Starting phenix.real_space_refine on Tue Apr 9 06:40:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ss5_40744/04_2024/8ss5_40744.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ss5_40744/04_2024/8ss5_40744.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ss5_40744/04_2024/8ss5_40744.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ss5_40744/04_2024/8ss5_40744.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ss5_40744/04_2024/8ss5_40744.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ss5_40744/04_2024/8ss5_40744.pdb" } resolution = 3.56 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= 0.005 sd= 0.075 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: 5 Type Number sf(0) Gaussians S 104 5.16 5 Na 1 4.78 5 C 10182 2.51 5 N 2524 2.21 5 O 2826 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 545": "NH1" <-> "NH2" Residue "A ARG 599": "NH1" <-> "NH2" Residue "A ARG 675": "NH1" <-> "NH2" Residue "A ARG 819": "NH1" <-> "NH2" Residue "A ARG 926": "NH1" <-> "NH2" Residue "A ARG 952": "NH1" <-> "NH2" Residue "A ARG 955": "NH1" <-> "NH2" Residue "A ARG 991": "NH1" <-> "NH2" Residue "A ARG 1031": "NH1" <-> "NH2" Residue "B PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 594": "NH1" <-> "NH2" Residue "B ARG 628": "NH1" <-> "NH2" Residue "B TYR 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 660": "NH1" <-> "NH2" Residue "B ARG 684": "NH1" <-> "NH2" Residue "B TYR 816": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 819": "NH1" <-> "NH2" Residue "C TYR 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 545": "NH1" <-> "NH2" Residue "C ARG 599": "NH1" <-> "NH2" Residue "C ARG 675": "NH1" <-> "NH2" Residue "C ARG 819": "NH1" <-> "NH2" Residue "C ARG 926": "NH1" <-> "NH2" Residue "C ARG 952": "NH1" <-> "NH2" Residue "C ARG 955": "NH1" <-> "NH2" Residue "C ARG 991": "NH1" <-> "NH2" Residue "C ARG 1031": "NH1" <-> "NH2" Residue "D PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 594": "NH1" <-> "NH2" Residue "D ARG 628": "NH1" <-> "NH2" Residue "D TYR 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 660": "NH1" <-> "NH2" Residue "D ARG 684": "NH1" <-> "NH2" Residue "D TYR 816": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 819": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 15637 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4662 Classifications: {'peptide': 595} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 577} Chain breaks: 4 Chain: "B" Number of atoms: 3156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3156 Classifications: {'peptide': 404} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 390} Chain breaks: 2 Chain: "C" Number of atoms: 4662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4662 Classifications: {'peptide': 595} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 577} Chain breaks: 4 Chain: "D" Number of atoms: 3156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3156 Classifications: {'peptide': 404} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 390} Chain breaks: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.49, per 1000 atoms: 0.54 Number of scatterers: 15637 At special positions: 0 Unit cell: (120.84, 124.02, 135.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 104 16.00 Na 1 11.00 O 2826 8.00 N 2524 7.00 C 10182 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 718 " - pdb=" SG CYS A 773 " distance=2.03 Simple disulfide: pdb=" SG CYS A 890 " - pdb=" SG CYS A 900 " distance=2.04 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 890 " - pdb=" SG CYS C 900 " distance=2.04 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 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: 6.59 Conformation dependent library (CDL) restraints added in 3.2 seconds 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3656 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 22 sheets defined 54.0% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.74 Creating SS restraints... Processing helix chain 'A' and resid 423 through 437 removed outlier: 3.724A pdb=" N LYS A 434 " --> pdb=" O ALA A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 469 removed outlier: 3.632A pdb=" N TYR A 469 " --> pdb=" O GLY A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 487 removed outlier: 3.502A pdb=" N GLU A 486 " --> pdb=" O THR A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 546 removed outlier: 3.509A pdb=" N VAL A 530 " --> pdb=" O TRP A 526 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER A 544 " --> pdb=" O LEU A 540 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG A 545 " --> pdb=" O PHE A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 585 removed outlier: 3.886A pdb=" N TRP A 578 " --> pdb=" O PHE A 574 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N MET A 585 " --> pdb=" O LEU A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 630 removed outlier: 3.668A pdb=" N ILE A 600 " --> pdb=" O LEU A 596 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL A 601 " --> pdb=" O SER A 597 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY A 602 " --> pdb=" O GLY A 598 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TRP A 606 " --> pdb=" O GLY A 602 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE A 607 " --> pdb=" O GLY A 603 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU A 610 " --> pdb=" O TRP A 606 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE A 611 " --> pdb=" O PHE A 607 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER A 614 " --> pdb=" O LEU A 610 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA A 618 " --> pdb=" O SER A 614 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR A 625 " --> pdb=" O ALA A 621 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL A 626 " --> pdb=" O ALA A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 642 removed outlier: 3.789A pdb=" N LYS A 641 " --> pdb=" O GLU A 637 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN A 642 " --> pdb=" O ASP A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 661 removed outlier: 3.873A pdb=" N PHE A 659 " --> pdb=" O THR A 655 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG A 660 " --> pdb=" O LYS A 656 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ARG A 661 " --> pdb=" O GLU A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 676 Processing helix chain 'A' and resid 686 through 695 Processing helix chain 'A' and resid 706 through 714 removed outlier: 3.865A pdb=" N TYR A 711 " --> pdb=" O THR A 707 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN A 714 " --> pdb=" O GLU A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 752 removed outlier: 3.547A pdb=" N ASN A 747 " --> pdb=" O GLY A 743 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU A 751 " --> pdb=" O ASN A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 767 removed outlier: 3.845A pdb=" N LYS A 763 " --> pdb=" O LEU A 759 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN A 764 " --> pdb=" O ASP A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 822 removed outlier: 3.524A pdb=" N LEU A 805 " --> pdb=" O GLY A 801 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU A 808 " --> pdb=" O GLY A 804 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU A 811 " --> pdb=" O MET A 807 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE A 812 " --> pdb=" O LEU A 808 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE A 814 " --> pdb=" O ALA A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 858 removed outlier: 3.611A pdb=" N LEU A 852 " --> pdb=" O GLY A 848 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA A 855 " --> pdb=" O LEU A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 928 removed outlier: 4.169A pdb=" N ARG A 926 " --> pdb=" O LEU A 922 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 952 removed outlier: 3.761A pdb=" N SER A 935 " --> pdb=" O PHE A 931 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE A 941 " --> pdb=" O PHE A 937 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE A 944 " --> pdb=" O PHE A 940 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG A 952 " --> pdb=" O ILE A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 990 removed outlier: 3.655A pdb=" N PHE A 965 " --> pdb=" O VAL A 961 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE A 967 " --> pdb=" O GLY A 963 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU A 968 " --> pdb=" O ILE A 964 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER A 969 " --> pdb=" O PHE A 965 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1033 removed outlier: 3.645A pdb=" N LEU A1015 " --> pdb=" O ALA A1011 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N MET A1023 " --> pdb=" O SER A1019 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL A1025 " --> pdb=" O GLY A1021 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 419 Processing helix chain 'B' and resid 423 through 436 Processing helix chain 'B' and resid 461 through 470 removed outlier: 3.575A pdb=" N TYR B 469 " --> pdb=" O GLY B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.549A pdb=" N LEU B 518 " --> pdb=" O PHE B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 547 removed outlier: 3.504A pdb=" N MET B 527 " --> pdb=" O TYR B 523 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE B 546 " --> pdb=" O LEU B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 585 removed outlier: 3.717A pdb=" N LEU B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N TRP B 578 " --> pdb=" O PHE B 574 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER B 580 " --> pdb=" O SER B 576 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU B 581 " --> pdb=" O LEU B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 626 removed outlier: 3.882A pdb=" N TRP B 605 " --> pdb=" O VAL B 601 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE B 608 " --> pdb=" O VAL B 604 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU B 610 " --> pdb=" O TRP B 606 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE B 611 " --> pdb=" O PHE B 607 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE B 612 " --> pdb=" O PHE B 608 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL B 626 " --> pdb=" O ALA B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 642 removed outlier: 3.666A pdb=" N GLN B 642 " --> pdb=" O ASP B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 662 removed outlier: 3.619A pdb=" N PHE B 659 " --> pdb=" O THR B 655 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG B 660 " --> pdb=" O LYS B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 677 removed outlier: 3.606A pdb=" N MET B 674 " --> pdb=" O MET B 670 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER B 676 " --> pdb=" O THR B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 696 removed outlier: 3.525A pdb=" N ALA B 691 " --> pdb=" O ALA B 687 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 713 Processing helix chain 'B' and resid 742 through 757 removed outlier: 3.534A pdb=" N ASN B 747 " --> pdb=" O GLY B 743 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU B 751 " --> pdb=" O ASN B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 767 Processing helix chain 'B' and resid 793 through 820 removed outlier: 3.589A pdb=" N TYR B 797 " --> pdb=" O ALA B 793 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR B 816 " --> pdb=" O ILE B 812 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 437 removed outlier: 3.724A pdb=" N LYS C 434 " --> pdb=" O ALA C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 469 removed outlier: 3.632A pdb=" N TYR C 469 " --> pdb=" O GLY C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 487 removed outlier: 3.502A pdb=" N GLU C 486 " --> pdb=" O THR C 482 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 546 removed outlier: 3.510A pdb=" N VAL C 530 " --> pdb=" O TRP C 526 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER C 544 " --> pdb=" O LEU C 540 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG C 545 " --> pdb=" O PHE C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 585 removed outlier: 3.886A pdb=" N TRP C 578 " --> pdb=" O PHE C 574 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N MET C 585 " --> pdb=" O LEU C 581 " (cutoff:3.500A) Processing helix chain 'C' and resid 595 through 630 removed outlier: 3.667A pdb=" N ILE C 600 " --> pdb=" O LEU C 596 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL C 601 " --> pdb=" O SER C 597 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY C 602 " --> pdb=" O GLY C 598 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TRP C 606 " --> pdb=" O GLY C 602 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE C 607 " --> pdb=" O GLY C 603 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU C 610 " --> pdb=" O TRP C 606 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE C 611 " --> pdb=" O PHE C 607 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER C 614 " --> pdb=" O LEU C 610 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA C 618 " --> pdb=" O SER C 614 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR C 625 " --> pdb=" O ALA C 621 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL C 626 " --> pdb=" O ALA C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 635 through 642 removed outlier: 3.789A pdb=" N LYS C 641 " --> pdb=" O GLU C 637 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN C 642 " --> pdb=" O ASP C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 661 removed outlier: 3.874A pdb=" N PHE C 659 " --> pdb=" O THR C 655 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG C 660 " --> pdb=" O LYS C 656 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG C 661 " --> pdb=" O GLU C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 676 Processing helix chain 'C' and resid 686 through 695 Processing helix chain 'C' and resid 706 through 714 removed outlier: 3.865A pdb=" N TYR C 711 " --> pdb=" O THR C 707 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN C 714 " --> pdb=" O GLU C 710 " (cutoff:3.500A) Processing helix chain 'C' and resid 743 through 752 removed outlier: 3.547A pdb=" N ASN C 747 " --> pdb=" O GLY C 743 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU C 751 " --> pdb=" O ASN C 747 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 767 removed outlier: 3.845A pdb=" N LYS C 763 " --> pdb=" O LEU C 759 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN C 764 " --> pdb=" O ASP C 760 " (cutoff:3.500A) Processing helix chain 'C' and resid 793 through 822 removed outlier: 3.525A pdb=" N LEU C 805 " --> pdb=" O GLY C 801 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU C 808 " --> pdb=" O GLY C 804 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU C 811 " --> pdb=" O MET C 807 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE C 812 " --> pdb=" O LEU C 808 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE C 814 " --> pdb=" O ALA C 810 " (cutoff:3.500A) Processing helix chain 'C' and resid 834 through 858 removed outlier: 3.610A pdb=" N LEU C 852 " --> pdb=" O GLY C 848 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA C 855 " --> pdb=" O LEU C 851 " (cutoff:3.500A) Processing helix chain 'C' and resid 922 through 928 removed outlier: 4.170A pdb=" N ARG C 926 " --> pdb=" O LEU C 922 " (cutoff:3.500A) Processing helix chain 'C' and resid 929 through 952 removed outlier: 3.761A pdb=" N SER C 935 " --> pdb=" O PHE C 931 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE C 941 " --> pdb=" O PHE C 937 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE C 944 " --> pdb=" O PHE C 940 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG C 952 " --> pdb=" O ILE C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 956 through 990 removed outlier: 3.656A pdb=" N PHE C 965 " --> pdb=" O VAL C 961 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE C 967 " --> pdb=" O GLY C 963 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU C 968 " --> pdb=" O ILE C 964 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER C 969 " --> pdb=" O PHE C 965 " (cutoff:3.500A) Processing helix chain 'C' and resid 1004 through 1033 removed outlier: 3.644A pdb=" N LEU C1015 " --> pdb=" O ALA C1011 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N MET C1023 " --> pdb=" O SER C1019 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL C1025 " --> pdb=" O GLY C1021 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 419 Processing helix chain 'D' and resid 423 through 436 Processing helix chain 'D' and resid 461 through 470 removed outlier: 3.575A pdb=" N TYR D 469 " --> pdb=" O GLY D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 487 Processing helix chain 'D' and resid 515 through 519 removed outlier: 3.549A pdb=" N LEU D 518 " --> pdb=" O PHE D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 547 removed outlier: 3.503A pdb=" N MET D 527 " --> pdb=" O TYR D 523 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE D 546 " --> pdb=" O LEU D 542 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 585 removed outlier: 3.718A pdb=" N LEU D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TRP D 578 " --> pdb=" O PHE D 574 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER D 580 " --> pdb=" O SER D 576 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU D 581 " --> pdb=" O LEU D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 595 through 626 removed outlier: 3.883A pdb=" N TRP D 605 " --> pdb=" O VAL D 601 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE D 608 " --> pdb=" O VAL D 604 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU D 610 " --> pdb=" O TRP D 606 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE D 611 " --> pdb=" O PHE D 607 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE D 612 " --> pdb=" O PHE D 608 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL D 626 " --> pdb=" O ALA D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 635 through 642 removed outlier: 3.666A pdb=" N GLN D 642 " --> pdb=" O ASP D 638 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 662 removed outlier: 3.619A pdb=" N PHE D 659 " --> pdb=" O THR D 655 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG D 660 " --> pdb=" O LYS D 656 " (cutoff:3.500A) Processing helix chain 'D' and resid 666 through 677 removed outlier: 3.605A pdb=" N MET D 674 " --> pdb=" O MET D 670 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER D 676 " --> pdb=" O THR D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 686 through 696 removed outlier: 3.524A pdb=" N ALA D 691 " --> pdb=" O ALA D 687 " (cutoff:3.500A) Processing helix chain 'D' and resid 707 through 713 Processing helix chain 'D' and resid 742 through 757 removed outlier: 3.534A pdb=" N ASN D 747 " --> pdb=" O GLY D 743 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU D 751 " --> pdb=" O ASN D 747 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 767 Processing helix chain 'D' and resid 793 through 820 removed outlier: 3.591A pdb=" N TYR D 797 " --> pdb=" O ALA D 793 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR D 816 " --> pdb=" O ILE D 812 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 396 through 399 removed outlier: 6.240A pdb=" N VAL A 397 " --> pdb=" O THR A 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 407 through 408 Processing sheet with id=AA3, first strand: chain 'A' and resid 490 through 491 Processing sheet with id=AA4, first strand: chain 'A' and resid 702 through 705 removed outlier: 3.939A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 649 through 650 removed outlier: 5.957A pdb=" N THR A 649 " --> pdb=" O VAL A 683 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 863 through 867 Processing sheet with id=AA7, first strand: chain 'B' and resid 395 through 397 removed outlier: 6.899A pdb=" N VAL B 395 " --> pdb=" O LYS B 441 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AA9, first strand: chain 'B' and resid 489 through 490 Processing sheet with id=AB1, first strand: chain 'B' and resid 497 through 498 Processing sheet with id=AB2, first strand: chain 'B' and resid 702 through 705 removed outlier: 4.156A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 396 through 399 removed outlier: 6.239A pdb=" N VAL C 397 " --> pdb=" O THR C 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 407 through 408 Processing sheet with id=AB5, first strand: chain 'C' and resid 490 through 491 Processing sheet with id=AB6, first strand: chain 'C' and resid 702 through 705 removed outlier: 3.940A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 649 through 650 removed outlier: 5.956A pdb=" N THR C 649 " --> pdb=" O VAL C 683 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 863 through 867 Processing sheet with id=AB9, first strand: chain 'D' and resid 395 through 397 removed outlier: 6.899A pdb=" N VAL D 395 " --> pdb=" O LYS D 441 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AC2, first strand: chain 'D' and resid 489 through 490 Processing sheet with id=AC3, first strand: chain 'D' and resid 497 through 498 Processing sheet with id=AC4, first strand: chain 'D' and resid 702 through 705 removed outlier: 4.155A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) 716 hydrogen bonds defined for protein. 2082 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.20 Time building geometry restraints manager: 6.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4742 1.35 - 1.47: 4120 1.47 - 1.59: 6942 1.59 - 1.71: 0 1.71 - 1.84: 174 Bond restraints: 15978 Sorted by residual: bond pdb=" C THR C 929 " pdb=" N PRO C 930 " ideal model delta sigma weight residual 1.336 1.394 -0.058 1.25e-02 6.40e+03 2.13e+01 bond pdb=" C THR A 929 " pdb=" N PRO A 930 " ideal model delta sigma weight residual 1.336 1.393 -0.057 1.25e-02 6.40e+03 2.11e+01 bond pdb=" C THR B 744 " pdb=" N PRO B 745 " ideal model delta sigma weight residual 1.336 1.390 -0.055 1.23e-02 6.61e+03 1.99e+01 bond pdb=" C THR D 744 " pdb=" N PRO D 745 " ideal model delta sigma weight residual 1.336 1.390 -0.055 1.23e-02 6.61e+03 1.98e+01 bond pdb=" C ASP D 519 " pdb=" N PRO D 520 " ideal model delta sigma weight residual 1.335 1.380 -0.045 1.30e-02 5.92e+03 1.18e+01 ... (remaining 15973 not shown) Histogram of bond angle deviations from ideal: 99.76 - 106.69: 428 106.69 - 113.61: 8548 113.61 - 120.53: 6538 120.53 - 127.45: 5873 127.45 - 134.38: 183 Bond angle restraints: 21570 Sorted by residual: angle pdb=" N LEU C 862 " pdb=" CA LEU C 862 " pdb=" C LEU C 862 " ideal model delta sigma weight residual 110.42 118.07 -7.65 1.46e+00 4.69e-01 2.74e+01 angle pdb=" N LEU A 862 " pdb=" CA LEU A 862 " pdb=" C LEU A 862 " ideal model delta sigma weight residual 110.42 118.03 -7.61 1.46e+00 4.69e-01 2.71e+01 angle pdb=" C GLU D 416 " pdb=" N GLY D 417 " pdb=" CA GLY D 417 " ideal model delta sigma weight residual 119.99 125.64 -5.65 1.13e+00 7.83e-01 2.50e+01 angle pdb=" C GLY C 894 " pdb=" N GLU C 895 " pdb=" CA GLU C 895 " ideal model delta sigma weight residual 121.54 131.06 -9.52 1.91e+00 2.74e-01 2.48e+01 angle pdb=" C GLU B 416 " pdb=" N GLY B 417 " pdb=" CA GLY B 417 " ideal model delta sigma weight residual 119.99 125.61 -5.62 1.13e+00 7.83e-01 2.47e+01 ... (remaining 21565 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.25: 8664 14.25 - 28.51: 544 28.51 - 42.76: 196 42.76 - 57.02: 22 57.02 - 71.27: 14 Dihedral angle restraints: 9440 sinusoidal: 3710 harmonic: 5730 Sorted by residual: dihedral pdb=" CA LYS C 716 " pdb=" C LYS C 716 " pdb=" N PRO C 717 " pdb=" CA PRO C 717 " ideal model delta harmonic sigma weight residual -180.00 -119.81 -60.19 0 5.00e+00 4.00e-02 1.45e+02 dihedral pdb=" CA LYS A 716 " pdb=" C LYS A 716 " pdb=" N PRO A 717 " pdb=" CA PRO A 717 " ideal model delta harmonic sigma weight residual -180.00 -119.83 -60.17 0 5.00e+00 4.00e-02 1.45e+02 dihedral pdb=" CA GLU B 678 " pdb=" C GLU B 678 " pdb=" N PRO B 679 " pdb=" CA PRO B 679 " ideal model delta harmonic sigma weight residual 180.00 133.79 46.21 0 5.00e+00 4.00e-02 8.54e+01 ... (remaining 9437 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1751 0.057 - 0.113: 551 0.113 - 0.170: 104 0.170 - 0.226: 20 0.226 - 0.283: 2 Chirality restraints: 2428 Sorted by residual: chirality pdb=" CB ILE B 591 " pdb=" CA ILE B 591 " pdb=" CG1 ILE B 591 " pdb=" CG2 ILE B 591 " both_signs ideal model delta sigma weight residual False 2.64 2.93 -0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CB ILE D 591 " pdb=" CA ILE D 591 " pdb=" CG1 ILE D 591 " pdb=" CG2 ILE D 591 " both_signs ideal model delta sigma weight residual False 2.64 2.92 -0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" CA PRO B 494 " pdb=" N PRO B 494 " pdb=" C PRO B 494 " pdb=" CB PRO B 494 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 2425 not shown) Planarity restraints: 2654 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU D 678 " -0.079 5.00e-02 4.00e+02 1.21e-01 2.33e+01 pdb=" N PRO D 679 " 0.209 5.00e-02 4.00e+02 pdb=" CA PRO D 679 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO D 679 " -0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 678 " -0.079 5.00e-02 4.00e+02 1.20e-01 2.32e+01 pdb=" N PRO B 679 " 0.208 5.00e-02 4.00e+02 pdb=" CA PRO B 679 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO B 679 " -0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 878 " 0.018 2.00e-02 2.50e+03 3.59e-02 1.29e+01 pdb=" C VAL C 878 " -0.062 2.00e-02 2.50e+03 pdb=" O VAL C 878 " 0.023 2.00e-02 2.50e+03 pdb=" N LYS C 879 " 0.021 2.00e-02 2.50e+03 ... (remaining 2651 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2117 2.75 - 3.29: 14750 3.29 - 3.83: 24692 3.83 - 4.36: 29132 4.36 - 4.90: 50296 Nonbonded interactions: 120987 Sorted by model distance: nonbonded pdb=" O ILE C 925 " pdb=" OG1 THR C 929 " model vdw 2.218 2.440 nonbonded pdb=" O ILE A 925 " pdb=" OG1 THR A 929 " model vdw 2.219 2.440 nonbonded pdb=" O PHE C 966 " pdb=" OG SER C 969 " model vdw 2.292 2.440 nonbonded pdb=" O PHE A 966 " pdb=" OG SER A 969 " model vdw 2.293 2.440 nonbonded pdb=" O TRP B 606 " pdb=" OG1 THR B 609 " model vdw 2.313 2.440 ... (remaining 120982 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 392 through 1035) selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.410 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: 0.020 Extract box with map and model: 7.400 Check model and map are aligned: 0.270 Set scattering table: 0.170 Process input model: 44.560 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 15978 Z= 0.362 Angle : 1.224 10.908 21570 Z= 0.729 Chirality : 0.057 0.283 2428 Planarity : 0.008 0.121 2654 Dihedral : 11.205 71.275 5766 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 1.12 % Allowed : 10.63 % Favored : 88.25 % Rotamer: Outliers : 0.24 % Allowed : 6.58 % Favored : 93.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 10.00 % Twisted General : 0.42 % 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: -5.78 (0.13), residues: 1966 helix: -3.64 (0.10), residues: 1010 sheet: -3.71 (0.29), residues: 198 loop : -3.92 (0.17), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 861 HIS 0.005 0.001 HIS C 412 PHE 0.049 0.003 PHE C 891 TYR 0.021 0.003 TYR C 533 ARG 0.014 0.001 ARG C 897 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 392 time to evaluate : 1.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 527 MET cc_start: 0.7378 (ptm) cc_final: 0.5895 (mmt) REVERT: A 669 LYS cc_start: 0.8209 (mtpm) cc_final: 0.7398 (tmtt) REVERT: A 888 ARG cc_start: 0.6140 (mmp80) cc_final: 0.5806 (ttm-80) REVERT: A 1001 TYR cc_start: 0.5863 (p90) cc_final: 0.5556 (p90) REVERT: B 438 PHE cc_start: 0.8323 (p90) cc_final: 0.8008 (p90) REVERT: B 695 LYS cc_start: 0.7623 (mtmp) cc_final: 0.7256 (mmpt) REVERT: B 803 LEU cc_start: 0.8074 (mt) cc_final: 0.7812 (mp) REVERT: C 500 ILE cc_start: 0.8878 (mt) cc_final: 0.8654 (mt) REVERT: C 527 MET cc_start: 0.6397 (ptm) cc_final: 0.4304 (mmt) REVERT: C 619 ASN cc_start: 0.8508 (t0) cc_final: 0.8253 (t0) REVERT: C 814 PHE cc_start: 0.7335 (t80) cc_final: 0.7061 (t80) REVERT: D 527 MET cc_start: 0.6718 (mtp) cc_final: 0.6501 (mmt) outliers start: 4 outliers final: 2 residues processed: 394 average time/residue: 0.3222 time to fit residues: 179.9760 Evaluate side-chains 246 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 244 time to evaluate : 1.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain C residue 399 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 1.9990 chunk 150 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 80 optimal weight: 0.0070 chunk 155 optimal weight: 9.9990 chunk 60 optimal weight: 0.9990 chunk 94 optimal weight: 0.8980 chunk 115 optimal weight: 4.9990 chunk 179 optimal weight: 0.9990 overall best weight: 0.7402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 950 HIS A1000 ASN B 575 ASN B 764 ASN C 435 HIS C 747 ASN C 950 HIS C 990 ASN C1000 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15978 Z= 0.215 Angle : 0.702 8.931 21570 Z= 0.370 Chirality : 0.043 0.195 2428 Planarity : 0.006 0.084 2654 Dihedral : 6.483 48.439 2154 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.61 % Allowed : 10.07 % Favored : 89.32 % Rotamer: Outliers : 2.49 % Allowed : 11.51 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.10 % 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: -3.52 (0.16), residues: 1966 helix: -1.35 (0.14), residues: 1046 sheet: -3.48 (0.33), residues: 178 loop : -3.40 (0.19), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 766 HIS 0.003 0.001 HIS B 435 PHE 0.021 0.002 PHE D 623 TYR 0.024 0.002 TYR A 533 ARG 0.005 0.001 ARG B 594 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 256 time to evaluate : 1.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 443 THR cc_start: 0.8797 (p) cc_final: 0.8336 (t) REVERT: A 527 MET cc_start: 0.7125 (ptm) cc_final: 0.5347 (mmt) REVERT: A 669 LYS cc_start: 0.8533 (mtpm) cc_final: 0.7585 (tmtt) REVERT: A 695 LYS cc_start: 0.7895 (pptt) cc_final: 0.7218 (ptpt) REVERT: A 888 ARG cc_start: 0.6155 (mmp80) cc_final: 0.5763 (ttm-80) REVERT: A 975 VAL cc_start: 0.8684 (m) cc_final: 0.8318 (t) REVERT: A 1029 MET cc_start: 0.6651 (OUTLIER) cc_final: 0.5133 (tmm) REVERT: B 606 TRP cc_start: 0.7370 (m-10) cc_final: 0.6978 (m-10) REVERT: B 695 LYS cc_start: 0.7617 (mtmp) cc_final: 0.7326 (mmpt) REVERT: C 527 MET cc_start: 0.6358 (ptm) cc_final: 0.4250 (mmt) REVERT: C 684 ARG cc_start: 0.7145 (mtm110) cc_final: 0.6732 (mpp80) REVERT: C 807 MET cc_start: 0.5251 (mtp) cc_final: 0.4865 (mtp) REVERT: D 606 TRP cc_start: 0.6146 (m-10) cc_final: 0.5766 (m-10) REVERT: D 699 LYS cc_start: 0.6947 (mmtt) cc_final: 0.6648 (mmtt) outliers start: 42 outliers final: 20 residues processed: 288 average time/residue: 0.2551 time to fit residues: 112.3646 Evaluate side-chains 236 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 215 time to evaluate : 1.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 519 ASP Chi-restraints excluded: chain A residue 533 TYR Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain B residue 411 ASN Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 456 ASP Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 412 HIS Chi-restraints excluded: chain C residue 447 ASP Chi-restraints excluded: chain C residue 533 TYR Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain D residue 401 LEU Chi-restraints excluded: chain D residue 406 VAL Chi-restraints excluded: chain D residue 411 ASN Chi-restraints excluded: chain D residue 456 ASP Chi-restraints excluded: chain D residue 482 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 99 optimal weight: 2.9990 chunk 55 optimal weight: 20.0000 chunk 149 optimal weight: 8.9990 chunk 122 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 180 optimal weight: 0.4980 chunk 194 optimal weight: 8.9990 chunk 160 optimal weight: 9.9990 chunk 178 optimal weight: 0.5980 chunk 61 optimal weight: 7.9990 chunk 144 optimal weight: 8.9990 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 726 ASN ** A 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 990 ASN C 508 GLN C 726 ASN ** D 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.4352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.100 15978 Z= 0.652 Angle : 0.908 10.144 21570 Z= 0.474 Chirality : 0.054 0.247 2428 Planarity : 0.007 0.090 2654 Dihedral : 6.828 51.408 2153 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.61 % Allowed : 13.22 % Favored : 86.16 % Rotamer: Outliers : 4.03 % Allowed : 12.34 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.21 % 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: -3.11 (0.17), residues: 1966 helix: -0.85 (0.15), residues: 1038 sheet: -3.70 (0.32), residues: 190 loop : -3.31 (0.20), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 606 HIS 0.006 0.002 HIS D 435 PHE 0.031 0.003 PHE C 495 TYR 0.039 0.003 TYR A 533 ARG 0.005 0.001 ARG D 692 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 235 time to evaluate : 1.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 420 ARG cc_start: 0.7752 (mtm180) cc_final: 0.7363 (mtp85) REVERT: A 440 TYR cc_start: 0.8556 (OUTLIER) cc_final: 0.7918 (p90) REVERT: A 527 MET cc_start: 0.7200 (ptm) cc_final: 0.5870 (mmt) REVERT: A 585 MET cc_start: 0.7470 (mmt) cc_final: 0.7267 (mmt) REVERT: A 669 LYS cc_start: 0.8402 (mtpm) cc_final: 0.7601 (tmtt) REVERT: A 674 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.8277 (mtp) REVERT: A 888 ARG cc_start: 0.6489 (mmp80) cc_final: 0.5868 (ttm-80) REVERT: A 975 VAL cc_start: 0.8697 (m) cc_final: 0.8343 (p) REVERT: A 1001 TYR cc_start: 0.6033 (p90) cc_final: 0.5665 (p90) REVERT: B 601 VAL cc_start: 0.8448 (t) cc_final: 0.8190 (p) REVERT: B 639 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8338 (tt) REVERT: C 408 MET cc_start: 0.8073 (mmt) cc_final: 0.7806 (mmm) REVERT: C 440 TYR cc_start: 0.8504 (p90) cc_final: 0.8112 (p90) REVERT: C 518 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8403 (pp) REVERT: C 527 MET cc_start: 0.6538 (ptm) cc_final: 0.4998 (mmt) REVERT: C 634 GLU cc_start: 0.8548 (tm-30) cc_final: 0.7862 (tm-30) REVERT: C 638 ASP cc_start: 0.8303 (m-30) cc_final: 0.8056 (m-30) REVERT: C 669 LYS cc_start: 0.8173 (mtpm) cc_final: 0.7198 (tmtt) REVERT: C 684 ARG cc_start: 0.7309 (mtm110) cc_final: 0.6994 (mpp80) REVERT: C 988 MET cc_start: 0.7269 (tmm) cc_final: 0.6992 (tmm) REVERT: D 633 ILE cc_start: 0.8151 (OUTLIER) cc_final: 0.7912 (pp) REVERT: D 639 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8506 (tt) outliers start: 68 outliers final: 30 residues processed: 287 average time/residue: 0.2589 time to fit residues: 112.9774 Evaluate side-chains 251 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 215 time to evaluate : 1.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 440 TYR Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 519 ASP Chi-restraints excluded: chain A residue 533 TYR Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 674 MET Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 411 ASN Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 741 SER Chi-restraints excluded: chain B residue 785 SER Chi-restraints excluded: chain B residue 790 SER Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 447 ASP Chi-restraints excluded: chain C residue 459 ILE Chi-restraints excluded: chain C residue 500 ILE Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 533 TYR Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 645 ILE Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 492 SER Chi-restraints excluded: chain D residue 543 VAL Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 639 LEU Chi-restraints excluded: chain D residue 790 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 177 optimal weight: 0.5980 chunk 135 optimal weight: 5.9990 chunk 93 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 85 optimal weight: 3.9990 chunk 120 optimal weight: 0.8980 chunk 180 optimal weight: 0.9980 chunk 191 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 171 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 642 GLN ** D 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.4529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15978 Z= 0.202 Angle : 0.636 8.867 21570 Z= 0.332 Chirality : 0.042 0.152 2428 Planarity : 0.005 0.075 2654 Dihedral : 6.060 45.522 2153 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.31 % Allowed : 10.38 % Favored : 89.32 % Rotamer: Outliers : 2.73 % Allowed : 15.36 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.10 % 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: -2.19 (0.18), residues: 1966 helix: 0.01 (0.16), residues: 1046 sheet: -3.41 (0.35), residues: 156 loop : -3.13 (0.20), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 766 HIS 0.003 0.001 HIS A 412 PHE 0.023 0.002 PHE D 623 TYR 0.020 0.001 TYR A 980 ARG 0.004 0.000 ARG B 594 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 237 time to evaluate : 1.674 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 420 ARG cc_start: 0.7563 (mtm180) cc_final: 0.7161 (mtp85) REVERT: A 527 MET cc_start: 0.7139 (ptm) cc_final: 0.5498 (mmt) REVERT: A 669 LYS cc_start: 0.8496 (mtpm) cc_final: 0.7584 (tmtt) REVERT: A 670 MET cc_start: 0.8317 (ttm) cc_final: 0.8053 (mtp) REVERT: A 674 MET cc_start: 0.8375 (OUTLIER) cc_final: 0.8033 (mtp) REVERT: A 888 ARG cc_start: 0.6362 (mmp80) cc_final: 0.5918 (ttm-80) REVERT: A 936 LEU cc_start: 0.6424 (OUTLIER) cc_final: 0.6051 (mt) REVERT: A 975 VAL cc_start: 0.8581 (m) cc_final: 0.8194 (p) REVERT: A 981 ILE cc_start: 0.7199 (mt) cc_final: 0.6881 (mm) REVERT: A 1001 TYR cc_start: 0.5906 (p90) cc_final: 0.5575 (p90) REVERT: B 527 MET cc_start: 0.7620 (mtp) cc_final: 0.6904 (mmt) REVERT: B 601 VAL cc_start: 0.8280 (t) cc_final: 0.7989 (m) REVERT: C 518 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8168 (pp) REVERT: C 527 MET cc_start: 0.6353 (ptm) cc_final: 0.4808 (mmt) REVERT: C 585 MET cc_start: 0.5878 (mmt) cc_final: 0.5663 (mmt) REVERT: C 634 GLU cc_start: 0.8526 (tm-30) cc_final: 0.7818 (tm-30) REVERT: C 638 ASP cc_start: 0.8212 (m-30) cc_final: 0.7933 (m-30) REVERT: C 669 LYS cc_start: 0.8171 (mtpm) cc_final: 0.7226 (tmtt) REVERT: C 684 ARG cc_start: 0.7246 (mtm110) cc_final: 0.6941 (mpp80) REVERT: C 975 VAL cc_start: 0.7855 (t) cc_final: 0.7629 (p) REVERT: C 988 MET cc_start: 0.7410 (tmm) cc_final: 0.7185 (tmm) outliers start: 46 outliers final: 28 residues processed: 272 average time/residue: 0.2626 time to fit residues: 108.0186 Evaluate side-chains 246 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 215 time to evaluate : 1.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 533 TYR Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 674 MET Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain B residue 411 ASN Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 456 ASP Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 741 SER Chi-restraints excluded: chain B residue 785 SER Chi-restraints excluded: chain B residue 790 SER Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 447 ASP Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 525 ILE Chi-restraints excluded: chain C residue 533 TYR Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain D residue 411 ASN Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 482 THR Chi-restraints excluded: chain D residue 741 SER Chi-restraints excluded: chain D residue 790 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 159 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 142 optimal weight: 20.0000 chunk 78 optimal weight: 1.9990 chunk 163 optimal weight: 6.9990 chunk 132 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 171 optimal weight: 0.8980 chunk 48 optimal weight: 0.0980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 747 ASN C 435 HIS C 642 GLN ** D 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.4776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15978 Z= 0.191 Angle : 0.613 10.404 21570 Z= 0.319 Chirality : 0.041 0.183 2428 Planarity : 0.005 0.073 2654 Dihedral : 5.738 42.121 2153 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.14 % Favored : 88.66 % Rotamer: Outliers : 2.85 % Allowed : 16.55 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.05 % 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: -1.81 (0.19), residues: 1966 helix: 0.41 (0.16), residues: 1042 sheet: -3.39 (0.34), residues: 156 loop : -3.06 (0.20), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP D 606 HIS 0.002 0.001 HIS D 435 PHE 0.023 0.001 PHE D 623 TYR 0.021 0.001 TYR A 980 ARG 0.004 0.000 ARG D 599 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 228 time to evaluate : 1.764 Fit side-chains REVERT: A 408 MET cc_start: 0.8014 (mmm) cc_final: 0.7473 (mmm) REVERT: A 420 ARG cc_start: 0.7669 (mtm180) cc_final: 0.7099 (mtp85) REVERT: A 527 MET cc_start: 0.7169 (ptm) cc_final: 0.5466 (mmt) REVERT: A 669 LYS cc_start: 0.8541 (mtpm) cc_final: 0.7837 (tmtt) REVERT: A 674 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.8191 (mtp) REVERT: A 888 ARG cc_start: 0.6155 (mmp80) cc_final: 0.5902 (ttm-80) REVERT: A 936 LEU cc_start: 0.6538 (OUTLIER) cc_final: 0.6173 (mt) REVERT: A 981 ILE cc_start: 0.7070 (mt) cc_final: 0.6682 (mm) REVERT: A 1001 TYR cc_start: 0.5965 (p90) cc_final: 0.5640 (p90) REVERT: B 527 MET cc_start: 0.7563 (mtp) cc_final: 0.6879 (mmt) REVERT: B 688 GLU cc_start: 0.7726 (mp0) cc_final: 0.7496 (mp0) REVERT: C 527 MET cc_start: 0.6402 (ptm) cc_final: 0.4670 (mmt) REVERT: C 634 GLU cc_start: 0.8458 (tm-30) cc_final: 0.7781 (tm-30) REVERT: C 669 LYS cc_start: 0.8325 (mtpm) cc_final: 0.7260 (tmtt) REVERT: C 674 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.7883 (mtp) REVERT: C 988 MET cc_start: 0.7384 (tmm) cc_final: 0.7169 (tmm) REVERT: C 1001 TYR cc_start: 0.6591 (p90) cc_final: 0.6063 (p90) REVERT: C 1029 MET cc_start: 0.5957 (mmm) cc_final: 0.5212 (mmm) REVERT: D 531 PHE cc_start: 0.5642 (m-10) cc_final: 0.5431 (m-10) REVERT: D 633 ILE cc_start: 0.8112 (OUTLIER) cc_final: 0.7862 (pp) REVERT: D 650 LEU cc_start: 0.7584 (OUTLIER) cc_final: 0.7358 (tt) outliers start: 48 outliers final: 28 residues processed: 262 average time/residue: 0.2536 time to fit residues: 102.5739 Evaluate side-chains 245 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 212 time to evaluate : 1.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 533 TYR Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 674 MET Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain B residue 411 ASN Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 456 ASP Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 790 SER Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 447 ASP Chi-restraints excluded: chain C residue 533 TYR Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 674 MET Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain D residue 411 ASN Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 456 ASP Chi-restraints excluded: chain D residue 482 THR Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 650 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 64 optimal weight: 3.9990 chunk 172 optimal weight: 8.9990 chunk 37 optimal weight: 0.9980 chunk 112 optimal weight: 0.5980 chunk 47 optimal weight: 20.0000 chunk 191 optimal weight: 2.9990 chunk 159 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 15 optimal weight: 10.0000 chunk 63 optimal weight: 0.9980 chunk 100 optimal weight: 0.1980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 642 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.4992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15978 Z= 0.192 Angle : 0.599 11.378 21570 Z= 0.311 Chirality : 0.041 0.180 2428 Planarity : 0.005 0.069 2654 Dihedral : 5.534 39.480 2153 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.73 % Favored : 89.06 % Rotamer: Outliers : 2.97 % Allowed : 17.85 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 6.67 % 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: -1.51 (0.19), residues: 1966 helix: 0.64 (0.17), residues: 1040 sheet: -3.31 (0.34), residues: 156 loop : -2.86 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP D 606 HIS 0.002 0.001 HIS D 435 PHE 0.027 0.001 PHE C1028 TYR 0.022 0.001 TYR A 980 ARG 0.003 0.000 ARG B 594 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 229 time to evaluate : 1.687 Fit side-chains REVERT: A 408 MET cc_start: 0.7958 (mmm) cc_final: 0.7367 (mmm) REVERT: A 420 ARG cc_start: 0.7697 (mtm180) cc_final: 0.7039 (mtp85) REVERT: A 527 MET cc_start: 0.7194 (ptm) cc_final: 0.5485 (mmt) REVERT: A 669 LYS cc_start: 0.8481 (mtpm) cc_final: 0.7813 (tmtt) REVERT: A 674 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.8249 (mtp) REVERT: A 907 MET cc_start: 0.6912 (ptp) cc_final: 0.6671 (ptp) REVERT: A 936 LEU cc_start: 0.6542 (OUTLIER) cc_final: 0.6180 (mt) REVERT: A 1001 TYR cc_start: 0.5870 (p90) cc_final: 0.5543 (p90) REVERT: B 527 MET cc_start: 0.7451 (mtp) cc_final: 0.6858 (mmt) REVERT: B 688 GLU cc_start: 0.7949 (mp0) cc_final: 0.7594 (mp0) REVERT: C 527 MET cc_start: 0.6335 (ptm) cc_final: 0.4671 (mmt) REVERT: C 634 GLU cc_start: 0.8482 (tm-30) cc_final: 0.7778 (tm-30) REVERT: C 669 LYS cc_start: 0.8324 (mtpm) cc_final: 0.7332 (tmtt) REVERT: C 674 MET cc_start: 0.8348 (OUTLIER) cc_final: 0.7859 (mtp) REVERT: C 975 VAL cc_start: 0.7729 (OUTLIER) cc_final: 0.7456 (p) REVERT: C 1001 TYR cc_start: 0.6369 (p90) cc_final: 0.6004 (p90) REVERT: D 633 ILE cc_start: 0.8063 (OUTLIER) cc_final: 0.7841 (pp) REVERT: D 650 LEU cc_start: 0.7293 (OUTLIER) cc_final: 0.7089 (tt) outliers start: 50 outliers final: 32 residues processed: 260 average time/residue: 0.2537 time to fit residues: 100.6704 Evaluate side-chains 242 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 204 time to evaluate : 1.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 533 TYR Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 674 MET Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain B residue 411 ASN Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 456 ASP Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 741 SER Chi-restraints excluded: chain B residue 785 SER Chi-restraints excluded: chain B residue 790 SER Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 447 ASP Chi-restraints excluded: chain C residue 533 TYR Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 674 MET Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 889 VAL Chi-restraints excluded: chain C residue 975 VAL Chi-restraints excluded: chain D residue 411 ASN Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 482 THR Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 790 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 184 optimal weight: 0.4980 chunk 21 optimal weight: 0.5980 chunk 109 optimal weight: 0.0970 chunk 139 optimal weight: 20.0000 chunk 108 optimal weight: 0.5980 chunk 161 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 190 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 116 optimal weight: 6.9990 chunk 88 optimal weight: 0.7980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 642 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.5163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15978 Z= 0.172 Angle : 0.596 11.335 21570 Z= 0.307 Chirality : 0.041 0.166 2428 Planarity : 0.004 0.072 2654 Dihedral : 5.411 39.068 2153 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.22 % Favored : 89.62 % Rotamer: Outliers : 3.14 % Allowed : 18.03 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 6.67 % 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: -1.29 (0.19), residues: 1966 helix: 0.79 (0.17), residues: 1042 sheet: -3.03 (0.37), residues: 144 loop : -2.81 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP D 606 HIS 0.002 0.001 HIS C 412 PHE 0.027 0.001 PHE C1028 TYR 0.019 0.001 TYR A 980 ARG 0.003 0.000 ARG B 594 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 222 time to evaluate : 1.619 Fit side-chains revert: symmetry clash REVERT: A 408 MET cc_start: 0.7968 (mmm) cc_final: 0.7326 (mmm) REVERT: A 414 MET cc_start: 0.6965 (ptp) cc_final: 0.6540 (ptp) REVERT: A 527 MET cc_start: 0.7085 (ptm) cc_final: 0.5450 (mmt) REVERT: A 585 MET cc_start: 0.5025 (mmt) cc_final: 0.4744 (mmt) REVERT: A 669 LYS cc_start: 0.8482 (mtpm) cc_final: 0.7854 (tmtt) REVERT: A 674 MET cc_start: 0.8636 (OUTLIER) cc_final: 0.8332 (mtp) REVERT: A 907 MET cc_start: 0.6885 (ptp) cc_final: 0.6614 (ptp) REVERT: A 936 LEU cc_start: 0.6602 (OUTLIER) cc_final: 0.6320 (mt) REVERT: A 1001 TYR cc_start: 0.5845 (p90) cc_final: 0.5546 (p90) REVERT: B 527 MET cc_start: 0.7313 (mtp) cc_final: 0.6821 (mmt) REVERT: B 688 GLU cc_start: 0.7951 (mp0) cc_final: 0.7604 (mp0) REVERT: C 527 MET cc_start: 0.6515 (ptm) cc_final: 0.4718 (mmt) REVERT: C 627 GLU cc_start: 0.7968 (tm-30) cc_final: 0.7715 (tm-30) REVERT: C 634 GLU cc_start: 0.8476 (tm-30) cc_final: 0.7804 (tm-30) REVERT: C 669 LYS cc_start: 0.8345 (mtpm) cc_final: 0.7343 (tmtt) REVERT: C 674 MET cc_start: 0.8350 (OUTLIER) cc_final: 0.7872 (mtp) REVERT: C 880 MET cc_start: 0.4941 (mpp) cc_final: 0.3700 (mmp) REVERT: C 1001 TYR cc_start: 0.6239 (p90) cc_final: 0.5810 (p90) REVERT: D 633 ILE cc_start: 0.8055 (OUTLIER) cc_final: 0.7835 (pp) outliers start: 53 outliers final: 37 residues processed: 253 average time/residue: 0.2524 time to fit residues: 98.2271 Evaluate side-chains 245 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 204 time to evaluate : 1.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain A residue 533 TYR Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 546 PHE Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 674 MET Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain B residue 411 ASN Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 456 ASP Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 741 SER Chi-restraints excluded: chain B residue 785 SER Chi-restraints excluded: chain B residue 790 SER Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 447 ASP Chi-restraints excluded: chain C residue 533 TYR Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 649 THR Chi-restraints excluded: chain C residue 674 MET Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 889 VAL Chi-restraints excluded: chain D residue 411 ASN Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 456 ASP Chi-restraints excluded: chain D residue 482 THR Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 741 SER Chi-restraints excluded: chain D residue 790 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 118 optimal weight: 0.8980 chunk 76 optimal weight: 9.9990 chunk 113 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 36 optimal weight: 0.2980 chunk 121 optimal weight: 8.9990 chunk 130 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 150 optimal weight: 7.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 642 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.5288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15978 Z= 0.204 Angle : 0.614 14.071 21570 Z= 0.314 Chirality : 0.042 0.228 2428 Planarity : 0.005 0.089 2654 Dihedral : 5.357 39.367 2153 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.20 % Allowed : 10.68 % Favored : 89.11 % Rotamer: Outliers : 2.97 % Allowed : 18.33 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 6.67 % 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: -1.28 (0.19), residues: 1966 helix: 0.84 (0.17), residues: 1042 sheet: -2.97 (0.35), residues: 180 loop : -2.81 (0.21), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP D 606 HIS 0.002 0.001 HIS C 883 PHE 0.029 0.001 PHE C1028 TYR 0.019 0.001 TYR A 980 ARG 0.011 0.000 ARG D 661 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 215 time to evaluate : 1.769 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 408 MET cc_start: 0.7964 (mmm) cc_final: 0.7299 (mmm) REVERT: A 414 MET cc_start: 0.6938 (ptp) cc_final: 0.6541 (ptp) REVERT: A 527 MET cc_start: 0.7199 (ptm) cc_final: 0.5449 (mmt) REVERT: A 585 MET cc_start: 0.5185 (mmt) cc_final: 0.4811 (mmt) REVERT: A 669 LYS cc_start: 0.8562 (mtpm) cc_final: 0.7881 (tmtt) REVERT: A 936 LEU cc_start: 0.6637 (OUTLIER) cc_final: 0.6365 (mt) REVERT: A 1001 TYR cc_start: 0.5967 (p90) cc_final: 0.5666 (p90) REVERT: B 527 MET cc_start: 0.7328 (mtp) cc_final: 0.6867 (mmt) REVERT: B 639 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7796 (tt) REVERT: B 688 GLU cc_start: 0.7983 (mp0) cc_final: 0.7638 (mp0) REVERT: C 527 MET cc_start: 0.6494 (ptm) cc_final: 0.4718 (mmt) REVERT: C 627 GLU cc_start: 0.7999 (tm-30) cc_final: 0.7691 (tm-30) REVERT: C 634 GLU cc_start: 0.8504 (tm-30) cc_final: 0.7839 (tm-30) REVERT: C 669 LYS cc_start: 0.8325 (mtpm) cc_final: 0.7297 (tmtt) REVERT: C 674 MET cc_start: 0.8436 (OUTLIER) cc_final: 0.7897 (mtp) REVERT: C 880 MET cc_start: 0.4476 (mpp) cc_final: 0.3145 (mmp) REVERT: C 1001 TYR cc_start: 0.6315 (p90) cc_final: 0.5886 (p90) REVERT: D 633 ILE cc_start: 0.8095 (OUTLIER) cc_final: 0.7879 (pp) outliers start: 50 outliers final: 38 residues processed: 245 average time/residue: 0.2501 time to fit residues: 94.4662 Evaluate side-chains 246 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 204 time to evaluate : 2.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 435 HIS Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain A residue 533 TYR Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 649 THR Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain A residue 674 MET Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain B residue 411 ASN Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 741 SER Chi-restraints excluded: chain B residue 785 SER Chi-restraints excluded: chain B residue 790 SER Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 447 ASP Chi-restraints excluded: chain C residue 533 TYR Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 674 MET Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain D residue 411 ASN Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 456 ASP Chi-restraints excluded: chain D residue 482 THR Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 741 SER Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain D residue 790 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 173 optimal weight: 9.9990 chunk 182 optimal weight: 0.8980 chunk 166 optimal weight: 1.9990 chunk 177 optimal weight: 0.5980 chunk 107 optimal weight: 0.9990 chunk 77 optimal weight: 10.0000 chunk 139 optimal weight: 30.0000 chunk 54 optimal weight: 9.9990 chunk 160 optimal weight: 0.0980 chunk 168 optimal weight: 0.8980 chunk 116 optimal weight: 3.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 508 GLN C 642 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.5387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15978 Z= 0.191 Angle : 0.612 14.683 21570 Z= 0.312 Chirality : 0.041 0.221 2428 Planarity : 0.005 0.088 2654 Dihedral : 5.305 38.679 2153 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.68 % Favored : 89.17 % Rotamer: Outliers : 2.97 % Allowed : 18.86 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 6.67 % 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: -1.21 (0.19), residues: 1966 helix: 0.90 (0.17), residues: 1042 sheet: -2.92 (0.35), residues: 180 loop : -2.80 (0.21), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP D 606 HIS 0.002 0.001 HIS C 883 PHE 0.028 0.001 PHE C1028 TYR 0.021 0.001 TYR D 647 ARG 0.012 0.000 ARG D 661 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 209 time to evaluate : 1.912 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 408 MET cc_start: 0.7936 (mmm) cc_final: 0.7257 (mmm) REVERT: A 414 MET cc_start: 0.6953 (ptp) cc_final: 0.6575 (ptp) REVERT: A 527 MET cc_start: 0.7028 (ptm) cc_final: 0.5325 (mmt) REVERT: A 585 MET cc_start: 0.5144 (mmt) cc_final: 0.4730 (mmt) REVERT: A 669 LYS cc_start: 0.8597 (mtpm) cc_final: 0.7989 (tmtt) REVERT: A 936 LEU cc_start: 0.6684 (OUTLIER) cc_final: 0.6412 (mt) REVERT: A 1001 TYR cc_start: 0.5928 (p90) cc_final: 0.5665 (p90) REVERT: B 527 MET cc_start: 0.7285 (mtp) cc_final: 0.6867 (mmp) REVERT: B 639 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7795 (tt) REVERT: B 688 GLU cc_start: 0.8050 (mp0) cc_final: 0.7802 (mp0) REVERT: C 527 MET cc_start: 0.6407 (ptm) cc_final: 0.4690 (mmt) REVERT: C 586 GLN cc_start: 0.7435 (OUTLIER) cc_final: 0.7193 (mm110) REVERT: C 627 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7656 (tm-30) REVERT: C 634 GLU cc_start: 0.8505 (tm-30) cc_final: 0.7839 (tm-30) REVERT: C 669 LYS cc_start: 0.8321 (mtpm) cc_final: 0.7253 (tptp) REVERT: C 880 MET cc_start: 0.4276 (mpp) cc_final: 0.2962 (mmp) REVERT: C 1001 TYR cc_start: 0.6420 (p90) cc_final: 0.6007 (p90) REVERT: D 633 ILE cc_start: 0.8035 (OUTLIER) cc_final: 0.7832 (pp) outliers start: 50 outliers final: 40 residues processed: 242 average time/residue: 0.2558 time to fit residues: 95.3108 Evaluate side-chains 247 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 203 time to evaluate : 1.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 435 HIS Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain A residue 533 TYR Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 674 MET Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain B residue 411 ASN Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 456 ASP Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 741 SER Chi-restraints excluded: chain B residue 785 SER Chi-restraints excluded: chain B residue 790 SER Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 447 ASP Chi-restraints excluded: chain C residue 533 TYR Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 586 GLN Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 649 THR Chi-restraints excluded: chain C residue 683 VAL Chi-restraints excluded: chain C residue 742 LEU Chi-restraints excluded: chain C residue 889 VAL Chi-restraints excluded: chain D residue 411 ASN Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 456 ASP Chi-restraints excluded: chain D residue 482 THR Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 741 SER Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain D residue 790 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 188 optimal weight: 1.9990 chunk 114 optimal weight: 10.0000 chunk 89 optimal weight: 0.6980 chunk 130 optimal weight: 0.7980 chunk 197 optimal weight: 6.9990 chunk 181 optimal weight: 0.9990 chunk 157 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 121 optimal weight: 0.0980 chunk 96 optimal weight: 0.7980 chunk 124 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 642 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.5520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15978 Z= 0.176 Angle : 0.606 15.660 21570 Z= 0.309 Chirality : 0.041 0.217 2428 Planarity : 0.005 0.083 2654 Dihedral : 5.152 37.903 2152 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.17 % Favored : 89.73 % Rotamer: Outliers : 2.43 % Allowed : 19.28 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 6.67 % 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: -1.08 (0.20), residues: 1966 helix: 1.05 (0.17), residues: 1044 sheet: -2.89 (0.35), residues: 180 loop : -2.82 (0.21), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP D 606 HIS 0.002 0.001 HIS C 883 PHE 0.029 0.001 PHE C1028 TYR 0.018 0.001 TYR A 980 ARG 0.011 0.000 ARG D 661 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3932 Ramachandran restraints generated. 1966 Oldfield, 0 Emsley, 1966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 212 time to evaluate : 1.773 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 408 MET cc_start: 0.7931 (mmm) cc_final: 0.7243 (mmm) REVERT: A 414 MET cc_start: 0.6911 (ptp) cc_final: 0.6536 (ptp) REVERT: A 527 MET cc_start: 0.7035 (ptm) cc_final: 0.5246 (mmt) REVERT: A 585 MET cc_start: 0.5023 (mmt) cc_final: 0.4666 (mmt) REVERT: A 669 LYS cc_start: 0.8584 (mtpm) cc_final: 0.7995 (tmtt) REVERT: A 936 LEU cc_start: 0.6783 (OUTLIER) cc_final: 0.6537 (mt) REVERT: A 1001 TYR cc_start: 0.5994 (p90) cc_final: 0.5659 (p90) REVERT: B 527 MET cc_start: 0.7211 (mtp) cc_final: 0.6912 (mmt) REVERT: B 639 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7676 (tt) REVERT: C 527 MET cc_start: 0.6361 (ptm) cc_final: 0.4550 (mmt) REVERT: C 627 GLU cc_start: 0.7948 (tm-30) cc_final: 0.7637 (tm-30) REVERT: C 634 GLU cc_start: 0.8517 (tm-30) cc_final: 0.7849 (tm-30) REVERT: C 669 LYS cc_start: 0.8547 (mtpm) cc_final: 0.7370 (tptp) REVERT: C 714 GLN cc_start: 0.7951 (mm-40) cc_final: 0.7565 (mm110) REVERT: C 880 MET cc_start: 0.4020 (mpp) cc_final: 0.2688 (mmp) REVERT: C 1001 TYR cc_start: 0.5955 (p90) cc_final: 0.5493 (p90) REVERT: D 684 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.7116 (ptt-90) REVERT: D 688 GLU cc_start: 0.7588 (mp0) cc_final: 0.7171 (mp0) outliers start: 41 outliers final: 34 residues processed: 237 average time/residue: 0.2568 time to fit residues: 93.1929 Evaluate side-chains 237 residues out of total 1686 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 200 time to evaluate : 1.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain A residue 435 HIS Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain A residue 533 TYR Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 647 TYR Chi-restraints excluded: chain A residue 868 ILE Chi-restraints excluded: chain A residue 936 LEU Chi-restraints excluded: chain B residue 411 ASN Chi-restraints excluded: chain B residue 456 ASP Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 639 LEU Chi-restraints excluded: chain B residue 644 GLU Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 741 SER Chi-restraints excluded: chain B residue 785 SER Chi-restraints excluded: chain B residue 790 SER Chi-restraints excluded: chain C residue 407 MET Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 447 ASP Chi-restraints excluded: chain C residue 533 TYR Chi-restraints excluded: chain C residue 581 LEU Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 889 VAL Chi-restraints excluded: chain D residue 411 ASN Chi-restraints excluded: chain D residue 445 VAL Chi-restraints excluded: chain D residue 456 ASP Chi-restraints excluded: chain D residue 482 THR Chi-restraints excluded: chain D residue 684 ARG Chi-restraints excluded: chain D residue 741 SER Chi-restraints excluded: chain D residue 762 LEU Chi-restraints excluded: chain D residue 790 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 144 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 chunk 157 optimal weight: 7.9990 chunk 65 optimal weight: 0.8980 chunk 161 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 138 optimal weight: 8.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 HIS C 642 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.202154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.172959 restraints weight = 18136.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.166304 restraints weight = 29697.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.164097 restraints weight = 29712.425| |-----------------------------------------------------------------------------| r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.5570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 15978 Z= 0.391 Angle : 0.725 15.755 21570 Z= 0.372 Chirality : 0.047 0.277 2428 Planarity : 0.006 0.089 2654 Dihedral : 5.644 40.533 2152 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.36 % Allowed : 12.21 % Favored : 87.44 % Rotamer: Outliers : 2.43 % Allowed : 19.63 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 6.67 % 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: -1.48 (0.19), residues: 1966 helix: 0.68 (0.16), residues: 1034 sheet: -3.11 (0.35), residues: 156 loop : -2.91 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP D 606 HIS 0.004 0.001 HIS B 435 PHE 0.028 0.002 PHE C1028 TYR 0.026 0.002 TYR D 647 ARG 0.010 0.001 ARG D 661 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3076.03 seconds wall clock time: 57 minutes 24.88 seconds (3444.88 seconds total)