Starting phenix.real_space_refine on Fri Sep 27 14:41:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryy_24748/09_2024/7ryy_24748.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryy_24748/09_2024/7ryy_24748.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryy_24748/09_2024/7ryy_24748.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryy_24748/09_2024/7ryy_24748.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryy_24748/09_2024/7ryy_24748.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryy_24748/09_2024/7ryy_24748.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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 P 2 5.49 5 S 106 5.16 5 C 10288 2.51 5 N 2538 2.21 5 O 2902 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 15836 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4698 Classifications: {'peptide': 602} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 585} Chain breaks: 4 Chain: "B" Number of atoms: 3177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3177 Classifications: {'peptide': 408} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 394} Chain breaks: 1 Chain: "C" Number of atoms: 4698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4698 Classifications: {'peptide': 602} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 585} Chain breaks: 4 Chain: "D" Number of atoms: 3177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3177 Classifications: {'peptide': 408} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 394} Chain breaks: 1 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {'PCW': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'PCW:plan-1': 1, 'PCW:plan-2': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {'PCW': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'PCW:plan-1': 1, 'PCW:plan-2': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 9.56, per 1000 atoms: 0.60 Number of scatterers: 15836 At special positions: 0 Unit cell: (120.512, 133.424, 129.12, 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 106 16.00 P 2 15.00 O 2902 8.00 N 2538 7.00 C 10288 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=2.03 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.07 Conformation dependent library (CDL) restraints added in 2.1 seconds 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3700 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 20 sheets defined 56.5% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'A' and resid 416 through 421 removed outlier: 3.739A pdb=" N TYR A 421 " --> pdb=" O ASN A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 462 through 469 Processing helix chain 'A' and resid 482 through 487 Processing helix chain 'A' and resid 515 through 519 removed outlier: 3.669A pdb=" N LEU A 518 " --> pdb=" O PHE A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 545 removed outlier: 3.761A pdb=" N SER A 537 " --> pdb=" O TYR A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 585 Processing helix chain 'A' and resid 595 through 630 removed outlier: 3.711A pdb=" N ILE A 611 " --> pdb=" O PHE A 607 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER A 614 " --> pdb=" O LEU A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 642 Processing helix chain 'A' and resid 654 through 661 Processing helix chain 'A' and resid 664 through 676 Processing helix chain 'A' and resid 685 through 697 removed outlier: 3.721A pdb=" N VAL A 693 " --> pdb=" O GLY A 689 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS A 697 " --> pdb=" O VAL A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 715 Processing helix chain 'A' and resid 742 through 756 removed outlier: 3.562A pdb=" N LEU A 751 " --> pdb=" O ASN A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 769 removed outlier: 4.153A pdb=" N TRP A 767 " --> pdb=" O LYS A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 822 removed outlier: 3.967A pdb=" N PHE A 796 " --> pdb=" O VAL A 792 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 805 " --> pdb=" O GLY A 801 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER A 818 " --> pdb=" O PHE A 814 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA A 822 " --> pdb=" O SER A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 858 removed outlier: 4.165A pdb=" N ALA A 836 " --> pdb=" O CYS A 832 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N SER A 857 " --> pdb=" O GLY A 853 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR A 858 " --> pdb=" O ILE A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 926 removed outlier: 3.780A pdb=" N ARG A 926 " --> pdb=" O LEU A 922 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 951 removed outlier: 3.851A pdb=" N LEU A 933 " --> pdb=" O THR A 929 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE A 938 " --> pdb=" O VAL A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 957 through 990 removed outlier: 3.687A pdb=" N SER A 962 " --> pdb=" O LEU A 958 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE A 964 " --> pdb=" O PHE A 960 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE A 984 " --> pdb=" O TYR A 980 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 989 " --> pdb=" O ASN A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1035 removed outlier: 3.641A pdb=" N LEU A1016 " --> pdb=" O ILE A1012 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR A1017 " --> pdb=" O SER A1013 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL A1022 " --> pdb=" O GLU A1018 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 437 Processing helix chain 'B' and resid 463 through 469 Processing helix chain 'B' and resid 482 through 488 removed outlier: 3.836A pdb=" N VAL B 488 " --> pdb=" O VAL B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.784A pdb=" N LEU B 518 " --> pdb=" O PHE B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 546 removed outlier: 3.776A pdb=" N SER B 537 " --> pdb=" O TYR B 533 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N PHE B 546 " --> pdb=" O LEU B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 585 removed outlier: 3.782A pdb=" N LEU B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N TRP B 578 " --> pdb=" O PHE B 574 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY B 582 " --> pdb=" O TRP B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 595 through 626 removed outlier: 3.825A pdb=" N VAL B 601 " --> pdb=" O SER B 597 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE B 611 " --> pdb=" O PHE B 607 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER B 614 " --> pdb=" O LEU B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 642 removed outlier: 3.598A pdb=" N SER B 640 " --> pdb=" O ALA B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 661 removed outlier: 3.513A pdb=" N PHE B 659 " --> pdb=" O THR B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 676 Processing helix chain 'B' and resid 685 through 697 removed outlier: 3.500A pdb=" N VAL B 693 " --> pdb=" O GLY B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 715 Processing helix chain 'B' and resid 742 through 757 removed outlier: 4.296A pdb=" N GLN B 756 " --> pdb=" O LYS B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 770 removed outlier: 3.691A pdb=" N LYS B 763 " --> pdb=" O LEU B 759 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TYR B 768 " --> pdb=" O ASN B 764 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LYS B 770 " --> pdb=" O TRP B 766 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 781 removed outlier: 3.631A pdb=" N GLY B 779 " --> pdb=" O ALA B 775 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N SER B 780 " --> pdb=" O LYS B 776 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS B 781 " --> pdb=" O ASP B 777 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 775 through 781' Processing helix chain 'B' and resid 792 through 819 removed outlier: 3.952A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU B 808 " --> pdb=" O GLY B 804 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE B 814 " --> pdb=" O ALA B 810 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR B 816 " --> pdb=" O ILE B 812 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 421 removed outlier: 3.739A pdb=" N TYR C 421 " --> pdb=" O ASN C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 437 Processing helix chain 'C' and resid 462 through 469 Processing helix chain 'C' and resid 482 through 487 Processing helix chain 'C' and resid 515 through 519 removed outlier: 3.669A pdb=" N LEU C 518 " --> pdb=" O PHE C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 545 removed outlier: 3.762A pdb=" N SER C 537 " --> pdb=" O TYR C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 585 Processing helix chain 'C' and resid 595 through 630 removed outlier: 3.711A pdb=" N ILE C 611 " --> pdb=" O PHE C 607 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER C 614 " --> pdb=" O LEU C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 642 Processing helix chain 'C' and resid 654 through 661 Processing helix chain 'C' and resid 664 through 676 Processing helix chain 'C' and resid 685 through 697 removed outlier: 3.720A pdb=" N VAL C 693 " --> pdb=" O GLY C 689 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS C 697 " --> pdb=" O VAL C 693 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 715 Processing helix chain 'C' and resid 742 through 756 removed outlier: 3.563A pdb=" N LEU C 751 " --> pdb=" O ASN C 747 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 769 removed outlier: 4.153A pdb=" N TRP C 767 " --> pdb=" O LYS C 763 " (cutoff:3.500A) Processing helix chain 'C' and resid 792 through 822 removed outlier: 3.966A pdb=" N PHE C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU C 805 " --> pdb=" O GLY C 801 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER C 818 " --> pdb=" O PHE C 814 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA C 822 " --> pdb=" O SER C 818 " (cutoff:3.500A) Processing helix chain 'C' and resid 832 through 858 removed outlier: 4.163A pdb=" N ALA C 836 " --> pdb=" O CYS C 832 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N SER C 857 " --> pdb=" O GLY C 853 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR C 858 " --> pdb=" O ILE C 854 " (cutoff:3.500A) Processing helix chain 'C' and resid 917 through 926 removed outlier: 3.780A pdb=" N ARG C 926 " --> pdb=" O LEU C 922 " (cutoff:3.500A) Processing helix chain 'C' and resid 929 through 951 removed outlier: 3.851A pdb=" N LEU C 933 " --> pdb=" O THR C 929 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE C 938 " --> pdb=" O VAL C 934 " (cutoff:3.500A) Processing helix chain 'C' and resid 957 through 990 removed outlier: 3.687A pdb=" N SER C 962 " --> pdb=" O LEU C 958 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE C 964 " --> pdb=" O PHE C 960 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE C 984 " --> pdb=" O TYR C 980 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU C 989 " --> pdb=" O ASN C 985 " (cutoff:3.500A) Processing helix chain 'C' and resid 1004 through 1035 removed outlier: 3.641A pdb=" N LEU C1016 " --> pdb=" O ILE C1012 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR C1017 " --> pdb=" O SER C1013 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL C1022 " --> pdb=" O GLU C1018 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 437 Processing helix chain 'D' and resid 463 through 469 Processing helix chain 'D' and resid 482 through 488 removed outlier: 3.836A pdb=" N VAL D 488 " --> pdb=" O VAL D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 519 removed outlier: 3.784A pdb=" N LEU D 518 " --> pdb=" O PHE D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 546 removed outlier: 3.776A pdb=" N SER D 537 " --> pdb=" O TYR D 533 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE D 546 " --> pdb=" O LEU D 542 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 585 removed outlier: 3.782A pdb=" N LEU D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N TRP D 578 " --> pdb=" O PHE D 574 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY D 582 " --> pdb=" O TRP D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 595 through 626 removed outlier: 3.823A pdb=" N VAL D 601 " --> pdb=" O SER D 597 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE D 611 " --> pdb=" O PHE D 607 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER D 614 " --> pdb=" O LEU D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 642 removed outlier: 3.599A pdb=" N SER D 640 " --> pdb=" O ALA D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 661 removed outlier: 3.512A pdb=" N PHE D 659 " --> pdb=" O THR D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 676 Processing helix chain 'D' and resid 685 through 697 removed outlier: 3.501A pdb=" N VAL D 693 " --> pdb=" O GLY D 689 " (cutoff:3.500A) Processing helix chain 'D' and resid 706 through 715 Processing helix chain 'D' and resid 742 through 757 removed outlier: 4.296A pdb=" N GLN D 756 " --> pdb=" O LYS D 752 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 770 removed outlier: 3.691A pdb=" N LYS D 763 " --> pdb=" O LEU D 759 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TYR D 768 " --> pdb=" O ASN D 764 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LYS D 770 " --> pdb=" O TRP D 766 " (cutoff:3.500A) Processing helix chain 'D' and resid 775 through 781 removed outlier: 3.630A pdb=" N GLY D 779 " --> pdb=" O ALA D 775 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N SER D 780 " --> pdb=" O LYS D 776 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS D 781 " --> pdb=" O ASP D 777 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 775 through 781' Processing helix chain 'D' and resid 792 through 819 removed outlier: 3.953A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU D 808 " --> pdb=" O GLY D 804 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE D 814 " --> pdb=" O ALA D 810 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR D 816 " --> pdb=" O ILE D 812 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 440 through 444 removed outlier: 5.649A pdb=" N VAL A 395 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N THR A 443 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N VAL A 397 " --> pdb=" O THR A 443 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N VAL A 396 " --> pdb=" O ILE A 474 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 489 through 491 Processing sheet with id=AA3, first strand: chain 'A' and resid 496 through 498 removed outlier: 4.015A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR A 732 " --> pdb=" O MET A 496 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU A 498 " --> pdb=" O LYS A 730 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 646 through 649 removed outlier: 6.293A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.455A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 8.667A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N MET A 721 " --> pdb=" O ILE A 504 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 900 through 902 removed outlier: 3.564A pdb=" N CYS A 890 " --> pdb=" O HIS A 883 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N HIS A 883 " --> pdb=" O CYS A 890 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N THR A 876 " --> pdb=" O LEU A 870 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU A 870 " --> pdb=" O THR A 876 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N VAL A 878 " --> pdb=" O ILE A 868 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ILE A 868 " --> pdb=" O VAL A 878 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER A 884 " --> pdb=" O LEU A 862 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS A1002 " --> pdb=" O TYR A 863 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY A 867 " --> pdb=" O TYR A 998 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 397 through 399 removed outlier: 5.701A pdb=" N VAL B 397 " --> pdb=" O THR B 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AA8, first strand: chain 'B' and resid 489 through 491 Processing sheet with id=AA9, first strand: chain 'B' and resid 497 through 498 Processing sheet with id=AB1, first strand: chain 'B' and resid 702 through 705 removed outlier: 4.355A pdb=" N ILE B 502 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL B 723 " --> pdb=" O ILE B 502 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 440 through 444 removed outlier: 5.648A pdb=" N VAL C 395 " --> pdb=" O LYS C 441 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N THR C 443 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N VAL C 397 " --> pdb=" O THR C 443 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N VAL C 396 " --> pdb=" O ILE C 474 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 489 through 491 Processing sheet with id=AB4, first strand: chain 'C' and resid 496 through 498 removed outlier: 4.015A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR C 732 " --> pdb=" O MET C 496 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU C 498 " --> pdb=" O LYS C 730 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 646 through 649 removed outlier: 6.291A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.454A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 8.666A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N MET C 721 " --> pdb=" O ILE C 504 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 900 through 902 removed outlier: 3.564A pdb=" N CYS C 890 " --> pdb=" O HIS C 883 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N HIS C 883 " --> pdb=" O CYS C 890 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N THR C 876 " --> pdb=" O LEU C 870 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU C 870 " --> pdb=" O THR C 876 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N VAL C 878 " --> pdb=" O ILE C 868 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ILE C 868 " --> pdb=" O VAL C 878 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N SER C 884 " --> pdb=" O LEU C 862 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS C1002 " --> pdb=" O TYR C 863 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY C 867 " --> pdb=" O TYR C 998 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 397 through 399 removed outlier: 5.701A pdb=" N VAL D 397 " --> pdb=" O THR D 443 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AB9, first strand: chain 'D' and resid 489 through 491 Processing sheet with id=AC1, first strand: chain 'D' and resid 497 through 498 Processing sheet with id=AC2, first strand: chain 'D' and resid 702 through 705 removed outlier: 4.355A pdb=" N ILE D 502 " --> pdb=" O VAL D 723 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL D 723 " --> pdb=" O ILE D 502 " (cutoff:3.500A) 818 hydrogen bonds defined for protein. 2400 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: 4.72 Time building geometry restraints manager: 4.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2516 1.31 - 1.44: 4378 1.44 - 1.57: 9092 1.57 - 1.69: 6 1.69 - 1.82: 176 Bond restraints: 16168 Sorted by residual: bond pdb=" C31 PCW C1101 " pdb=" O2 PCW C1101 " ideal model delta sigma weight residual 1.333 1.428 -0.095 2.00e-02 2.50e+03 2.25e+01 bond pdb=" C31 PCW A1101 " pdb=" O2 PCW A1101 " ideal model delta sigma weight residual 1.333 1.427 -0.094 2.00e-02 2.50e+03 2.22e+01 bond pdb=" C31 PCW C1101 " pdb=" C32 PCW C1101 " ideal model delta sigma weight residual 1.502 1.554 -0.052 2.00e-02 2.50e+03 6.88e+00 bond pdb=" C31 PCW A1101 " pdb=" C32 PCW A1101 " ideal model delta sigma weight residual 1.502 1.554 -0.052 2.00e-02 2.50e+03 6.81e+00 bond pdb=" C36 PCW A1101 " pdb=" C37 PCW A1101 " ideal model delta sigma weight residual 1.524 1.573 -0.049 2.00e-02 2.50e+03 6.06e+00 ... (remaining 16163 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.86: 21390 2.86 - 5.72: 359 5.72 - 8.58: 49 8.58 - 11.43: 14 11.43 - 14.29: 4 Bond angle restraints: 21816 Sorted by residual: angle pdb=" C LYS C 716 " pdb=" N PRO C 717 " pdb=" CA PRO C 717 " ideal model delta sigma weight residual 119.84 112.01 7.83 1.25e+00 6.40e-01 3.93e+01 angle pdb=" C LYS A 716 " pdb=" N PRO A 717 " pdb=" CA PRO A 717 " ideal model delta sigma weight residual 119.84 112.02 7.82 1.25e+00 6.40e-01 3.91e+01 angle pdb=" C SER C 635 " pdb=" N ALA C 636 " pdb=" CA ALA C 636 " ideal model delta sigma weight residual 121.54 129.94 -8.40 1.91e+00 2.74e-01 1.93e+01 angle pdb=" C SER A 635 " pdb=" N ALA A 636 " pdb=" CA ALA A 636 " ideal model delta sigma weight residual 121.54 129.88 -8.34 1.91e+00 2.74e-01 1.91e+01 angle pdb=" CA LEU C 882 " pdb=" CB LEU C 882 " pdb=" CG LEU C 882 " ideal model delta sigma weight residual 116.30 130.59 -14.29 3.50e+00 8.16e-02 1.67e+01 ... (remaining 21811 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.16: 8814 15.16 - 30.32: 538 30.32 - 45.48: 191 45.48 - 60.64: 21 60.64 - 75.81: 10 Dihedral angle restraints: 9574 sinusoidal: 3778 harmonic: 5796 Sorted by residual: dihedral pdb=" CA LYS D 716 " pdb=" C LYS D 716 " pdb=" N PRO D 717 " pdb=" CA PRO D 717 " ideal model delta harmonic sigma weight residual 180.00 140.51 39.49 0 5.00e+00 4.00e-02 6.24e+01 dihedral pdb=" CA LYS B 716 " pdb=" C LYS B 716 " pdb=" N PRO B 717 " pdb=" CA PRO B 717 " ideal model delta harmonic sigma weight residual 180.00 140.52 39.48 0 5.00e+00 4.00e-02 6.24e+01 dihedral pdb=" CB CYS A 718 " pdb=" SG CYS A 718 " pdb=" SG CYS A 773 " pdb=" CB CYS A 773 " ideal model delta sinusoidal sigma weight residual 93.00 161.74 -68.74 1 1.00e+01 1.00e-02 6.12e+01 ... (remaining 9571 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1859 0.054 - 0.107: 476 0.107 - 0.161: 90 0.161 - 0.214: 21 0.214 - 0.268: 8 Chirality restraints: 2454 Sorted by residual: chirality pdb=" CG LEU A 882 " pdb=" CB LEU A 882 " pdb=" CD1 LEU A 882 " pdb=" CD2 LEU A 882 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CG LEU C 882 " pdb=" CB LEU C 882 " pdb=" CD1 LEU C 882 " pdb=" CD2 LEU C 882 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CG LEU C 989 " pdb=" CB LEU C 989 " pdb=" CD1 LEU C 989 " pdb=" CD2 LEU C 989 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 2451 not shown) Planarity restraints: 2684 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 716 " 0.068 5.00e-02 4.00e+02 1.04e-01 1.73e+01 pdb=" N PRO A 717 " -0.180 5.00e-02 4.00e+02 pdb=" CA PRO A 717 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 717 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 716 " -0.068 5.00e-02 4.00e+02 1.04e-01 1.72e+01 pdb=" N PRO C 717 " 0.179 5.00e-02 4.00e+02 pdb=" CA PRO C 717 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO C 717 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 716 " 0.066 5.00e-02 4.00e+02 1.01e-01 1.64e+01 pdb=" N PRO B 717 " -0.175 5.00e-02 4.00e+02 pdb=" CA PRO B 717 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO B 717 " 0.057 5.00e-02 4.00e+02 ... (remaining 2681 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2980 2.76 - 3.30: 15245 3.30 - 3.83: 26184 3.83 - 4.37: 30805 4.37 - 4.90: 50570 Nonbonded interactions: 125784 Sorted by model distance: nonbonded pdb=" O LEU D 639 " pdb=" OH TYR D 647 " model vdw 2.230 3.040 nonbonded pdb=" O LEU B 639 " pdb=" OH TYR B 647 " model vdw 2.230 3.040 nonbonded pdb=" OG SER D 706 " pdb=" OD1 ASN D 726 " model vdw 2.278 3.040 nonbonded pdb=" OG SER B 706 " pdb=" OD1 ASN B 726 " model vdw 2.278 3.040 nonbonded pdb=" O PHE C 943 " pdb=" OG SER C 946 " model vdw 2.321 3.040 ... (remaining 125779 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' 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: 6.450 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: 0.010 Extract box with map and model: 0.680 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 36.200 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5203 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 : 0.005 0.095 16168 Z= 0.331 Angle : 1.006 14.292 21816 Z= 0.550 Chirality : 0.052 0.268 2454 Planarity : 0.007 0.104 2684 Dihedral : 11.501 75.805 5856 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.59 % Allowed : 5.74 % Favored : 93.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 6.90 % 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: -4.08 (0.14), residues: 1992 helix: -2.72 (0.10), residues: 1048 sheet: -2.53 (0.33), residues: 156 loop : -2.46 (0.19), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP D 767 HIS 0.004 0.001 HIS D 435 PHE 0.019 0.002 PHE C 901 TYR 0.018 0.002 TYR C 647 ARG 0.006 0.001 ARG B 599 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 465 time to evaluate : 1.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 531 PHE cc_start: 0.7408 (m-10) cc_final: 0.6976 (m-80) REVERT: A 684 ARG cc_start: 0.7965 (mpp-170) cc_final: 0.7309 (tmt-80) REVERT: A 704 LEU cc_start: 0.7584 (pt) cc_final: 0.7083 (pt) REVERT: A 708 MET cc_start: 0.8204 (mtt) cc_final: 0.7428 (ptm) REVERT: A 712 ILE cc_start: 0.8670 (mm) cc_final: 0.8073 (mm) REVERT: A 721 MET cc_start: 0.3323 (ptm) cc_final: 0.2641 (ppp) REVERT: A 860 TYR cc_start: 0.3924 (m-80) cc_final: 0.3608 (m-80) REVERT: B 519 ASP cc_start: 0.8301 (t0) cc_final: 0.8021 (t0) REVERT: B 579 PHE cc_start: 0.4285 (t80) cc_final: 0.3702 (t80) REVERT: B 593 PRO cc_start: 0.7307 (Cg_exo) cc_final: 0.6683 (Cg_endo) REVERT: B 699 LYS cc_start: 0.8576 (mptt) cc_final: 0.7978 (mmmt) REVERT: B 708 MET cc_start: 0.8146 (mtt) cc_final: 0.7457 (tpt) REVERT: C 402 GLU cc_start: 0.7329 (tp30) cc_final: 0.7022 (tp30) REVERT: C 424 TYR cc_start: 0.7162 (t80) cc_final: 0.6601 (t80) REVERT: C 457 THR cc_start: 0.7661 (p) cc_final: 0.7451 (p) REVERT: C 479 LEU cc_start: 0.8689 (tp) cc_final: 0.8390 (tp) REVERT: C 519 ASP cc_start: 0.6552 (m-30) cc_final: 0.5893 (t0) REVERT: C 521 LEU cc_start: 0.6881 (mt) cc_final: 0.6569 (mt) REVERT: C 672 THR cc_start: 0.7772 (m) cc_final: 0.7570 (p) REVERT: C 710 GLU cc_start: 0.8897 (mt-10) cc_final: 0.8569 (tp30) REVERT: C 713 GLU cc_start: 0.9093 (tt0) cc_final: 0.8865 (mt-10) REVERT: C 720 THR cc_start: 0.8104 (p) cc_final: 0.7598 (t) REVERT: C 732 TYR cc_start: 0.3989 (m-10) cc_final: 0.3700 (m-10) REVERT: C 762 LEU cc_start: 0.9086 (mt) cc_final: 0.8673 (mm) REVERT: C 796 PHE cc_start: 0.7147 (m-80) cc_final: 0.6712 (m-80) REVERT: C 880 MET cc_start: 0.5000 (tmm) cc_final: 0.4424 (ttt) REVERT: C 1003 TYR cc_start: 0.5709 (m-80) cc_final: 0.5490 (m-80) REVERT: D 407 MET cc_start: 0.3927 (mtm) cc_final: 0.2923 (mmp) REVERT: D 463 MET cc_start: 0.7744 (mtm) cc_final: 0.7325 (mtm) REVERT: D 527 MET cc_start: 0.5979 (ttm) cc_final: 0.5643 (ttm) REVERT: D 629 MET cc_start: 0.6645 (mmm) cc_final: 0.4964 (tpp) REVERT: D 649 THR cc_start: 0.2950 (p) cc_final: 0.2688 (p) REVERT: D 760 ASP cc_start: 0.7170 (m-30) cc_final: 0.6946 (t0) REVERT: D 763 LYS cc_start: 0.9012 (ttpt) cc_final: 0.8747 (tptt) outliers start: 10 outliers final: 2 residues processed: 472 average time/residue: 0.3202 time to fit residues: 212.4265 Evaluate side-chains 279 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 277 time to evaluate : 1.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 0.9980 chunk 151 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 80 optimal weight: 0.7980 chunk 156 optimal weight: 3.9990 chunk 60 optimal weight: 9.9990 chunk 95 optimal weight: 6.9990 chunk 116 optimal weight: 0.9990 chunk 181 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS A 575 ASN A 586 GLN A 619 ASN A 642 GLN A 714 GLN A 872 GLN A 874 GLN A 950 HIS ** A 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 ASN B 569 ASN B 619 ASN B 747 ASN B 764 ASN B 791 ASN C 587 GLN C 619 ASN ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 714 GLN C 726 ASN C 985 ASN D 461 ASN D 575 ASN D 587 GLN ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5803 moved from start: 0.4914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16168 Z= 0.232 Angle : 0.719 10.536 21816 Z= 0.377 Chirality : 0.045 0.351 2454 Planarity : 0.006 0.082 2684 Dihedral : 7.147 59.775 2208 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.23 % Allowed : 5.04 % Favored : 94.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 6.90 % 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: -1.40 (0.17), residues: 1992 helix: -0.03 (0.14), residues: 1094 sheet: -1.64 (0.33), residues: 202 loop : -2.06 (0.21), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C1005 HIS 0.003 0.001 HIS C 883 PHE 0.026 0.002 PHE C 901 TYR 0.024 0.002 TYR A1003 ARG 0.008 0.001 ARG B 715 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 346 time to evaluate : 1.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 585 MET cc_start: 0.7987 (tpp) cc_final: 0.7758 (tpp) REVERT: A 684 ARG cc_start: 0.8091 (mpp-170) cc_final: 0.7360 (tmt-80) REVERT: A 704 LEU cc_start: 0.7831 (pt) cc_final: 0.6855 (pt) REVERT: A 707 THR cc_start: 0.8062 (m) cc_final: 0.7854 (p) REVERT: A 708 MET cc_start: 0.8325 (mtt) cc_final: 0.7702 (ptm) REVERT: A 709 ASN cc_start: 0.6708 (t0) cc_final: 0.6471 (t0) REVERT: A 721 MET cc_start: 0.2862 (ptm) cc_final: 0.1092 (ppp) REVERT: A 860 TYR cc_start: 0.3962 (m-80) cc_final: 0.3295 (m-80) REVERT: A 939 MET cc_start: 0.4957 (ttt) cc_final: 0.4419 (ttt) REVERT: A 941 ILE cc_start: 0.7607 (mt) cc_final: 0.7364 (mt) REVERT: B 408 MET cc_start: 0.4945 (mmt) cc_final: 0.4512 (mpp) REVERT: B 519 ASP cc_start: 0.8619 (t0) cc_final: 0.8242 (t0) REVERT: B 629 MET cc_start: 0.2796 (tpp) cc_final: 0.2527 (tpt) REVERT: B 661 ARG cc_start: 0.8617 (tpm170) cc_final: 0.8220 (tpp80) REVERT: B 708 MET cc_start: 0.8179 (mtt) cc_final: 0.7447 (tpt) REVERT: C 414 MET cc_start: 0.5585 (mpp) cc_final: 0.5158 (mpp) REVERT: C 424 TYR cc_start: 0.7391 (t80) cc_final: 0.6734 (t80) REVERT: C 519 ASP cc_start: 0.7315 (m-30) cc_final: 0.7030 (t0) REVERT: C 527 MET cc_start: 0.8690 (mtm) cc_final: 0.8020 (ptm) REVERT: C 710 GLU cc_start: 0.9002 (mt-10) cc_final: 0.8611 (mm-30) REVERT: C 762 LEU cc_start: 0.9208 (mt) cc_final: 0.8734 (mm) REVERT: C 764 ASN cc_start: 0.7415 (t0) cc_final: 0.7078 (m110) REVERT: C 796 PHE cc_start: 0.7493 (m-80) cc_final: 0.7136 (m-80) REVERT: C 980 TYR cc_start: 0.7378 (t80) cc_final: 0.7122 (t80) REVERT: C 1003 TYR cc_start: 0.5974 (m-80) cc_final: 0.5153 (m-80) REVERT: C 1032 TYR cc_start: 0.8365 (t80) cc_final: 0.8089 (t80) REVERT: D 405 TYR cc_start: 0.8131 (m-80) cc_final: 0.7856 (m-80) REVERT: D 407 MET cc_start: 0.4824 (mtm) cc_final: 0.4062 (mmp) REVERT: D 424 TYR cc_start: 0.7361 (t80) cc_final: 0.6504 (t80) REVERT: D 458 LYS cc_start: 0.8773 (mmtp) cc_final: 0.8408 (mmmt) REVERT: D 527 MET cc_start: 0.6171 (ttm) cc_final: 0.5709 (ttm) REVERT: D 629 MET cc_start: 0.6682 (mmm) cc_final: 0.4924 (tpp) REVERT: D 760 ASP cc_start: 0.7120 (m-30) cc_final: 0.6386 (t0) REVERT: D 763 LYS cc_start: 0.9012 (ttpt) cc_final: 0.8732 (tmmt) outliers start: 4 outliers final: 0 residues processed: 350 average time/residue: 0.2885 time to fit residues: 146.3575 Evaluate side-chains 243 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 243 time to evaluate : 1.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 100 optimal weight: 9.9990 chunk 56 optimal weight: 2.9990 chunk 151 optimal weight: 0.8980 chunk 123 optimal weight: 7.9990 chunk 50 optimal weight: 0.9980 chunk 181 optimal weight: 7.9990 chunk 196 optimal weight: 0.3980 chunk 162 optimal weight: 8.9990 chunk 180 optimal weight: 0.7980 chunk 62 optimal weight: 8.9990 chunk 145 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS A 619 ASN A 709 ASN ** A 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 586 GLN ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 791 ASN C 575 ASN C 619 ASN ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 411 ASN D 575 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5961 moved from start: 0.6037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16168 Z= 0.176 Angle : 0.631 11.150 21816 Z= 0.327 Chirality : 0.042 0.244 2454 Planarity : 0.005 0.069 2684 Dihedral : 6.569 55.797 2208 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.12 % Allowed : 3.52 % Favored : 96.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 6.90 % 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: -0.30 (0.18), residues: 1992 helix: 0.97 (0.15), residues: 1094 sheet: -1.62 (0.34), residues: 184 loop : -1.61 (0.22), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 861 HIS 0.002 0.001 HIS A 950 PHE 0.023 0.001 PHE D 623 TYR 0.028 0.002 TYR A 980 ARG 0.006 0.001 ARG D 594 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 327 time to evaluate : 1.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 527 MET cc_start: 0.6345 (mmt) cc_final: 0.5885 (tpp) REVERT: A 684 ARG cc_start: 0.7955 (mpp-170) cc_final: 0.7056 (tmt-80) REVERT: A 704 LEU cc_start: 0.7647 (pt) cc_final: 0.5756 (pt) REVERT: A 708 MET cc_start: 0.8624 (mtt) cc_final: 0.8211 (ptm) REVERT: A 721 MET cc_start: 0.2328 (ptm) cc_final: 0.1872 (ppp) REVERT: A 939 MET cc_start: 0.5197 (ttt) cc_final: 0.4667 (ttt) REVERT: A 1023 MET cc_start: 0.4500 (ttm) cc_final: 0.4267 (ttp) REVERT: B 460 TRP cc_start: 0.6990 (m100) cc_final: 0.6517 (m-90) REVERT: B 536 VAL cc_start: 0.8320 (t) cc_final: 0.6049 (t) REVERT: B 587 GLN cc_start: 0.5926 (tp40) cc_final: 0.5406 (mm110) REVERT: B 619 ASN cc_start: 0.6167 (t0) cc_final: 0.4280 (t0) REVERT: B 620 LEU cc_start: 0.8787 (tt) cc_final: 0.8494 (tt) REVERT: B 623 PHE cc_start: 0.8160 (m-10) cc_final: 0.7792 (m-10) REVERT: B 629 MET cc_start: 0.2879 (tpp) cc_final: 0.2645 (tpp) REVERT: B 661 ARG cc_start: 0.8643 (tpm170) cc_final: 0.8246 (tpp80) REVERT: B 708 MET cc_start: 0.8146 (mtt) cc_final: 0.7368 (tpt) REVERT: C 414 MET cc_start: 0.5655 (mpp) cc_final: 0.5373 (mpp) REVERT: C 519 ASP cc_start: 0.7755 (m-30) cc_final: 0.7369 (t0) REVERT: C 624 LEU cc_start: 0.7216 (mt) cc_final: 0.6980 (mp) REVERT: C 633 ILE cc_start: 0.5956 (pt) cc_final: 0.5639 (pt) REVERT: C 710 GLU cc_start: 0.9057 (mt-10) cc_final: 0.8678 (tp30) REVERT: C 714 GLN cc_start: 0.7385 (pt0) cc_final: 0.6784 (pt0) REVERT: C 726 ASN cc_start: 0.7437 (m-40) cc_final: 0.7219 (t0) REVERT: C 764 ASN cc_start: 0.7226 (t0) cc_final: 0.6830 (m110) REVERT: C 811 LEU cc_start: 0.9597 (tp) cc_final: 0.9288 (mt) REVERT: C 1003 TYR cc_start: 0.6420 (m-80) cc_final: 0.5451 (m-80) REVERT: C 1032 TYR cc_start: 0.8366 (t80) cc_final: 0.8046 (t80) REVERT: D 405 TYR cc_start: 0.8095 (m-80) cc_final: 0.7708 (m-80) REVERT: D 407 MET cc_start: 0.4873 (mtm) cc_final: 0.4224 (mmp) REVERT: D 428 LEU cc_start: 0.8330 (mt) cc_final: 0.8070 (mm) REVERT: D 458 LYS cc_start: 0.8857 (mmtp) cc_final: 0.8491 (mmmt) REVERT: D 463 MET cc_start: 0.8068 (mtm) cc_final: 0.7863 (mtm) REVERT: D 496 MET cc_start: 0.4178 (pmm) cc_final: 0.3968 (pmm) REVERT: D 503 MET cc_start: 0.7817 (ppp) cc_final: 0.7601 (ppp) REVERT: D 527 MET cc_start: 0.6252 (ttm) cc_final: 0.5817 (ttm) REVERT: D 629 MET cc_start: 0.6586 (mmm) cc_final: 0.4909 (tpp) REVERT: D 709 ASN cc_start: 0.7327 (t0) cc_final: 0.6824 (t0) REVERT: D 760 ASP cc_start: 0.7110 (m-30) cc_final: 0.6756 (t0) outliers start: 2 outliers final: 0 residues processed: 327 average time/residue: 0.2705 time to fit residues: 130.5172 Evaluate side-chains 253 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 253 time to evaluate : 1.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 179 optimal weight: 0.7980 chunk 136 optimal weight: 9.9990 chunk 94 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 182 optimal weight: 9.9990 chunk 193 optimal weight: 0.6980 chunk 95 optimal weight: 0.9980 chunk 173 optimal weight: 4.9990 chunk 52 optimal weight: 10.0000 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 586 GLN A 619 ASN A 883 HIS A 985 ASN B 508 GLN ** B 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 ASN B 709 ASN B 764 ASN ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 587 GLN ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6858 moved from start: 1.0221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 16168 Z= 0.321 Angle : 0.815 12.253 21816 Z= 0.431 Chirality : 0.047 0.234 2454 Planarity : 0.006 0.073 2684 Dihedral : 7.027 56.583 2208 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 18.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.18 % Allowed : 5.28 % Favored : 94.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 6.90 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.18), residues: 1992 helix: 0.38 (0.15), residues: 1108 sheet: -1.62 (0.36), residues: 186 loop : -1.84 (0.22), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.004 TRP C 526 HIS 0.007 0.002 HIS B 412 PHE 0.045 0.003 PHE C 517 TYR 0.034 0.003 TYR A 700 ARG 0.018 0.001 ARG B 485 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 421 time to evaluate : 1.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 424 TYR cc_start: 0.8230 (t80) cc_final: 0.7604 (t80) REVERT: A 440 TYR cc_start: 0.7208 (p90) cc_final: 0.6810 (p90) REVERT: A 527 MET cc_start: 0.6881 (mmt) cc_final: 0.6600 (tpp) REVERT: A 533 TYR cc_start: 0.8357 (t80) cc_final: 0.8086 (t80) REVERT: A 578 TRP cc_start: 0.8405 (t60) cc_final: 0.8077 (t60) REVERT: A 586 GLN cc_start: 0.8838 (tp40) cc_final: 0.7307 (tp-100) REVERT: A 604 VAL cc_start: 0.9032 (m) cc_final: 0.8805 (p) REVERT: A 709 ASN cc_start: 0.8293 (t0) cc_final: 0.8016 (t0) REVERT: A 721 MET cc_start: 0.5463 (ptm) cc_final: 0.4495 (ppp) REVERT: A 939 MET cc_start: 0.6804 (ttt) cc_final: 0.6240 (tmm) REVERT: A 1014 PHE cc_start: 0.7217 (t80) cc_final: 0.6965 (t80) REVERT: B 460 TRP cc_start: 0.7177 (m100) cc_final: 0.6603 (m-90) REVERT: B 578 TRP cc_start: 0.8290 (t-100) cc_final: 0.7740 (t-100) REVERT: B 587 GLN cc_start: 0.8503 (tp40) cc_final: 0.8029 (mm-40) REVERT: B 619 ASN cc_start: 0.7192 (t160) cc_final: 0.6640 (t0) REVERT: B 623 PHE cc_start: 0.8247 (m-10) cc_final: 0.7656 (m-10) REVERT: B 647 TYR cc_start: 0.6951 (OUTLIER) cc_final: 0.5755 (m-10) REVERT: B 708 MET cc_start: 0.8406 (mtt) cc_final: 0.7636 (tpt) REVERT: B 803 LEU cc_start: 0.9066 (mt) cc_final: 0.8819 (mt) REVERT: B 807 MET cc_start: 0.8674 (mtp) cc_final: 0.8249 (mtp) REVERT: C 424 TYR cc_start: 0.8024 (t80) cc_final: 0.7605 (t80) REVERT: C 431 GLU cc_start: 0.8955 (mm-30) cc_final: 0.8538 (tp30) REVERT: C 480 THR cc_start: 0.9220 (m) cc_final: 0.8850 (p) REVERT: C 496 MET cc_start: 0.5382 (mmm) cc_final: 0.4958 (mmm) REVERT: C 570 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7528 (pm20) REVERT: C 607 PHE cc_start: 0.9041 (t80) cc_final: 0.8727 (t80) REVERT: C 614 SER cc_start: 0.9302 (m) cc_final: 0.8953 (p) REVERT: C 620 LEU cc_start: 0.8628 (mt) cc_final: 0.8415 (mp) REVERT: C 629 MET cc_start: 0.9211 (mtm) cc_final: 0.8931 (mtp) REVERT: C 654 SER cc_start: 0.8380 (t) cc_final: 0.8111 (t) REVERT: C 670 MET cc_start: 0.8978 (mmp) cc_final: 0.8698 (mmp) REVERT: C 713 GLU cc_start: 0.9028 (pt0) cc_final: 0.8728 (mt-10) REVERT: C 714 GLN cc_start: 0.7381 (pt0) cc_final: 0.6059 (pt0) REVERT: C 811 LEU cc_start: 0.9650 (tp) cc_final: 0.9385 (mt) REVERT: C 817 LYS cc_start: 0.8350 (tppp) cc_final: 0.7636 (ptmt) REVERT: C 840 LEU cc_start: 0.8650 (mt) cc_final: 0.8423 (mt) REVERT: C 931 PHE cc_start: 0.8075 (m-10) cc_final: 0.7871 (m-80) REVERT: C 999 PHE cc_start: 0.8175 (t80) cc_final: 0.7900 (t80) REVERT: D 458 LYS cc_start: 0.8982 (mmtp) cc_final: 0.8684 (mmmt) REVERT: D 463 MET cc_start: 0.8008 (mtm) cc_final: 0.7524 (mmm) REVERT: D 496 MET cc_start: 0.6550 (pmm) cc_final: 0.6001 (pmm) REVERT: D 612 ILE cc_start: 0.9369 (mm) cc_final: 0.8977 (mm) REVERT: D 626 VAL cc_start: 0.7724 (t) cc_final: 0.7211 (t) REVERT: D 720 THR cc_start: 0.8089 (p) cc_final: 0.7479 (p) REVERT: D 763 LYS cc_start: 0.8538 (tptp) cc_final: 0.8271 (tptt) outliers start: 3 outliers final: 0 residues processed: 423 average time/residue: 0.2694 time to fit residues: 168.9053 Evaluate side-chains 320 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 319 time to evaluate : 1.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 161 optimal weight: 10.0000 chunk 109 optimal weight: 0.0970 chunk 2 optimal weight: 1.9990 chunk 143 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 164 optimal weight: 0.9980 chunk 133 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 173 optimal weight: 2.9990 chunk 48 optimal weight: 0.0470 overall best weight: 1.0280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 642 GLN A 709 ASN ** A 874 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 950 HIS A 985 ASN B 508 GLN B 586 GLN B 619 ASN ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6893 moved from start: 1.0986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 16168 Z= 0.184 Angle : 0.642 8.470 21816 Z= 0.333 Chirality : 0.043 0.159 2454 Planarity : 0.005 0.061 2684 Dihedral : 6.273 52.838 2208 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.18 % Allowed : 2.75 % Favored : 97.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 6.90 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.19), residues: 1992 helix: 1.12 (0.15), residues: 1132 sheet: -1.33 (0.34), residues: 196 loop : -1.66 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 767 HIS 0.002 0.001 HIS C 435 PHE 0.022 0.001 PHE A 965 TYR 0.023 0.002 TYR C 768 ARG 0.005 0.000 ARG A 684 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 391 time to evaluate : 1.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 424 TYR cc_start: 0.8196 (t80) cc_final: 0.7632 (t80) REVERT: A 527 MET cc_start: 0.6880 (mmt) cc_final: 0.6000 (tpp) REVERT: A 574 PHE cc_start: 0.8159 (p90) cc_final: 0.7168 (m-80) REVERT: A 586 GLN cc_start: 0.8860 (tp40) cc_final: 0.8150 (tp-100) REVERT: A 627 GLU cc_start: 0.8684 (pp20) cc_final: 0.8015 (tp30) REVERT: A 939 MET cc_start: 0.6957 (ttt) cc_final: 0.6241 (tmm) REVERT: B 460 TRP cc_start: 0.7025 (m100) cc_final: 0.6448 (m-90) REVERT: B 463 MET cc_start: 0.4928 (ptm) cc_final: 0.4476 (ppp) REVERT: B 527 MET cc_start: 0.7534 (mtt) cc_final: 0.7007 (mmm) REVERT: B 578 TRP cc_start: 0.8487 (t-100) cc_final: 0.7693 (t-100) REVERT: B 587 GLN cc_start: 0.8502 (mm110) cc_final: 0.7710 (mm110) REVERT: B 606 TRP cc_start: 0.8872 (m-10) cc_final: 0.8657 (m-10) REVERT: B 619 ASN cc_start: 0.7335 (t0) cc_final: 0.6805 (t0) REVERT: B 623 PHE cc_start: 0.7929 (m-10) cc_final: 0.7679 (m-10) REVERT: B 627 GLU cc_start: 0.7957 (pp20) cc_final: 0.7597 (pp20) REVERT: B 708 MET cc_start: 0.8589 (mtt) cc_final: 0.7848 (tpt) REVERT: B 721 MET cc_start: 0.6033 (ttp) cc_final: 0.5697 (ptm) REVERT: B 807 MET cc_start: 0.8645 (mtp) cc_final: 0.8338 (ppp) REVERT: B 808 LEU cc_start: 0.8679 (mm) cc_final: 0.8104 (mm) REVERT: C 424 TYR cc_start: 0.8264 (t80) cc_final: 0.7683 (t80) REVERT: C 431 GLU cc_start: 0.8938 (mm-30) cc_final: 0.8704 (tp30) REVERT: C 479 LEU cc_start: 0.8800 (tp) cc_final: 0.8579 (tp) REVERT: C 496 MET cc_start: 0.6254 (mmm) cc_final: 0.5580 (tmm) REVERT: C 500 ILE cc_start: 0.7875 (mt) cc_final: 0.7615 (mt) REVERT: C 570 GLU cc_start: 0.8369 (mm-30) cc_final: 0.7744 (pm20) REVERT: C 585 MET cc_start: 0.8486 (mpp) cc_final: 0.7907 (mpp) REVERT: C 586 GLN cc_start: 0.5467 (tm-30) cc_final: 0.5000 (tm-30) REVERT: C 607 PHE cc_start: 0.9199 (t80) cc_final: 0.8961 (t80) REVERT: C 620 LEU cc_start: 0.8655 (mt) cc_final: 0.8390 (mp) REVERT: C 654 SER cc_start: 0.8388 (t) cc_final: 0.7709 (p) REVERT: C 658 PHE cc_start: 0.7834 (t80) cc_final: 0.7262 (m-80) REVERT: C 670 MET cc_start: 0.9069 (mmp) cc_final: 0.8672 (mmp) REVERT: C 726 ASN cc_start: 0.8523 (m-40) cc_final: 0.8294 (m-40) REVERT: C 762 LEU cc_start: 0.9330 (mm) cc_final: 0.8719 (mp) REVERT: C 811 LEU cc_start: 0.9656 (tp) cc_final: 0.9442 (mt) REVERT: C 840 LEU cc_start: 0.8743 (mt) cc_final: 0.8508 (mt) REVERT: C 965 PHE cc_start: 0.8289 (m-80) cc_final: 0.8050 (m-80) REVERT: C 999 PHE cc_start: 0.8195 (t80) cc_final: 0.7698 (t80) REVERT: C 1003 TYR cc_start: 0.6377 (m-80) cc_final: 0.3960 (m-80) REVERT: C 1032 TYR cc_start: 0.8360 (t80) cc_final: 0.7633 (t80) REVERT: D 428 LEU cc_start: 0.8092 (mm) cc_final: 0.7774 (mm) REVERT: D 458 LYS cc_start: 0.8961 (mmtp) cc_final: 0.8501 (mmmt) REVERT: D 460 TRP cc_start: 0.4920 (m100) cc_final: 0.4271 (m100) REVERT: D 463 MET cc_start: 0.8019 (mtm) cc_final: 0.7581 (mmm) REVERT: D 493 LYS cc_start: 0.7450 (mptt) cc_final: 0.7220 (mppt) REVERT: D 576 SER cc_start: 0.8142 (m) cc_final: 0.7202 (t) REVERT: D 626 VAL cc_start: 0.8196 (t) cc_final: 0.7222 (t) REVERT: D 649 THR cc_start: 0.5417 (p) cc_final: 0.5106 (p) REVERT: D 670 MET cc_start: 0.8417 (tmm) cc_final: 0.7780 (tmm) REVERT: D 763 LYS cc_start: 0.8490 (tptp) cc_final: 0.8174 (tptt) outliers start: 3 outliers final: 0 residues processed: 392 average time/residue: 0.2503 time to fit residues: 147.3542 Evaluate side-chains 310 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 310 time to evaluate : 1.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 65 optimal weight: 0.3980 chunk 174 optimal weight: 5.9990 chunk 38 optimal weight: 0.6980 chunk 113 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 193 optimal weight: 3.9990 chunk 160 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 101 optimal weight: 8.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 586 GLN ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 950 HIS ** A 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 HIS ** B 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 586 GLN B 619 ASN ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 619 ASN ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 1.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 16168 Z= 0.189 Angle : 0.636 7.910 21816 Z= 0.329 Chirality : 0.042 0.153 2454 Planarity : 0.005 0.065 2684 Dihedral : 6.120 50.731 2208 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.06 % Allowed : 2.23 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 6.90 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.19), residues: 1992 helix: 1.42 (0.16), residues: 1112 sheet: -1.30 (0.36), residues: 196 loop : -1.45 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 526 HIS 0.002 0.001 HIS D 435 PHE 0.035 0.002 PHE A 844 TYR 0.021 0.001 TYR C 533 ARG 0.006 0.001 ARG C 675 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 388 time to evaluate : 1.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 LEU cc_start: 0.7845 (mm) cc_final: 0.7091 (mm) REVERT: A 424 TYR cc_start: 0.8279 (t80) cc_final: 0.7666 (t80) REVERT: A 503 MET cc_start: 0.6858 (tpp) cc_final: 0.5952 (tpt) REVERT: A 524 GLU cc_start: 0.9332 (pm20) cc_final: 0.9006 (pm20) REVERT: A 527 MET cc_start: 0.7145 (mmt) cc_final: 0.6454 (tpp) REVERT: A 531 PHE cc_start: 0.8692 (m-10) cc_final: 0.8393 (m-80) REVERT: A 574 PHE cc_start: 0.8287 (p90) cc_final: 0.7199 (m-80) REVERT: A 577 LEU cc_start: 0.8884 (mm) cc_final: 0.8542 (mm) REVERT: A 584 PHE cc_start: 0.8701 (t80) cc_final: 0.8460 (t80) REVERT: A 586 GLN cc_start: 0.8962 (tp-100) cc_final: 0.8577 (mm-40) REVERT: A 609 THR cc_start: 0.8360 (t) cc_final: 0.7926 (t) REVERT: A 624 LEU cc_start: 0.8980 (mt) cc_final: 0.8533 (mt) REVERT: A 627 GLU cc_start: 0.8865 (pp20) cc_final: 0.8622 (pp20) REVERT: A 711 TYR cc_start: 0.7612 (t80) cc_final: 0.7370 (t80) REVERT: A 939 MET cc_start: 0.7220 (ttt) cc_final: 0.6562 (tmm) REVERT: B 460 TRP cc_start: 0.6947 (m100) cc_final: 0.6372 (m-90) REVERT: B 463 MET cc_start: 0.5112 (ptm) cc_final: 0.4656 (ppp) REVERT: B 527 MET cc_start: 0.7547 (mtt) cc_final: 0.7042 (mmm) REVERT: B 586 GLN cc_start: 0.8612 (OUTLIER) cc_final: 0.8379 (mm-40) REVERT: B 587 GLN cc_start: 0.8339 (mm110) cc_final: 0.7852 (mm110) REVERT: B 608 PHE cc_start: 0.8952 (t80) cc_final: 0.8715 (t80) REVERT: B 619 ASN cc_start: 0.7606 (t0) cc_final: 0.7186 (t0) REVERT: B 627 GLU cc_start: 0.8061 (pp20) cc_final: 0.7794 (pp20) REVERT: B 708 MET cc_start: 0.8603 (mtt) cc_final: 0.8003 (tpt) REVERT: B 721 MET cc_start: 0.6100 (ttp) cc_final: 0.5753 (ptm) REVERT: B 807 MET cc_start: 0.8745 (mtp) cc_final: 0.8453 (ppp) REVERT: B 808 LEU cc_start: 0.8741 (mm) cc_final: 0.8135 (mm) REVERT: C 431 GLU cc_start: 0.8959 (mm-30) cc_final: 0.8755 (tp30) REVERT: C 479 LEU cc_start: 0.8708 (tp) cc_final: 0.8433 (tp) REVERT: C 490 ASP cc_start: 0.7382 (m-30) cc_final: 0.7175 (m-30) REVERT: C 496 MET cc_start: 0.6557 (mmm) cc_final: 0.6171 (tpp) REVERT: C 524 GLU cc_start: 0.9091 (mp0) cc_final: 0.8803 (mp0) REVERT: C 570 GLU cc_start: 0.8619 (mm-30) cc_final: 0.7959 (pm20) REVERT: C 594 ARG cc_start: 0.8152 (mtm-85) cc_final: 0.7887 (mtm-85) REVERT: C 607 PHE cc_start: 0.9319 (t80) cc_final: 0.8766 (t80) REVERT: C 620 LEU cc_start: 0.8806 (mt) cc_final: 0.8011 (mp) REVERT: C 670 MET cc_start: 0.9103 (mmp) cc_final: 0.8683 (mmp) REVERT: C 726 ASN cc_start: 0.8399 (m-40) cc_final: 0.8150 (m-40) REVERT: C 811 LEU cc_start: 0.9643 (tp) cc_final: 0.9435 (mt) REVERT: C 861 TRP cc_start: 0.7617 (m100) cc_final: 0.7406 (m100) REVERT: C 965 PHE cc_start: 0.8220 (m-80) cc_final: 0.7997 (m-80) REVERT: C 999 PHE cc_start: 0.8250 (t80) cc_final: 0.7827 (t80) REVERT: C 1032 TYR cc_start: 0.8358 (t80) cc_final: 0.7649 (t80) REVERT: D 407 MET cc_start: 0.5511 (mpp) cc_final: 0.5167 (mpp) REVERT: D 428 LEU cc_start: 0.8269 (mm) cc_final: 0.7939 (mm) REVERT: D 458 LYS cc_start: 0.9018 (mmtp) cc_final: 0.8717 (mmmt) REVERT: D 463 MET cc_start: 0.7903 (mtm) cc_final: 0.7467 (mmm) REVERT: D 493 LYS cc_start: 0.7448 (mptt) cc_final: 0.7169 (mppt) REVERT: D 576 SER cc_start: 0.8133 (m) cc_final: 0.7293 (t) REVERT: D 626 VAL cc_start: 0.8791 (t) cc_final: 0.8512 (t) REVERT: D 649 THR cc_start: 0.5472 (p) cc_final: 0.5205 (p) REVERT: D 667 PHE cc_start: 0.8290 (m-80) cc_final: 0.7246 (m-80) REVERT: D 670 MET cc_start: 0.8498 (tmm) cc_final: 0.7824 (tmm) REVERT: D 720 THR cc_start: 0.8375 (p) cc_final: 0.7860 (t) REVERT: D 763 LYS cc_start: 0.8501 (tptp) cc_final: 0.8184 (tptt) outliers start: 1 outliers final: 0 residues processed: 389 average time/residue: 0.2521 time to fit residues: 147.7055 Evaluate side-chains 330 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 329 time to evaluate : 1.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 186 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 110 optimal weight: 0.9980 chunk 141 optimal weight: 6.9990 chunk 109 optimal weight: 0.0970 chunk 162 optimal weight: 4.9990 chunk 108 optimal weight: 0.9990 chunk 192 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 950 HIS A 985 ASN B 508 GLN B 619 ASN ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 642 GLN C 920 ASN ** D 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 1.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 16168 Z= 0.166 Angle : 0.624 9.382 21816 Z= 0.320 Chirality : 0.041 0.143 2454 Planarity : 0.005 0.066 2684 Dihedral : 5.945 48.028 2208 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 6.90 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.19), residues: 1992 helix: 1.56 (0.16), residues: 1112 sheet: -1.27 (0.36), residues: 196 loop : -1.42 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 526 HIS 0.002 0.001 HIS D 435 PHE 0.021 0.001 PHE A 965 TYR 0.021 0.001 TYR C 616 ARG 0.013 0.001 ARG A 715 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 390 time to evaluate : 1.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 LEU cc_start: 0.7897 (mm) cc_final: 0.7105 (mm) REVERT: A 424 TYR cc_start: 0.8431 (t80) cc_final: 0.8003 (t80) REVERT: A 476 ILE cc_start: 0.8687 (mm) cc_final: 0.8103 (tp) REVERT: A 524 GLU cc_start: 0.9376 (pm20) cc_final: 0.8722 (pm20) REVERT: A 527 MET cc_start: 0.7290 (mmt) cc_final: 0.6339 (tpp) REVERT: A 531 PHE cc_start: 0.8902 (m-10) cc_final: 0.8424 (m-80) REVERT: A 533 TYR cc_start: 0.8737 (t80) cc_final: 0.8363 (t80) REVERT: A 574 PHE cc_start: 0.8377 (p90) cc_final: 0.7338 (m-80) REVERT: A 577 LEU cc_start: 0.9003 (mm) cc_final: 0.8641 (mm) REVERT: A 584 PHE cc_start: 0.8675 (t80) cc_final: 0.7953 (t80) REVERT: A 586 GLN cc_start: 0.8914 (tp-100) cc_final: 0.8466 (mm-40) REVERT: A 611 ILE cc_start: 0.9565 (mm) cc_final: 0.9352 (mm) REVERT: A 624 LEU cc_start: 0.8933 (mt) cc_final: 0.8502 (mt) REVERT: A 627 GLU cc_start: 0.8881 (pp20) cc_final: 0.8629 (pp20) REVERT: A 629 MET cc_start: 0.8485 (mpp) cc_final: 0.8186 (mpp) REVERT: A 708 MET cc_start: 0.8837 (ptt) cc_final: 0.8180 (mmm) REVERT: A 711 TYR cc_start: 0.7784 (t80) cc_final: 0.7454 (t80) REVERT: A 753 LEU cc_start: 0.7471 (mp) cc_final: 0.6762 (mp) REVERT: A 921 VAL cc_start: 0.9197 (t) cc_final: 0.8707 (m) REVERT: A 938 PHE cc_start: 0.9072 (m-80) cc_final: 0.8760 (m-80) REVERT: A 939 MET cc_start: 0.7429 (ttt) cc_final: 0.6858 (tmm) REVERT: A 1023 MET cc_start: 0.5861 (ttt) cc_final: 0.5399 (ptm) REVERT: B 460 TRP cc_start: 0.6857 (m100) cc_final: 0.6292 (m-90) REVERT: B 463 MET cc_start: 0.5255 (ptm) cc_final: 0.4811 (ppp) REVERT: B 527 MET cc_start: 0.7440 (mtt) cc_final: 0.6942 (mmm) REVERT: B 578 TRP cc_start: 0.8724 (t-100) cc_final: 0.8229 (t-100) REVERT: B 587 GLN cc_start: 0.8187 (mm110) cc_final: 0.7665 (mm110) REVERT: B 627 GLU cc_start: 0.8090 (pp20) cc_final: 0.7742 (pp20) REVERT: B 708 MET cc_start: 0.8631 (mtt) cc_final: 0.8042 (tpt) REVERT: B 721 MET cc_start: 0.6249 (ttp) cc_final: 0.5998 (ptm) REVERT: B 807 MET cc_start: 0.8735 (mtp) cc_final: 0.8462 (ppp) REVERT: B 808 LEU cc_start: 0.8758 (mm) cc_final: 0.8195 (mm) REVERT: C 424 TYR cc_start: 0.8375 (t80) cc_final: 0.7838 (t80) REVERT: C 479 LEU cc_start: 0.8662 (tp) cc_final: 0.8348 (tp) REVERT: C 524 GLU cc_start: 0.9096 (mp0) cc_final: 0.8858 (mp0) REVERT: C 570 GLU cc_start: 0.8729 (mm-30) cc_final: 0.8025 (pm20) REVERT: C 594 ARG cc_start: 0.8375 (mtm-85) cc_final: 0.8159 (mtm-85) REVERT: C 620 LEU cc_start: 0.8872 (mt) cc_final: 0.8281 (mp) REVERT: C 726 ASN cc_start: 0.8549 (m-40) cc_final: 0.8285 (m-40) REVERT: C 762 LEU cc_start: 0.9455 (mp) cc_final: 0.8966 (mm) REVERT: C 934 VAL cc_start: 0.8661 (t) cc_final: 0.8102 (t) REVERT: C 965 PHE cc_start: 0.8196 (m-80) cc_final: 0.7976 (m-80) REVERT: C 1032 TYR cc_start: 0.8076 (t80) cc_final: 0.7833 (t80) REVERT: D 407 MET cc_start: 0.5703 (mpp) cc_final: 0.5356 (mpp) REVERT: D 463 MET cc_start: 0.7887 (mtm) cc_final: 0.7463 (mmm) REVERT: D 576 SER cc_start: 0.8424 (m) cc_final: 0.7594 (t) REVERT: D 670 MET cc_start: 0.8539 (tmm) cc_final: 0.8023 (tmm) REVERT: D 720 THR cc_start: 0.8487 (p) cc_final: 0.7893 (t) REVERT: D 763 LYS cc_start: 0.8530 (tptp) cc_final: 0.8245 (tptt) outliers start: 0 outliers final: 0 residues processed: 390 average time/residue: 0.2445 time to fit residues: 145.6969 Evaluate side-chains 312 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 312 time to evaluate : 1.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 119 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 115 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 131 optimal weight: 9.9990 chunk 95 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 151 optimal weight: 9.9990 chunk 175 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 709 ASN ** A 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 412 HIS B 508 GLN B 586 GLN B 619 ASN ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 461 ASN ** D 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 1.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 16168 Z= 0.268 Angle : 0.746 20.547 21816 Z= 0.390 Chirality : 0.045 0.162 2454 Planarity : 0.005 0.066 2684 Dihedral : 6.492 50.807 2208 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 18.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.06 % Allowed : 1.99 % Favored : 97.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 6.90 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.19), residues: 1992 helix: 1.13 (0.16), residues: 1116 sheet: -1.40 (0.41), residues: 152 loop : -1.61 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP D 578 HIS 0.003 0.001 HIS C 435 PHE 0.038 0.002 PHE A 844 TYR 0.031 0.002 TYR C 616 ARG 0.008 0.001 ARG C 599 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 402 time to evaluate : 1.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 LEU cc_start: 0.8173 (mm) cc_final: 0.7338 (mm) REVERT: A 424 TYR cc_start: 0.8784 (t80) cc_final: 0.8393 (t80) REVERT: A 511 LYS cc_start: 0.8046 (mmpt) cc_final: 0.7825 (mmmm) REVERT: A 524 GLU cc_start: 0.9335 (pm20) cc_final: 0.8784 (pm20) REVERT: A 527 MET cc_start: 0.7685 (mmt) cc_final: 0.6866 (tpp) REVERT: A 528 CYS cc_start: 0.8748 (p) cc_final: 0.8489 (p) REVERT: A 531 PHE cc_start: 0.8908 (m-10) cc_final: 0.8502 (m-80) REVERT: A 540 LEU cc_start: 0.9453 (mm) cc_final: 0.9160 (tp) REVERT: A 574 PHE cc_start: 0.8211 (p90) cc_final: 0.7738 (m-80) REVERT: A 577 LEU cc_start: 0.9282 (mm) cc_final: 0.8946 (mm) REVERT: A 586 GLN cc_start: 0.8930 (tp-100) cc_final: 0.8512 (mm-40) REVERT: A 634 GLU cc_start: 0.7809 (pp20) cc_final: 0.7515 (pm20) REVERT: A 708 MET cc_start: 0.8889 (ptt) cc_final: 0.8235 (mmm) REVERT: A 710 GLU cc_start: 0.9179 (mp0) cc_final: 0.8908 (mp0) REVERT: A 807 MET cc_start: 0.9185 (mmp) cc_final: 0.8852 (mpp) REVERT: A 815 CYS cc_start: 0.6472 (m) cc_final: 0.6056 (t) REVERT: A 938 PHE cc_start: 0.9246 (m-80) cc_final: 0.9030 (m-80) REVERT: A 939 MET cc_start: 0.8029 (ttt) cc_final: 0.7660 (mmm) REVERT: A 980 TYR cc_start: 0.8076 (t80) cc_final: 0.7778 (t80) REVERT: A 981 ILE cc_start: 0.8844 (tt) cc_final: 0.8595 (tt) REVERT: B 412 HIS cc_start: 0.5917 (p-80) cc_final: 0.5679 (p90) REVERT: B 460 TRP cc_start: 0.6999 (m100) cc_final: 0.6368 (m-90) REVERT: B 493 LYS cc_start: 0.3402 (mptt) cc_final: 0.2983 (mppt) REVERT: B 527 MET cc_start: 0.7868 (mtt) cc_final: 0.7323 (mmm) REVERT: B 587 GLN cc_start: 0.8253 (mm110) cc_final: 0.7772 (mm110) REVERT: B 619 ASN cc_start: 0.8166 (t160) cc_final: 0.7961 (t0) REVERT: B 708 MET cc_start: 0.8947 (mtt) cc_final: 0.8442 (tpt) REVERT: B 721 MET cc_start: 0.7708 (ttp) cc_final: 0.6474 (ptm) REVERT: B 807 MET cc_start: 0.9047 (mtp) cc_final: 0.8843 (tmm) REVERT: B 808 LEU cc_start: 0.9092 (mm) cc_final: 0.8681 (mm) REVERT: B 814 PHE cc_start: 0.8193 (t80) cc_final: 0.7766 (t80) REVERT: C 432 ILE cc_start: 0.9323 (mm) cc_final: 0.9114 (tp) REVERT: C 528 CYS cc_start: 0.9354 (m) cc_final: 0.9151 (m) REVERT: C 570 GLU cc_start: 0.8928 (mm-30) cc_final: 0.8295 (pm20) REVERT: C 594 ARG cc_start: 0.8674 (mtm-85) cc_final: 0.8467 (mtm-85) REVERT: C 608 PHE cc_start: 0.9049 (t80) cc_final: 0.8843 (t80) REVERT: C 616 TYR cc_start: 0.9245 (t80) cc_final: 0.8977 (t80) REVERT: C 620 LEU cc_start: 0.8978 (mt) cc_final: 0.8348 (mp) REVERT: C 629 MET cc_start: 0.9430 (mtt) cc_final: 0.8984 (mtt) REVERT: C 852 LEU cc_start: 0.8770 (tp) cc_final: 0.8437 (tp) REVERT: C 861 TRP cc_start: 0.7603 (m100) cc_final: 0.7345 (m100) REVERT: C 880 MET cc_start: 0.4971 (mtp) cc_final: 0.4658 (mtp) REVERT: C 939 MET cc_start: 0.8808 (ppp) cc_final: 0.8223 (ptm) REVERT: C 987 GLU cc_start: 0.8413 (tm-30) cc_final: 0.8095 (tm-30) REVERT: C 988 MET cc_start: 0.7982 (mmp) cc_final: 0.7217 (mmp) REVERT: C 999 PHE cc_start: 0.8185 (t80) cc_final: 0.7878 (t80) REVERT: C 1026 TYR cc_start: 0.8621 (m-10) cc_final: 0.8397 (m-80) REVERT: C 1032 TYR cc_start: 0.8276 (t80) cc_final: 0.8054 (t80) REVERT: D 407 MET cc_start: 0.6392 (mpp) cc_final: 0.6005 (mpp) REVERT: D 414 MET cc_start: 0.6222 (mpp) cc_final: 0.6000 (mpp) REVERT: D 463 MET cc_start: 0.8147 (mtm) cc_final: 0.7642 (mmm) REVERT: D 524 GLU cc_start: 0.8924 (pt0) cc_final: 0.8557 (pm20) REVERT: D 576 SER cc_start: 0.8676 (m) cc_final: 0.7813 (t) REVERT: D 649 THR cc_start: 0.5668 (p) cc_final: 0.5152 (p) REVERT: D 667 PHE cc_start: 0.8143 (m-80) cc_final: 0.7009 (m-80) REVERT: D 670 MET cc_start: 0.8607 (tmm) cc_final: 0.7900 (tmm) REVERT: D 674 MET cc_start: 0.8048 (ppp) cc_final: 0.7798 (ppp) REVERT: D 763 LYS cc_start: 0.8531 (tptp) cc_final: 0.8285 (tptt) outliers start: 1 outliers final: 0 residues processed: 403 average time/residue: 0.2316 time to fit residues: 146.3464 Evaluate side-chains 323 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 323 time to evaluate : 1.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 184 optimal weight: 5.9990 chunk 168 optimal weight: 8.9990 chunk 179 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 141 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 162 optimal weight: 5.9990 chunk 169 optimal weight: 0.7980 chunk 117 optimal weight: 3.9990 chunk 189 optimal weight: 0.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 756 GLN B 508 GLN ** B 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 ASN ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 508 GLN ** D 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 709 ASN D 726 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 1.5032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 16168 Z= 0.237 Angle : 0.698 8.158 21816 Z= 0.365 Chirality : 0.044 0.161 2454 Planarity : 0.005 0.063 2684 Dihedral : 6.299 54.903 2208 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 5.17 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.19), residues: 1992 helix: 1.24 (0.16), residues: 1118 sheet: -1.56 (0.40), residues: 152 loop : -1.64 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP D 578 HIS 0.004 0.001 HIS C 412 PHE 0.030 0.002 PHE A 844 TYR 0.017 0.002 TYR C 768 ARG 0.006 0.001 ARG B 594 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 423 time to evaluate : 1.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 424 TYR cc_start: 0.8706 (t80) cc_final: 0.8348 (t80) REVERT: A 511 LYS cc_start: 0.8002 (mmpt) cc_final: 0.7726 (mmmm) REVERT: A 527 MET cc_start: 0.7817 (mmt) cc_final: 0.6993 (tpp) REVERT: A 528 CYS cc_start: 0.8753 (p) cc_final: 0.8493 (p) REVERT: A 531 PHE cc_start: 0.8966 (m-10) cc_final: 0.8538 (m-80) REVERT: A 574 PHE cc_start: 0.8131 (p90) cc_final: 0.7809 (m-80) REVERT: A 577 LEU cc_start: 0.9326 (mm) cc_final: 0.9050 (mm) REVERT: A 607 PHE cc_start: 0.9249 (t80) cc_final: 0.8576 (t80) REVERT: A 629 MET cc_start: 0.8783 (mpp) cc_final: 0.8518 (mpp) REVERT: A 634 GLU cc_start: 0.8171 (pp20) cc_final: 0.7934 (pm20) REVERT: A 705 GLU cc_start: 0.9096 (mm-30) cc_final: 0.8465 (mm-30) REVERT: A 708 MET cc_start: 0.8948 (ptt) cc_final: 0.8420 (mmp) REVERT: A 796 PHE cc_start: 0.8791 (m-80) cc_final: 0.8475 (m-80) REVERT: A 803 LEU cc_start: 0.9217 (mt) cc_final: 0.8919 (mt) REVERT: A 807 MET cc_start: 0.9286 (mmp) cc_final: 0.9070 (mpp) REVERT: A 815 CYS cc_start: 0.6561 (m) cc_final: 0.6171 (t) REVERT: A 849 LEU cc_start: 0.8059 (mt) cc_final: 0.7569 (mm) REVERT: A 938 PHE cc_start: 0.9238 (m-80) cc_final: 0.8966 (m-80) REVERT: A 966 PHE cc_start: 0.8485 (m-10) cc_final: 0.7977 (m-80) REVERT: A 980 TYR cc_start: 0.8145 (t80) cc_final: 0.7929 (t80) REVERT: A 981 ILE cc_start: 0.8929 (tt) cc_final: 0.8679 (tt) REVERT: A 987 GLU cc_start: 0.8738 (mm-30) cc_final: 0.8293 (mt-10) REVERT: B 460 TRP cc_start: 0.6964 (m100) cc_final: 0.6322 (m-90) REVERT: B 463 MET cc_start: 0.5833 (ptm) cc_final: 0.5437 (ppp) REVERT: B 493 LYS cc_start: 0.3340 (mptt) cc_final: 0.2526 (mptt) REVERT: B 527 MET cc_start: 0.8220 (mtt) cc_final: 0.7647 (mmm) REVERT: B 578 TRP cc_start: 0.9158 (t-100) cc_final: 0.8567 (t-100) REVERT: B 619 ASN cc_start: 0.8306 (t160) cc_final: 0.8008 (t0) REVERT: B 707 THR cc_start: 0.9137 (m) cc_final: 0.8480 (m) REVERT: B 708 MET cc_start: 0.9297 (mtt) cc_final: 0.8755 (tpp) REVERT: B 710 GLU cc_start: 0.8813 (mp0) cc_final: 0.8555 (pp20) REVERT: B 721 MET cc_start: 0.7330 (ttp) cc_final: 0.6739 (ptm) REVERT: B 808 LEU cc_start: 0.9122 (mm) cc_final: 0.8719 (mm) REVERT: B 814 PHE cc_start: 0.8274 (t80) cc_final: 0.7948 (t80) REVERT: C 424 TYR cc_start: 0.8734 (t80) cc_final: 0.8063 (t80) REVERT: C 428 LEU cc_start: 0.9816 (tp) cc_final: 0.9520 (mt) REVERT: C 463 MET cc_start: 0.9073 (mmm) cc_final: 0.8758 (mpp) REVERT: C 524 GLU cc_start: 0.9452 (pm20) cc_final: 0.9128 (pm20) REVERT: C 527 MET cc_start: 0.9084 (ptp) cc_final: 0.8446 (ttt) REVERT: C 531 PHE cc_start: 0.9406 (m-10) cc_final: 0.9093 (m-10) REVERT: C 570 GLU cc_start: 0.9035 (mm-30) cc_final: 0.8434 (pm20) REVERT: C 620 LEU cc_start: 0.8869 (mt) cc_final: 0.8518 (mt) REVERT: C 762 LEU cc_start: 0.9441 (mp) cc_final: 0.8818 (mp) REVERT: C 811 LEU cc_start: 0.8918 (mt) cc_final: 0.8659 (pp) REVERT: C 938 PHE cc_start: 0.7804 (m-80) cc_final: 0.7595 (m-80) REVERT: C 940 PHE cc_start: 0.9313 (t80) cc_final: 0.9113 (t80) REVERT: C 965 PHE cc_start: 0.8425 (m-80) cc_final: 0.8110 (m-80) REVERT: C 980 TYR cc_start: 0.8939 (t80) cc_final: 0.8718 (t80) REVERT: D 407 MET cc_start: 0.6477 (mpp) cc_final: 0.5964 (mpp) REVERT: D 463 MET cc_start: 0.8216 (mtm) cc_final: 0.7735 (mmm) REVERT: D 496 MET cc_start: 0.7876 (pmm) cc_final: 0.7580 (pmm) REVERT: D 667 PHE cc_start: 0.8140 (m-80) cc_final: 0.7025 (m-80) REVERT: D 670 MET cc_start: 0.8692 (tmm) cc_final: 0.8018 (tmm) REVERT: D 763 LYS cc_start: 0.8627 (tptp) cc_final: 0.8235 (tptt) outliers start: 0 outliers final: 0 residues processed: 423 average time/residue: 0.2397 time to fit residues: 155.8173 Evaluate side-chains 326 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 326 time to evaluate : 1.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 115 optimal weight: 0.0270 chunk 90 optimal weight: 0.7980 chunk 132 optimal weight: 0.9980 chunk 199 optimal weight: 4.9990 chunk 183 optimal weight: 6.9990 chunk 158 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 126 optimal weight: 5.9990 chunk 169 optimal weight: 1.9990 overall best weight: 1.1642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 990 ASN B 508 GLN B 586 GLN B 619 ASN ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 726 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 1.5504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 16168 Z= 0.201 Angle : 0.689 8.835 21816 Z= 0.355 Chirality : 0.044 0.302 2454 Planarity : 0.004 0.066 2684 Dihedral : 6.234 58.122 2208 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 6.90 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.19), residues: 1992 helix: 1.37 (0.16), residues: 1108 sheet: -1.62 (0.41), residues: 138 loop : -1.55 (0.22), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 526 HIS 0.003 0.001 HIS D 435 PHE 0.021 0.002 PHE C 658 TYR 0.022 0.001 TYR C 768 ARG 0.012 0.001 ARG A 899 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 407 time to evaluate : 1.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 424 TYR cc_start: 0.8664 (t80) cc_final: 0.8347 (t80) REVERT: A 427 ASP cc_start: 0.8870 (m-30) cc_final: 0.8385 (m-30) REVERT: A 476 ILE cc_start: 0.8818 (mm) cc_final: 0.8377 (tp) REVERT: A 485 ARG cc_start: 0.8447 (mtt90) cc_final: 0.8224 (mtt180) REVERT: A 511 LYS cc_start: 0.8039 (mmpt) cc_final: 0.7734 (mmmm) REVERT: A 527 MET cc_start: 0.7822 (mmt) cc_final: 0.7100 (tpp) REVERT: A 528 CYS cc_start: 0.8742 (p) cc_final: 0.8502 (p) REVERT: A 531 PHE cc_start: 0.8960 (m-10) cc_final: 0.8630 (m-80) REVERT: A 577 LEU cc_start: 0.9343 (mm) cc_final: 0.8935 (mm) REVERT: A 605 TRP cc_start: 0.8925 (t-100) cc_final: 0.8614 (t-100) REVERT: A 627 GLU cc_start: 0.9097 (pp20) cc_final: 0.8745 (pp20) REVERT: A 629 MET cc_start: 0.8765 (mpp) cc_final: 0.8468 (mpp) REVERT: A 685 THR cc_start: 0.8365 (t) cc_final: 0.7993 (p) REVERT: A 705 GLU cc_start: 0.9076 (mm-30) cc_final: 0.8379 (mm-30) REVERT: A 708 MET cc_start: 0.8968 (ptt) cc_final: 0.8319 (mmm) REVERT: A 762 LEU cc_start: 0.9067 (mt) cc_final: 0.8782 (mt) REVERT: A 796 PHE cc_start: 0.8745 (m-80) cc_final: 0.8480 (m-80) REVERT: A 803 LEU cc_start: 0.9201 (mt) cc_final: 0.8771 (mt) REVERT: A 938 PHE cc_start: 0.9143 (m-80) cc_final: 0.8887 (m-80) REVERT: A 981 ILE cc_start: 0.8971 (tt) cc_final: 0.8756 (tt) REVERT: A 987 GLU cc_start: 0.8854 (mm-30) cc_final: 0.8391 (mt-10) REVERT: A 1023 MET cc_start: 0.6671 (ttt) cc_final: 0.5946 (ptp) REVERT: B 414 MET cc_start: 0.7241 (pmm) cc_final: 0.5145 (mtt) REVERT: B 460 TRP cc_start: 0.7024 (m100) cc_final: 0.6343 (m-90) REVERT: B 463 MET cc_start: 0.5942 (ptm) cc_final: 0.5418 (ppp) REVERT: B 493 LYS cc_start: 0.3476 (mptt) cc_final: 0.2892 (mptt) REVERT: B 527 MET cc_start: 0.8257 (mtt) cc_final: 0.7766 (mmm) REVERT: B 578 TRP cc_start: 0.9075 (t-100) cc_final: 0.8418 (t-100) REVERT: B 596 LEU cc_start: 0.9202 (pt) cc_final: 0.8816 (tt) REVERT: B 619 ASN cc_start: 0.8314 (t160) cc_final: 0.8073 (t0) REVERT: B 707 THR cc_start: 0.9173 (m) cc_final: 0.8618 (m) REVERT: B 708 MET cc_start: 0.9265 (mtt) cc_final: 0.8848 (tpp) REVERT: B 710 GLU cc_start: 0.8749 (mp0) cc_final: 0.8477 (pp20) REVERT: B 721 MET cc_start: 0.8227 (ttp) cc_final: 0.7172 (ptm) REVERT: B 808 LEU cc_start: 0.9248 (mm) cc_final: 0.8733 (mm) REVERT: B 814 PHE cc_start: 0.8281 (t80) cc_final: 0.7818 (t80) REVERT: C 424 TYR cc_start: 0.8863 (t80) cc_final: 0.8028 (t80) REVERT: C 428 LEU cc_start: 0.9800 (tp) cc_final: 0.9466 (mt) REVERT: C 463 MET cc_start: 0.9009 (mmm) cc_final: 0.8711 (mpp) REVERT: C 524 GLU cc_start: 0.9373 (pm20) cc_final: 0.9152 (pm20) REVERT: C 527 MET cc_start: 0.9147 (ptp) cc_final: 0.8446 (ttt) REVERT: C 531 PHE cc_start: 0.9420 (m-10) cc_final: 0.9077 (m-10) REVERT: C 570 GLU cc_start: 0.9034 (mm-30) cc_final: 0.8447 (pm20) REVERT: C 586 GLN cc_start: 0.6292 (tm-30) cc_final: 0.5911 (tm-30) REVERT: C 594 ARG cc_start: 0.8476 (mtm-85) cc_final: 0.7818 (mtm-85) REVERT: C 616 TYR cc_start: 0.9301 (t80) cc_final: 0.9030 (t80) REVERT: C 620 LEU cc_start: 0.8938 (mt) cc_final: 0.8034 (mt) REVERT: C 729 SER cc_start: 0.7477 (m) cc_final: 0.6931 (p) REVERT: C 762 LEU cc_start: 0.9434 (mp) cc_final: 0.8872 (mp) REVERT: C 768 TYR cc_start: 0.8358 (p90) cc_final: 0.8054 (p90) REVERT: C 811 LEU cc_start: 0.8929 (mt) cc_final: 0.8643 (pp) REVERT: C 939 MET cc_start: 0.8718 (ppp) cc_final: 0.8235 (tmm) REVERT: C 965 PHE cc_start: 0.8381 (m-80) cc_final: 0.8074 (m-80) REVERT: C 980 TYR cc_start: 0.8877 (t80) cc_final: 0.8672 (t80) REVERT: C 985 ASN cc_start: 0.9428 (m-40) cc_final: 0.9209 (m-40) REVERT: C 999 PHE cc_start: 0.8247 (t80) cc_final: 0.7949 (t80) REVERT: D 407 MET cc_start: 0.6462 (mpp) cc_final: 0.6060 (mpp) REVERT: D 463 MET cc_start: 0.8205 (mtm) cc_final: 0.7742 (mtp) REVERT: D 496 MET cc_start: 0.7884 (pmm) cc_final: 0.7564 (pmm) REVERT: D 503 MET cc_start: 0.8471 (ppp) cc_final: 0.8121 (ppp) REVERT: D 585 MET cc_start: 0.8730 (mmm) cc_final: 0.8403 (mmm) REVERT: D 667 PHE cc_start: 0.8261 (m-80) cc_final: 0.7193 (m-80) REVERT: D 670 MET cc_start: 0.8774 (tmm) cc_final: 0.8124 (tmm) REVERT: D 708 MET cc_start: 0.8779 (tpp) cc_final: 0.8324 (ttm) REVERT: D 763 LYS cc_start: 0.8541 (tptp) cc_final: 0.8183 (tptt) outliers start: 0 outliers final: 0 residues processed: 407 average time/residue: 0.2727 time to fit residues: 174.1010 Evaluate side-chains 338 residues out of total 1706 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 338 time to evaluate : 1.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 48 optimal weight: 7.9990 chunk 146 optimal weight: 0.2980 chunk 23 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 chunk 158 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 163 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 139 optimal weight: 4.9990 chunk 9 optimal weight: 0.3980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 508 GLN B 586 GLN B 619 ASN ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.082763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.063977 restraints weight = 70442.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.065534 restraints weight = 51525.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.066701 restraints weight = 40563.893| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 1.5850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 16168 Z= 0.183 Angle : 0.678 10.264 21816 Z= 0.344 Chirality : 0.043 0.318 2454 Planarity : 0.004 0.064 2684 Dihedral : 6.072 57.836 2208 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.06 % Allowed : 0.35 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 5.17 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.19), residues: 1992 helix: 1.39 (0.16), residues: 1122 sheet: -1.38 (0.40), residues: 158 loop : -1.56 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 526 HIS 0.003 0.001 HIS D 435 PHE 0.041 0.002 PHE D 571 TYR 0.021 0.001 TYR C 616 ARG 0.007 0.001 ARG C 594 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3584.50 seconds wall clock time: 64 minutes 44.34 seconds (3884.34 seconds total)