Starting phenix.real_space_refine on Wed Mar 4 20:39:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ryy_24748/03_2026/7ryy_24748.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ryy_24748/03_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_24748/03_2026/7ryy_24748.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ryy_24748/03_2026/7ryy_24748.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ryy_24748/03_2026/7ryy_24748.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ryy_24748/03_2026/7ryy_24748.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: 30 Planarities with less than four sites: {'PCW:plan-1': 1, 'PCW:plan-2': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {'PCW': 1} Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'PCW:plan-1': 1, 'PCW:plan-2': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 3.60, 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: 1.33 Conformation dependent library (CDL) restraints added in 716.0 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: 0.44 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: 2.42 Time building geometry restraints manager: 1.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2516 1.31 - 1.44: 4378 1.44 - 1.57: 9092 1.57 - 1.69: 6 1.69 - 1.82: 176 Bond restraints: 16168 Sorted by residual: bond pdb=" C31 PCW C1101 " pdb=" O2 PCW C1101 " ideal model delta sigma weight residual 1.333 1.428 -0.095 2.00e-02 2.50e+03 2.25e+01 bond pdb=" C31 PCW A1101 " pdb=" O2 PCW A1101 " ideal model delta sigma weight residual 1.333 1.427 -0.094 2.00e-02 2.50e+03 2.22e+01 bond pdb=" C31 PCW C1101 " pdb=" C32 PCW C1101 " ideal model delta sigma weight residual 1.502 1.554 -0.052 2.00e-02 2.50e+03 6.88e+00 bond pdb=" C31 PCW A1101 " pdb=" C32 PCW A1101 " ideal model delta sigma weight residual 1.502 1.554 -0.052 2.00e-02 2.50e+03 6.81e+00 bond pdb=" C36 PCW A1101 " pdb=" C37 PCW A1101 " ideal model delta sigma weight residual 1.524 1.573 -0.049 2.00e-02 2.50e+03 6.06e+00 ... (remaining 16163 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.86: 21390 2.86 - 5.72: 359 5.72 - 8.58: 49 8.58 - 11.43: 14 11.43 - 14.29: 4 Bond angle restraints: 21816 Sorted by residual: angle pdb=" C LYS C 716 " pdb=" N PRO C 717 " pdb=" CA PRO C 717 " ideal model delta sigma weight residual 119.84 112.01 7.83 1.25e+00 6.40e-01 3.93e+01 angle pdb=" C LYS A 716 " pdb=" N PRO A 717 " pdb=" CA PRO A 717 " ideal model delta sigma weight residual 119.84 112.02 7.82 1.25e+00 6.40e-01 3.91e+01 angle pdb=" C SER C 635 " pdb=" N ALA C 636 " pdb=" CA ALA C 636 " ideal model delta sigma weight residual 121.54 129.94 -8.40 1.91e+00 2.74e-01 1.93e+01 angle pdb=" C SER A 635 " pdb=" N ALA A 636 " pdb=" CA ALA A 636 " ideal model delta sigma weight residual 121.54 129.88 -8.34 1.91e+00 2.74e-01 1.91e+01 angle pdb=" CA LEU C 882 " pdb=" CB LEU C 882 " pdb=" CG LEU C 882 " ideal model delta sigma weight residual 116.30 130.59 -14.29 3.50e+00 8.16e-02 1.67e+01 ... (remaining 21811 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.16: 8814 15.16 - 30.32: 538 30.32 - 45.48: 191 45.48 - 60.64: 21 60.64 - 75.81: 10 Dihedral angle restraints: 9574 sinusoidal: 3778 harmonic: 5796 Sorted by residual: dihedral pdb=" CA LYS D 716 " pdb=" C LYS D 716 " pdb=" N PRO D 717 " pdb=" CA PRO D 717 " ideal model delta harmonic sigma weight residual 180.00 140.51 39.49 0 5.00e+00 4.00e-02 6.24e+01 dihedral pdb=" CA LYS B 716 " pdb=" C LYS B 716 " pdb=" N PRO B 717 " pdb=" CA PRO B 717 " ideal model delta harmonic sigma weight residual 180.00 140.52 39.48 0 5.00e+00 4.00e-02 6.24e+01 dihedral pdb=" CB CYS A 718 " pdb=" SG CYS A 718 " pdb=" SG CYS A 773 " pdb=" CB CYS A 773 " ideal model delta sinusoidal sigma weight residual 93.00 161.74 -68.74 1 1.00e+01 1.00e-02 6.12e+01 ... (remaining 9571 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1859 0.054 - 0.107: 476 0.107 - 0.161: 90 0.161 - 0.214: 21 0.214 - 0.268: 8 Chirality restraints: 2454 Sorted by residual: chirality pdb=" CG LEU A 882 " pdb=" CB LEU A 882 " pdb=" CD1 LEU A 882 " pdb=" CD2 LEU A 882 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CG LEU C 882 " pdb=" CB LEU C 882 " pdb=" CD1 LEU C 882 " pdb=" CD2 LEU C 882 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CG LEU C 989 " pdb=" CB LEU C 989 " pdb=" CD1 LEU C 989 " pdb=" CD2 LEU C 989 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 2451 not shown) Planarity restraints: 2684 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 716 " 0.068 5.00e-02 4.00e+02 1.04e-01 1.73e+01 pdb=" N PRO A 717 " -0.180 5.00e-02 4.00e+02 pdb=" CA PRO A 717 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 717 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 716 " -0.068 5.00e-02 4.00e+02 1.04e-01 1.72e+01 pdb=" N PRO C 717 " 0.179 5.00e-02 4.00e+02 pdb=" CA PRO C 717 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO C 717 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 716 " 0.066 5.00e-02 4.00e+02 1.01e-01 1.64e+01 pdb=" N PRO B 717 " -0.175 5.00e-02 4.00e+02 pdb=" CA PRO B 717 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO B 717 " 0.057 5.00e-02 4.00e+02 ... (remaining 2681 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2980 2.76 - 3.30: 15245 3.30 - 3.83: 26184 3.83 - 4.37: 30805 4.37 - 4.90: 50570 Nonbonded interactions: 125784 Sorted by model distance: nonbonded pdb=" O LEU D 639 " pdb=" OH TYR D 647 " model vdw 2.230 3.040 nonbonded pdb=" O LEU B 639 " pdb=" OH TYR B 647 " model vdw 2.230 3.040 nonbonded pdb=" OG SER D 706 " pdb=" OD1 ASN D 726 " model vdw 2.278 3.040 nonbonded pdb=" OG SER B 706 " pdb=" OD1 ASN B 726 " model vdw 2.278 3.040 nonbonded pdb=" O PHE C 943 " pdb=" OG SER C 946 " model vdw 2.321 3.040 ... (remaining 125779 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 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: 3.070 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: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.640 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5203 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 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 : 11.501 75.805 5856 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.59 % Allowed : 5.74 % Favored : 93.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 6.90 % Twisted General : 0.00 % Rama-Z 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 covalent geometry : bond 0.00521 (16168) covalent geometry : angle 1.00570 (21816) SS BOND : bond 0.00440 ( 6) SS BOND : angle 1.77159 ( 12) hydrogen bonds : bond 0.28054 ( 818) hydrogen bonds : angle 8.98911 ( 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 : 0.573 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: 0.1476 time to fit residues: 98.9319 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 : 0.562 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3644 r_free = 0.3644 target = 0.083924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.064909 restraints weight = 69068.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.066457 restraints weight = 50187.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.067443 restraints weight = 39402.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.068373 restraints weight = 33404.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.068896 restraints weight = 28994.707| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5690 moved from start: 0.4821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16174 Z= 0.173 Angle : 0.695 11.144 21828 Z= 0.363 Chirality : 0.044 0.273 2454 Planarity : 0.006 0.083 2684 Dihedral : 7.063 59.546 2208 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.23 % Allowed : 5.33 % Favored : 94.43 % 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: -1.37 (0.17), residues: 1992 helix: -0.03 (0.14), residues: 1068 sheet: -1.63 (0.33), residues: 202 loop : -1.94 (0.21), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 715 TYR 0.023 0.002 TYR D 797 PHE 0.026 0.002 PHE C 901 TRP 0.031 0.002 TRP B 767 HIS 0.004 0.001 HIS C 883 Details of bonding type rmsd covalent geometry : bond 0.00352 (16168) covalent geometry : angle 0.69500 (21816) SS BOND : bond 0.00354 ( 6) SS BOND : angle 1.26904 ( 12) hydrogen bonds : bond 0.04785 ( 818) hydrogen bonds : angle 4.83601 ( 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 348 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 344 time to evaluate : 0.591 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: 0.5563 (tp) cc_final: 0.5180 (tp) REVERT: A 684 ARG cc_start: 0.7977 (mpp-170) cc_final: 0.7367 (tmt-80) REVERT: A 704 LEU cc_start: 0.7307 (pt) cc_final: 0.6158 (pt) REVERT: A 707 THR cc_start: 0.7929 (m) cc_final: 0.7617 (p) REVERT: A 708 MET cc_start: 0.8050 (mtt) cc_final: 0.7428 (ptm) REVERT: A 721 MET cc_start: 0.1651 (tmm) cc_final: 0.0145 (tmm) REVERT: A 860 TYR cc_start: 0.3781 (m-80) cc_final: 0.3085 (m-80) REVERT: A 939 MET cc_start: 0.4773 (ttt) cc_final: 0.4218 (ttt) REVERT: A 941 ILE cc_start: 0.7390 (mt) cc_final: 0.7148 (mt) REVERT: A 988 MET cc_start: 0.1319 (tpt) cc_final: 0.0943 (tpt) REVERT: B 520 PRO cc_start: 0.8213 (Cg_endo) cc_final: 0.7772 (Cg_exo) REVERT: B 527 MET cc_start: 0.7200 (ttm) cc_final: 0.6861 (mmm) REVERT: B 531 PHE cc_start: 0.7947 (t80) cc_final: 0.7660 (t80) REVERT: B 629 MET cc_start: 0.3232 (tpp) cc_final: 0.2995 (tpt) REVERT: B 661 ARG cc_start: 0.8527 (tpm170) cc_final: 0.8299 (tpp80) REVERT: B 708 MET cc_start: 0.8133 (mtt) cc_final: 0.7355 (tpt) REVERT: C 414 MET cc_start: 0.4953 (mpp) cc_final: 0.4672 (mpp) REVERT: C 424 TYR cc_start: 0.6629 (t80) cc_final: 0.6082 (t80) REVERT: C 519 ASP cc_start: 0.7128 (m-30) cc_final: 0.6879 (t0) REVERT: C 527 MET cc_start: 0.8369 (mtm) cc_final: 0.7840 (ptm) REVERT: C 710 GLU cc_start: 0.8919 (mt-10) cc_final: 0.8602 (mm-30) REVERT: C 762 LEU cc_start: 0.9154 (mt) cc_final: 0.8508 (mm) REVERT: C 796 PHE cc_start: 0.7173 (m-80) cc_final: 0.6754 (m-80) REVERT: C 939 MET cc_start: 0.7865 (ptt) cc_final: 0.7569 (ptm) REVERT: C 1003 TYR cc_start: 0.6075 (m-80) cc_final: 0.5216 (m-80) REVERT: C 1032 TYR cc_start: 0.8306 (t80) cc_final: 0.8024 (t80) REVERT: D 424 TYR cc_start: 0.7261 (t80) cc_final: 0.6481 (t80) REVERT: D 527 MET cc_start: 0.6010 (ttm) cc_final: 0.5553 (ttm) REVERT: D 629 MET cc_start: 0.6952 (mmm) cc_final: 0.5340 (tpp) REVERT: D 721 MET cc_start: 0.8281 (mtm) cc_final: 0.8000 (ptm) REVERT: D 760 ASP cc_start: 0.7117 (m-30) cc_final: 0.6718 (t0) REVERT: D 763 LYS cc_start: 0.8968 (ttpt) cc_final: 0.8656 (tttt) REVERT: D 790 SER cc_start: 0.7629 (m) cc_final: 0.7407 (p) outliers start: 4 outliers final: 0 residues processed: 348 average time/residue: 0.1366 time to fit residues: 68.9111 Evaluate side-chains 238 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 0.572 ------------------------------------------------------------------------------- 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: 1.9990 chunk 147 optimal weight: 6.9990 chunk 83 optimal weight: 9.9990 chunk 4 optimal weight: 0.0050 chunk 106 optimal weight: 8.9990 chunk 101 optimal weight: 0.3980 chunk 12 optimal weight: 0.3980 chunk 34 optimal weight: 4.9990 chunk 186 optimal weight: 5.9990 chunk 122 optimal weight: 0.0870 chunk 159 optimal weight: 3.9990 overall best weight: 0.5774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 985 ASN B 569 ASN B 791 ASN C 619 ASN ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 ASN D 411 ASN D 619 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.084216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.065284 restraints weight = 70372.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.066892 restraints weight = 50245.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.068066 restraints weight = 38970.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.068862 restraints weight = 32337.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.069537 restraints weight = 28176.390| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5794 moved from start: 0.5704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.106 16174 Z= 0.126 Angle : 0.619 11.691 21828 Z= 0.320 Chirality : 0.042 0.264 2454 Planarity : 0.005 0.068 2684 Dihedral : 6.518 57.072 2208 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.18 % Allowed : 2.99 % Favored : 96.83 % 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: -0.39 (0.18), residues: 1992 helix: 0.84 (0.15), residues: 1106 sheet: -1.65 (0.36), residues: 176 loop : -1.60 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 715 TYR 0.024 0.002 TYR A 980 PHE 0.024 0.001 PHE A 965 TRP 0.040 0.002 TRP A 861 HIS 0.003 0.001 HIS B 412 Details of bonding type rmsd covalent geometry : bond 0.00266 (16168) covalent geometry : angle 0.61894 (21816) SS BOND : bond 0.00369 ( 6) SS BOND : angle 1.07916 ( 12) hydrogen bonds : bond 0.04021 ( 818) hydrogen bonds : angle 4.41609 ( 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 330 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 327 time to evaluate : 0.550 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: 0.6285 (mmt) cc_final: 0.5896 (tpp) REVERT: A 585 MET cc_start: 0.8404 (tpt) cc_final: 0.8200 (tpt) REVERT: A 591 ILE cc_start: 0.5933 (tp) cc_final: 0.5491 (tp) REVERT: A 684 ARG cc_start: 0.7997 (mpp-170) cc_final: 0.7289 (tmt-80) REVERT: A 704 LEU cc_start: 0.7097 (pt) cc_final: 0.5247 (pt) REVERT: A 707 THR cc_start: 0.7986 (m) cc_final: 0.7709 (p) REVERT: A 708 MET cc_start: 0.8287 (mtt) cc_final: 0.7802 (ptm) REVERT: A 712 ILE cc_start: 0.8753 (mm) cc_final: 0.8372 (mm) REVERT: A 939 MET cc_start: 0.4951 (ttt) cc_final: 0.4650 (ttt) REVERT: A 988 MET cc_start: 0.1782 (tpt) cc_final: 0.1405 (tpt) REVERT: B 460 TRP cc_start: 0.6806 (m100) cc_final: 0.6396 (m-90) REVERT: B 519 ASP cc_start: 0.8683 (t0) cc_final: 0.8345 (t0) REVERT: B 520 PRO cc_start: 0.7929 (Cg_endo) cc_final: 0.7215 (Cg_exo) REVERT: B 531 PHE cc_start: 0.7934 (t80) cc_final: 0.7730 (t80) REVERT: B 629 MET cc_start: 0.3374 (tpp) cc_final: 0.2990 (tpt) REVERT: B 708 MET cc_start: 0.8131 (mtt) cc_final: 0.7375 (tpt) REVERT: B 734 ILE cc_start: 0.7315 (mm) cc_final: 0.7092 (tp) REVERT: C 424 TYR cc_start: 0.6450 (t80) cc_final: 0.6114 (t80) REVERT: C 463 MET cc_start: 0.8464 (mpp) cc_final: 0.8070 (mpp) REVERT: C 610 LEU cc_start: 0.8012 (tp) cc_final: 0.7778 (tp) REVERT: C 633 ILE cc_start: 0.5704 (pt) cc_final: 0.5359 (pt) REVERT: C 637 GLU cc_start: 0.8087 (mp0) cc_final: 0.7849 (mp0) REVERT: C 762 LEU cc_start: 0.9166 (mt) cc_final: 0.8673 (mm) REVERT: C 811 LEU cc_start: 0.9506 (tp) cc_final: 0.9219 (mt) REVERT: C 840 LEU cc_start: 0.8840 (mt) cc_final: 0.8434 (mt) REVERT: C 1003 TYR cc_start: 0.6387 (m-80) cc_final: 0.5308 (m-80) REVERT: C 1032 TYR cc_start: 0.8251 (t80) cc_final: 0.7989 (t80) REVERT: D 405 TYR cc_start: 0.7965 (m-80) cc_final: 0.7620 (m-80) REVERT: D 407 MET cc_start: 0.4533 (mpp) cc_final: 0.4021 (mpp) REVERT: D 428 LEU cc_start: 0.8302 (mt) cc_final: 0.8101 (mm) REVERT: D 458 LYS cc_start: 0.8761 (mmtp) cc_final: 0.8364 (mmmt) REVERT: D 527 MET cc_start: 0.6058 (ttm) cc_final: 0.5640 (ttm) REVERT: D 629 MET cc_start: 0.6715 (mmm) cc_final: 0.5385 (tpp) REVERT: D 721 MET cc_start: 0.8620 (mtm) cc_final: 0.8388 (mtp) REVERT: D 760 ASP cc_start: 0.7157 (m-30) cc_final: 0.6342 (t0) outliers start: 3 outliers final: 0 residues processed: 329 average time/residue: 0.1338 time to fit residues: 64.8825 Evaluate side-chains 237 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.566 ------------------------------------------------------------------------------- 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: 4.9990 chunk 1 optimal weight: 7.9990 chunk 134 optimal weight: 8.9990 chunk 91 optimal weight: 0.5980 chunk 100 optimal weight: 10.0000 chunk 122 optimal weight: 0.9980 chunk 164 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 113 optimal weight: 0.5980 chunk 160 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 985 ASN B 508 GLN ** B 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 764 ASN C 575 ASN ** C 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 883 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 586 GLN D 587 GLN D 619 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.083805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.064635 restraints weight = 70984.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.066258 restraints weight = 51059.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.067501 restraints weight = 39792.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.068396 restraints weight = 32976.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.069088 restraints weight = 28513.187| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6390 moved from start: 0.8014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16174 Z= 0.180 Angle : 0.691 12.820 21828 Z= 0.360 Chirality : 0.044 0.292 2454 Planarity : 0.006 0.070 2684 Dihedral : 6.409 59.691 2208 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.06 % Allowed : 4.57 % Favored : 95.37 % 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: -0.24 (0.18), residues: 1992 helix: 0.98 (0.15), residues: 1108 sheet: -1.51 (0.35), residues: 190 loop : -1.59 (0.22), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 599 TYR 0.020 0.002 TYR B 523 PHE 0.026 0.002 PHE D 579 TRP 0.035 0.003 TRP C 526 HIS 0.005 0.001 HIS A 950 Details of bonding type rmsd covalent geometry : bond 0.00364 (16168) covalent geometry : angle 0.69081 (21816) SS BOND : bond 0.00272 ( 6) SS BOND : angle 1.18876 ( 12) hydrogen bonds : bond 0.03931 ( 818) hydrogen bonds : angle 4.52568 ( 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 359 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 358 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 527 MET cc_start: 0.6430 (mmt) cc_final: 0.5738 (tpp) REVERT: A 704 LEU cc_start: 0.7809 (pt) cc_final: 0.6348 (pt) REVERT: A 708 MET cc_start: 0.8617 (mtt) cc_final: 0.8372 (ptm) REVERT: A 939 MET cc_start: 0.5631 (ttt) cc_final: 0.4376 (tmm) REVERT: A 988 MET cc_start: 0.3235 (tpt) cc_final: 0.2765 (tpt) REVERT: B 460 TRP cc_start: 0.6871 (m100) cc_final: 0.6358 (m-90) REVERT: B 519 ASP cc_start: 0.8921 (t0) cc_final: 0.8705 (t0) REVERT: B 520 PRO cc_start: 0.8230 (Cg_endo) cc_final: 0.7602 (Cg_exo) REVERT: B 527 MET cc_start: 0.6685 (mtt) cc_final: 0.5940 (mmm) REVERT: B 586 GLN cc_start: 0.8369 (mm110) cc_final: 0.7779 (mm-40) REVERT: B 708 MET cc_start: 0.8220 (mtt) cc_final: 0.7462 (tpt) REVERT: B 797 TYR cc_start: 0.7325 (m-80) cc_final: 0.6915 (m-10) REVERT: C 424 TYR cc_start: 0.6880 (t80) cc_final: 0.6590 (t80) REVERT: C 463 MET cc_start: 0.8645 (mpp) cc_final: 0.8132 (mpp) REVERT: C 480 THR cc_start: 0.8925 (m) cc_final: 0.8269 (p) REVERT: C 585 MET cc_start: 0.8188 (mpp) cc_final: 0.7913 (mpp) REVERT: C 637 GLU cc_start: 0.8320 (mp0) cc_final: 0.8074 (mp0) REVERT: C 710 GLU cc_start: 0.8901 (tm-30) cc_final: 0.8691 (tm-30) REVERT: C 762 LEU cc_start: 0.9235 (mt) cc_final: 0.8789 (mm) REVERT: C 811 LEU cc_start: 0.9616 (tp) cc_final: 0.9295 (mt) REVERT: C 840 LEU cc_start: 0.8873 (mt) cc_final: 0.8572 (mt) REVERT: C 1003 TYR cc_start: 0.6266 (m-80) cc_final: 0.4790 (m-80) REVERT: C 1032 TYR cc_start: 0.8198 (t80) cc_final: 0.7869 (t80) REVERT: D 428 LEU cc_start: 0.8436 (mt) cc_final: 0.8115 (mm) REVERT: D 432 ILE cc_start: 0.5351 (tp) cc_final: 0.5116 (tp) REVERT: D 463 MET cc_start: 0.7766 (mtm) cc_final: 0.7444 (mtp) REVERT: D 527 MET cc_start: 0.6625 (ttm) cc_final: 0.6110 (ttm) REVERT: D 585 MET cc_start: 0.7341 (mmt) cc_final: 0.7129 (mmt) REVERT: D 670 MET cc_start: 0.8152 (tmm) cc_final: 0.7525 (tmm) REVERT: D 721 MET cc_start: 0.8737 (mtm) cc_final: 0.8358 (mtp) REVERT: D 760 ASP cc_start: 0.7260 (m-30) cc_final: 0.6960 (t0) outliers start: 1 outliers final: 0 residues processed: 358 average time/residue: 0.1259 time to fit residues: 66.8143 Evaluate side-chains 271 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 0.564 ------------------------------------------------------------------------------- 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: 1.9990 chunk 54 optimal weight: 0.9990 chunk 2 optimal weight: 0.0870 chunk 61 optimal weight: 0.5980 chunk 60 optimal weight: 10.0000 chunk 115 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 88 optimal weight: 10.0000 chunk 167 optimal weight: 0.8980 chunk 104 optimal weight: 4.9990 chunk 130 optimal weight: 0.0980 overall best weight: 0.5360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 874 GLN 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 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 883 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.085082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.066342 restraints weight = 68453.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.067925 restraints weight = 50453.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.069092 restraints weight = 39880.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.069974 restraints weight = 33319.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.070640 restraints weight = 28908.023| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6379 moved from start: 0.8573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 16174 Z= 0.115 Angle : 0.607 7.557 21828 Z= 0.311 Chirality : 0.041 0.154 2454 Planarity : 0.004 0.069 2684 Dihedral : 6.098 57.908 2208 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.12 % Allowed : 2.23 % Favored : 97.66 % 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: 0.17 (0.19), residues: 1992 helix: 1.29 (0.15), residues: 1122 sheet: -1.44 (0.40), residues: 152 loop : -1.42 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 715 TYR 0.024 0.001 TYR A 860 PHE 0.022 0.001 PHE A 965 TRP 0.039 0.002 TRP B 767 HIS 0.003 0.001 HIS C 435 Details of bonding type rmsd covalent geometry : bond 0.00248 (16168) covalent geometry : angle 0.60677 (21816) SS BOND : bond 0.00273 ( 6) SS BOND : angle 1.00543 ( 12) hydrogen bonds : bond 0.03513 ( 818) hydrogen bonds : angle 4.16505 ( 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 367 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 365 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 424 TYR cc_start: 0.6540 (t80) cc_final: 0.6071 (t80) REVERT: A 510 SER cc_start: 0.4984 (m) cc_final: 0.4630 (t) REVERT: A 527 MET cc_start: 0.6555 (mmt) cc_final: 0.6029 (tpp) REVERT: A 619 ASN cc_start: 0.7733 (t160) cc_final: 0.6918 (t0) REVERT: A 624 LEU cc_start: 0.8761 (mt) cc_final: 0.8508 (mt) REVERT: A 704 LEU cc_start: 0.7370 (pt) cc_final: 0.4975 (pt) REVERT: A 939 MET cc_start: 0.5574 (ttt) cc_final: 0.4179 (tmm) REVERT: A 1023 MET cc_start: 0.2682 (ptm) cc_final: 0.2413 (ptm) REVERT: B 460 TRP cc_start: 0.6455 (m100) cc_final: 0.5876 (m-90) REVERT: B 519 ASP cc_start: 0.8885 (t0) cc_final: 0.8621 (t0) REVERT: B 520 PRO cc_start: 0.8313 (Cg_endo) cc_final: 0.7776 (Cg_exo) REVERT: B 523 TYR cc_start: 0.4072 (t80) cc_final: 0.2770 (t80) REVERT: B 527 MET cc_start: 0.7199 (mtt) cc_final: 0.5897 (mpp) REVERT: B 533 TYR cc_start: 0.8086 (t80) cc_final: 0.7349 (t80) REVERT: B 584 PHE cc_start: 0.9104 (t80) cc_final: 0.8891 (t80) REVERT: B 587 GLN cc_start: 0.7673 (mm110) cc_final: 0.7282 (mm110) REVERT: B 708 MET cc_start: 0.8257 (mtt) cc_final: 0.7362 (tpt) REVERT: C 463 MET cc_start: 0.8465 (mpp) cc_final: 0.8213 (mpp) REVERT: C 585 MET cc_start: 0.8153 (mpp) cc_final: 0.7584 (mpp) REVERT: C 586 GLN cc_start: 0.5485 (tm-30) cc_final: 0.4827 (tm-30) REVERT: C 637 GLU cc_start: 0.8090 (mp0) cc_final: 0.7752 (mp0) REVERT: C 762 LEU cc_start: 0.9275 (mt) cc_final: 0.8823 (mm) REVERT: C 811 LEU cc_start: 0.9589 (tp) cc_final: 0.9305 (mt) REVERT: C 840 LEU cc_start: 0.8833 (mt) cc_final: 0.8517 (mt) REVERT: C 882 LEU cc_start: 0.7488 (pp) cc_final: 0.7255 (pp) REVERT: C 999 PHE cc_start: 0.8126 (t80) cc_final: 0.7798 (t80) REVERT: C 1003 TYR cc_start: 0.6256 (m-80) cc_final: 0.4711 (m-80) REVERT: C 1026 TYR cc_start: 0.6268 (m-80) cc_final: 0.5733 (m-80) REVERT: C 1032 TYR cc_start: 0.8003 (t80) cc_final: 0.7676 (t80) REVERT: D 414 MET cc_start: 0.6263 (mpp) cc_final: 0.5995 (mpp) REVERT: D 428 LEU cc_start: 0.8820 (mt) cc_final: 0.8465 (mt) REVERT: D 432 ILE cc_start: 0.5267 (tp) cc_final: 0.4992 (tp) REVERT: D 463 MET cc_start: 0.7510 (mtm) cc_final: 0.7213 (mmm) REVERT: D 527 MET cc_start: 0.6527 (ttm) cc_final: 0.5944 (ttm) REVERT: D 670 MET cc_start: 0.8053 (tmm) cc_final: 0.7550 (tmm) REVERT: D 720 THR cc_start: 0.7757 (p) cc_final: 0.7303 (p) REVERT: D 760 ASP cc_start: 0.7161 (m-30) cc_final: 0.6820 (t0) outliers start: 2 outliers final: 0 residues processed: 366 average time/residue: 0.1188 time to fit residues: 65.6497 Evaluate side-chains 276 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 276 time to evaluate : 0.514 ------------------------------------------------------------------------------- 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: 2.9990 chunk 76 optimal weight: 1.9990 chunk 123 optimal weight: 4.9990 chunk 193 optimal weight: 0.9980 chunk 129 optimal weight: 5.9990 chunk 186 optimal weight: 0.0030 chunk 162 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 chunk 95 optimal weight: 0.8980 chunk 160 optimal weight: 10.0000 chunk 179 optimal weight: 0.9990 overall best weight: 0.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 587 GLN A 619 ASN A 709 ASN A 874 GLN A 985 ASN ** B 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 619 ASN ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 619 ASN D 709 ASN D 791 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.084674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.065394 restraints weight = 69798.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.066968 restraints weight = 51460.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.068187 restraints weight = 40764.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.068928 restraints weight = 33951.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.069703 restraints weight = 29980.292| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6646 moved from start: 0.9715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 16174 Z= 0.132 Angle : 0.629 7.543 21828 Z= 0.322 Chirality : 0.041 0.168 2454 Planarity : 0.005 0.067 2684 Dihedral : 6.039 59.866 2208 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.06 % Allowed : 2.99 % Favored : 96.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 6.90 % Twisted General : 0.00 % Rama-Z 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: 0.24 (0.19), residues: 1992 helix: 1.37 (0.15), residues: 1124 sheet: -1.37 (0.36), residues: 184 loop : -1.43 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 660 TYR 0.026 0.001 TYR C 732 PHE 0.030 0.002 PHE A 607 TRP 0.039 0.002 TRP C 526 HIS 0.002 0.001 HIS A 435 Details of bonding type rmsd covalent geometry : bond 0.00291 (16168) covalent geometry : angle 0.62867 (21816) SS BOND : bond 0.00266 ( 6) SS BOND : angle 0.96636 ( 12) hydrogen bonds : bond 0.03466 ( 818) hydrogen bonds : angle 4.23918 ( 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 356 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 355 time to evaluate : 0.496 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 527 MET cc_start: 0.6755 (mmt) cc_final: 0.6171 (tpp) REVERT: A 584 PHE cc_start: 0.8708 (t80) cc_final: 0.7729 (t80) REVERT: A 587 GLN cc_start: 0.8342 (tp40) cc_final: 0.7577 (tp-100) REVERT: A 611 ILE cc_start: 0.8986 (mm) cc_final: 0.8713 (mm) REVERT: A 627 GLU cc_start: 0.8558 (pp20) cc_final: 0.7873 (mm-30) REVERT: A 705 GLU cc_start: 0.8297 (mm-30) cc_final: 0.7117 (mp0) REVERT: A 868 ILE cc_start: 0.8605 (pt) cc_final: 0.8401 (pt) REVERT: A 938 PHE cc_start: 0.8561 (m-80) cc_final: 0.7986 (m-80) REVERT: A 939 MET cc_start: 0.6115 (ttt) cc_final: 0.5028 (tmm) REVERT: A 988 MET cc_start: 0.4594 (tpt) cc_final: 0.4012 (mmm) REVERT: B 519 ASP cc_start: 0.8935 (t0) cc_final: 0.8699 (t0) REVERT: B 520 PRO cc_start: 0.8262 (Cg_endo) cc_final: 0.7757 (Cg_exo) REVERT: B 527 MET cc_start: 0.7204 (mtt) cc_final: 0.6925 (mmm) REVERT: B 708 MET cc_start: 0.8442 (mtt) cc_final: 0.7659 (tpt) REVERT: B 721 MET cc_start: 0.5798 (tmm) cc_final: 0.4680 (tmm) REVERT: C 424 TYR cc_start: 0.7181 (t80) cc_final: 0.6830 (t80) REVERT: C 525 ILE cc_start: 0.9095 (mt) cc_final: 0.8853 (mt) REVERT: C 624 LEU cc_start: 0.7849 (mt) cc_final: 0.7604 (mp) REVERT: C 637 GLU cc_start: 0.8146 (mp0) cc_final: 0.7802 (mp0) REVERT: C 656 LYS cc_start: 0.7997 (tmtt) cc_final: 0.7319 (tptp) REVERT: C 730 LYS cc_start: 0.5941 (tttt) cc_final: 0.5726 (ttmt) REVERT: C 762 LEU cc_start: 0.9262 (mt) cc_final: 0.8901 (mm) REVERT: C 811 LEU cc_start: 0.9634 (tp) cc_final: 0.9300 (mt) REVERT: C 817 LYS cc_start: 0.8319 (tppp) cc_final: 0.7700 (ptmt) REVERT: C 840 LEU cc_start: 0.8789 (mt) cc_final: 0.8533 (mt) REVERT: C 880 MET cc_start: 0.4125 (ttt) cc_final: 0.3666 (mtp) REVERT: C 934 VAL cc_start: 0.8557 (t) cc_final: 0.7794 (t) REVERT: C 939 MET cc_start: 0.8361 (ptt) cc_final: 0.8079 (tmm) REVERT: C 999 PHE cc_start: 0.8049 (t80) cc_final: 0.7791 (t80) REVERT: C 1003 TYR cc_start: 0.6366 (m-80) cc_final: 0.5003 (m-80) REVERT: C 1032 TYR cc_start: 0.8118 (t80) cc_final: 0.7842 (t80) REVERT: D 407 MET cc_start: 0.5119 (mpp) cc_final: 0.4826 (mpp) REVERT: D 414 MET cc_start: 0.6207 (mpp) cc_final: 0.5907 (mpp) REVERT: D 428 LEU cc_start: 0.8884 (mt) cc_final: 0.8561 (mt) REVERT: D 463 MET cc_start: 0.7553 (mtm) cc_final: 0.7206 (mmm) REVERT: D 503 MET cc_start: 0.8491 (ppp) cc_final: 0.7943 (ppp) REVERT: D 629 MET cc_start: 0.7026 (mmm) cc_final: 0.6788 (mmm) REVERT: D 667 PHE cc_start: 0.8093 (m-80) cc_final: 0.7689 (m-80) REVERT: D 670 MET cc_start: 0.8260 (tmm) cc_final: 0.7763 (tmm) REVERT: D 720 THR cc_start: 0.7969 (p) cc_final: 0.7577 (t) REVERT: D 760 ASP cc_start: 0.7159 (m-30) cc_final: 0.6794 (t0) outliers start: 1 outliers final: 0 residues processed: 355 average time/residue: 0.1086 time to fit residues: 59.3956 Evaluate side-chains 286 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 286 time to evaluate : 0.415 ------------------------------------------------------------------------------- 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: 1.9990 chunk 75 optimal weight: 6.9990 chunk 51 optimal weight: 7.9990 chunk 125 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 148 optimal weight: 0.7980 chunk 134 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 1 optimal weight: 9.9990 chunk 135 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 619 ASN ** A 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 874 GLN A 950 HIS A 985 ASN B 508 GLN B 586 GLN B 709 ASN ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 587 GLN ** C 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 791 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.084340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.065393 restraints weight = 70512.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.066931 restraints weight = 52135.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.068058 restraints weight = 41418.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.068835 restraints weight = 34772.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.069468 restraints weight = 30523.653| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6873 moved from start: 1.1027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 16174 Z= 0.141 Angle : 0.665 7.582 21828 Z= 0.342 Chirality : 0.042 0.155 2454 Planarity : 0.005 0.099 2684 Dihedral : 6.086 56.338 2208 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.71 % Favored : 96.23 % Rotamer: Outliers : 0.12 % Allowed : 1.58 % Favored : 98.30 % 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: 0.17 (0.19), residues: 1992 helix: 1.41 (0.15), residues: 1112 sheet: -1.53 (0.36), residues: 174 loop : -1.57 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 661 TYR 0.014 0.002 TYR C 533 PHE 0.028 0.002 PHE C 938 TRP 0.036 0.002 TRP A 605 HIS 0.006 0.001 HIS A 950 Details of bonding type rmsd covalent geometry : bond 0.00304 (16168) covalent geometry : angle 0.66486 (21816) SS BOND : bond 0.00285 ( 6) SS BOND : angle 0.97305 ( 12) hydrogen bonds : bond 0.03706 ( 818) hydrogen bonds : angle 4.40795 ( 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 373 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 371 time to evaluate : 0.580 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 401 LEU cc_start: 0.7491 (mm) cc_final: 0.6965 (mm) REVERT: A 527 MET cc_start: 0.6812 (mmt) cc_final: 0.5695 (tpp) REVERT: A 528 CYS cc_start: 0.7811 (m) cc_final: 0.7489 (m) REVERT: A 534 ILE cc_start: 0.8835 (mm) cc_final: 0.8603 (mm) REVERT: A 624 LEU cc_start: 0.8857 (mt) cc_final: 0.8220 (mt) REVERT: A 627 GLU cc_start: 0.8790 (pp20) cc_final: 0.8502 (pp20) REVERT: A 705 GLU cc_start: 0.8559 (mm-30) cc_final: 0.7520 (mm-30) REVERT: A 721 MET cc_start: 0.6393 (tmm) cc_final: 0.5967 (tpp) REVERT: A 938 PHE cc_start: 0.8781 (m-80) cc_final: 0.8402 (m-80) REVERT: A 939 MET cc_start: 0.6712 (ttt) cc_final: 0.6193 (tmm) REVERT: A 988 MET cc_start: 0.5252 (tpt) cc_final: 0.5037 (tpt) REVERT: A 1023 MET cc_start: 0.3893 (ptm) cc_final: 0.3493 (ptm) REVERT: B 478 PRO cc_start: 0.6210 (Cg_exo) cc_final: 0.5965 (Cg_endo) REVERT: B 527 MET cc_start: 0.7579 (mtt) cc_final: 0.7077 (mmm) REVERT: B 578 TRP cc_start: 0.8643 (t-100) cc_final: 0.8009 (t-100) REVERT: B 708 MET cc_start: 0.8530 (mtt) cc_final: 0.7834 (tpp) REVERT: B 721 MET cc_start: 0.6341 (tmm) cc_final: 0.5938 (tmm) REVERT: B 814 PHE cc_start: 0.7341 (t80) cc_final: 0.7068 (t80) REVERT: C 424 TYR cc_start: 0.7349 (t80) cc_final: 0.6980 (t80) REVERT: C 431 GLU cc_start: 0.8763 (mm-30) cc_final: 0.8396 (mm-30) REVERT: C 500 ILE cc_start: 0.7459 (mt) cc_final: 0.7164 (mt) REVERT: C 524 GLU cc_start: 0.8944 (mp0) cc_final: 0.8714 (mp0) REVERT: C 570 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7726 (pm20) REVERT: C 762 LEU cc_start: 0.9282 (mt) cc_final: 0.8625 (mp) REVERT: C 811 LEU cc_start: 0.9648 (tp) cc_final: 0.9409 (mt) REVERT: C 861 TRP cc_start: 0.7595 (m100) cc_final: 0.7023 (m100) REVERT: C 999 PHE cc_start: 0.7959 (t80) cc_final: 0.7692 (t80) REVERT: C 1032 TYR cc_start: 0.8016 (t80) cc_final: 0.7622 (t80) REVERT: D 414 MET cc_start: 0.6266 (mpp) cc_final: 0.5991 (mpp) REVERT: D 428 LEU cc_start: 0.8797 (mt) cc_final: 0.8481 (mt) REVERT: D 463 MET cc_start: 0.7613 (mtm) cc_final: 0.7155 (mmm) REVERT: D 493 LYS cc_start: 0.7661 (mptt) cc_final: 0.7367 (mppt) REVERT: D 612 ILE cc_start: 0.8922 (mm) cc_final: 0.8701 (mm) REVERT: D 626 VAL cc_start: 0.8274 (t) cc_final: 0.7931 (t) REVERT: D 649 THR cc_start: 0.4578 (p) cc_final: 0.4369 (p) REVERT: D 667 PHE cc_start: 0.8084 (m-80) cc_final: 0.7541 (m-80) REVERT: D 670 MET cc_start: 0.8330 (tmm) cc_final: 0.7857 (tmm) outliers start: 2 outliers final: 0 residues processed: 372 average time/residue: 0.1135 time to fit residues: 64.8565 Evaluate side-chains 291 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 291 time to evaluate : 0.553 ------------------------------------------------------------------------------- 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: 3.9990 chunk 164 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 123 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 95 optimal weight: 0.1980 chunk 198 optimal weight: 0.7980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 586 GLN ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 709 ASN ** A 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 642 GLN ** D 586 GLN ** 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 = 0.3644 r_free = 0.3644 target = 0.082998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.064228 restraints weight = 72074.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.065841 restraints weight = 52648.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.067027 restraints weight = 41216.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.067915 restraints weight = 34275.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.068454 restraints weight = 29750.062| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 1.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 16174 Z= 0.166 Angle : 0.706 9.992 21828 Z= 0.364 Chirality : 0.043 0.172 2454 Planarity : 0.005 0.064 2684 Dihedral : 6.059 46.465 2208 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.06 % Allowed : 1.93 % Favored : 98.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 5.17 % 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: -0.00 (0.19), residues: 1992 helix: 1.12 (0.15), residues: 1136 sheet: -1.52 (0.34), residues: 190 loop : -1.44 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 599 TYR 0.020 0.002 TYR C 647 PHE 0.025 0.002 PHE C 844 TRP 0.044 0.002 TRP C 526 HIS 0.004 0.001 HIS C 435 Details of bonding type rmsd covalent geometry : bond 0.00367 (16168) covalent geometry : angle 0.70526 (21816) SS BOND : bond 0.00224 ( 6) SS BOND : angle 1.09204 ( 12) hydrogen bonds : bond 0.03688 ( 818) hydrogen bonds : angle 4.55495 ( 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 388 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 387 time to evaluate : 0.605 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 420 ARG cc_start: 0.8439 (ptp-170) cc_final: 0.8217 (ptp90) REVERT: A 424 TYR cc_start: 0.7164 (t80) cc_final: 0.6689 (t80) REVERT: A 524 GLU cc_start: 0.9146 (pm20) cc_final: 0.8570 (pm20) REVERT: A 527 MET cc_start: 0.7390 (mmt) cc_final: 0.6345 (tpp) REVERT: A 531 PHE cc_start: 0.8836 (m-80) cc_final: 0.8415 (m-80) REVERT: A 537 SER cc_start: 0.9288 (m) cc_final: 0.8994 (p) REVERT: A 577 LEU cc_start: 0.9107 (mm) cc_final: 0.8847 (mm) REVERT: A 671 TRP cc_start: 0.8026 (t-100) cc_final: 0.7446 (t-100) REVERT: A 705 GLU cc_start: 0.8636 (mm-30) cc_final: 0.7660 (mm-30) REVERT: A 753 LEU cc_start: 0.7557 (mt) cc_final: 0.6833 (mt) REVERT: A 807 MET cc_start: 0.9190 (mmp) cc_final: 0.8941 (mmt) REVERT: A 815 CYS cc_start: 0.6178 (m) cc_final: 0.5833 (t) REVERT: A 938 PHE cc_start: 0.9091 (m-80) cc_final: 0.8686 (m-80) REVERT: A 939 MET cc_start: 0.7208 (ttt) cc_final: 0.6696 (tmm) REVERT: A 988 MET cc_start: 0.6213 (tpt) cc_final: 0.5780 (mmm) REVERT: B 463 MET cc_start: 0.5180 (ptm) cc_final: 0.4574 (ppp) REVERT: B 527 MET cc_start: 0.7951 (mtt) cc_final: 0.7368 (mmm) REVERT: B 545 ARG cc_start: 0.5966 (ttt180) cc_final: 0.5748 (ttt180) REVERT: B 578 TRP cc_start: 0.8815 (t-100) cc_final: 0.8082 (t-100) REVERT: B 629 MET cc_start: 0.4828 (tpt) cc_final: 0.4299 (tpt) REVERT: B 708 MET cc_start: 0.8671 (mtt) cc_final: 0.7931 (tpt) REVERT: B 721 MET cc_start: 0.7816 (tmm) cc_final: 0.7524 (tmm) REVERT: B 803 LEU cc_start: 0.9418 (mt) cc_final: 0.9129 (mt) REVERT: B 807 MET cc_start: 0.8810 (mtp) cc_final: 0.8502 (mtp) REVERT: C 424 TYR cc_start: 0.7672 (t80) cc_final: 0.7301 (t80) REVERT: C 570 GLU cc_start: 0.8483 (mm-30) cc_final: 0.7955 (pm20) REVERT: C 585 MET cc_start: 0.8795 (mpp) cc_final: 0.8291 (mpp) REVERT: C 625 THR cc_start: 0.9547 (p) cc_final: 0.9345 (p) REVERT: C 629 MET cc_start: 0.9221 (mtm) cc_final: 0.8717 (mtp) REVERT: C 762 LEU cc_start: 0.9268 (mt) cc_final: 0.8680 (mp) REVERT: C 811 LEU cc_start: 0.9624 (tp) cc_final: 0.9406 (mt) REVERT: C 965 PHE cc_start: 0.8477 (m-80) cc_final: 0.8031 (m-80) REVERT: C 999 PHE cc_start: 0.8104 (t80) cc_final: 0.7493 (t80) REVERT: C 1032 TYR cc_start: 0.8139 (t80) cc_final: 0.7598 (t80) REVERT: D 414 MET cc_start: 0.6385 (mpp) cc_final: 0.6137 (mpp) REVERT: D 428 LEU cc_start: 0.8839 (mt) cc_final: 0.8546 (mt) REVERT: D 463 MET cc_start: 0.7713 (mtm) cc_final: 0.7307 (mmm) REVERT: D 524 GLU cc_start: 0.8417 (pt0) cc_final: 0.7748 (pt0) REVERT: D 541 PHE cc_start: 0.8631 (t80) cc_final: 0.8384 (t80) REVERT: D 626 VAL cc_start: 0.8597 (t) cc_final: 0.8340 (t) REVERT: D 649 THR cc_start: 0.5009 (p) cc_final: 0.4457 (p) REVERT: D 667 PHE cc_start: 0.8073 (m-80) cc_final: 0.7095 (m-80) REVERT: D 670 MET cc_start: 0.8384 (tmm) cc_final: 0.7631 (tmm) REVERT: D 720 THR cc_start: 0.8384 (p) cc_final: 0.7904 (t) REVERT: D 760 ASP cc_start: 0.7449 (m-30) cc_final: 0.7116 (t0) REVERT: D 797 TYR cc_start: 0.8299 (m-80) cc_final: 0.7999 (m-80) outliers start: 1 outliers final: 0 residues processed: 387 average time/residue: 0.1082 time to fit residues: 65.4576 Evaluate side-chains 301 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 301 time to evaluate : 0.610 ------------------------------------------------------------------------------- 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: 8.9990 chunk 177 optimal weight: 0.7980 chunk 58 optimal weight: 6.9990 chunk 134 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 187 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 51 optimal weight: 9.9990 chunk 40 optimal weight: 0.6980 chunk 96 optimal weight: 6.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 642 GLN A 709 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 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 709 ASN ** 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 = 0.3643 r_free = 0.3643 target = 0.083414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.064561 restraints weight = 71250.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.066167 restraints weight = 52116.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.067388 restraints weight = 40917.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.068275 restraints weight = 33917.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.068932 restraints weight = 29426.483| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 1.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 16174 Z= 0.145 Angle : 0.688 8.267 21828 Z= 0.355 Chirality : 0.044 0.179 2454 Planarity : 0.005 0.064 2684 Dihedral : 6.064 51.563 2208 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % 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: 0.04 (0.19), residues: 1992 helix: 1.25 (0.15), residues: 1120 sheet: -1.71 (0.41), residues: 132 loop : -1.55 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 599 TYR 0.020 0.002 TYR C 768 PHE 0.030 0.002 PHE A 844 TRP 0.064 0.003 TRP D 578 HIS 0.004 0.001 HIS D 435 Details of bonding type rmsd covalent geometry : bond 0.00319 (16168) covalent geometry : angle 0.68805 (21816) SS BOND : bond 0.00197 ( 6) SS BOND : angle 0.92122 ( 12) hydrogen bonds : bond 0.03692 ( 818) hydrogen bonds : angle 4.59338 ( 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 379 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 379 time to evaluate : 0.583 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 511 LYS cc_start: 0.7989 (mmpt) cc_final: 0.7759 (mmmm) REVERT: A 524 GLU cc_start: 0.9291 (pm20) cc_final: 0.8901 (pm20) REVERT: A 527 MET cc_start: 0.7434 (mmt) cc_final: 0.7017 (mmt) REVERT: A 577 LEU cc_start: 0.9258 (mm) cc_final: 0.8954 (mm) REVERT: A 605 TRP cc_start: 0.8726 (t-100) cc_final: 0.8403 (t-100) REVERT: A 611 ILE cc_start: 0.9505 (mm) cc_final: 0.9256 (tp) REVERT: A 634 GLU cc_start: 0.7487 (pp20) cc_final: 0.7222 (pm20) REVERT: A 671 TRP cc_start: 0.8074 (t-100) cc_final: 0.7281 (t-100) REVERT: A 705 GLU cc_start: 0.8515 (mm-30) cc_final: 0.7612 (mm-30) REVERT: A 921 VAL cc_start: 0.9320 (t) cc_final: 0.8916 (t) REVERT: A 938 PHE cc_start: 0.9108 (m-80) cc_final: 0.8754 (m-80) REVERT: A 939 MET cc_start: 0.7567 (ttt) cc_final: 0.7039 (tmm) REVERT: A 988 MET cc_start: 0.6982 (tpt) cc_final: 0.6693 (mmm) REVERT: B 407 MET cc_start: 0.6568 (mtm) cc_final: 0.6274 (mpp) REVERT: B 460 TRP cc_start: 0.6347 (m100) cc_final: 0.5726 (m-90) REVERT: B 509 LYS cc_start: 0.7993 (tptp) cc_final: 0.7213 (mmmt) REVERT: B 527 MET cc_start: 0.7967 (mtt) cc_final: 0.7401 (mmm) REVERT: B 545 ARG cc_start: 0.5705 (ttt180) cc_final: 0.5394 (ttt180) REVERT: B 578 TRP cc_start: 0.8940 (t-100) cc_final: 0.8340 (t-100) REVERT: B 708 MET cc_start: 0.8669 (mtt) cc_final: 0.7992 (tpt) REVERT: B 808 LEU cc_start: 0.8787 (mm) cc_final: 0.8269 (mm) REVERT: B 814 PHE cc_start: 0.7975 (t80) cc_final: 0.7563 (t80) REVERT: C 431 GLU cc_start: 0.9038 (mm-30) cc_final: 0.8660 (tp30) REVERT: C 570 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8268 (pm20) REVERT: C 629 MET cc_start: 0.9238 (mtm) cc_final: 0.8760 (mtm) REVERT: C 763 LYS cc_start: 0.8133 (tptt) cc_final: 0.7918 (tptt) REVERT: C 807 MET cc_start: 0.8995 (tmm) cc_final: 0.8642 (tmm) REVERT: C 965 PHE cc_start: 0.8373 (m-80) cc_final: 0.7963 (m-80) REVERT: C 1005 TRP cc_start: 0.7425 (p90) cc_final: 0.6727 (m100) REVERT: C 1032 TYR cc_start: 0.8061 (t80) cc_final: 0.7680 (t80) REVERT: D 407 MET cc_start: 0.6279 (mpp) cc_final: 0.5910 (mpp) REVERT: D 414 MET cc_start: 0.6628 (mpp) cc_final: 0.6388 (mpp) REVERT: D 428 LEU cc_start: 0.8769 (mt) cc_final: 0.8477 (mt) REVERT: D 463 MET cc_start: 0.7790 (mtm) cc_final: 0.7452 (mtm) REVERT: D 524 GLU cc_start: 0.8764 (pt0) cc_final: 0.8411 (pm20) REVERT: D 541 PHE cc_start: 0.8716 (t80) cc_final: 0.8487 (t80) REVERT: D 626 VAL cc_start: 0.8801 (t) cc_final: 0.8498 (t) REVERT: D 649 THR cc_start: 0.5101 (p) cc_final: 0.4830 (p) REVERT: D 670 MET cc_start: 0.8414 (tmm) cc_final: 0.7967 (tmm) REVERT: D 702 TYR cc_start: 0.8333 (t80) cc_final: 0.8111 (t80) REVERT: D 760 ASP cc_start: 0.7677 (m-30) cc_final: 0.7195 (t0) REVERT: D 763 LYS cc_start: 0.8658 (pttm) cc_final: 0.8439 (ptmt) REVERT: D 797 TYR cc_start: 0.8332 (m-80) cc_final: 0.8017 (m-80) REVERT: A 1102 GLU cc_start: 0.6215 (tp30) cc_final: 0.5205 (tp30) outliers start: 0 outliers final: 0 residues processed: 379 average time/residue: 0.1023 time to fit residues: 61.4714 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 : 0.530 ------------------------------------------------------------------------------- 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: 2.9990 chunk 74 optimal weight: 0.9980 chunk 94 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 chunk 96 optimal weight: 4.9990 chunk 79 optimal weight: 0.8980 chunk 164 optimal weight: 0.0000 chunk 117 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 67 optimal weight: 8.9990 chunk 161 optimal weight: 2.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 756 GLN A 985 ASN B 508 GLN ** 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 586 GLN ** 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 = 0.3643 r_free = 0.3643 target = 0.083240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.064447 restraints weight = 70170.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.066071 restraints weight = 51162.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.067273 restraints weight = 40254.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.068095 restraints weight = 33448.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.068764 restraints weight = 29182.517| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 1.4249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 16174 Z= 0.146 Angle : 0.696 9.553 21828 Z= 0.357 Chirality : 0.044 0.233 2454 Planarity : 0.004 0.065 2684 Dihedral : 6.047 53.104 2208 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 5.17 % Twisted General : 0.00 % Rama-Z 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: 0.01 (0.19), residues: 1992 helix: 1.17 (0.15), residues: 1132 sheet: -1.71 (0.41), residues: 132 loop : -1.51 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 594 TYR 0.016 0.001 TYR C 768 PHE 0.039 0.002 PHE A 844 TRP 0.053 0.002 TRP D 578 HIS 0.005 0.001 HIS C 883 Details of bonding type rmsd covalent geometry : bond 0.00328 (16168) covalent geometry : angle 0.69574 (21816) SS BOND : bond 0.00227 ( 6) SS BOND : angle 1.03868 ( 12) hydrogen bonds : bond 0.03661 ( 818) hydrogen bonds : angle 4.63739 ( 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 386 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 386 time to evaluate : 0.630 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: A 424 TYR cc_start: 0.7587 (t80) cc_final: 0.7156 (t80) REVERT: A 524 GLU cc_start: 0.9368 (pm20) cc_final: 0.8335 (pm20) REVERT: A 527 MET cc_start: 0.7689 (mmt) cc_final: 0.7016 (tpp) REVERT: A 531 PHE cc_start: 0.8960 (m-80) cc_final: 0.8718 (m-80) REVERT: A 540 LEU cc_start: 0.9347 (mm) cc_final: 0.9013 (tp) REVERT: A 577 LEU cc_start: 0.9285 (mm) cc_final: 0.8977 (mm) REVERT: A 586 GLN cc_start: 0.8478 (mm-40) cc_final: 0.8023 (tp40) REVERT: A 605 TRP cc_start: 0.8705 (t-100) cc_final: 0.7571 (t-100) REVERT: A 629 MET cc_start: 0.8637 (mpp) cc_final: 0.8324 (mpp) REVERT: A 634 GLU cc_start: 0.7798 (pp20) cc_final: 0.7521 (pm20) REVERT: A 671 TRP cc_start: 0.8075 (t-100) cc_final: 0.7387 (t-100) REVERT: A 705 GLU cc_start: 0.8448 (mm-30) cc_final: 0.7675 (mm-30) REVERT: A 763 LYS cc_start: 0.8313 (pttt) cc_final: 0.7898 (pttp) REVERT: A 815 CYS cc_start: 0.6619 (m) cc_final: 0.6184 (t) REVERT: A 938 PHE cc_start: 0.9173 (m-80) cc_final: 0.8912 (m-80) REVERT: A 939 MET cc_start: 0.7796 (ttt) cc_final: 0.7422 (tmm) REVERT: A 988 MET cc_start: 0.7481 (tpt) cc_final: 0.7216 (mmm) REVERT: B 407 MET cc_start: 0.6649 (mtm) cc_final: 0.6212 (mpp) REVERT: B 408 MET cc_start: 0.5733 (mpp) cc_final: 0.3957 (ttp) REVERT: B 460 TRP cc_start: 0.6443 (m100) cc_final: 0.6037 (m-90) REVERT: B 463 MET cc_start: 0.5556 (ptm) cc_final: 0.5022 (ppp) REVERT: B 485 ARG cc_start: 0.8191 (mmt90) cc_final: 0.7705 (mmm160) REVERT: B 509 LYS cc_start: 0.8108 (tptp) cc_final: 0.7485 (mmmt) REVERT: B 527 MET cc_start: 0.8050 (mtt) cc_final: 0.7513 (mmm) REVERT: B 578 TRP cc_start: 0.8955 (t-100) cc_final: 0.8263 (t-100) REVERT: B 610 LEU cc_start: 0.9278 (mp) cc_final: 0.9009 (mp) REVERT: B 627 GLU cc_start: 0.8061 (pp20) cc_final: 0.7758 (pp20) REVERT: B 708 MET cc_start: 0.9014 (mtt) cc_final: 0.8305 (tpt) REVERT: B 814 PHE cc_start: 0.8001 (t80) cc_final: 0.7672 (t80) REVERT: C 424 TYR cc_start: 0.8048 (t80) cc_final: 0.7671 (t80) REVERT: C 431 GLU cc_start: 0.8954 (mm-30) cc_final: 0.8575 (tp30) REVERT: C 524 GLU cc_start: 0.9563 (pm20) cc_final: 0.9036 (pm20) REVERT: C 570 GLU cc_start: 0.8596 (mm-30) cc_final: 0.8272 (pm20) REVERT: C 585 MET cc_start: 0.8586 (mpp) cc_final: 0.8245 (mmm) REVERT: C 594 ARG cc_start: 0.8407 (mtm-85) cc_final: 0.7934 (mtm-85) REVERT: C 625 THR cc_start: 0.9670 (p) cc_final: 0.9291 (t) REVERT: C 629 MET cc_start: 0.9183 (mtm) cc_final: 0.8697 (mtp) REVERT: C 762 LEU cc_start: 0.9399 (mp) cc_final: 0.8413 (mp) REVERT: C 768 TYR cc_start: 0.8045 (p90) cc_final: 0.7757 (p90) REVERT: C 861 TRP cc_start: 0.6988 (m100) cc_final: 0.6007 (m100) REVERT: C 965 PHE cc_start: 0.8447 (m-80) cc_final: 0.7995 (m-80) REVERT: C 999 PHE cc_start: 0.7809 (t80) cc_final: 0.7365 (t80) REVERT: C 1005 TRP cc_start: 0.7529 (p90) cc_final: 0.6615 (m100) REVERT: C 1032 TYR cc_start: 0.7990 (t80) cc_final: 0.7745 (t80) REVERT: D 407 MET cc_start: 0.6262 (mpp) cc_final: 0.5758 (mpp) REVERT: D 414 MET cc_start: 0.6584 (mpp) cc_final: 0.6375 (mpp) REVERT: D 428 LEU cc_start: 0.8860 (mt) cc_final: 0.8598 (mt) REVERT: D 463 MET cc_start: 0.7787 (mtm) cc_final: 0.7363 (mmm) REVERT: D 649 THR cc_start: 0.5350 (p) cc_final: 0.5120 (p) REVERT: D 670 MET cc_start: 0.8499 (tmm) cc_final: 0.8116 (tmm) REVERT: D 760 ASP cc_start: 0.7678 (m-30) cc_final: 0.7215 (t0) REVERT: D 763 LYS cc_start: 0.8697 (pttm) cc_final: 0.8430 (ptmt) REVERT: D 797 TYR cc_start: 0.8515 (m-80) cc_final: 0.8237 (m-80) REVERT: A 1102 GLU cc_start: 0.6417 (tp30) cc_final: 0.5474 (tp30) outliers start: 0 outliers final: 0 residues processed: 386 average time/residue: 0.1036 time to fit residues: 63.0775 Evaluate side-chains 311 residues out of total 1706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 311 time to evaluate : 0.527 ------------------------------------------------------------------------------- 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: 0.2980 chunk 50 optimal weight: 0.3980 chunk 76 optimal weight: 3.9990 chunk 168 optimal weight: 4.9990 chunk 41 optimal weight: 0.4980 chunk 54 optimal weight: 0.8980 chunk 57 optimal weight: 10.0000 chunk 163 optimal weight: 6.9990 chunk 94 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 985 ASN B 508 GLN ** 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** ** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.084023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.064919 restraints weight = 71794.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.066527 restraints weight = 52409.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.067761 restraints weight = 41244.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.068665 restraints weight = 34422.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.069273 restraints weight = 29912.358| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 1.4642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 16174 Z= 0.129 Angle : 0.673 8.688 21828 Z= 0.342 Chirality : 0.043 0.249 2454 Planarity : 0.004 0.063 2684 Dihedral : 5.972 59.445 2208 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.79 % Cis-general : 0.00 % Twisted Proline : 6.90 % Twisted General : 0.00 % Rama-Z 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: 0.10 (0.19), residues: 1992 helix: 1.25 (0.16), residues: 1142 sheet: -1.49 (0.44), residues: 112 loop : -1.58 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 594 TYR 0.020 0.001 TYR C 768 PHE 0.033 0.002 PHE A 531 TRP 0.044 0.002 TRP D 578 HIS 0.005 0.001 HIS C 883 Details of bonding type rmsd covalent geometry : bond 0.00285 (16168) covalent geometry : angle 0.67295 (21816) SS BOND : bond 0.00215 ( 6) SS BOND : angle 1.03738 ( 12) hydrogen bonds : bond 0.03546 ( 818) hydrogen bonds : angle 4.49957 ( 2400) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2665.99 seconds wall clock time: 47 minutes 3.45 seconds (2823.45 seconds total)