 561 THR Chi-restraints excluded: chain 7 residue 598 PHE Chi-restraints excluded: chain 7 residue 622 HIS Chi-restraints excluded: chain 7 residue 696 SER Chi-restraints excluded: chain 2 residue 515 VAL Chi-restraints excluded: chain 2 residue 526 ASN Chi-restraints excluded: chain 2 residue 552 ILE Chi-restraints excluded: chain 2 residue 622 GLU Chi-restraints excluded: chain 2 residue 624 MET Chi-restraints excluded: chain 2 residue 651 ASN 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 517 THR Chi-restraints excluded: chain 5 residue 518 SER Chi-restraints excluded: chain 3 residue 410 ASP Chi-restraints excluded: chain 3 residue 530 HIS Chi-restraints excluded: chain 4 residue 572 THR Chi-restraints excluded: chain 4 residue 643 SER Chi-restraints excluded: chain 4 residue 707 LEU 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 74 optimal weight: 10.0000 chunk 111 optimal weight: 5.9990 chunk 56 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 118 optimal weight: 5.9990 chunk 127 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 chunk 170 optimal weight: 0.5980 chunk 179 optimal weight: 0.9980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 508 HIS 2 856 GLN ** 3 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.5241 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= 0.188 Angle : 0.503 6.314 21605 Z= 0.271 Chirality : 0.040 0.155 2553 Planarity : 0.003 0.057 2678 Dihedral : 11.990 161.112 2432 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.49 % Allowed : 12.51 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.19), residues: 1903 helix: 0.53 (0.17), residues: 960 sheet: -0.85 (0.30), residues: 262 loop : -0.60 (0.24), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP 2 589 HIS 0.006 0.001 HIS 7 615 PHE 0.012 0.001 PHE 5 554 TYR 0.024 0.001 TYR 6 793 ARG 0.008 0.000 ARG 3 455 *********************** 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 154 residues out of total 1685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 129 time to evaluate : 2.795 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: 6 649 GLN cc_start: 0.8144 (mt0) cc_final: 0.7282 (tm-30) REVERT: 3 462 MET cc_start: 0.9163 (mmm) cc_final: 0.8805 (mmm) outliers start: 25 outliers final: 21 residues processed: 147 average time/residue: 0.5714 time to fit residues: 132.2893 Evaluate side-chains 144 residues out of total 1685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 123 time to evaluate : 2.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 7 residue 622 HIS Chi-restraints excluded: chain 7 residue 696 SER Chi-restraints excluded: chain 2 residue 515 VAL Chi-restraints excluded: chain 2 residue 552 ILE Chi-restraints excluded: chain 2 residue 622 GLU Chi-restraints excluded: chain 2 residue 624 MET Chi-restraints excluded: chain 2 residue 651 ASN 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 517 THR Chi-restraints excluded: chain 3 residue 410 ASP Chi-restraints excluded: chain 3 residue 530 HIS Chi-restraints excluded: chain 4 residue 572 THR Chi-restraints excluded: chain 4 residue 643 SER Chi-restraints excluded: chain 4 residue 707 LEU 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 163 optimal weight: 1.9990 chunk 174 optimal weight: 2.9990 chunk 179 optimal weight: 0.9980 chunk 104 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 173 optimal weight: 1.9990 chunk 114 optimal weight: 0.0980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 508 HIS ** 3 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.5438 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= 0.202 Angle : 0.506 6.419 21605 Z= 0.272 Chirality : 0.039 0.161 2553 Planarity : 0.003 0.089 2678 Dihedral : 11.784 162.146 2432 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.49 % Allowed : 12.45 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.19), residues: 1903 helix: 0.62 (0.17), residues: 960 sheet: -0.88 (0.30), residues: 260 loop : -0.50 (0.24), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP 2 476 HIS 0.006 0.001 HIS 2 508 PHE 0.013 0.001 PHE 5 554 TYR 0.007 0.001 TYR 2 555 ARG 0.012 0.000 ARG 7 673 *********************** 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 152 residues out of total 1685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 127 time to evaluate : 2.565 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: 6 649 GLN cc_start: 0.8162 (mt0) cc_final: 0.7365 (tm-30) REVERT: 3 462 MET cc_start: 0.9159 (mmm) cc_final: 0.8888 (mmm) outliers start: 25 outliers final: 19 residues processed: 147 average time/residue: 0.5519 time to fit residues: 127.7347 Evaluate side-chains 139 residues out of total 1685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 120 time to evaluate : 2.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 7 residue 622 HIS Chi-restraints excluded: chain 7 residue 696 SER Chi-restraints excluded: chain 2 residue 515 VAL Chi-restraints excluded: chain 2 residue 607 ASP Chi-restraints excluded: chain 2 residue 622 GLU Chi-restraints excluded: chain 2 residue 624 MET Chi-restraints excluded: chain 2 residue 651 ASN Chi-restraints excluded: chain 5 residue 433 SER Chi-restraints excluded: chain 5 residue 476 VAL Chi-restraints excluded: chain 5 residue 517 THR Chi-restraints excluded: chain 3 residue 410 ASP Chi-restraints excluded: chain 3 residue 530 HIS Chi-restraints excluded: chain 4 residue 572 THR Chi-restraints excluded: chain 4 residue 643 SER 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 184 optimal weight: 1.9990 chunk 112 optimal weight: 9.9990 chunk 87 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 193 optimal weight: 7.9990 chunk 177 optimal weight: 0.5980 chunk 153 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 118 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 508 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.5582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15943 Z= 0.184 Angle : 0.494 6.712 21605 Z= 0.266 Chirality : 0.040 0.156 2553 Planarity : 0.003 0.049 2678 Dihedral : 11.673 161.925 2432 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.25 % Allowed : 12.45 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.19), residues: 1903 helix: 0.70 (0.17), residues: 964 sheet: -0.87 (0.30), residues: 261 loop : -0.52 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP 2 589 HIS 0.005 0.001 HIS 7 622 PHE 0.013 0.001 PHE 5 554 TYR 0.011 0.001 TYR 6 793 ARG 0.010 0.000 ARG 7 673 ********************** 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 143 residues out of total 1685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 122 time to evaluate : 2.449 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: 6 649 GLN cc_start: 0.8157 (mt0) cc_final: 0.7367 (tm-30) REVERT: 3 462 MET cc_start: 0.9177 (mmm) cc_final: 0.8910 (mmm) REVERT: 3 673 GLN cc_start: 0.9285 (tt0) cc_final: 0.8979 (tp-100) outliers start: 21 outliers final: 20 residues processed: 138 average time/residue: 0.5140 time to fit residues: 116.0345 Evaluate side-chains 139 residues out of total 1685 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 119 time to evaluate : 2.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 7 residue 622 HIS Chi-restraints excluded: chain 7 residue 696 SER Chi-restraints excluded: chain 2 residue 515 VAL Chi-restraints excluded: chain 2 residue 607 ASP Chi-restraints excluded: chain 2 residue 622 GLU Chi-restraints excluded: chain 2 residue 624 MET Chi-restraints excluded: chain 2 residue 651 ASN 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 517 THR Chi-restraints excluded: chain 3 residue 410 ASP Chi-restraints excluded: chain 3 residue 530 HIS Chi-restraints excluded: chain 4 residue 572 THR Chi-restraints excluded: chain 4 residue 643 SER 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 163 optimal weight: 0.2980 chunk 47 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 158 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 135 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 6 700 ASN 2 508 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.092551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.071173 restraints weight = 136046.388| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 3.69 r_work: 0.3109 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.5741 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= 0.198 Angle : 0.496 6.497 21605 Z= 0.267 Chirality : 0.039 0.159 2553 Planarity : 0.003 0.062 2678 Dihedral : 11.556 161.055 2432 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.37 % Allowed : 12.57 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.19), residues: 1903 helix: 0.75 (0.17), residues: 964 sheet: -0.81 (0.30), residues: 263 loop : -0.52 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP 2 476 HIS 0.006 0.001 HIS 2 508 PHE 0.014 0.001 PHE 5 554 TYR 0.009 0.001 TYR 2 555 ARG 0.010 0.000 ARG 7 673 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6264.62 seconds wall clock time: 112 minutes 32.34 seconds (6752.34 seconds total)