Starting phenix.real_space_refine on Fri Jul 3 21:06:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ryy_24748/07_2026/7ryy_24748.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ryy_24748/07_2026/7ryy_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 { model { file = "/net/cci-nas-00/data/ceres_data/7ryy_24748/07_2026/7ryy_24748.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ryy_24748/07_2026/7ryy_24748.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ryy_24748/07_2026/7ryy_24748.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ryy_24748/07_2026/7ryy_24748.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7ryy_24748/07_2026/7ryy_24748.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ryy_24748/07_2026/7ryy_24748.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: 28 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: 28 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: 3.70, per 1000 atoms: 0.23 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: 1.21 Conformation dependent library (CDL) restraints added in 829.2 milliseconds 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: 0.63 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: 2.82 Time building geometry restraints manager: 1.64 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: 8810 15.16 - 30.32: 536 30.32 - 45.48: 182 45.48 - 60.64: 20 60.64 - 75.81: 10 Dihedral angle restraints: 9558 sinusoidal: 3762 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 9555 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: 0.03 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: 3.100 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: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.630 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5064 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 16174 Z= 0.254 Angle : 1.006 14.292 21828 Z= 0.550 Chirality : 0.052 0.268 2454 Planarity : 0.007 0.104 2684 Dihedral : 11.370 75.805 5840 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.006 0.001 ARG B 599 TYR 0.018 0.002 TYR C 647 PHE 0.019 0.002 PHE C 901 TRP 0.031 0.003 TRP D 767 HIS 0.004 0.001 HIS D 435 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.25 (16168) covalent geometry : angle 1.00570 / 0.55 (21816) SS BOND : bond 0.00440 / 0.22 ( 6) SS BOND : angle 1.77159 / 0.99 ( 12) hydrogen bonds : bond 0.28054 / 18.61 ( 818) hydrogen bonds : angle 8.98911 / 6.36 ( 2400) *********************** 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 to be fit. rotamer outliers: 10 poor density : 465 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 531 PHE cc_start: 0.7408 (m-10) cc_final: 0.6979 (m-80) REVERT: A 684 ARG cc_start: 0.7965 (mpp-170) cc_final: 0.7307 (tmt-80) REVERT: A 704 LEU cc_start: 0.7584 (pt) cc_final: 0.7084 (pt) REVERT: A 708 MET cc_start: 0.8204 (mtt) cc_final: 0.7417 (ptm) REVERT: A 712 ILE cc_start: 0.8670 (mm) cc_final: 0.8071 (mm) REVERT: A 860 TYR cc_start: 0.3924 (m-80) cc_final: 0.3621 (m-80) REVERT: B 579 PHE cc_start: 0.4285 (t80) cc_final: 0.3703 (t80) REVERT: B 593 PRO cc_start: 0.7307 (Cg_exo) cc_final: 0.6677 (Cg_endo) REVERT: B 619 ASN cc_start: 0.5720 (t160) cc_final: 0.4484 (t0) REVERT: B 620 LEU cc_start: 0.8419 (tt) cc_final: 0.8144 (tt) REVERT: B 699 LYS cc_start: 0.8576 (mptt) cc_final: 0.7977 (mmmt) REVERT: B 708 MET cc_start: 0.8146 (mtt) cc_final: 0.7453 (tpt) REVERT: C 400 ILE cc_start: 0.5221 (tt) cc_final: 0.4988 (mt) REVERT: C 424 TYR cc_start: 0.7163 (t80) cc_final: 0.6547 (t80) REVERT: C 457 THR cc_start: 0.7661 (p) cc_final: 0.7451 (p) REVERT: C 479 LEU cc_start: 0.8688 (tp) cc_final: 0.8386 (tp) REVERT: C 519 ASP cc_start: 0.6552 (m-30) cc_final: 0.5899 (t0) REVERT: C 521 LEU cc_start: 0.6881 (mt) cc_final: 0.6563 (mt) REVERT: C 672 THR cc_start: 0.7772 (m) cc_final: 0.7569 (p) REVERT: C 710 GLU cc_start: 0.8897 (mt-10) cc_final: 0.8570 (tp30) REVERT: C 713 GLU cc_start: 0.9093 (tt0) cc_final: 0.8869 (mt-10) REVERT: C 720 THR cc_start: 0.8104 (p) cc_final: 0.7596 (t) REVERT: C 762 LEU cc_start: 0.9086 (mt) cc_final: 0.8692 (mm) REVERT: C 764 ASN cc_start: 0.6756 (t0) cc_final: 0.6269 (m110) REVERT: C 796 PHE cc_start: 0.7147 (m-80) cc_final: 0.6713 (m-80) REVERT: C 880 MET cc_start: 0.5000 (tmm) cc_final: 0.4425 (ttt) REVERT: C 1003 TYR cc_start: 0.5709 (m-80) cc_final: 0.5493 (m-80) REVERT: D 405 TYR cc_start: 0.7647 (m-80) cc_final: 0.7403 (m-80) REVERT: D 407 MET cc_start: 0.3927 (mtm) cc_final: 0.2929 (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: 0.5642 (ttm) REVERT: D 629 MET cc_start: 0.6645 (mmm) cc_final: 0.4966 (tpp) REVERT: D 649 THR cc_start: 0.2950 (p) cc_final: 0.2687 (p) REVERT: D 760 ASP cc_start: 0.7170 (m-30) cc_final: 0.6953 (t0) REVERT: D 763 LYS cc_start: 0.9012 (ttpt) cc_final: 0.8751 (tptt) outliers start: 10 outliers final: 2 residues processed: 472 average time/residue: 0.1474 time to fit residues: 99.7573 Evaluate side-chains 283 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 281 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 8.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 575 ASN A 619 ASN A 642 GLN ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 714 GLN A 872 GLN A 874 GLN A 950 HIS A 985 ASN B 461 ASN B 569 ASN B 586 GLN ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 586 GLN D 587 GLN D 619 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.083863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.064858 restraints weight = 69257.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.066415 restraints weight = 50327.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.067577 restraints weight = 39463.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.068336 restraints weight = 32885.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.069072 restraints weight = 28784.837| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5475 moved from start: 0.4677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16174 Z= 0.156 Angle : 0.685 10.915 21828 Z= 0.358 Chirality : 0.044 0.334 2454 Planarity : 0.006 0.083 2684 Dihedral : 6.449 59.575 2192 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 12.30 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.17), residues: 1992 helix: 0.02 (0.14), residues: 1068 sheet: -1.64 (0.33), residues: 202 loop : -1.95 (0.21), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 715 TYR 0.020 0.002 TYR A1003 PHE 0.024 0.002 PHE C 901 TRP 0.030 0.002 TRP C1005 HIS 0.004 0.001 HIS C 883 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.16 (16168) covalent geometry : angle 0.68429 / 0.36 (21816) SS BOND : bond 0.00379 / 0.17 ( 6) SS BOND : angle 1.25853 / 0.65 ( 12) hydrogen bonds : bond 0.04841 / 3.22 ( 818) hydrogen bonds : angle 4.85263 / 3.52 ( 2400) *********************** 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 343 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 339 time to evaluate : 0.552 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 591 ILE cc_start: 0.5354 (tp) cc_final: 0.4921 (tp) REVERT: A 684 ARG cc_start: 0.7899 (mpp-170) cc_final: 0.7381 (tmt-80) REVERT: A 704 LEU cc_start: 0.7131 (pt) cc_final: 0.6062 (pt) REVERT: A 707 THR cc_start: 0.7893 (m) cc_final: 0.7573 (p) REVERT: A 708 MET cc_start: 0.7955 (mtt) cc_final: 0.7364 (ptm) REVERT: A 721 MET cc_start: 0.1740 (tmm) cc_final: 0.0257 (tmm) REVERT: A 860 TYR cc_start: 0.3778 (m-80) cc_final: 0.3371 (m-80) REVERT: A 879 LYS cc_start: 0.7510 (ptpt) cc_final: 0.7255 (ptmm) REVERT: A 939 MET cc_start: 0.4760 (ttt) cc_final: 0.4181 (ttt) REVERT: A 941 ILE cc_start: 0.7316 (mt) cc_final: 0.7073 (mt) REVERT: B 520 PRO cc_start: 0.8166 (Cg_endo) cc_final: 0.7734 (Cg_exo) REVERT: B 531 PHE cc_start: 0.7865 (t80) cc_final: 0.7626 (t80) REVERT: B 629 MET cc_start: 0.2973 (tpp) cc_final: 0.2762 (tpt) REVERT: B 661 ARG cc_start: 0.8487 (tpm170) cc_final: 0.8256 (tpp80) REVERT: B 708 MET cc_start: 0.8146 (mtt) cc_final: 0.7347 (tpt) REVERT: C 414 MET cc_start: 0.4822 (mpp) cc_final: 0.4614 (mpp) REVERT: C 424 TYR cc_start: 0.6523 (t80) cc_final: 0.6026 (t80) REVERT: C 519 ASP cc_start: 0.7064 (m-30) cc_final: 0.6818 (t0) REVERT: C 527 MET cc_start: 0.8260 (mtm) cc_final: 0.6729 (mtp) REVERT: C 672 THR cc_start: 0.8091 (m) cc_final: 0.7885 (p) REVERT: C 710 GLU cc_start: 0.8872 (mt-10) cc_final: 0.8353 (mm-30) REVERT: C 762 LEU cc_start: 0.9149 (mt) cc_final: 0.8517 (mm) REVERT: C 796 PHE cc_start: 0.7096 (m-80) cc_final: 0.6700 (m-80) REVERT: C 1003 TYR cc_start: 0.6067 (m-80) cc_final: 0.5127 (m-80) REVERT: C 1032 TYR cc_start: 0.8249 (t80) cc_final: 0.7963 (t80) REVERT: D 424 TYR cc_start: 0.7160 (t80) cc_final: 0.6349 (t80) REVERT: D 527 MET cc_start: 0.5905 (ttm) cc_final: 0.5457 (ttm) REVERT: D 629 MET cc_start: 0.6845 (mmm) cc_final: 0.5225 (tpp) REVERT: D 760 ASP cc_start: 0.7122 (m-30) cc_final: 0.6445 (t0) REVERT: D 763 LYS cc_start: 0.8959 (ttpt) cc_final: 0.8752 (tmmt) REVERT: D 790 SER cc_start: 0.7522 (m) cc_final: 0.7252 (p) outliers start: 4 outliers final: 0 residues processed: 343 average time/residue: 0.1361 time to fit residues: 68.2593 Evaluate side-chains 240 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 113 optimal weight: 2.9990 chunk 147 optimal weight: 7.9990 chunk 83 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 106 optimal weight: 10.0000 chunk 101 optimal weight: 1.9990 chunk 12 optimal weight: 0.0370 chunk 34 optimal weight: 3.9990 chunk 186 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 chunk 159 optimal weight: 0.8980 overall best weight: 1.3862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 619 ASN ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 985 ASN C 575 ASN ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN ** D 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 587 GLN D 619 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.083456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.064424 restraints weight = 71446.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.065994 restraints weight = 50903.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.067205 restraints weight = 39918.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.067936 restraints weight = 32952.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.068690 restraints weight = 29069.758| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6114 moved from start: 0.7164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 16174 Z= 0.192 Angle : 0.709 10.734 21828 Z= 0.372 Chirality : 0.044 0.218 2454 Planarity : 0.006 0.073 2684 Dihedral : 6.018 51.420 2192 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.06 % Allowed : 4.28 % Favored : 95.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 6.90 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.18), residues: 1992 helix: 0.60 (0.15), residues: 1116 sheet: -1.67 (0.34), residues: 190 loop : -1.74 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 715 TYR 0.025 0.002 TYR D 768 PHE 0.019 0.002 PHE A 965 TRP 0.033 0.003 TRP D 767 HIS 0.009 0.002 HIS A 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.19 (16168) covalent geometry : angle 0.70842 / 0.37 (21816) SS BOND : bond 0.00346 / 0.17 ( 6) SS BOND : angle 1.37622 / 0.75 ( 12) hydrogen bonds : bond 0.04323 / 2.86 ( 818) hydrogen bonds : angle 4.70143 / 3.39 ( 2400) *********************** 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 374 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 373 time to evaluate : 0.564 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: A 527 MET cc_start: 0.6426 (mmt) cc_final: 0.5829 (mpp) REVERT: A 581 LEU cc_start: 0.8446 (tp) cc_final: 0.8033 (tp) REVERT: A 644 GLU cc_start: 0.6782 (pt0) cc_final: 0.6298 (tm-30) REVERT: A 656 LYS cc_start: 0.8380 (ptmt) cc_final: 0.8134 (ptmt) REVERT: A 657 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7436 (mp0) REVERT: A 704 LEU cc_start: 0.7626 (pt) cc_final: 0.5840 (pt) REVERT: A 707 THR cc_start: 0.8361 (m) cc_final: 0.8082 (p) REVERT: A 708 MET cc_start: 0.8284 (mtt) cc_final: 0.7980 (ptm) REVERT: A 939 MET cc_start: 0.5860 (ttt) cc_final: 0.4805 (tmm) REVERT: B 460 TRP cc_start: 0.6829 (m100) cc_final: 0.6341 (m-90) REVERT: B 463 MET cc_start: 0.4766 (ptm) cc_final: 0.3627 (ttp) REVERT: B 519 ASP cc_start: 0.8820 (t0) cc_final: 0.8591 (t0) REVERT: B 520 PRO cc_start: 0.8106 (Cg_endo) cc_final: 0.7383 (Cg_exo) REVERT: B 531 PHE cc_start: 0.8349 (t80) cc_final: 0.8067 (t80) REVERT: B 536 VAL cc_start: 0.8658 (t) cc_final: 0.7684 (t) REVERT: B 620 LEU cc_start: 0.8885 (tt) cc_final: 0.8598 (tt) REVERT: B 708 MET cc_start: 0.8284 (mtt) cc_final: 0.7501 (tpt) REVERT: B 734 ILE cc_start: 0.7461 (mm) cc_final: 0.7184 (tp) REVERT: C 424 TYR cc_start: 0.6839 (t80) cc_final: 0.6619 (t80) REVERT: C 463 MET cc_start: 0.8448 (mpp) cc_final: 0.8239 (mpp) REVERT: C 581 LEU cc_start: 0.8689 (tp) cc_final: 0.8459 (tp) REVERT: C 610 LEU cc_start: 0.8608 (tp) cc_final: 0.8381 (tp) REVERT: C 637 GLU cc_start: 0.8224 (mp0) cc_final: 0.7755 (mp0) REVERT: C 657 GLU cc_start: 0.7435 (pt0) cc_final: 0.6992 (tp30) REVERT: C 668 ASP cc_start: 0.8694 (m-30) cc_final: 0.8449 (m-30) REVERT: C 672 THR cc_start: 0.8192 (m) cc_final: 0.7945 (p) REVERT: C 762 LEU cc_start: 0.9254 (mt) cc_final: 0.8794 (mm) REVERT: C 807 MET cc_start: 0.8474 (tmm) cc_final: 0.8271 (tmm) REVERT: C 811 LEU cc_start: 0.9606 (tp) cc_final: 0.9216 (mt) REVERT: C 840 LEU cc_start: 0.8920 (mt) cc_final: 0.8638 (mt) REVERT: C 980 TYR cc_start: 0.8056 (t80) cc_final: 0.7788 (t80) REVERT: C 999 PHE cc_start: 0.8021 (t80) cc_final: 0.7789 (t80) REVERT: C 1003 TYR cc_start: 0.5170 (m-80) cc_final: 0.4872 (m-80) REVERT: C 1032 TYR cc_start: 0.8061 (t80) cc_final: 0.7755 (t80) REVERT: D 458 LYS cc_start: 0.8910 (mmtp) cc_final: 0.8583 (mmmt) REVERT: D 463 MET cc_start: 0.7707 (mtm) cc_final: 0.7405 (mtp) REVERT: D 503 MET cc_start: 0.7922 (ppp) cc_final: 0.7613 (ppp) REVERT: D 527 MET cc_start: 0.6535 (ttm) cc_final: 0.6060 (ttm) REVERT: D 585 MET cc_start: 0.7168 (mmm) cc_final: 0.6821 (mmt) REVERT: D 586 GLN cc_start: 0.8762 (mt0) cc_final: 0.8437 (mt0) REVERT: D 760 ASP cc_start: 0.7160 (m-30) cc_final: 0.6927 (t0) REVERT: D 767 TRP cc_start: 0.6385 (m-90) cc_final: 0.6077 (m100) REVERT: D 815 CYS cc_start: 0.6490 (m) cc_final: 0.6045 (t) outliers start: 1 outliers final: 0 residues processed: 373 average time/residue: 0.1261 time to fit residues: 70.5697 Evaluate side-chains 279 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 279 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 180 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 134 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 100 optimal weight: 7.9990 chunk 122 optimal weight: 0.0980 chunk 164 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 113 optimal weight: 0.5980 chunk 160 optimal weight: 9.9990 chunk 61 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 586 GLN A 619 ASN ** A 874 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 985 ASN B 508 GLN ** B 586 GLN ** 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 619 ASN ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 411 ASN D 619 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.083317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.064456 restraints weight = 70925.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.065950 restraints weight = 51931.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.067143 restraints weight = 41197.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.067982 restraints weight = 34251.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.068665 restraints weight = 29868.462| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6489 moved from start: 0.9243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.199 16174 Z= 0.186 Angle : 0.706 13.121 21828 Z= 0.365 Chirality : 0.043 0.232 2454 Planarity : 0.006 0.075 2684 Dihedral : 6.002 58.649 2192 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 6.90 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.18), residues: 1992 helix: 0.95 (0.15), residues: 1108 sheet: -1.44 (0.35), residues: 190 loop : -1.58 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 897 TYR 0.036 0.002 TYR A 980 PHE 0.024 0.002 PHE A 608 TRP 0.085 0.003 TRP A 861 HIS 0.006 0.001 HIS A 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.19 (16168) covalent geometry : angle 0.70593 / 0.36 (21816) SS BOND : bond 0.00302 / 0.14 ( 6) SS BOND : angle 1.09026 / 0.59 ( 12) hydrogen bonds : bond 0.04032 / 2.65 ( 818) hydrogen bonds : angle 4.52919 / 3.29 ( 2400) *********************** 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 388 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 388 time to evaluate : 0.571 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: A 527 MET cc_start: 0.6390 (mmt) cc_final: 0.5980 (tpp) REVERT: A 534 ILE cc_start: 0.9066 (mm) cc_final: 0.8857 (mm) REVERT: A 584 PHE cc_start: 0.8882 (t80) cc_final: 0.8083 (t80) REVERT: A 585 MET cc_start: 0.9076 (tpt) cc_final: 0.8667 (mmm) REVERT: A 587 GLN cc_start: 0.8047 (tp40) cc_final: 0.7740 (tp-100) REVERT: A 596 LEU cc_start: 0.8030 (mt) cc_final: 0.7672 (mt) REVERT: A 619 ASN cc_start: 0.8082 (t160) cc_final: 0.7455 (t0) REVERT: A 624 LEU cc_start: 0.9001 (mt) cc_final: 0.8613 (mt) REVERT: A 939 MET cc_start: 0.6022 (ttt) cc_final: 0.4860 (tmm) REVERT: A 1023 MET cc_start: 0.5786 (ttt) cc_final: 0.4766 (ptp) REVERT: B 407 MET cc_start: 0.7341 (mtm) cc_final: 0.7053 (mpp) REVERT: B 460 TRP cc_start: 0.6814 (m100) cc_final: 0.6259 (m-90) REVERT: B 587 GLN cc_start: 0.7892 (tp40) cc_final: 0.7584 (mm110) REVERT: B 708 MET cc_start: 0.8448 (mtt) cc_final: 0.7588 (tpt) REVERT: B 721 MET cc_start: 0.5087 (ttm) cc_final: 0.4529 (ptm) REVERT: C 402 GLU cc_start: 0.7404 (tt0) cc_final: 0.7127 (tm-30) REVERT: C 424 TYR cc_start: 0.6971 (t80) cc_final: 0.6761 (t80) REVERT: C 586 GLN cc_start: 0.5578 (tm-30) cc_final: 0.5305 (tm-30) REVERT: C 607 PHE cc_start: 0.8468 (t80) cc_final: 0.8253 (t80) REVERT: C 637 GLU cc_start: 0.8256 (mp0) cc_final: 0.7757 (mp0) REVERT: C 670 MET cc_start: 0.8628 (mmp) cc_final: 0.8336 (mmp) REVERT: C 705 GLU cc_start: 0.6729 (tm-30) cc_final: 0.6125 (tp30) REVERT: C 762 LEU cc_start: 0.9134 (mt) cc_final: 0.8756 (mm) REVERT: C 811 LEU cc_start: 0.9619 (tp) cc_final: 0.9312 (mt) REVERT: C 817 LYS cc_start: 0.8367 (tppp) cc_final: 0.7678 (ptmt) REVERT: C 840 LEU cc_start: 0.8721 (mt) cc_final: 0.8429 (mt) REVERT: C 891 PHE cc_start: 0.6457 (m-10) cc_final: 0.6118 (m-80) REVERT: C 1003 TYR cc_start: 0.6353 (m-80) cc_final: 0.4993 (m-80) REVERT: C 1032 TYR cc_start: 0.8093 (t80) cc_final: 0.7701 (t80) REVERT: D 414 MET cc_start: 0.6164 (mpp) cc_final: 0.5879 (mpp) REVERT: D 428 LEU cc_start: 0.8572 (mt) cc_final: 0.8221 (mt) REVERT: D 458 LYS cc_start: 0.8953 (mmtp) cc_final: 0.8617 (mmmt) REVERT: D 463 MET cc_start: 0.7797 (mtm) cc_final: 0.7479 (mtp) REVERT: D 503 MET cc_start: 0.8407 (ppp) cc_final: 0.8143 (ppp) REVERT: D 612 ILE cc_start: 0.8764 (mm) cc_final: 0.8489 (mm) REVERT: D 670 MET cc_start: 0.8107 (tmm) cc_final: 0.7527 (tmm) REVERT: D 760 ASP cc_start: 0.7172 (m-30) cc_final: 0.6859 (t0) outliers start: 0 outliers final: 0 residues processed: 388 average time/residue: 0.1250 time to fit residues: 73.1000 Evaluate side-chains 274 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 274 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 108 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 61 optimal weight: 8.9990 chunk 60 optimal weight: 9.9990 chunk 115 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 88 optimal weight: 0.0980 chunk 167 optimal weight: 8.9990 chunk 104 optimal weight: 1.9990 chunk 130 optimal weight: 10.0000 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 412 HIS A 619 ASN A 642 GLN A 756 GLN A 883 HIS A 985 ASN B 508 GLN B 586 GLN ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 764 ASN ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 619 ASN C 642 GLN C 985 ASN ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 747 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.080874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.062847 restraints weight = 71741.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.064395 restraints weight = 52131.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.065558 restraints weight = 40810.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.066343 restraints weight = 33847.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.067012 restraints weight = 29360.315| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 1.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 16174 Z= 0.242 Angle : 0.808 8.141 21828 Z= 0.426 Chirality : 0.047 0.205 2454 Planarity : 0.006 0.068 2684 Dihedral : 6.392 62.948 2192 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 19.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.12 % Allowed : 4.04 % Favored : 95.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 6.90 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.18), residues: 1992 helix: 0.48 (0.15), residues: 1112 sheet: -1.77 (0.40), residues: 142 loop : -1.69 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 628 TYR 0.024 0.003 TYR D 424 PHE 0.024 0.003 PHE A 608 TRP 0.031 0.003 TRP D 767 HIS 0.003 0.001 HIS B 435 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.24 (16168) covalent geometry : angle 0.80809 / 0.43 (21816) SS BOND : bond 0.00285 / 0.14 ( 6) SS BOND : angle 1.32395 / 0.74 ( 12) hydrogen bonds : bond 0.04745 / 3.15 ( 818) hydrogen bonds : angle 5.16767 / 3.76 ( 2400) *********************** 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 413 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 411 time to evaluate : 0.616 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: A 401 LEU cc_start: 0.7542 (mm) cc_final: 0.6786 (mm) REVERT: A 511 LYS cc_start: 0.7964 (mmpt) cc_final: 0.7677 (mmmm) REVERT: A 527 MET cc_start: 0.7503 (mmt) cc_final: 0.7048 (mmt) REVERT: A 581 LEU cc_start: 0.9281 (tp) cc_final: 0.8981 (tp) REVERT: A 586 GLN cc_start: 0.9279 (tp40) cc_final: 0.8770 (tp40) REVERT: A 627 GLU cc_start: 0.8958 (pp20) cc_final: 0.8353 (tp30) REVERT: A 705 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7293 (mm-30) REVERT: A 939 MET cc_start: 0.7489 (ttt) cc_final: 0.6615 (tmm) REVERT: B 406 VAL cc_start: 0.8509 (t) cc_final: 0.8305 (t) REVERT: B 460 TRP cc_start: 0.6542 (m100) cc_final: 0.5890 (m-90) REVERT: B 527 MET cc_start: 0.8005 (mtt) cc_final: 0.6994 (mpp) REVERT: B 545 ARG cc_start: 0.5937 (ttt180) cc_final: 0.5634 (ttt180) REVERT: B 578 TRP cc_start: 0.8777 (t-100) cc_final: 0.8413 (t-100) REVERT: B 627 GLU cc_start: 0.8214 (pp20) cc_final: 0.7749 (pp20) REVERT: B 629 MET cc_start: 0.5330 (tpt) cc_final: 0.4909 (tpt) REVERT: B 708 MET cc_start: 0.8889 (mtt) cc_final: 0.8160 (tpt) REVERT: B 721 MET cc_start: 0.7651 (ttm) cc_final: 0.6749 (ttm) REVERT: B 807 MET cc_start: 0.8873 (mtp) cc_final: 0.8658 (tmm) REVERT: B 808 LEU cc_start: 0.8903 (mm) cc_final: 0.8233 (mm) REVERT: C 424 TYR cc_start: 0.7636 (t80) cc_final: 0.7285 (t80) REVERT: C 519 ASP cc_start: 0.8426 (t70) cc_final: 0.8142 (t0) REVERT: C 570 GLU cc_start: 0.8485 (mm-30) cc_final: 0.7866 (pm20) REVERT: C 670 MET cc_start: 0.8676 (mmp) cc_final: 0.8182 (mmp) REVERT: C 762 LEU cc_start: 0.9195 (mt) cc_final: 0.8585 (mt) REVERT: C 796 PHE cc_start: 0.8573 (m-80) cc_final: 0.8150 (m-80) REVERT: C 811 LEU cc_start: 0.9643 (tp) cc_final: 0.9388 (mt) REVERT: C 891 PHE cc_start: 0.6681 (m-10) cc_final: 0.6329 (m-10) REVERT: C 965 PHE cc_start: 0.8713 (m-80) cc_final: 0.8281 (m-80) REVERT: C 987 GLU cc_start: 0.8276 (tm-30) cc_final: 0.8042 (tm-30) REVERT: C 999 PHE cc_start: 0.7997 (t80) cc_final: 0.7725 (t80) REVERT: C 1032 TYR cc_start: 0.8109 (t80) cc_final: 0.7657 (t80) REVERT: D 407 MET cc_start: 0.5711 (mpp) cc_final: 0.5396 (mpp) REVERT: D 408 MET cc_start: 0.5223 (mmm) cc_final: 0.4864 (mmt) REVERT: D 414 MET cc_start: 0.6208 (mpp) cc_final: 0.5746 (mpp) REVERT: D 463 MET cc_start: 0.7859 (mtm) cc_final: 0.7474 (mtm) REVERT: D 541 PHE cc_start: 0.8674 (t80) cc_final: 0.8389 (t80) REVERT: D 649 THR cc_start: 0.5154 (p) cc_final: 0.4701 (p) REVERT: D 670 MET cc_start: 0.8274 (tmm) cc_final: 0.7667 (tmm) REVERT: D 760 ASP cc_start: 0.7643 (m-30) cc_final: 0.6742 (t0) REVERT: D 763 LYS cc_start: 0.8891 (ttpt) cc_final: 0.8647 (ttpp) outliers start: 2 outliers final: 0 residues processed: 412 average time/residue: 0.1159 time to fit residues: 73.7430 Evaluate side-chains 308 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 308 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 189 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 123 optimal weight: 4.9990 chunk 193 optimal weight: 6.9990 chunk 129 optimal weight: 1.9990 chunk 186 optimal weight: 8.9990 chunk 162 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 160 optimal weight: 10.0000 chunk 179 optimal weight: 0.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 619 ASN A 642 GLN ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 874 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 950 HIS A 985 ASN B 412 HIS ** B 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 619 ASN D 508 GLN ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.080585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.062008 restraints weight = 73931.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.063570 restraints weight = 53748.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.064712 restraints weight = 42247.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.065486 restraints weight = 35254.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.066159 restraints weight = 30913.521| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 1.3815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16174 Z= 0.181 Angle : 0.703 8.470 21828 Z= 0.366 Chirality : 0.043 0.162 2454 Planarity : 0.005 0.067 2684 Dihedral : 6.056 60.192 2192 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 6.90 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.19), residues: 1992 helix: 0.87 (0.15), residues: 1114 sheet: -1.68 (0.41), residues: 138 loop : -1.57 (0.23), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 628 TYR 0.022 0.002 TYR C 768 PHE 0.034 0.002 PHE A 844 TRP 0.054 0.003 TRP B 767 HIS 0.003 0.001 HIS A 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.18 (16168) covalent geometry : angle 0.70254 / 0.37 (21816) SS BOND : bond 0.00254 / 0.12 ( 6) SS BOND : angle 1.08809 / 0.57 ( 12) hydrogen bonds : bond 0.04011 / 2.66 ( 818) hydrogen bonds : angle 4.89074 / 3.53 ( 2400) *********************** 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 398 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 398 time to evaluate : 0.623 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: A 424 TYR cc_start: 0.7781 (t80) cc_final: 0.7273 (t80) REVERT: A 511 LYS cc_start: 0.8182 (mmpt) cc_final: 0.7917 (mmmm) REVERT: A 524 GLU cc_start: 0.9384 (pm20) cc_final: 0.8680 (pm20) REVERT: A 527 MET cc_start: 0.7482 (mmt) cc_final: 0.6641 (tpp) REVERT: A 531 PHE cc_start: 0.8762 (m-80) cc_final: 0.8222 (m-80) REVERT: A 577 LEU cc_start: 0.9280 (mm) cc_final: 0.8936 (mm) REVERT: A 586 GLN cc_start: 0.9071 (tp40) cc_final: 0.8864 (tp40) REVERT: A 629 MET cc_start: 0.8598 (mpp) cc_final: 0.8376 (mpp) REVERT: A 634 GLU cc_start: 0.7308 (pp20) cc_final: 0.7079 (pm20) REVERT: A 670 MET cc_start: 0.8141 (mmp) cc_final: 0.7939 (mmm) REVERT: A 671 TRP cc_start: 0.8092 (t-100) cc_final: 0.7359 (t-100) REVERT: A 807 MET cc_start: 0.9302 (mmp) cc_final: 0.9008 (mpp) REVERT: A 921 VAL cc_start: 0.9256 (t) cc_final: 0.8742 (m) REVERT: A 939 MET cc_start: 0.7774 (ttt) cc_final: 0.7242 (tmm) REVERT: A 980 TYR cc_start: 0.7853 (t80) cc_final: 0.7483 (t80) REVERT: A 981 ILE cc_start: 0.8984 (pt) cc_final: 0.8631 (pt) REVERT: A 988 MET cc_start: 0.6695 (tpt) cc_final: 0.6458 (mmm) REVERT: B 460 TRP cc_start: 0.6725 (m100) cc_final: 0.5981 (m-90) REVERT: B 545 ARG cc_start: 0.5960 (ttt180) cc_final: 0.5604 (ttt180) REVERT: B 578 TRP cc_start: 0.8935 (t-100) cc_final: 0.8581 (t-100) REVERT: B 596 LEU cc_start: 0.9064 (pt) cc_final: 0.8772 (tt) REVERT: B 708 MET cc_start: 0.9026 (mtt) cc_final: 0.8400 (tpt) REVERT: B 721 MET cc_start: 0.7562 (ttp) cc_final: 0.6824 (ptm) REVERT: B 808 LEU cc_start: 0.9085 (mm) cc_final: 0.8452 (mm) REVERT: B 814 PHE cc_start: 0.7982 (t80) cc_final: 0.7675 (t80) REVERT: C 428 LEU cc_start: 0.9519 (mm) cc_final: 0.9292 (mm) REVERT: C 519 ASP cc_start: 0.8471 (t70) cc_final: 0.7992 (t0) REVERT: C 528 CYS cc_start: 0.8983 (m) cc_final: 0.8759 (m) REVERT: C 570 GLU cc_start: 0.8664 (mm-30) cc_final: 0.8124 (pm20) REVERT: C 586 GLN cc_start: 0.6376 (tm-30) cc_final: 0.5996 (tm-30) REVERT: C 762 LEU cc_start: 0.9126 (mt) cc_final: 0.8914 (tp) REVERT: C 796 PHE cc_start: 0.8660 (m-80) cc_final: 0.8408 (t80) REVERT: C 811 LEU cc_start: 0.9622 (tp) cc_final: 0.9403 (mt) REVERT: C 999 PHE cc_start: 0.8095 (t80) cc_final: 0.7703 (t80) REVERT: C 1032 TYR cc_start: 0.8063 (t80) cc_final: 0.7803 (t80) REVERT: D 407 MET cc_start: 0.6328 (mpp) cc_final: 0.5883 (mpp) REVERT: D 414 MET cc_start: 0.6484 (mpp) cc_final: 0.6155 (mpp) REVERT: D 428 LEU cc_start: 0.8475 (mm) cc_final: 0.8237 (mm) REVERT: D 463 MET cc_start: 0.7944 (mtm) cc_final: 0.7610 (mtm) REVERT: D 607 PHE cc_start: 0.9062 (t80) cc_final: 0.8724 (t80) REVERT: D 670 MET cc_start: 0.8425 (tmm) cc_final: 0.7822 (tmm) REVERT: D 721 MET cc_start: 0.8801 (mmp) cc_final: 0.8545 (mmm) REVERT: D 760 ASP cc_start: 0.7603 (m-30) cc_final: 0.6772 (t0) REVERT: D 763 LYS cc_start: 0.8851 (ttpt) cc_final: 0.8598 (ttpp) outliers start: 0 outliers final: 0 residues processed: 398 average time/residue: 0.1110 time to fit residues: 69.7478 Evaluate side-chains 304 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 304 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 10 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 125 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 148 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 67 optimal weight: 0.0470 chunk 1 optimal weight: 9.9990 chunk 135 optimal weight: 0.7980 overall best weight: 1.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 586 GLN A 619 ASN B 508 GLN ** B 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 714 GLN ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 619 ASN ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.081321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.062657 restraints weight = 72860.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.064258 restraints weight = 52718.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.065456 restraints weight = 41263.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.066323 restraints weight = 34346.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.066671 restraints weight = 29836.139| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 1.4361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16174 Z= 0.138 Angle : 0.666 8.051 21828 Z= 0.343 Chirality : 0.043 0.153 2454 Planarity : 0.004 0.066 2684 Dihedral : 5.749 58.263 2192 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.06 % Allowed : 1.76 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.19), residues: 1992 helix: 1.16 (0.16), residues: 1098 sheet: -1.68 (0.39), residues: 150 loop : -1.50 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 675 TYR 0.016 0.002 TYR C1026 PHE 0.042 0.002 PHE C 531 TRP 0.046 0.002 TRP B 767 HIS 0.003 0.001 HIS B 435 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 (16168) covalent geometry : angle 0.66513 / 0.34 (21816) SS BOND : bond 0.00277 / 0.14 ( 6) SS BOND : angle 1.16544 / 0.65 ( 12) hydrogen bonds : bond 0.03809 / 2.55 ( 818) hydrogen bonds : angle 4.63626 / 3.38 ( 2400) *********************** 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 412 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 411 time to evaluate : 0.615 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: A 424 TYR cc_start: 0.7690 (t80) cc_final: 0.7306 (t80) REVERT: A 511 LYS cc_start: 0.8061 (mmpt) cc_final: 0.7738 (mmmm) REVERT: A 524 GLU cc_start: 0.9406 (pm20) cc_final: 0.8728 (pm20) REVERT: A 527 MET cc_start: 0.7596 (mmt) cc_final: 0.6685 (tpp) REVERT: A 528 CYS cc_start: 0.8633 (p) cc_final: 0.8294 (p) REVERT: A 531 PHE cc_start: 0.8776 (m-10) cc_final: 0.8312 (m-80) REVERT: A 540 LEU cc_start: 0.9463 (mm) cc_final: 0.9187 (tp) REVERT: A 577 LEU cc_start: 0.9377 (mm) cc_final: 0.9066 (mm) REVERT: A 580 SER cc_start: 0.9212 (m) cc_final: 0.8804 (p) REVERT: A 586 GLN cc_start: 0.9002 (OUTLIER) cc_final: 0.8636 (tp40) REVERT: A 605 TRP cc_start: 0.8935 (t-100) cc_final: 0.8148 (t-100) REVERT: A 627 GLU cc_start: 0.8836 (pp20) cc_final: 0.8503 (mt-10) REVERT: A 705 GLU cc_start: 0.8439 (mm-30) cc_final: 0.7389 (mm-30) REVERT: A 803 LEU cc_start: 0.9215 (mt) cc_final: 0.8956 (mt) REVERT: A 807 MET cc_start: 0.9316 (mmp) cc_final: 0.9071 (mpp) REVERT: A 939 MET cc_start: 0.7994 (ttt) cc_final: 0.7791 (mmm) REVERT: A 980 TYR cc_start: 0.7839 (t80) cc_final: 0.7566 (t80) REVERT: A 981 ILE cc_start: 0.9065 (pt) cc_final: 0.8756 (pt) REVERT: A 988 MET cc_start: 0.6891 (tpt) cc_final: 0.6662 (mmt) REVERT: A 1023 MET cc_start: 0.6475 (ttt) cc_final: 0.5695 (ptp) REVERT: B 460 TRP cc_start: 0.6785 (m100) cc_final: 0.6050 (m-90) REVERT: B 503 MET cc_start: 0.8712 (tpt) cc_final: 0.8281 (tpt) REVERT: B 527 MET cc_start: 0.8213 (mtt) cc_final: 0.7412 (mpp) REVERT: B 578 TRP cc_start: 0.9022 (t-100) cc_final: 0.8440 (t-100) REVERT: B 585 MET cc_start: 0.8242 (mtp) cc_final: 0.7878 (ttm) REVERT: B 596 LEU cc_start: 0.9114 (pt) cc_final: 0.8811 (tt) REVERT: B 708 MET cc_start: 0.9051 (mtt) cc_final: 0.8274 (tpt) REVERT: B 721 MET cc_start: 0.7830 (ttp) cc_final: 0.7289 (ptm) REVERT: B 808 LEU cc_start: 0.9089 (mm) cc_final: 0.8766 (mm) REVERT: B 814 PHE cc_start: 0.8094 (t80) cc_final: 0.7834 (t80) REVERT: C 428 LEU cc_start: 0.9501 (mm) cc_final: 0.9076 (mm) REVERT: C 519 ASP cc_start: 0.8521 (t70) cc_final: 0.8262 (t0) REVERT: C 570 GLU cc_start: 0.8603 (mm-30) cc_final: 0.8249 (pm20) REVERT: C 585 MET cc_start: 0.9178 (mmm) cc_final: 0.8634 (mmm) REVERT: C 586 GLN cc_start: 0.6570 (tm-30) cc_final: 0.6240 (tm-30) REVERT: C 629 MET cc_start: 0.9255 (mtm) cc_final: 0.9036 (mtm) REVERT: C 789 LEU cc_start: 0.9223 (tt) cc_final: 0.9005 (pt) REVERT: C 796 PHE cc_start: 0.8673 (m-80) cc_final: 0.8321 (m-80) REVERT: C 965 PHE cc_start: 0.8596 (m-80) cc_final: 0.8267 (m-80) REVERT: C 999 PHE cc_start: 0.8057 (t80) cc_final: 0.7780 (t80) REVERT: C 1005 TRP cc_start: 0.7346 (p90) cc_final: 0.6767 (m100) REVERT: C 1032 TYR cc_start: 0.8066 (t80) cc_final: 0.7819 (t80) REVERT: D 407 MET cc_start: 0.6187 (mpp) cc_final: 0.5768 (mpp) REVERT: D 414 MET cc_start: 0.6505 (mpp) cc_final: 0.6241 (mpp) REVERT: D 428 LEU cc_start: 0.8742 (mm) cc_final: 0.8538 (mm) REVERT: D 463 MET cc_start: 0.7909 (mtm) cc_final: 0.7581 (mtm) REVERT: D 585 MET cc_start: 0.8217 (mmm) cc_final: 0.7766 (mmm) REVERT: D 607 PHE cc_start: 0.9030 (t80) cc_final: 0.8610 (t80) REVERT: D 670 MET cc_start: 0.8391 (tmm) cc_final: 0.7823 (tmm) REVERT: D 721 MET cc_start: 0.8892 (mmp) cc_final: 0.8620 (mmm) REVERT: D 760 ASP cc_start: 0.7736 (m-30) cc_final: 0.7240 (t0) outliers start: 1 outliers final: 0 residues processed: 411 average time/residue: 0.1123 time to fit residues: 71.6958 Evaluate side-chains 309 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 308 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 77 optimal weight: 0.0770 chunk 164 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 123 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 68 optimal weight: 9.9990 chunk 40 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 95 optimal weight: 0.8980 chunk 198 optimal weight: 0.9980 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 412 HIS A 619 ASN A 950 HIS ** B 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 619 ASN ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.082033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.063013 restraints weight = 73132.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.064656 restraints weight = 52690.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.065878 restraints weight = 41017.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.066678 restraints weight = 34120.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.067358 restraints weight = 29828.978| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 1.4729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16174 Z= 0.125 Angle : 0.667 8.262 21828 Z= 0.340 Chirality : 0.043 0.305 2454 Planarity : 0.004 0.065 2684 Dihedral : 5.577 59.781 2192 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 6.90 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.19), residues: 1992 helix: 1.28 (0.16), residues: 1112 sheet: -1.71 (0.40), residues: 138 loop : -1.54 (0.23), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 675 TYR 0.019 0.001 TYR C 768 PHE 0.035 0.001 PHE A 844 TRP 0.031 0.002 TRP B 767 HIS 0.003 0.001 HIS B 435 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 (16168) covalent geometry : angle 0.66662 / 0.34 (21816) SS BOND : bond 0.00239 / 0.12 ( 6) SS BOND : angle 0.98491 / 0.53 ( 12) hydrogen bonds : bond 0.03587 / 2.40 ( 818) hydrogen bonds : angle 4.46590 / 3.27 ( 2400) *********************** 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 395 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 395 time to evaluate : 0.628 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: A 424 TYR cc_start: 0.7860 (t80) cc_final: 0.7111 (t80) REVERT: A 511 LYS cc_start: 0.8139 (mmpt) cc_final: 0.7800 (mmmm) REVERT: A 524 GLU cc_start: 0.9376 (pm20) cc_final: 0.8670 (pm20) REVERT: A 527 MET cc_start: 0.7564 (mmt) cc_final: 0.6624 (tpp) REVERT: A 528 CYS cc_start: 0.8641 (p) cc_final: 0.8344 (p) REVERT: A 531 PHE cc_start: 0.8830 (m-10) cc_final: 0.8385 (m-80) REVERT: A 540 LEU cc_start: 0.9513 (mm) cc_final: 0.9244 (tp) REVERT: A 577 LEU cc_start: 0.9398 (mm) cc_final: 0.8977 (mm) REVERT: A 605 TRP cc_start: 0.9040 (t-100) cc_final: 0.8412 (t-100) REVERT: A 627 GLU cc_start: 0.8851 (pp20) cc_final: 0.8525 (mt-10) REVERT: A 674 MET cc_start: 0.7783 (ttt) cc_final: 0.7582 (ttt) REVERT: A 705 GLU cc_start: 0.8793 (mm-30) cc_final: 0.7806 (mm-30) REVERT: A 763 LYS cc_start: 0.8494 (pttm) cc_final: 0.8230 (pttm) REVERT: A 796 PHE cc_start: 0.8618 (m-80) cc_final: 0.8313 (m-80) REVERT: A 803 LEU cc_start: 0.9213 (mt) cc_final: 0.8816 (mt) REVERT: A 849 LEU cc_start: 0.7903 (mt) cc_final: 0.6990 (mt) REVERT: A 938 PHE cc_start: 0.9152 (m-80) cc_final: 0.8951 (m-80) REVERT: A 939 MET cc_start: 0.8237 (ttt) cc_final: 0.8034 (mmm) REVERT: A 980 TYR cc_start: 0.7935 (t80) cc_final: 0.7574 (t80) REVERT: A 981 ILE cc_start: 0.9075 (pt) cc_final: 0.8705 (pt) REVERT: A 987 GLU cc_start: 0.8587 (mm-30) cc_final: 0.7915 (mt-10) REVERT: A 1023 MET cc_start: 0.6420 (ttt) cc_final: 0.5985 (ptm) REVERT: B 460 TRP cc_start: 0.6868 (m100) cc_final: 0.6027 (m-90) REVERT: B 493 LYS cc_start: 0.3436 (mptt) cc_final: 0.2745 (mppt) REVERT: B 503 MET cc_start: 0.8791 (tpt) cc_final: 0.8351 (tpt) REVERT: B 527 MET cc_start: 0.8271 (mtt) cc_final: 0.7437 (mpp) REVERT: B 578 TRP cc_start: 0.8997 (t-100) cc_final: 0.8219 (t-100) REVERT: B 596 LEU cc_start: 0.9141 (pt) cc_final: 0.8901 (tt) REVERT: B 708 MET cc_start: 0.8923 (mtt) cc_final: 0.8409 (tpt) REVERT: B 721 MET cc_start: 0.7376 (ttp) cc_final: 0.6884 (ptm) REVERT: B 814 PHE cc_start: 0.8066 (t80) cc_final: 0.7685 (t80) REVERT: C 424 TYR cc_start: 0.7965 (t80) cc_final: 0.7355 (t80) REVERT: C 519 ASP cc_start: 0.8586 (t70) cc_final: 0.8355 (t70) REVERT: C 527 MET cc_start: 0.8864 (ptp) cc_final: 0.8523 (ptp) REVERT: C 570 GLU cc_start: 0.8701 (mm-30) cc_final: 0.8270 (pm20) REVERT: C 586 GLN cc_start: 0.6298 (tm-30) cc_final: 0.5623 (tm-30) REVERT: C 629 MET cc_start: 0.9263 (mtm) cc_final: 0.8972 (mtm) REVERT: C 762 LEU cc_start: 0.9252 (tp) cc_final: 0.8272 (tp) REVERT: C 768 TYR cc_start: 0.7992 (p90) cc_final: 0.7754 (p90) REVERT: C 796 PHE cc_start: 0.8646 (m-80) cc_final: 0.8264 (m-80) REVERT: C 939 MET cc_start: 0.8621 (ppp) cc_final: 0.8170 (tmm) REVERT: C 965 PHE cc_start: 0.8525 (m-80) cc_final: 0.8191 (m-80) REVERT: C 1032 TYR cc_start: 0.8040 (t80) cc_final: 0.7495 (t80) REVERT: D 407 MET cc_start: 0.6570 (mpp) cc_final: 0.6070 (mpp) REVERT: D 414 MET cc_start: 0.6592 (mpp) cc_final: 0.6390 (mpp) REVERT: D 428 LEU cc_start: 0.8944 (mm) cc_final: 0.8743 (mm) REVERT: D 463 MET cc_start: 0.7775 (mtm) cc_final: 0.7392 (mtp) REVERT: D 607 PHE cc_start: 0.9068 (t80) cc_final: 0.8606 (t80) REVERT: D 649 THR cc_start: 0.5711 (p) cc_final: 0.5336 (p) REVERT: D 670 MET cc_start: 0.8537 (tmm) cc_final: 0.8211 (tmm) REVERT: D 721 MET cc_start: 0.8878 (mmp) cc_final: 0.8617 (mmm) REVERT: D 760 ASP cc_start: 0.7580 (m-30) cc_final: 0.7068 (t0) outliers start: 0 outliers final: 0 residues processed: 395 average time/residue: 0.1104 time to fit residues: 68.0422 Evaluate side-chains 307 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 307 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 75 optimal weight: 0.0040 chunk 177 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 187 optimal weight: 4.9990 chunk 55 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 40 optimal weight: 0.1980 chunk 96 optimal weight: 9.9990 overall best weight: 0.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 619 ASN A 950 HIS A 985 ASN ** B 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 619 ASN ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.082997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.063923 restraints weight = 72041.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.065533 restraints weight = 52690.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.066737 restraints weight = 41444.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.067513 restraints weight = 34601.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.068120 restraints weight = 30366.538| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 1.5095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 16174 Z= 0.123 Angle : 0.671 8.118 21828 Z= 0.340 Chirality : 0.043 0.332 2454 Planarity : 0.004 0.067 2684 Dihedral : 5.428 58.562 2192 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 6.90 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.19), residues: 1992 helix: 1.29 (0.16), residues: 1126 sheet: -1.72 (0.38), residues: 150 loop : -1.49 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 594 TYR 0.018 0.001 TYR C 768 PHE 0.030 0.001 PHE A 844 TRP 0.025 0.002 TRP B 767 HIS 0.003 0.001 HIS A 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (16168) covalent geometry : angle 0.67059 / 0.34 (21816) SS BOND : bond 0.00259 / 0.13 ( 6) SS BOND : angle 1.01856 / 0.54 ( 12) hydrogen bonds : bond 0.03509 / 2.34 ( 818) hydrogen bonds : angle 4.40731 / 3.22 ( 2400) *********************** 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 392 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 392 time to evaluate : 0.637 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: 0.7753 (t80) cc_final: 0.7330 (t80) REVERT: A 511 LYS cc_start: 0.8147 (mmpt) cc_final: 0.7790 (mmmm) REVERT: A 527 MET cc_start: 0.7565 (mmt) cc_final: 0.6727 (tpp) REVERT: A 528 CYS cc_start: 0.8694 (p) cc_final: 0.8366 (p) REVERT: A 531 PHE cc_start: 0.8814 (m-10) cc_final: 0.8478 (m-80) REVERT: A 540 LEU cc_start: 0.9457 (mm) cc_final: 0.9197 (tp) REVERT: A 577 LEU cc_start: 0.9396 (mm) cc_final: 0.8972 (mm) REVERT: A 605 TRP cc_start: 0.8967 (t-100) cc_final: 0.8440 (t-100) REVERT: A 627 GLU cc_start: 0.8832 (pp20) cc_final: 0.8442 (mt-10) REVERT: A 670 MET cc_start: 0.7972 (mmp) cc_final: 0.7739 (mmm) REVERT: A 674 MET cc_start: 0.7808 (ttt) cc_final: 0.7604 (ttt) REVERT: A 705 GLU cc_start: 0.8634 (mm-30) cc_final: 0.7590 (mm-30) REVERT: A 710 GLU cc_start: 0.8886 (mp0) cc_final: 0.8494 (mp0) REVERT: A 729 SER cc_start: 0.7929 (m) cc_final: 0.7652 (t) REVERT: A 759 LEU cc_start: 0.8320 (pt) cc_final: 0.8024 (pt) REVERT: A 796 PHE cc_start: 0.8592 (m-80) cc_final: 0.8325 (m-80) REVERT: A 807 MET cc_start: 0.8996 (mpp) cc_final: 0.8701 (mpp) REVERT: A 815 CYS cc_start: 0.6687 (m) cc_final: 0.6274 (t) REVERT: A 849 LEU cc_start: 0.7982 (mt) cc_final: 0.7094 (mt) REVERT: A 864 LEU cc_start: 0.5382 (tt) cc_final: 0.5058 (mt) REVERT: A 880 MET cc_start: 0.5864 (mmm) cc_final: 0.5421 (mmm) REVERT: A 938 PHE cc_start: 0.9145 (m-80) cc_final: 0.8937 (m-80) REVERT: A 966 PHE cc_start: 0.8360 (m-10) cc_final: 0.8010 (m-80) REVERT: A 980 TYR cc_start: 0.7779 (t80) cc_final: 0.7531 (t80) REVERT: A 981 ILE cc_start: 0.9094 (pt) cc_final: 0.8675 (pt) REVERT: A 987 GLU cc_start: 0.8628 (mm-30) cc_final: 0.7913 (mt-10) REVERT: A 1023 MET cc_start: 0.6375 (ttt) cc_final: 0.5660 (ptp) REVERT: B 414 MET cc_start: 0.7310 (pmm) cc_final: 0.4841 (ttm) REVERT: B 460 TRP cc_start: 0.6868 (m100) cc_final: 0.6040 (m-90) REVERT: B 493 LYS cc_start: 0.3581 (mptt) cc_final: 0.2920 (mppt) REVERT: B 503 MET cc_start: 0.8672 (tpt) cc_final: 0.8193 (tpt) REVERT: B 527 MET cc_start: 0.8237 (mtt) cc_final: 0.7594 (mpp) REVERT: B 578 TRP cc_start: 0.9021 (t-100) cc_final: 0.8323 (t-100) REVERT: B 596 LEU cc_start: 0.9142 (pt) cc_final: 0.8919 (tt) REVERT: B 708 MET cc_start: 0.8856 (mtt) cc_final: 0.8386 (tpt) REVERT: B 814 PHE cc_start: 0.8040 (t80) cc_final: 0.7743 (t80) REVERT: C 424 TYR cc_start: 0.8048 (t80) cc_final: 0.7793 (t80) REVERT: C 519 ASP cc_start: 0.8551 (t70) cc_final: 0.8334 (t70) REVERT: C 524 GLU cc_start: 0.9459 (pm20) cc_final: 0.9242 (pm20) REVERT: C 527 MET cc_start: 0.8946 (ptp) cc_final: 0.8648 (ptp) REVERT: C 570 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8237 (pm20) REVERT: C 586 GLN cc_start: 0.6303 (tm-30) cc_final: 0.5736 (tm-30) REVERT: C 625 THR cc_start: 0.9618 (p) cc_final: 0.9258 (t) REVERT: C 629 MET cc_start: 0.9251 (mtm) cc_final: 0.8757 (mtm) REVERT: C 641 LYS cc_start: 0.8433 (mppt) cc_final: 0.8090 (mptt) REVERT: C 729 SER cc_start: 0.7994 (m) cc_final: 0.7310 (p) REVERT: C 768 TYR cc_start: 0.7928 (p90) cc_final: 0.7627 (p90) REVERT: C 796 PHE cc_start: 0.8543 (m-80) cc_final: 0.8207 (m-80) REVERT: C 965 PHE cc_start: 0.8577 (m-80) cc_final: 0.8221 (m-80) REVERT: C 975 VAL cc_start: 0.9174 (t) cc_final: 0.8909 (p) REVERT: C 1007 PHE cc_start: 0.8357 (t80) cc_final: 0.8105 (t80) REVERT: C 1032 TYR cc_start: 0.8049 (t80) cc_final: 0.7610 (t80) REVERT: D 407 MET cc_start: 0.6492 (mpp) cc_final: 0.6130 (mpp) REVERT: D 414 MET cc_start: 0.6679 (mpp) cc_final: 0.6471 (mpp) REVERT: D 463 MET cc_start: 0.7907 (mtm) cc_final: 0.7522 (mtp) REVERT: D 629 MET cc_start: 0.6711 (mmm) cc_final: 0.6337 (mmm) REVERT: D 649 THR cc_start: 0.5512 (p) cc_final: 0.5115 (p) REVERT: D 670 MET cc_start: 0.8514 (tmm) cc_final: 0.8069 (tmm) REVERT: D 721 MET cc_start: 0.8839 (mmp) cc_final: 0.8551 (mmm) REVERT: D 760 ASP cc_start: 0.7611 (m-30) cc_final: 0.7149 (t0) outliers start: 0 outliers final: 0 residues processed: 392 average time/residue: 0.1116 time to fit residues: 68.1897 Evaluate side-chains 317 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 317 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 11 optimal weight: 6.9990 chunk 74 optimal weight: 0.4980 chunk 94 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 96 optimal weight: 9.9990 chunk 79 optimal weight: 3.9990 chunk 164 optimal weight: 20.0000 chunk 117 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 161 optimal weight: 0.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 619 ASN A 985 ASN B 508 GLN ** 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 619 ASN ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.081616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.062567 restraints weight = 72258.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.064130 restraints weight = 52478.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.065297 restraints weight = 41390.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.066089 restraints weight = 34605.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.066455 restraints weight = 30348.019| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 1.5722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 16174 Z= 0.142 Angle : 0.691 8.946 21828 Z= 0.354 Chirality : 0.043 0.311 2454 Planarity : 0.004 0.064 2684 Dihedral : 5.456 57.034 2192 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 6.90 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.19), residues: 1992 helix: 1.32 (0.16), residues: 1114 sheet: -1.89 (0.37), residues: 162 loop : -1.47 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 594 TYR 0.024 0.002 TYR C1026 PHE 0.023 0.002 PHE D 517 TRP 0.019 0.002 TRP A 605 HIS 0.003 0.001 HIS A 412 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (16168) covalent geometry : angle 0.69094 / 0.35 (21816) SS BOND : bond 0.00262 / 0.13 ( 6) SS BOND : angle 1.06316 / 0.58 ( 12) hydrogen bonds : bond 0.03625 / 2.44 ( 818) hydrogen bonds : angle 4.50584 / 3.29 ( 2400) ********************** 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 384 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 384 time to evaluate : 0.609 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: 0.7866 (t80) cc_final: 0.7052 (t80) REVERT: A 511 LYS cc_start: 0.8077 (mmpt) cc_final: 0.7719 (mmmm) REVERT: A 524 GLU cc_start: 0.9307 (pm20) cc_final: 0.9052 (pm20) REVERT: A 527 MET cc_start: 0.7642 (mmt) cc_final: 0.6829 (tpp) REVERT: A 528 CYS cc_start: 0.8833 (p) cc_final: 0.8585 (p) REVERT: A 531 PHE cc_start: 0.8846 (m-10) cc_final: 0.8487 (m-80) REVERT: A 577 LEU cc_start: 0.9429 (mm) cc_final: 0.8974 (mm) REVERT: A 580 SER cc_start: 0.9244 (m) cc_final: 0.8901 (p) REVERT: A 586 GLN cc_start: 0.8798 (mm-40) cc_final: 0.8400 (tp40) REVERT: A 605 TRP cc_start: 0.9009 (t-100) cc_final: 0.8567 (t-100) REVERT: A 625 THR cc_start: 0.9509 (p) cc_final: 0.8829 (t) REVERT: A 629 MET cc_start: 0.8583 (mpp) cc_final: 0.8285 (mpp) REVERT: A 670 MET cc_start: 0.7994 (mmp) cc_final: 0.7792 (mmm) REVERT: A 674 MET cc_start: 0.7813 (ttt) cc_final: 0.7592 (ttt) REVERT: A 705 GLU cc_start: 0.8701 (mm-30) cc_final: 0.7936 (mm-30) REVERT: A 710 GLU cc_start: 0.8957 (mp0) cc_final: 0.8697 (mp0) REVERT: A 762 LEU cc_start: 0.8661 (mt) cc_final: 0.8325 (mt) REVERT: A 763 LYS cc_start: 0.8850 (ptpp) cc_final: 0.7856 (pttm) REVERT: A 796 PHE cc_start: 0.8700 (m-80) cc_final: 0.8448 (m-80) REVERT: A 866 GLU cc_start: 0.6399 (pm20) cc_final: 0.5127 (pm20) REVERT: A 966 PHE cc_start: 0.8583 (m-10) cc_final: 0.8307 (m-80) REVERT: A 987 GLU cc_start: 0.8874 (mm-30) cc_final: 0.8249 (mt-10) REVERT: B 414 MET cc_start: 0.7271 (pmm) cc_final: 0.4768 (ttm) REVERT: B 460 TRP cc_start: 0.6978 (m100) cc_final: 0.6190 (m-90) REVERT: B 493 LYS cc_start: 0.4134 (mptt) cc_final: 0.3321 (mppt) REVERT: B 503 MET cc_start: 0.8647 (tpt) cc_final: 0.8118 (tpt) REVERT: B 527 MET cc_start: 0.8282 (mtt) cc_final: 0.7653 (mpp) REVERT: B 596 LEU cc_start: 0.9205 (pt) cc_final: 0.8999 (tt) REVERT: B 708 MET cc_start: 0.9015 (mtt) cc_final: 0.8549 (tpt) REVERT: B 814 PHE cc_start: 0.8151 (t80) cc_final: 0.7863 (t80) REVERT: C 414 MET cc_start: 0.7271 (mpp) cc_final: 0.6437 (mmm) REVERT: C 424 TYR cc_start: 0.8188 (t80) cc_final: 0.7765 (t80) REVERT: C 519 ASP cc_start: 0.8522 (t70) cc_final: 0.8208 (t0) REVERT: C 524 GLU cc_start: 0.9414 (pm20) cc_final: 0.8971 (pm20) REVERT: C 527 MET cc_start: 0.8989 (ptp) cc_final: 0.8635 (ptp) REVERT: C 570 GLU cc_start: 0.8621 (mm-30) cc_final: 0.8370 (pm20) REVERT: C 581 LEU cc_start: 0.9072 (tp) cc_final: 0.8833 (tp) REVERT: C 620 LEU cc_start: 0.9301 (mm) cc_final: 0.9063 (mm) REVERT: C 625 THR cc_start: 0.9653 (p) cc_final: 0.9348 (t) REVERT: C 629 MET cc_start: 0.9250 (mtm) cc_final: 0.8667 (mtm) REVERT: C 641 LYS cc_start: 0.8453 (mppt) cc_final: 0.8101 (mptt) REVERT: C 729 SER cc_start: 0.8291 (m) cc_final: 0.7725 (p) REVERT: C 762 LEU cc_start: 0.9349 (mp) cc_final: 0.8617 (mp) REVERT: C 768 TYR cc_start: 0.7913 (p90) cc_final: 0.7590 (p90) REVERT: C 796 PHE cc_start: 0.8615 (m-80) cc_final: 0.8285 (m-80) REVERT: C 811 LEU cc_start: 0.8969 (mt) cc_final: 0.8730 (pp) REVERT: C 1007 PHE cc_start: 0.8534 (t80) cc_final: 0.8206 (t80) REVERT: C 1032 TYR cc_start: 0.8147 (t80) cc_final: 0.7693 (t80) REVERT: D 407 MET cc_start: 0.6632 (mpp) cc_final: 0.6134 (mpp) REVERT: D 463 MET cc_start: 0.8030 (mtm) cc_final: 0.7619 (mtp) REVERT: D 649 THR cc_start: 0.5815 (p) cc_final: 0.5403 (p) REVERT: D 670 MET cc_start: 0.8619 (tmm) cc_final: 0.8254 (tmm) REVERT: D 721 MET cc_start: 0.8826 (mmp) cc_final: 0.8531 (mmm) REVERT: D 760 ASP cc_start: 0.7643 (m-30) cc_final: 0.7156 (t0) outliers start: 0 outliers final: 0 residues processed: 384 average time/residue: 0.1067 time to fit residues: 63.9606 Evaluate side-chains 320 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 320 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 166 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 168 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 54 optimal weight: 0.5980 chunk 57 optimal weight: 10.0000 chunk 163 optimal weight: 6.9990 chunk 94 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 106 optimal weight: 4.9990 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 575 ASN A 619 ASN ** A 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 508 GLN B 586 GLN ** B 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 619 ASN D 508 GLN D 586 GLN ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.080767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.061608 restraints weight = 73080.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.063197 restraints weight = 53015.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.064355 restraints weight = 41612.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.065207 restraints weight = 34660.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.065785 restraints weight = 30432.411| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 1.6306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 16174 Z= 0.147 Angle : 0.720 11.833 21828 Z= 0.367 Chirality : 0.044 0.339 2454 Planarity : 0.005 0.095 2684 Dihedral : 5.501 55.243 2192 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.06 % Allowed : 0.53 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 6.90 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.19), residues: 1992 helix: 1.25 (0.16), residues: 1116 sheet: -1.75 (0.38), residues: 160 loop : -1.55 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 485 TYR 0.025 0.002 TYR A 711 PHE 0.027 0.002 PHE A 844 TRP 0.017 0.002 TRP C 861 HIS 0.003 0.001 HIS D 435 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 (16168) covalent geometry : angle 0.71917 / 0.37 (21816) SS BOND : bond 0.00269 / 0.14 ( 6) SS BOND : angle 1.24276 / 0.68 ( 12) hydrogen bonds : bond 0.03747 / 2.50 ( 818) hydrogen bonds : angle 4.60062 / 3.35 ( 2400) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2845.08 seconds wall clock time: 50 minutes 14.76 seconds (3014.76 seconds total)