Starting phenix.real_space_refine on Sat Jul 4 00:23:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7rz8_24754/07_2026/7rz8_24754.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rz8_24754/07_2026/7rz8_24754.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7rz8_24754/07_2026/7rz8_24754.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7rz8_24754/07_2026/7rz8_24754.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rz8_24754/07_2026/7rz8_24754.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rz8_24754/07_2026/7rz8_24754.map" model { file = "/net/cci-nas-00/data/ceres_data/7rz8_24754/07_2026/7rz8_24754.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rz8_24754/07_2026/7rz8_24754.cif" } resolution = 4.1 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 14 5.49 5 S 106 5.16 5 C 10960 2.51 5 N 2600 2.21 5 O 3042 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16722 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 609, 4762 Classifications: {'peptide': 609} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 591} Chain breaks: 3 Chain: "B" Number of atoms: 3216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3216 Classifications: {'peptide': 413} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 399} Chain breaks: 1 Chain: "C" Number of atoms: 4762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 609, 4762 Classifications: {'peptide': 609} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 591} Chain breaks: 3 Chain: "D" Number of atoms: 3216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3216 Classifications: {'peptide': 413} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 399} Chain breaks: 1 Chain: "A" Number of atoms: 222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 222 Unusual residues: {'PCW': 7, 'QUS': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 196 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PCW:plan-2': 3, 'PCW:plan-1': 3, 'PCW:plan-3': 3, 'PCW:plan-4': 3} Unresolved non-hydrogen planarities: 40 Chain: "B" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 161 Unusual residues: {'PCW': 4, 'QUS': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PCW:plan-2': 2, 'PCW:plan-1': 1, 'PCW:plan-3': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 222 Unusual residues: {'PCW': 7, 'QUS': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 196 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PCW:plan-2': 3, 'PCW:plan-1': 3, 'PCW:plan-3': 3, 'PCW:plan-4': 3} Unresolved non-hydrogen planarities: 40 Chain: "D" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 161 Unusual residues: {'PCW': 4, 'QUS': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PCW:plan-1': 1, 'PCW:plan-3': 1, 'PCW:plan-4': 1, 'PCW:plan-2': 2} Unresolved non-hydrogen planarities: 14 Time building chain proxies: 3.71, per 1000 atoms: 0.22 Number of scatterers: 16722 At special positions: 0 Unit cell: (118.659, 131.487, 132.556, 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 14 15.00 O 3042 8.00 N 2600 7.00 C 10960 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=2.04 Simple disulfide: pdb=" SG CYS A 890 " - pdb=" SG CYS A 900 " distance=2.05 Simple disulfide: pdb=" SG CYS B 718 " - pdb=" SG CYS B 773 " distance=2.03 Simple disulfide: pdb=" SG CYS C 718 " - pdb=" SG CYS C 773 " distance=2.04 Simple disulfide: pdb=" SG CYS C 890 " - pdb=" SG CYS C 900 " distance=2.05 Simple disulfide: pdb=" SG CYS D 718 " - pdb=" SG CYS D 773 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 1.35 Conformation dependent library (CDL) restraints added in 888.1 milliseconds 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3740 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 22 sheets defined 57.7% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 416 through 421 removed outlier: 3.521A pdb=" N GLU A 419 " --> pdb=" O GLU A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 437 removed outlier: 3.524A pdb=" N HIS A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 469 Processing helix chain 'A' and resid 482 through 488 removed outlier: 3.946A pdb=" N VAL A 488 " --> pdb=" O VAL A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 519 removed outlier: 3.678A pdb=" N LEU A 518 " --> pdb=" O PHE A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 545 Processing helix chain 'A' and resid 572 through 585 Processing helix chain 'A' and resid 595 through 630 removed outlier: 3.605A pdb=" N ILE A 611 " --> pdb=" O PHE A 607 " (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: 3.830A pdb=" N VAL A 693 " --> pdb=" O GLY A 689 " (cutoff:3.500A) removed outlier: 3.772A 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 755 Processing helix chain 'A' and resid 757 through 770 removed outlier: 3.668A pdb=" N TRP A 766 " --> pdb=" O LEU A 762 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N TRP A 767 " --> pdb=" O LYS A 763 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS A 770 " --> pdb=" O TRP A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 780 removed outlier: 3.659A pdb=" N GLY A 779 " --> pdb=" O ALA A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 822 removed outlier: 3.752A pdb=" N PHE A 796 " --> pdb=" O VAL A 792 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER A 818 " --> pdb=" O PHE A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 858 removed outlier: 3.546A pdb=" N LEU A 852 " --> pdb=" O GLY A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 893 through 897 removed outlier: 3.667A pdb=" N ARG A 897 " --> pdb=" O GLY A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 926 removed outlier: 3.585A pdb=" N ARG A 926 " --> pdb=" O LEU A 922 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 952 removed outlier: 3.919A pdb=" N LEU A 933 " --> pdb=" O THR A 929 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE A 944 " --> pdb=" O PHE A 940 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE A 951 " --> pdb=" O ASN A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 990 removed outlier: 4.193A pdb=" N PHE A 960 " --> pdb=" O THR A 956 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLU A 987 " --> pdb=" O SER A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1035 removed outlier: 3.633A pdb=" N LEU A1015 " --> pdb=" O ALA A1011 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A1025 " --> pdb=" O GLY A1021 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 437 Processing helix chain 'B' and resid 462 through 469 Processing helix chain 'B' and resid 482 through 489 removed outlier: 4.120A pdb=" N VAL B 488 " --> pdb=" O VAL B 484 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE B 489 " --> pdb=" O ARG B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 519 removed outlier: 3.684A pdb=" N LEU B 518 " --> pdb=" O PHE B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 547 removed outlier: 3.567A pdb=" N ARG B 545 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N PHE B 546 " --> pdb=" O LEU B 542 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N SER B 547 " --> pdb=" O VAL B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 585 Processing helix chain 'B' and resid 595 through 626 removed outlier: 4.042A pdb=" N VAL B 601 " --> pdb=" O SER B 597 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE B 611 " --> pdb=" O PHE B 607 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER B 614 " --> pdb=" O LEU B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 642 removed outlier: 3.604A pdb=" N SER B 640 " --> pdb=" O ALA B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 661 removed outlier: 3.535A pdb=" N GLU B 657 " --> pdb=" O GLY B 653 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE B 659 " --> pdb=" O THR B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 676 removed outlier: 3.805A pdb=" N MET B 670 " --> pdb=" O VAL B 666 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR B 672 " --> pdb=" O ASP B 668 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR B 673 " --> pdb=" O LYS B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 695 Processing helix chain 'B' and resid 706 through 715 removed outlier: 3.545A pdb=" N GLU B 713 " --> pdb=" O ASN B 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 756 removed outlier: 3.507A pdb=" N GLN B 756 " --> pdb=" O LYS B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 770 removed outlier: 3.904A pdb=" N TRP B 767 " --> pdb=" O LYS B 763 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR B 768 " --> pdb=" O ASN B 764 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LYS B 770 " --> pdb=" O TRP B 766 " (cutoff:3.500A) Processing helix chain 'B' and resid 774 through 781 removed outlier: 3.860A pdb=" N SER B 778 " --> pdb=" O GLY B 774 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N SER B 780 " --> pdb=" O LYS B 776 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 791 No H-bonds generated for 'chain 'B' and resid 789 through 791' Processing helix chain 'B' and resid 792 through 819 removed outlier: 3.928A pdb=" N PHE B 796 " --> pdb=" O VAL B 792 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 421 removed outlier: 3.521A pdb=" N GLU C 419 " --> pdb=" O GLU C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 437 removed outlier: 3.524A pdb=" N HIS C 435 " --> pdb=" O GLU C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 469 Processing helix chain 'C' and resid 482 through 488 removed outlier: 3.945A pdb=" N VAL C 488 " --> pdb=" O VAL C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 519 removed outlier: 3.678A pdb=" N LEU C 518 " --> pdb=" O PHE C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 545 Processing helix chain 'C' and resid 572 through 585 Processing helix chain 'C' and resid 595 through 630 removed outlier: 3.605A pdb=" N ILE C 611 " --> pdb=" O PHE C 607 " (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: 3.831A pdb=" N VAL C 693 " --> pdb=" O GLY C 689 " (cutoff:3.500A) removed outlier: 3.773A 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 755 Processing helix chain 'C' and resid 757 through 770 removed outlier: 3.668A pdb=" N TRP C 766 " --> pdb=" O LEU C 762 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N TRP C 767 " --> pdb=" O LYS C 763 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS C 770 " --> pdb=" O TRP C 766 " (cutoff:3.500A) Processing helix chain 'C' and resid 775 through 780 removed outlier: 3.660A pdb=" N GLY C 779 " --> pdb=" O ALA C 775 " (cutoff:3.500A) Processing helix chain 'C' and resid 792 through 822 removed outlier: 3.752A pdb=" N PHE C 796 " --> pdb=" O VAL C 792 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER C 818 " --> pdb=" O PHE C 814 " (cutoff:3.500A) Processing helix chain 'C' and resid 832 through 858 removed outlier: 3.547A pdb=" N LEU C 852 " --> pdb=" O GLY C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 893 through 897 removed outlier: 3.667A pdb=" N ARG C 897 " --> pdb=" O GLY C 894 " (cutoff:3.500A) Processing helix chain 'C' and resid 917 through 926 removed outlier: 3.585A pdb=" N ARG C 926 " --> pdb=" O LEU C 922 " (cutoff:3.500A) Processing helix chain 'C' and resid 929 through 952 removed outlier: 3.918A pdb=" N LEU C 933 " --> pdb=" O THR C 929 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE C 944 " --> pdb=" O PHE C 940 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE C 951 " --> pdb=" O ASN C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 956 through 990 removed outlier: 4.193A pdb=" N PHE C 960 " --> pdb=" O THR C 956 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLU C 987 " --> pdb=" O SER C 983 " (cutoff:3.500A) Processing helix chain 'C' and resid 1004 through 1035 removed outlier: 3.633A pdb=" N LEU C1015 " --> pdb=" O ALA C1011 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL C1025 " --> pdb=" O GLY C1021 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 437 Processing helix chain 'D' and resid 462 through 469 Processing helix chain 'D' and resid 482 through 489 removed outlier: 4.120A pdb=" N VAL D 488 " --> pdb=" O VAL D 484 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE D 489 " --> pdb=" O ARG D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 519 removed outlier: 3.685A pdb=" N LEU D 518 " --> pdb=" O PHE D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 547 removed outlier: 3.569A pdb=" N ARG D 545 " --> pdb=" O PHE D 541 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N PHE D 546 " --> pdb=" O LEU D 542 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N SER D 547 " --> pdb=" O VAL D 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 585 Processing helix chain 'D' and resid 595 through 626 removed outlier: 4.042A pdb=" N VAL D 601 " --> pdb=" O SER D 597 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE D 611 " --> pdb=" O PHE D 607 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER D 614 " --> pdb=" O LEU D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 642 removed outlier: 3.604A pdb=" N SER D 640 " --> pdb=" O ALA D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 661 removed outlier: 3.535A pdb=" N GLU D 657 " --> pdb=" O GLY D 653 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N PHE D 659 " --> pdb=" O THR D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 676 removed outlier: 3.805A pdb=" N MET D 670 " --> pdb=" O VAL D 666 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR D 672 " --> pdb=" O ASP D 668 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR D 673 " --> pdb=" O LYS D 669 " (cutoff:3.500A) Processing helix chain 'D' and resid 685 through 695 Processing helix chain 'D' and resid 706 through 715 removed outlier: 3.544A pdb=" N GLU D 713 " --> pdb=" O ASN D 709 " (cutoff:3.500A) Processing helix chain 'D' and resid 742 through 756 removed outlier: 3.508A pdb=" N GLN D 756 " --> pdb=" O LYS D 752 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 770 removed outlier: 3.905A pdb=" N TRP D 767 " --> pdb=" O LYS D 763 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR D 768 " --> pdb=" O ASN D 764 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LYS D 770 " --> pdb=" O TRP D 766 " (cutoff:3.500A) Processing helix chain 'D' and resid 774 through 781 removed outlier: 3.860A pdb=" N SER D 778 " --> pdb=" O GLY D 774 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N SER D 780 " --> pdb=" O LYS D 776 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 791 No H-bonds generated for 'chain 'D' and resid 789 through 791' Processing helix chain 'D' and resid 792 through 819 removed outlier: 3.928A pdb=" N PHE D 796 " --> pdb=" O VAL D 792 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 440 through 444 removed outlier: 6.286A pdb=" N VAL A 395 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N THR A 443 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N VAL A 397 " --> pdb=" O THR A 443 " (cutoff:3.500A) removed outlier: 6.001A 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: 4.214A pdb=" N MET A 496 " --> pdb=" O TYR A 732 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N TYR A 732 " --> pdb=" O MET A 496 " (cutoff:3.500A) removed outlier: 3.762A 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: 6.204A pdb=" N ALA A 646 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N LEU A 703 " --> pdb=" O ALA A 646 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N GLY A 648 " --> pdb=" O LEU A 703 " (cutoff:3.500A) removed outlier: 9.274A pdb=" N GLU A 705 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N TYR A 700 " --> pdb=" O LYS A 505 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N LYS A 505 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILE A 502 " --> pdb=" O VAL A 723 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 890 through 891 removed outlier: 3.570A pdb=" N CYS A 890 " --> pdb=" O HIS A 883 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N HIS A 883 " --> pdb=" O CYS A 890 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 862 " --> pdb=" O SER A 884 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 867 through 869 Processing sheet with id=AA7, 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=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 407 through 408 Processing sheet with id=AA9, first strand: chain 'B' and resid 497 through 498 Processing sheet with id=AB1, first strand: chain 'B' and resid 500 through 501 Processing sheet with id=AB2, first strand: chain 'B' and resid 503 through 505 Processing sheet with id=AB3, first strand: chain 'C' and resid 440 through 444 removed outlier: 6.286A pdb=" N VAL C 395 " --> pdb=" O LYS C 441 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N THR C 443 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N VAL C 397 " --> pdb=" O THR C 443 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N VAL C 396 " --> pdb=" O ILE C 474 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 489 through 491 Processing sheet with id=AB5, first strand: chain 'C' and resid 496 through 498 removed outlier: 4.214A pdb=" N MET C 496 " --> pdb=" O TYR C 732 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR C 732 " --> pdb=" O MET C 496 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU C 498 " --> pdb=" O LYS C 730 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 646 through 649 removed outlier: 6.205A pdb=" N ALA C 646 " --> pdb=" O ALA C 701 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N LEU C 703 " --> pdb=" O ALA C 646 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N GLY C 648 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 9.275A pdb=" N GLU C 705 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N TYR C 700 " --> pdb=" O LYS C 505 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LYS C 505 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ILE C 502 " --> pdb=" O VAL C 723 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 890 through 891 removed outlier: 3.570A pdb=" N CYS C 890 " --> pdb=" O HIS C 883 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N HIS C 883 " --> pdb=" O CYS C 890 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU C 862 " --> pdb=" O SER C 884 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 867 through 869 Processing sheet with id=AB9, 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=AB9 Processing sheet with id=AC1, first strand: chain 'D' and resid 407 through 408 Processing sheet with id=AC2, first strand: chain 'D' and resid 497 through 498 Processing sheet with id=AC3, first strand: chain 'D' and resid 500 through 501 Processing sheet with id=AC4, first strand: chain 'D' and resid 503 through 505 824 hydrogen bonds defined for protein. 2412 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: 2.92 Time building geometry restraints manager: 1.81 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: 2564 1.31 - 1.44: 4584 1.44 - 1.56: 9572 1.56 - 1.69: 152 1.69 - 1.81: 176 Bond restraints: 17048 Sorted by residual: bond pdb=" C05 QUS B1104 " pdb=" O19 QUS B1104 " ideal model delta sigma weight residual 1.203 1.449 -0.246 2.00e-02 2.50e+03 1.52e+02 bond pdb=" C05 QUS D1105 " pdb=" O19 QUS D1105 " ideal model delta sigma weight residual 1.203 1.449 -0.246 2.00e-02 2.50e+03 1.51e+02 bond pdb=" C05 QUS C1106 " pdb=" O19 QUS C1106 " ideal model delta sigma weight residual 1.203 1.447 -0.244 2.00e-02 2.50e+03 1.48e+02 bond pdb=" C05 QUS A1106 " pdb=" O19 QUS A1106 " ideal model delta sigma weight residual 1.203 1.446 -0.243 2.00e-02 2.50e+03 1.48e+02 bond pdb=" C04 QUS B1104 " pdb=" O18 QUS B1104 " ideal model delta sigma weight residual 1.212 1.413 -0.201 2.00e-02 2.50e+03 1.01e+02 ... (remaining 17043 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.97: 22156 2.97 - 5.93: 506 5.93 - 8.90: 150 8.90 - 11.86: 33 11.86 - 14.83: 33 Bond angle restraints: 22878 Sorted by residual: angle pdb=" N ALA D 820 " pdb=" CA ALA D 820 " pdb=" C ALA D 820 " ideal model delta sigma weight residual 113.01 98.25 14.76 1.20e+00 6.94e-01 1.51e+02 angle pdb=" N ALA B 820 " pdb=" CA ALA B 820 " pdb=" C ALA B 820 " ideal model delta sigma weight residual 113.18 98.35 14.83 1.21e+00 6.83e-01 1.50e+02 angle pdb=" CA ARG B 819 " pdb=" C ARG B 819 " pdb=" N ALA B 820 " ideal model delta sigma weight residual 117.92 111.52 6.40 1.35e+00 5.49e-01 2.25e+01 angle pdb=" C GLY A 894 " pdb=" N GLU A 895 " pdb=" CA GLU A 895 " ideal model delta sigma weight residual 122.61 129.88 -7.27 1.56e+00 4.11e-01 2.17e+01 angle pdb=" C GLY C 894 " pdb=" N GLU C 895 " pdb=" CA GLU C 895 " ideal model delta sigma weight residual 122.61 129.86 -7.25 1.56e+00 4.11e-01 2.16e+01 ... (remaining 22873 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.75: 9792 35.75 - 71.50: 278 71.50 - 107.25: 22 107.25 - 143.00: 6 143.00 - 178.75: 8 Dihedral angle restraints: 10106 sinusoidal: 4240 harmonic: 5866 Sorted by residual: dihedral pdb=" CA LYS C 716 " pdb=" C LYS C 716 " pdb=" N PRO C 717 " pdb=" CA PRO C 717 " ideal model delta harmonic sigma weight residual 180.00 134.14 45.86 0 5.00e+00 4.00e-02 8.41e+01 dihedral pdb=" CA LYS A 716 " pdb=" C LYS A 716 " pdb=" N PRO A 717 " pdb=" CA PRO A 717 " ideal model delta harmonic sigma weight residual 180.00 134.15 45.85 0 5.00e+00 4.00e-02 8.41e+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 93.00 166.27 -73.27 1 1.00e+01 1.00e-02 6.84e+01 ... (remaining 10103 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 2286 0.091 - 0.182: 174 0.182 - 0.274: 30 0.274 - 0.365: 2 0.365 - 0.456: 2 Chirality restraints: 2494 Sorted by residual: chirality pdb=" CG LEU C 892 " pdb=" CB LEU C 892 " pdb=" CD1 LEU C 892 " pdb=" CD2 LEU C 892 " both_signs ideal model delta sigma weight residual False -2.59 -2.13 -0.46 2.00e-01 2.50e+01 5.20e+00 chirality pdb=" CG LEU A 892 " pdb=" CB LEU A 892 " pdb=" CD1 LEU A 892 " pdb=" CD2 LEU A 892 " both_signs ideal model delta sigma weight residual False -2.59 -2.14 -0.45 2.00e-01 2.50e+01 5.12e+00 chirality pdb=" CA ALA B 820 " pdb=" N ALA B 820 " pdb=" C ALA B 820 " pdb=" CB ALA B 820 " both_signs ideal model delta sigma weight residual False 2.48 2.83 -0.34 2.00e-01 2.50e+01 2.92e+00 ... (remaining 2491 not shown) Planarity restraints: 2778 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 716 " 0.077 5.00e-02 4.00e+02 1.18e-01 2.24e+01 pdb=" N PRO A 717 " -0.205 5.00e-02 4.00e+02 pdb=" CA PRO A 717 " 0.063 5.00e-02 4.00e+02 pdb=" CD PRO A 717 " 0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 716 " -0.077 5.00e-02 4.00e+02 1.18e-01 2.24e+01 pdb=" N PRO C 717 " 0.205 5.00e-02 4.00e+02 pdb=" CA PRO C 717 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO C 717 " -0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 819 " -0.018 2.00e-02 2.50e+03 3.84e-02 1.47e+01 pdb=" C ARG B 819 " 0.066 2.00e-02 2.50e+03 pdb=" O ARG B 819 " -0.026 2.00e-02 2.50e+03 pdb=" N ALA B 820 " -0.023 2.00e-02 2.50e+03 ... (remaining 2775 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3464 2.78 - 3.31: 15170 3.31 - 3.84: 26645 3.84 - 4.37: 31308 4.37 - 4.90: 52509 Nonbonded interactions: 129096 Sorted by model distance: nonbonded pdb=" O ARG D 692 " pdb=" OG SER D 696 " model vdw 2.246 3.040 nonbonded pdb=" O ARG B 692 " pdb=" OG SER B 696 " model vdw 2.247 3.040 nonbonded pdb=" O LEU B 639 " pdb=" OH TYR B 647 " model vdw 2.293 3.040 nonbonded pdb=" O LEU D 639 " pdb=" OH TYR D 647 " model vdw 2.293 3.040 nonbonded pdb=" OG SER D 706 " pdb=" OD1 ASN D 726 " model vdw 2.324 3.040 ... (remaining 129091 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = (chain 'B' and (resid 394 through 823 or (resid 1101 and (name C13 or name C14 o \ r name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name C \ 21 or name C22 or name C23)) or resid 1102 through 1103)) selection = (chain 'D' and (resid 394 through 1101 or (resid 1102 through 1103 and (name N o \ r name C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C1 \ 6 or name C17 or name C18 or name C19 or name C2 or name C20 or name C3 or name \ C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or n \ ame C38 or name C39 or name C4 or name C40 or name C41 or name C42 or name C43 o \ r name C44 or name C45 or name C5 or name C6 or name C7 or name C8 or name O11 o \ r name O1P or name O2 or name O2P or name O3 or name O31 or name O3P or name O4P \ or name P )))) } 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: 4.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.970 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 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 : 0.010 0.246 17054 Z= 0.527 Angle : 1.291 14.825 22890 Z= 0.605 Chirality : 0.058 0.456 2494 Planarity : 0.007 0.118 2778 Dihedral : 16.429 178.748 6348 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.11 % Favored : 95.79 % Rotamer: Outliers : 0.93 % Allowed : 5.28 % Favored : 93.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 6.67 % 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: -4.14 (0.13), residues: 2020 helix: -2.87 (0.09), residues: 1088 sheet: -2.11 (0.34), residues: 180 loop : -2.41 (0.19), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 599 TYR 0.020 0.002 TYR A 768 PHE 0.042 0.002 PHE C 901 TRP 0.022 0.002 TRP A 767 HIS 0.004 0.001 HIS C 883 Details of bonding type rmsd/Z covalent geometry : bond 0.01047 / 0.53 (17048) covalent geometry : angle 1.29172 / 0.60 (22878) SS BOND : bond 0.00910 / 0.59 ( 6) SS BOND : angle 0.63470 / 0.40 ( 12) hydrogen bonds : bond 0.29436 / 19.73 ( 824) hydrogen bonds : angle 8.44921 / 5.84 ( 2412) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 617 time to evaluate : 0.614 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 418 ASN cc_start: 0.7583 (m-40) cc_final: 0.7087 (m-40) REVERT: A 427 ASP cc_start: 0.8542 (m-30) cc_final: 0.8325 (m-30) REVERT: A 537 SER cc_start: 0.8812 (m) cc_final: 0.8219 (t) REVERT: A 545 ARG cc_start: 0.7383 (mmt180) cc_final: 0.6346 (tpp-160) REVERT: A 799 LEU cc_start: 0.9094 (tp) cc_final: 0.8863 (tt) REVERT: A 835 LYS cc_start: 0.8189 (tppt) cc_final: 0.7636 (mmtt) REVERT: A 880 MET cc_start: 0.8642 (tmm) cc_final: 0.7967 (tmm) REVERT: A 985 ASN cc_start: 0.8835 (m-40) cc_final: 0.8490 (m-40) REVERT: B 407 MET cc_start: 0.4615 (mtm) cc_final: 0.4314 (mmm) REVERT: B 411 ASN cc_start: 0.8043 (m-40) cc_final: 0.7744 (m-40) REVERT: B 418 ASN cc_start: 0.7509 (p0) cc_final: 0.6210 (p0) REVERT: B 497 SER cc_start: 0.8293 (m) cc_final: 0.7901 (p) REVERT: B 503 MET cc_start: 0.7793 (ttt) cc_final: 0.7253 (tpp) REVERT: B 669 LYS cc_start: 0.9133 (mttt) cc_final: 0.8811 (mmtt) REVERT: B 702 TYR cc_start: 0.7772 (t80) cc_final: 0.7159 (t80) REVERT: B 709 ASN cc_start: 0.8509 (t0) cc_final: 0.7579 (t0) REVERT: B 710 GLU cc_start: 0.8422 (tm-30) cc_final: 0.7914 (tp30) REVERT: B 715 ARG cc_start: 0.8039 (tpt-90) cc_final: 0.7717 (tmt-80) REVERT: B 756 GLN cc_start: 0.6367 (pt0) cc_final: 0.5790 (pm20) REVERT: C 427 ASP cc_start: 0.8444 (m-30) cc_final: 0.8209 (m-30) REVERT: C 461 ASN cc_start: 0.8531 (t0) cc_final: 0.8182 (p0) REVERT: C 519 ASP cc_start: 0.7813 (m-30) cc_final: 0.7524 (m-30) REVERT: C 527 MET cc_start: 0.8401 (ttm) cc_final: 0.8167 (ttm) REVERT: C 531 PHE cc_start: 0.8478 (m-10) cc_final: 0.8274 (m-10) REVERT: C 569 ASN cc_start: 0.7920 (t0) cc_final: 0.7288 (m-40) REVERT: C 577 LEU cc_start: 0.9192 (mm) cc_final: 0.8979 (mm) REVERT: C 613 ILE cc_start: 0.8862 (mt) cc_final: 0.8459 (mt) REVERT: C 835 LYS cc_start: 0.8303 (tppt) cc_final: 0.7897 (ttpt) REVERT: C 866 GLU cc_start: 0.6917 (tp30) cc_final: 0.6697 (tt0) REVERT: C 920 ASN cc_start: 0.8431 (t160) cc_final: 0.7816 (m-40) REVERT: C 924 MET cc_start: 0.8185 (mmt) cc_final: 0.7931 (mmp) REVERT: C 1013 SER cc_start: 0.8826 (t) cc_final: 0.8526 (p) REVERT: C 1023 MET cc_start: 0.8026 (mtp) cc_final: 0.7649 (mtp) REVERT: D 411 ASN cc_start: 0.7744 (m-40) cc_final: 0.7428 (m110) REVERT: D 460 TRP cc_start: 0.6804 (m100) cc_final: 0.6569 (m100) REVERT: D 524 GLU cc_start: 0.8354 (pm20) cc_final: 0.8000 (pm20) REVERT: D 531 PHE cc_start: 0.8400 (m-10) cc_final: 0.7791 (m-80) REVERT: D 544 SER cc_start: 0.8454 (m) cc_final: 0.7973 (t) REVERT: D 570 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7642 (mm-30) REVERT: D 609 THR cc_start: 0.9364 (p) cc_final: 0.9150 (t) REVERT: D 702 TYR cc_start: 0.7846 (t80) cc_final: 0.6955 (t80) REVERT: D 709 ASN cc_start: 0.8489 (t0) cc_final: 0.8260 (t0) REVERT: D 710 GLU cc_start: 0.8411 (tm-30) cc_final: 0.8073 (tm-30) REVERT: D 763 LYS cc_start: 0.9032 (tttt) cc_final: 0.8609 (tptt) REVERT: D 799 LEU cc_start: 0.9267 (tp) cc_final: 0.8979 (tt) outliers start: 16 outliers final: 6 residues processed: 632 average time/residue: 0.1325 time to fit residues: 126.0705 Evaluate side-chains 366 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 360 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.1980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.0040 chunk 200 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 435 HIS A 587 GLN ** A 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 642 GLN A 714 GLN A 950 HIS B 461 ASN B 587 GLN B 619 ASN C 435 HIS C 586 GLN C 619 ASN C 950 HIS D 461 ASN D 586 GLN D 587 GLN D 619 ASN D 791 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.125633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.098285 restraints weight = 43330.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.101231 restraints weight = 26231.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.102613 restraints weight = 17964.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.104017 restraints weight = 14307.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.103898 restraints weight = 13045.735| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.123 17054 Z= 0.144 Angle : 0.666 9.329 22890 Z= 0.350 Chirality : 0.044 0.206 2494 Planarity : 0.006 0.077 2778 Dihedral : 17.562 179.536 2662 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.23 % Allowed : 3.94 % Favored : 95.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 6.67 % 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: -1.41 (0.17), residues: 2020 helix: 0.07 (0.14), residues: 1094 sheet: -1.90 (0.31), residues: 236 loop : -2.11 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 715 TYR 0.022 0.002 TYR B 768 PHE 0.028 0.002 PHE C 901 TRP 0.045 0.002 TRP D 766 HIS 0.002 0.001 HIS A 435 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (17048) covalent geometry : angle 0.66461 / 0.35 (22878) SS BOND : bond 0.00738 / 0.38 ( 6) SS BOND : angle 2.12989 / 1.17 ( 12) hydrogen bonds : bond 0.05264 / 3.50 ( 824) hydrogen bonds : angle 4.36166 / 3.07 ( 2412) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 489 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 ASN cc_start: 0.7828 (m-40) cc_final: 0.7363 (m-40) REVERT: A 669 LYS cc_start: 0.9453 (ttpt) cc_final: 0.9039 (tttt) REVERT: A 835 LYS cc_start: 0.8489 (tppt) cc_final: 0.8104 (mmtt) REVERT: A 844 PHE cc_start: 0.8474 (m-80) cc_final: 0.8215 (m-80) REVERT: A 851 LEU cc_start: 0.8158 (tp) cc_final: 0.7898 (tp) REVERT: A 880 MET cc_start: 0.8240 (tmm) cc_final: 0.7648 (tmm) REVERT: A 937 PHE cc_start: 0.8687 (t80) cc_final: 0.8090 (t80) REVERT: A 947 ASN cc_start: 0.8320 (m110) cc_final: 0.7997 (m-40) REVERT: A 985 ASN cc_start: 0.8860 (m-40) cc_final: 0.8557 (m-40) REVERT: A 1023 MET cc_start: 0.8816 (mtp) cc_final: 0.8495 (mtp) REVERT: B 411 ASN cc_start: 0.8191 (m-40) cc_final: 0.7780 (m-40) REVERT: B 418 ASN cc_start: 0.7468 (p0) cc_final: 0.6949 (p0) REVERT: B 503 MET cc_start: 0.8061 (ttt) cc_final: 0.7831 (ttp) REVERT: B 702 TYR cc_start: 0.7807 (t80) cc_final: 0.7279 (t80) REVERT: B 813 GLU cc_start: 0.8267 (mt-10) cc_final: 0.8005 (mt-10) REVERT: C 502 ILE cc_start: 0.9486 (mp) cc_final: 0.9249 (mt) REVERT: C 527 MET cc_start: 0.8444 (ttm) cc_final: 0.8213 (ttm) REVERT: C 569 ASN cc_start: 0.7878 (t0) cc_final: 0.7038 (m-40) REVERT: C 573 ILE cc_start: 0.9010 (tp) cc_final: 0.8782 (tp) REVERT: C 604 VAL cc_start: 0.9636 (t) cc_final: 0.9422 (p) REVERT: C 616 TYR cc_start: 0.9122 (t80) cc_final: 0.8904 (t80) REVERT: C 655 THR cc_start: 0.9043 (m) cc_final: 0.8774 (p) REVERT: C 675 ARG cc_start: 0.7764 (ptm160) cc_final: 0.7369 (ptm160) REVERT: C 835 LYS cc_start: 0.8497 (tppt) cc_final: 0.8220 (ttpt) REVERT: C 866 GLU cc_start: 0.6840 (tp30) cc_final: 0.5949 (tt0) REVERT: C 880 MET cc_start: 0.8313 (tmm) cc_final: 0.7704 (tmm) REVERT: C 920 ASN cc_start: 0.8043 (t0) cc_final: 0.7730 (t0) REVERT: C 924 MET cc_start: 0.8113 (mmt) cc_final: 0.7467 (mmt) REVERT: C 950 HIS cc_start: 0.6366 (m-70) cc_final: 0.5911 (t-90) REVERT: C 1023 MET cc_start: 0.8380 (mtp) cc_final: 0.7912 (mtp) REVERT: C 1031 ARG cc_start: 0.6487 (ttp-110) cc_final: 0.6063 (mtp85) REVERT: D 411 ASN cc_start: 0.8056 (m-40) cc_final: 0.7489 (m110) REVERT: D 418 ASN cc_start: 0.7364 (p0) cc_final: 0.6504 (p0) REVERT: D 503 MET cc_start: 0.8331 (ttt) cc_final: 0.7839 (ttt) REVERT: D 524 GLU cc_start: 0.8673 (pm20) cc_final: 0.8370 (pm20) REVERT: D 537 SER cc_start: 0.9313 (p) cc_final: 0.8947 (t) REVERT: D 570 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7670 (mm-30) REVERT: D 702 TYR cc_start: 0.7928 (t80) cc_final: 0.7084 (t80) REVERT: D 710 GLU cc_start: 0.8320 (tm-30) cc_final: 0.7951 (tm-30) REVERT: D 714 GLN cc_start: 0.8206 (mm-40) cc_final: 0.7615 (mm-40) REVERT: D 746 VAL cc_start: 0.9045 (t) cc_final: 0.8772 (p) REVERT: D 763 LYS cc_start: 0.9094 (tttt) cc_final: 0.8580 (tptt) REVERT: D 798 ILE cc_start: 0.9445 (mt) cc_final: 0.9130 (tp) REVERT: D 813 GLU cc_start: 0.8304 (mt-10) cc_final: 0.8033 (mp0) outliers start: 4 outliers final: 0 residues processed: 492 average time/residue: 0.1135 time to fit residues: 87.3248 Evaluate side-chains 339 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 339 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 198 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 163 optimal weight: 8.9990 chunk 171 optimal weight: 2.9990 chunk 127 optimal weight: 5.9990 chunk 105 optimal weight: 0.2980 chunk 114 optimal weight: 0.7980 chunk 39 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 180 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 435 HIS A 587 GLN A 726 ASN B 586 GLN B 764 ASN C 411 ASN C 587 GLN C 619 ASN C 714 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.119660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.092280 restraints weight = 44389.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.094950 restraints weight = 26494.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.096498 restraints weight = 17174.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.096964 restraints weight = 14122.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.097035 restraints weight = 13040.187| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.4279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 17054 Z= 0.201 Angle : 0.704 8.884 22890 Z= 0.366 Chirality : 0.044 0.214 2494 Planarity : 0.005 0.073 2778 Dihedral : 16.742 177.361 2662 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.29 % Allowed : 4.12 % Favored : 95.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.05 % 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: -0.41 (0.19), residues: 2020 helix: 1.04 (0.15), residues: 1104 sheet: -1.81 (0.32), residues: 232 loop : -1.85 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 991 TYR 0.016 0.002 TYR B 700 PHE 0.029 0.002 PHE A 940 TRP 0.028 0.002 TRP C 767 HIS 0.004 0.001 HIS A 954 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.20 (17048) covalent geometry : angle 0.70207 / 0.37 (22878) SS BOND : bond 0.01472 / 0.94 ( 6) SS BOND : angle 2.39104 / 1.34 ( 12) hydrogen bonds : bond 0.04448 / 2.93 ( 824) hydrogen bonds : angle 4.38853 / 3.07 ( 2412) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 416 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 ASN cc_start: 0.8082 (m-40) cc_final: 0.7487 (m110) REVERT: A 419 GLU cc_start: 0.8576 (tp30) cc_final: 0.8149 (tp30) REVERT: A 425 CYS cc_start: 0.8821 (m) cc_final: 0.8510 (m) REVERT: A 537 SER cc_start: 0.9305 (m) cc_final: 0.8814 (t) REVERT: A 669 LYS cc_start: 0.9435 (ttpt) cc_final: 0.9152 (ttpt) REVERT: A 808 LEU cc_start: 0.8943 (tt) cc_final: 0.8601 (mp) REVERT: A 835 LYS cc_start: 0.8580 (tppt) cc_final: 0.8311 (mmtt) REVERT: A 851 LEU cc_start: 0.7996 (tp) cc_final: 0.7736 (tp) REVERT: A 880 MET cc_start: 0.8348 (tmm) cc_final: 0.7243 (tmm) REVERT: A 892 LEU cc_start: 0.7739 (tp) cc_final: 0.7472 (tp) REVERT: A 937 PHE cc_start: 0.8748 (t80) cc_final: 0.8375 (t80) REVERT: A 947 ASN cc_start: 0.8412 (m110) cc_final: 0.8136 (m110) REVERT: A 988 MET cc_start: 0.8150 (tpt) cc_final: 0.7920 (tpt) REVERT: A 1023 MET cc_start: 0.8738 (mtp) cc_final: 0.8304 (mtp) REVERT: B 411 ASN cc_start: 0.8129 (m-40) cc_final: 0.7711 (m-40) REVERT: B 418 ASN cc_start: 0.7553 (p0) cc_final: 0.6786 (p0) REVERT: B 604 VAL cc_start: 0.9774 (m) cc_final: 0.9546 (p) REVERT: B 708 MET cc_start: 0.8840 (mtm) cc_final: 0.8638 (mtt) REVERT: B 721 MET cc_start: 0.8362 (tpp) cc_final: 0.8105 (tpp) REVERT: B 789 LEU cc_start: 0.9533 (tp) cc_final: 0.9231 (tp) REVERT: B 813 GLU cc_start: 0.8264 (mt-10) cc_final: 0.7899 (mt-10) REVERT: C 427 ASP cc_start: 0.8656 (m-30) cc_final: 0.8452 (m-30) REVERT: C 503 MET cc_start: 0.8775 (ttm) cc_final: 0.8456 (ttt) REVERT: C 569 ASN cc_start: 0.8094 (t0) cc_final: 0.7159 (m-40) REVERT: C 596 LEU cc_start: 0.8906 (tt) cc_final: 0.8693 (tt) REVERT: C 655 THR cc_start: 0.9183 (m) cc_final: 0.8829 (p) REVERT: C 669 LYS cc_start: 0.9458 (ttpt) cc_final: 0.9164 (ttpt) REVERT: C 705 GLU cc_start: 0.8479 (mm-30) cc_final: 0.8278 (mm-30) REVERT: C 721 MET cc_start: 0.7917 (ptm) cc_final: 0.7584 (ptm) REVERT: C 815 CYS cc_start: 0.7408 (m) cc_final: 0.6527 (p) REVERT: C 835 LYS cc_start: 0.8652 (tppt) cc_final: 0.8437 (ttpt) REVERT: C 866 GLU cc_start: 0.6911 (tp30) cc_final: 0.6257 (tp30) REVERT: C 880 MET cc_start: 0.8341 (tmm) cc_final: 0.7651 (tmm) REVERT: C 939 MET cc_start: 0.8294 (mtm) cc_final: 0.7963 (mtm) REVERT: C 950 HIS cc_start: 0.6645 (m-70) cc_final: 0.5808 (t-90) REVERT: C 1013 SER cc_start: 0.9180 (t) cc_final: 0.8827 (p) REVERT: C 1023 MET cc_start: 0.8469 (mtp) cc_final: 0.8189 (mtp) REVERT: C 1029 MET cc_start: 0.8320 (mtp) cc_final: 0.7617 (tpp) REVERT: D 411 ASN cc_start: 0.7888 (m-40) cc_final: 0.7452 (m-40) REVERT: D 503 MET cc_start: 0.8702 (ttt) cc_final: 0.7628 (ttt) REVERT: D 537 SER cc_start: 0.9401 (p) cc_final: 0.9053 (t) REVERT: D 570 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7674 (mm-30) REVERT: D 710 GLU cc_start: 0.8426 (tm-30) cc_final: 0.8142 (tm-30) REVERT: D 746 VAL cc_start: 0.9168 (t) cc_final: 0.8848 (p) REVERT: D 813 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7649 (mt-10) outliers start: 5 outliers final: 0 residues processed: 418 average time/residue: 0.1086 time to fit residues: 71.5006 Evaluate side-chains 296 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 296 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 122 optimal weight: 4.9990 chunk 173 optimal weight: 3.9990 chunk 116 optimal weight: 0.5980 chunk 181 optimal weight: 0.6980 chunk 107 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 96 optimal weight: 30.0000 chunk 141 optimal weight: 6.9990 chunk 60 optimal weight: 10.0000 chunk 85 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 435 HIS ** C 435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 587 GLN C 619 ASN C 726 ASN D 586 GLN ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.117187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.089606 restraints weight = 45294.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.092386 restraints weight = 27123.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.094098 restraints weight = 18631.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.094935 restraints weight = 14232.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.094913 restraints weight = 13500.079| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.4871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 17054 Z= 0.236 Angle : 0.735 21.664 22890 Z= 0.381 Chirality : 0.046 0.341 2494 Planarity : 0.005 0.074 2778 Dihedral : 16.375 167.385 2662 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.17 % Allowed : 3.94 % Favored : 95.88 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.10 % 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: -0.21 (0.19), residues: 2020 helix: 1.28 (0.16), residues: 1092 sheet: -2.10 (0.35), residues: 180 loop : -1.79 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 715 TYR 0.019 0.002 TYR B 768 PHE 0.029 0.002 PHE A 901 TRP 0.029 0.002 TRP A 767 HIS 0.004 0.001 HIS A 954 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.23 (17048) covalent geometry : angle 0.73212 / 0.38 (22878) SS BOND : bond 0.02305 / 1.20 ( 6) SS BOND : angle 2.82348 / 1.63 ( 12) hydrogen bonds : bond 0.04243 / 2.77 ( 824) hydrogen bonds : angle 4.53344 / 3.18 ( 2412) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 373 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 ASN cc_start: 0.8132 (m-40) cc_final: 0.7644 (m110) REVERT: A 419 GLU cc_start: 0.8497 (tp30) cc_final: 0.8156 (tp30) REVERT: A 427 ASP cc_start: 0.8851 (m-30) cc_final: 0.8645 (m-30) REVERT: A 519 ASP cc_start: 0.7842 (m-30) cc_final: 0.7580 (m-30) REVERT: A 537 SER cc_start: 0.9335 (m) cc_final: 0.8810 (t) REVERT: A 705 GLU cc_start: 0.7813 (pm20) cc_final: 0.5888 (mp0) REVERT: A 808 LEU cc_start: 0.8946 (tt) cc_final: 0.8567 (mp) REVERT: A 835 LYS cc_start: 0.8558 (tppt) cc_final: 0.8243 (mmtt) REVERT: A 851 LEU cc_start: 0.7968 (tp) cc_final: 0.7736 (tp) REVERT: A 937 PHE cc_start: 0.8750 (t80) cc_final: 0.8298 (t80) REVERT: A 947 ASN cc_start: 0.8544 (m110) cc_final: 0.8256 (m110) REVERT: A 1023 MET cc_start: 0.8776 (mtp) cc_final: 0.8391 (mtp) REVERT: B 411 ASN cc_start: 0.8022 (m-40) cc_final: 0.7594 (m-40) REVERT: B 524 GLU cc_start: 0.8581 (pm20) cc_final: 0.8207 (pm20) REVERT: B 528 CYS cc_start: 0.8732 (m) cc_final: 0.8436 (m) REVERT: B 604 VAL cc_start: 0.9777 (m) cc_final: 0.9573 (p) REVERT: B 670 MET cc_start: 0.9120 (mmp) cc_final: 0.8608 (mmm) REVERT: B 714 GLN cc_start: 0.8371 (mm-40) cc_final: 0.7925 (tt0) REVERT: B 721 MET cc_start: 0.8399 (tpp) cc_final: 0.8181 (tpp) REVERT: B 747 ASN cc_start: 0.8678 (m-40) cc_final: 0.8418 (m-40) REVERT: B 813 GLU cc_start: 0.8375 (mt-10) cc_final: 0.7759 (mt-10) REVERT: C 569 ASN cc_start: 0.8200 (t0) cc_final: 0.7346 (m-40) REVERT: C 655 THR cc_start: 0.9178 (m) cc_final: 0.8932 (p) REVERT: C 669 LYS cc_start: 0.9399 (ttpt) cc_final: 0.9065 (tttt) REVERT: C 705 GLU cc_start: 0.8475 (mm-30) cc_final: 0.8186 (mm-30) REVERT: C 756 GLN cc_start: 0.8546 (tm-30) cc_final: 0.8119 (tm-30) REVERT: C 813 GLU cc_start: 0.8988 (pp20) cc_final: 0.8372 (tt0) REVERT: C 815 CYS cc_start: 0.7653 (m) cc_final: 0.6564 (p) REVERT: C 840 LEU cc_start: 0.8145 (tp) cc_final: 0.7785 (tp) REVERT: C 844 PHE cc_start: 0.7910 (m-80) cc_final: 0.7546 (m-80) REVERT: C 874 GLN cc_start: 0.7228 (pt0) cc_final: 0.5665 (mm110) REVERT: C 924 MET cc_start: 0.8246 (mmt) cc_final: 0.7382 (mmt) REVERT: C 950 HIS cc_start: 0.6488 (m-70) cc_final: 0.5733 (m-70) REVERT: C 1013 SER cc_start: 0.9184 (t) cc_final: 0.8895 (p) REVERT: C 1023 MET cc_start: 0.8623 (mtp) cc_final: 0.8119 (mtp) REVERT: C 1029 MET cc_start: 0.8232 (mtp) cc_final: 0.7577 (tpp) REVERT: D 411 ASN cc_start: 0.7839 (m-40) cc_final: 0.7439 (m-40) REVERT: D 503 MET cc_start: 0.8740 (ttt) cc_final: 0.7607 (ttt) REVERT: D 524 GLU cc_start: 0.8598 (pm20) cc_final: 0.8331 (pm20) REVERT: D 533 TYR cc_start: 0.9285 (t80) cc_final: 0.8952 (t80) REVERT: D 537 SER cc_start: 0.9397 (p) cc_final: 0.9092 (t) REVERT: D 747 ASN cc_start: 0.8857 (m110) cc_final: 0.8639 (m110) REVERT: D 813 GLU cc_start: 0.8301 (mt-10) cc_final: 0.7800 (mt-10) outliers start: 3 outliers final: 0 residues processed: 376 average time/residue: 0.1055 time to fit residues: 63.9646 Evaluate side-chains 295 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 295 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 144 optimal weight: 8.9990 chunk 7 optimal weight: 0.9980 chunk 129 optimal weight: 4.9990 chunk 143 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 154 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 192 optimal weight: 9.9990 chunk 163 optimal weight: 8.9990 chunk 103 optimal weight: 6.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 726 ASN C 587 GLN C 619 ASN ** D 587 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 = 0.3689 r_free = 0.3689 target = 0.115607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.088794 restraints weight = 45140.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.090959 restraints weight = 28803.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.092577 restraints weight = 19370.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.092900 restraints weight = 15779.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.092968 restraints weight = 15115.411| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.5324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 17054 Z= 0.274 Angle : 0.783 24.424 22890 Z= 0.404 Chirality : 0.047 0.397 2494 Planarity : 0.005 0.076 2778 Dihedral : 16.279 157.624 2662 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.23 % Allowed : 3.71 % Favored : 96.06 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.15 % 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: -0.37 (0.19), residues: 2020 helix: 1.21 (0.16), residues: 1098 sheet: -2.58 (0.32), residues: 194 loop : -1.83 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1031 TYR 0.020 0.002 TYR D 673 PHE 0.031 0.002 PHE A 901 TRP 0.028 0.002 TRP C 861 HIS 0.005 0.001 HIS C 954 Details of bonding type rmsd/Z covalent geometry : bond 0.00609 / 0.27 (17048) covalent geometry : angle 0.77842 / 0.40 (22878) SS BOND : bond 0.02586 / 1.48 ( 6) SS BOND : angle 3.80101 / 2.39 ( 12) hydrogen bonds : bond 0.04346 / 2.85 ( 824) hydrogen bonds : angle 4.76218 / 3.34 ( 2412) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 353 time to evaluate : 0.525 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: A 418 ASN cc_start: 0.8121 (m-40) cc_final: 0.7659 (m110) REVERT: A 419 GLU cc_start: 0.8546 (tp30) cc_final: 0.8259 (tp30) REVERT: A 503 MET cc_start: 0.8955 (tmm) cc_final: 0.8613 (tmm) REVERT: A 537 SER cc_start: 0.9303 (m) cc_final: 0.8810 (t) REVERT: A 710 GLU cc_start: 0.9190 (mt-10) cc_final: 0.8769 (mt-10) REVERT: A 808 LEU cc_start: 0.8910 (tt) cc_final: 0.8552 (mp) REVERT: A 835 LYS cc_start: 0.8431 (tppt) cc_final: 0.8219 (mmtt) REVERT: A 844 PHE cc_start: 0.8456 (m-80) cc_final: 0.8245 (m-80) REVERT: A 851 LEU cc_start: 0.7936 (tp) cc_final: 0.7725 (tp) REVERT: A 880 MET cc_start: 0.8257 (tmm) cc_final: 0.7908 (tmm) REVERT: A 937 PHE cc_start: 0.8786 (t80) cc_final: 0.8403 (t80) REVERT: A 947 ASN cc_start: 0.8692 (m110) cc_final: 0.8334 (m110) REVERT: A 1023 MET cc_start: 0.8781 (mtp) cc_final: 0.8344 (mtp) REVERT: B 411 ASN cc_start: 0.7949 (m-40) cc_final: 0.7435 (m-40) REVERT: B 463 MET cc_start: 0.7836 (mmm) cc_final: 0.7259 (mmt) REVERT: B 503 MET cc_start: 0.8851 (ttt) cc_final: 0.8628 (ttt) REVERT: B 524 GLU cc_start: 0.8512 (pm20) cc_final: 0.8135 (pm20) REVERT: B 528 CYS cc_start: 0.8684 (m) cc_final: 0.8417 (m) REVERT: B 544 SER cc_start: 0.9096 (m) cc_final: 0.8818 (t) REVERT: B 708 MET cc_start: 0.8969 (mtm) cc_final: 0.8721 (mtt) REVERT: B 714 GLN cc_start: 0.8671 (mm-40) cc_final: 0.7747 (tt0) REVERT: B 726 ASN cc_start: 0.8623 (OUTLIER) cc_final: 0.8401 (m110) REVERT: B 813 GLU cc_start: 0.8387 (mt-10) cc_final: 0.7725 (mt-10) REVERT: C 425 CYS cc_start: 0.8806 (m) cc_final: 0.8597 (m) REVERT: C 503 MET cc_start: 0.8811 (ttm) cc_final: 0.8445 (tmm) REVERT: C 705 GLU cc_start: 0.8396 (mm-30) cc_final: 0.8054 (mm-30) REVERT: C 756 GLN cc_start: 0.8675 (tm-30) cc_final: 0.8277 (tm-30) REVERT: C 813 GLU cc_start: 0.8939 (pp20) cc_final: 0.8573 (tt0) REVERT: C 815 CYS cc_start: 0.7958 (m) cc_final: 0.6693 (p) REVERT: C 840 LEU cc_start: 0.8243 (tp) cc_final: 0.7792 (tp) REVERT: C 844 PHE cc_start: 0.7845 (m-80) cc_final: 0.7468 (m-80) REVERT: C 880 MET cc_start: 0.8394 (tmm) cc_final: 0.8113 (tmm) REVERT: C 924 MET cc_start: 0.8112 (mmt) cc_final: 0.7753 (mmt) REVERT: C 955 ARG cc_start: 0.4999 (mmm-85) cc_final: 0.3250 (ptt-90) REVERT: C 1023 MET cc_start: 0.8607 (mtp) cc_final: 0.8046 (mtt) REVERT: C 1029 MET cc_start: 0.8188 (mtp) cc_final: 0.7624 (tpp) REVERT: D 407 MET cc_start: 0.6293 (mtp) cc_final: 0.5934 (mtm) REVERT: D 411 ASN cc_start: 0.7802 (m-40) cc_final: 0.7420 (m-40) REVERT: D 503 MET cc_start: 0.8849 (ttt) cc_final: 0.8346 (ttt) REVERT: D 524 GLU cc_start: 0.8563 (pm20) cc_final: 0.8331 (pm20) REVERT: D 709 ASN cc_start: 0.8516 (t0) cc_final: 0.8033 (m-40) REVERT: D 742 LEU cc_start: 0.9327 (pp) cc_final: 0.9117 (pp) REVERT: D 747 ASN cc_start: 0.8833 (m110) cc_final: 0.8607 (m-40) REVERT: D 764 ASN cc_start: 0.8694 (m110) cc_final: 0.8422 (m110) REVERT: D 813 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7571 (mt-10) outliers start: 4 outliers final: 0 residues processed: 356 average time/residue: 0.1014 time to fit residues: 57.9806 Evaluate side-chains 275 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 274 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 32 optimal weight: 0.9990 chunk 174 optimal weight: 0.6980 chunk 98 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 192 optimal weight: 7.9990 chunk 91 optimal weight: 7.9990 chunk 169 optimal weight: 6.9990 chunk 130 optimal weight: 0.9990 chunk 40 optimal weight: 9.9990 chunk 94 optimal weight: 0.8980 chunk 151 optimal weight: 7.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 435 HIS B 461 ASN B 619 ASN B 764 ASN C 508 GLN C 587 GLN C 619 ASN ** C 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 947 ASN ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 619 ASN D 764 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.119958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.093444 restraints weight = 43677.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.095599 restraints weight = 28652.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.097016 restraints weight = 19057.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.097782 restraints weight = 15644.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.097821 restraints weight = 14384.465| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.5443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17054 Z= 0.138 Angle : 0.674 19.660 22890 Z= 0.343 Chirality : 0.044 0.323 2494 Planarity : 0.005 0.075 2778 Dihedral : 15.291 154.440 2662 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.12 % Allowed : 2.26 % Favored : 97.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.15 % 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: 0.03 (0.20), residues: 2020 helix: 1.55 (0.16), residues: 1096 sheet: -2.27 (0.33), residues: 184 loop : -1.75 (0.24), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1031 TYR 0.018 0.001 TYR B 732 PHE 0.053 0.002 PHE A 938 TRP 0.023 0.001 TRP A 767 HIS 0.002 0.001 HIS A 883 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (17048) covalent geometry : angle 0.66951 / 0.34 (22878) SS BOND : bond 0.01489 / 0.85 ( 6) SS BOND : angle 3.36608 / 2.07 ( 12) hydrogen bonds : bond 0.03902 / 2.56 ( 824) hydrogen bonds : angle 4.23128 / 2.96 ( 2412) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 369 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 ASN cc_start: 0.8027 (m-40) cc_final: 0.7576 (m110) REVERT: A 419 GLU cc_start: 0.8478 (tp30) cc_final: 0.8257 (tp30) REVERT: A 529 ILE cc_start: 0.9691 (mt) cc_final: 0.9487 (mt) REVERT: A 616 TYR cc_start: 0.9470 (t80) cc_final: 0.9231 (t80) REVERT: A 808 LEU cc_start: 0.8860 (tt) cc_final: 0.8488 (mp) REVERT: A 835 LYS cc_start: 0.8411 (tppt) cc_final: 0.8170 (mmtt) REVERT: A 851 LEU cc_start: 0.7963 (tp) cc_final: 0.7731 (tp) REVERT: A 880 MET cc_start: 0.8378 (tmm) cc_final: 0.7986 (tmm) REVERT: A 937 PHE cc_start: 0.8621 (t80) cc_final: 0.8189 (t80) REVERT: A 947 ASN cc_start: 0.8622 (m110) cc_final: 0.8240 (m110) REVERT: A 987 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7730 (mt-10) REVERT: A 1023 MET cc_start: 0.8721 (mtp) cc_final: 0.8100 (mtp) REVERT: B 399 THR cc_start: 0.7576 (m) cc_final: 0.6995 (p) REVERT: B 407 MET cc_start: 0.6170 (mtp) cc_final: 0.5898 (mmp) REVERT: B 411 ASN cc_start: 0.8004 (m-40) cc_final: 0.7436 (m-40) REVERT: B 463 MET cc_start: 0.7790 (mmm) cc_final: 0.7237 (mmt) REVERT: B 524 GLU cc_start: 0.8489 (pm20) cc_final: 0.8051 (pm20) REVERT: B 528 CYS cc_start: 0.8688 (m) cc_final: 0.8384 (m) REVERT: B 537 SER cc_start: 0.9421 (p) cc_final: 0.8977 (t) REVERT: B 700 TYR cc_start: 0.6584 (t80) cc_final: 0.6336 (t80) REVERT: B 708 MET cc_start: 0.8870 (mtm) cc_final: 0.8659 (mtt) REVERT: B 714 GLN cc_start: 0.8400 (mm-40) cc_final: 0.7638 (tt0) REVERT: B 726 ASN cc_start: 0.8969 (m-40) cc_final: 0.8747 (m-40) REVERT: B 744 THR cc_start: 0.7896 (m) cc_final: 0.7682 (m) REVERT: B 747 ASN cc_start: 0.8697 (m110) cc_final: 0.8382 (m110) REVERT: B 813 GLU cc_start: 0.8311 (mt-10) cc_final: 0.7669 (mt-10) REVERT: C 585 MET cc_start: 0.9107 (mmm) cc_final: 0.8713 (mmm) REVERT: C 596 LEU cc_start: 0.8953 (tt) cc_final: 0.8679 (tt) REVERT: C 705 GLU cc_start: 0.8325 (mm-30) cc_final: 0.8030 (mm-30) REVERT: C 756 GLN cc_start: 0.8502 (tm-30) cc_final: 0.8239 (tm-30) REVERT: C 807 MET cc_start: 0.8862 (mmm) cc_final: 0.8498 (mmm) REVERT: C 813 GLU cc_start: 0.8871 (pp20) cc_final: 0.8631 (tt0) REVERT: C 815 CYS cc_start: 0.7810 (m) cc_final: 0.6477 (p) REVERT: C 840 LEU cc_start: 0.8139 (tp) cc_final: 0.7749 (tp) REVERT: C 844 PHE cc_start: 0.7825 (m-80) cc_final: 0.7475 (m-80) REVERT: C 924 MET cc_start: 0.8031 (mmt) cc_final: 0.7766 (mmt) REVERT: C 939 MET cc_start: 0.8197 (mtm) cc_final: 0.7990 (mtm) REVERT: C 950 HIS cc_start: 0.6763 (m-70) cc_final: 0.6160 (m-70) REVERT: C 955 ARG cc_start: 0.4825 (mmm-85) cc_final: 0.3070 (ptt-90) REVERT: C 1009 PHE cc_start: 0.8393 (m-10) cc_final: 0.8165 (m-10) REVERT: C 1023 MET cc_start: 0.8626 (mtp) cc_final: 0.8061 (mtp) REVERT: C 1029 MET cc_start: 0.8108 (mtp) cc_final: 0.7486 (tpp) REVERT: D 503 MET cc_start: 0.8829 (ttt) cc_final: 0.8291 (ttt) REVERT: D 529 ILE cc_start: 0.9734 (mp) cc_final: 0.9518 (mp) REVERT: D 533 TYR cc_start: 0.9320 (t80) cc_final: 0.8865 (t80) REVERT: D 537 SER cc_start: 0.9359 (p) cc_final: 0.9018 (t) REVERT: D 673 TYR cc_start: 0.7863 (t80) cc_final: 0.7627 (t80) REVERT: D 709 ASN cc_start: 0.8592 (t0) cc_final: 0.8002 (m-40) REVERT: D 714 GLN cc_start: 0.8271 (mm-40) cc_final: 0.7560 (mm-40) REVERT: D 742 LEU cc_start: 0.9325 (pp) cc_final: 0.9089 (pp) REVERT: D 747 ASN cc_start: 0.8792 (m110) cc_final: 0.8511 (m110) REVERT: D 764 ASN cc_start: 0.8758 (m-40) cc_final: 0.8484 (m110) REVERT: D 813 GLU cc_start: 0.8196 (mt-10) cc_final: 0.7501 (mt-10) outliers start: 2 outliers final: 0 residues processed: 371 average time/residue: 0.1103 time to fit residues: 65.9397 Evaluate side-chains 280 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 280 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 59 optimal weight: 6.9990 chunk 82 optimal weight: 4.9990 chunk 146 optimal weight: 0.3980 chunk 121 optimal weight: 0.7980 chunk 148 optimal weight: 0.8980 chunk 191 optimal weight: 6.9990 chunk 144 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 135 optimal weight: 6.9990 chunk 27 optimal weight: 0.2980 chunk 184 optimal weight: 9.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 435 HIS A 714 GLN B 764 ASN C 587 GLN C 619 ASN C 747 ASN C 947 ASN ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.119558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.092098 restraints weight = 44351.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.094939 restraints weight = 27236.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.096809 restraints weight = 18410.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.097671 restraints weight = 13773.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.097670 restraints weight = 13145.821| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.5658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 17054 Z= 0.148 Angle : 0.680 21.417 22890 Z= 0.347 Chirality : 0.044 0.379 2494 Planarity : 0.005 0.077 2778 Dihedral : 14.845 152.900 2662 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.10 % 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: 0.03 (0.19), residues: 2020 helix: 1.51 (0.16), residues: 1102 sheet: -2.22 (0.33), residues: 184 loop : -1.72 (0.24), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1031 TYR 0.020 0.002 TYR A 424 PHE 0.054 0.002 PHE A 901 TRP 0.028 0.002 TRP A 767 HIS 0.003 0.001 HIS A 883 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (17048) covalent geometry : angle 0.67430 / 0.34 (22878) SS BOND : bond 0.01892 / 1.21 ( 6) SS BOND : angle 4.01811 / 2.52 ( 12) hydrogen bonds : bond 0.03834 / 2.51 ( 824) hydrogen bonds : angle 4.23670 / 2.96 ( 2412) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 359 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 ASN cc_start: 0.8160 (m-40) cc_final: 0.7702 (m110) REVERT: A 419 GLU cc_start: 0.8574 (tp30) cc_final: 0.8155 (tp30) REVERT: A 434 LYS cc_start: 0.9017 (mmmt) cc_final: 0.8126 (ptmt) REVERT: A 491 PHE cc_start: 0.8257 (m-10) cc_final: 0.7944 (m-10) REVERT: A 537 SER cc_start: 0.9330 (m) cc_final: 0.8890 (t) REVERT: A 616 TYR cc_start: 0.9477 (t80) cc_final: 0.9229 (t80) REVERT: A 708 MET cc_start: 0.8975 (mpp) cc_final: 0.8556 (mtm) REVERT: A 808 LEU cc_start: 0.8817 (tt) cc_final: 0.8429 (mp) REVERT: A 835 LYS cc_start: 0.8401 (tppt) cc_final: 0.8191 (mmtt) REVERT: A 851 LEU cc_start: 0.7898 (tp) cc_final: 0.7637 (tp) REVERT: A 874 GLN cc_start: 0.6944 (pt0) cc_final: 0.6695 (pt0) REVERT: A 880 MET cc_start: 0.8213 (tmm) cc_final: 0.7884 (tmm) REVERT: A 937 PHE cc_start: 0.8659 (t80) cc_final: 0.8176 (t80) REVERT: A 947 ASN cc_start: 0.8653 (m110) cc_final: 0.8297 (m110) REVERT: A 1023 MET cc_start: 0.8658 (mtp) cc_final: 0.8142 (mtp) REVERT: B 407 MET cc_start: 0.6055 (mtp) cc_final: 0.5837 (mmp) REVERT: B 411 ASN cc_start: 0.8014 (m-40) cc_final: 0.7425 (m-40) REVERT: B 496 MET cc_start: 0.7820 (pmm) cc_final: 0.7397 (pmm) REVERT: B 524 GLU cc_start: 0.8509 (pm20) cc_final: 0.8070 (pm20) REVERT: B 528 CYS cc_start: 0.8773 (m) cc_final: 0.8458 (m) REVERT: B 537 SER cc_start: 0.9335 (p) cc_final: 0.9069 (t) REVERT: B 700 TYR cc_start: 0.6552 (t80) cc_final: 0.6283 (t80) REVERT: B 726 ASN cc_start: 0.9010 (m-40) cc_final: 0.8717 (m-40) REVERT: B 744 THR cc_start: 0.7904 (m) cc_final: 0.7689 (m) REVERT: B 747 ASN cc_start: 0.8816 (m110) cc_final: 0.8465 (m110) REVERT: B 813 GLU cc_start: 0.8342 (mt-10) cc_final: 0.7717 (mt-10) REVERT: C 569 ASN cc_start: 0.8235 (t0) cc_final: 0.7294 (m-40) REVERT: C 596 LEU cc_start: 0.8907 (tt) cc_final: 0.8578 (tt) REVERT: C 655 THR cc_start: 0.8995 (p) cc_final: 0.8639 (p) REVERT: C 813 GLU cc_start: 0.8895 (pp20) cc_final: 0.8658 (tt0) REVERT: C 815 CYS cc_start: 0.7744 (m) cc_final: 0.6431 (p) REVERT: C 840 LEU cc_start: 0.8157 (tp) cc_final: 0.7845 (tp) REVERT: C 874 GLN cc_start: 0.7180 (pt0) cc_final: 0.5395 (mm110) REVERT: C 924 MET cc_start: 0.8138 (mmt) cc_final: 0.7787 (mmt) REVERT: C 939 MET cc_start: 0.8301 (mtm) cc_final: 0.8093 (mtm) REVERT: C 950 HIS cc_start: 0.6772 (m-70) cc_final: 0.6209 (m-70) REVERT: C 955 ARG cc_start: 0.5051 (mmm-85) cc_final: 0.3099 (ptt90) REVERT: C 1009 PHE cc_start: 0.8349 (m-10) cc_final: 0.8112 (m-10) REVERT: C 1023 MET cc_start: 0.8654 (mtp) cc_final: 0.8076 (mtp) REVERT: C 1029 MET cc_start: 0.8161 (mtp) cc_final: 0.7553 (tpp) REVERT: D 503 MET cc_start: 0.8919 (ttt) cc_final: 0.8262 (ttt) REVERT: D 529 ILE cc_start: 0.9709 (mp) cc_final: 0.9482 (mp) REVERT: D 533 TYR cc_start: 0.9312 (t80) cc_final: 0.8865 (t80) REVERT: D 537 SER cc_start: 0.9353 (p) cc_final: 0.9066 (t) REVERT: D 709 ASN cc_start: 0.8638 (t0) cc_final: 0.8032 (m-40) REVERT: D 714 GLN cc_start: 0.8181 (mm-40) cc_final: 0.7756 (mm-40) REVERT: D 747 ASN cc_start: 0.8798 (m110) cc_final: 0.8524 (m-40) REVERT: D 764 ASN cc_start: 0.8818 (m-40) cc_final: 0.8552 (m110) REVERT: D 813 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7543 (mt-10) outliers start: 0 outliers final: 0 residues processed: 359 average time/residue: 0.1075 time to fit residues: 62.2833 Evaluate side-chains 280 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 280 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 17 optimal weight: 0.5980 chunk 201 optimal weight: 0.8980 chunk 61 optimal weight: 7.9990 chunk 114 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 chunk 116 optimal weight: 0.5980 chunk 37 optimal weight: 7.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 435 HIS A 714 GLN A 947 ASN B 619 ASN B 714 GLN B 764 ASN C 587 GLN C 619 ASN ** D 587 GLN ** 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 = 0.3794 r_free = 0.3794 target = 0.122047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.094164 restraints weight = 44625.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.096949 restraints weight = 28495.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.098752 restraints weight = 18315.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.099144 restraints weight = 14938.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.099139 restraints weight = 14055.698| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.5880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17054 Z= 0.126 Angle : 0.660 15.405 22890 Z= 0.336 Chirality : 0.043 0.318 2494 Planarity : 0.005 0.078 2778 Dihedral : 14.280 151.321 2662 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.15 % 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: 0.16 (0.20), residues: 2020 helix: 1.60 (0.16), residues: 1102 sheet: -2.34 (0.34), residues: 184 loop : -1.57 (0.24), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 628 TYR 0.020 0.001 TYR A 424 PHE 0.050 0.002 PHE C 938 TRP 0.025 0.001 TRP A 767 HIS 0.003 0.001 HIS C 883 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (17048) covalent geometry : angle 0.65560 / 0.33 (22878) SS BOND : bond 0.01438 / 0.82 ( 6) SS BOND : angle 3.46307 / 2.10 ( 12) hydrogen bonds : bond 0.03615 / 2.36 ( 824) hydrogen bonds : angle 4.12327 / 2.86 ( 2412) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 372 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 ASN cc_start: 0.7981 (m-40) cc_final: 0.7576 (m110) REVERT: A 419 GLU cc_start: 0.8510 (tp30) cc_final: 0.7985 (tp30) REVERT: A 434 LYS cc_start: 0.8895 (mmmt) cc_final: 0.8009 (ptmt) REVERT: A 537 SER cc_start: 0.9298 (m) cc_final: 0.8867 (t) REVERT: A 585 MET cc_start: 0.9205 (mmm) cc_final: 0.8610 (mmm) REVERT: A 616 TYR cc_start: 0.9430 (t80) cc_final: 0.9163 (t80) REVERT: A 708 MET cc_start: 0.8861 (mpp) cc_final: 0.8494 (mtm) REVERT: A 808 LEU cc_start: 0.8694 (tt) cc_final: 0.8372 (mp) REVERT: A 851 LEU cc_start: 0.7991 (tp) cc_final: 0.7761 (tp) REVERT: A 874 GLN cc_start: 0.6859 (pt0) cc_final: 0.6608 (pt0) REVERT: A 937 PHE cc_start: 0.8644 (t80) cc_final: 0.8135 (t80) REVERT: A 947 ASN cc_start: 0.8394 (m-40) cc_final: 0.8095 (m-40) REVERT: A 1023 MET cc_start: 0.8610 (mtp) cc_final: 0.8179 (mtp) REVERT: B 407 MET cc_start: 0.5967 (mtp) cc_final: 0.5693 (mmp) REVERT: B 411 ASN cc_start: 0.7963 (m-40) cc_final: 0.7348 (m-40) REVERT: B 496 MET cc_start: 0.7758 (pmm) cc_final: 0.7227 (pmm) REVERT: B 533 TYR cc_start: 0.9276 (t80) cc_final: 0.8962 (t80) REVERT: B 537 SER cc_start: 0.9226 (p) cc_final: 0.8947 (t) REVERT: B 714 GLN cc_start: 0.7788 (tt0) cc_final: 0.7508 (tt0) REVERT: B 726 ASN cc_start: 0.8950 (m-40) cc_final: 0.8679 (m-40) REVERT: B 744 THR cc_start: 0.7876 (m) cc_final: 0.7647 (m) REVERT: B 747 ASN cc_start: 0.8668 (m110) cc_final: 0.8345 (m110) REVERT: B 767 TRP cc_start: 0.7750 (m-10) cc_final: 0.7451 (m-10) REVERT: B 813 GLU cc_start: 0.8249 (mt-10) cc_final: 0.7654 (mt-10) REVERT: C 585 MET cc_start: 0.8993 (mmm) cc_final: 0.8413 (mmm) REVERT: C 596 LEU cc_start: 0.8836 (tt) cc_final: 0.8487 (tt) REVERT: C 655 THR cc_start: 0.9037 (p) cc_final: 0.8477 (p) REVERT: C 708 MET cc_start: 0.8907 (mpp) cc_final: 0.8350 (mtm) REVERT: C 807 MET cc_start: 0.8772 (mmm) cc_final: 0.8437 (mmm) REVERT: C 813 GLU cc_start: 0.8830 (pp20) cc_final: 0.8581 (tt0) REVERT: C 815 CYS cc_start: 0.7751 (m) cc_final: 0.6427 (p) REVERT: C 840 LEU cc_start: 0.8043 (tp) cc_final: 0.7796 (mt) REVERT: C 874 GLN cc_start: 0.7167 (pt0) cc_final: 0.5386 (mm110) REVERT: C 892 LEU cc_start: 0.7978 (tp) cc_final: 0.7653 (tp) REVERT: C 924 MET cc_start: 0.8168 (mmt) cc_final: 0.7807 (mmt) REVERT: C 937 PHE cc_start: 0.8436 (t80) cc_final: 0.8030 (t80) REVERT: C 955 ARG cc_start: 0.5004 (mmm-85) cc_final: 0.2929 (ttp80) REVERT: C 1023 MET cc_start: 0.8656 (mtp) cc_final: 0.8167 (mtp) REVERT: C 1029 MET cc_start: 0.8098 (mtp) cc_final: 0.7528 (tpp) REVERT: D 503 MET cc_start: 0.8860 (ttt) cc_final: 0.8332 (ttt) REVERT: D 529 ILE cc_start: 0.9678 (mp) cc_final: 0.9467 (mp) REVERT: D 533 TYR cc_start: 0.9312 (t80) cc_final: 0.8949 (t80) REVERT: D 537 SER cc_start: 0.9321 (p) cc_final: 0.9015 (t) REVERT: D 709 ASN cc_start: 0.8516 (t0) cc_final: 0.7959 (m-40) REVERT: D 747 ASN cc_start: 0.8842 (m110) cc_final: 0.8612 (m-40) REVERT: D 764 ASN cc_start: 0.8823 (m-40) cc_final: 0.8555 (m110) REVERT: D 813 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7527 (mt-10) outliers start: 0 outliers final: 0 residues processed: 372 average time/residue: 0.1074 time to fit residues: 64.2081 Evaluate side-chains 287 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 287 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 21 optimal weight: 0.6980 chunk 109 optimal weight: 5.9990 chunk 94 optimal weight: 7.9990 chunk 24 optimal weight: 6.9990 chunk 176 optimal weight: 0.7980 chunk 168 optimal weight: 10.0000 chunk 172 optimal weight: 0.5980 chunk 131 optimal weight: 0.5980 chunk 58 optimal weight: 8.9990 chunk 152 optimal weight: 5.9990 chunk 93 optimal weight: 10.0000 overall best weight: 1.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 435 HIS A 947 ASN B 619 ASN B 714 GLN B 764 ASN C 619 ASN ** C 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.119660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.092192 restraints weight = 45114.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.094600 restraints weight = 29757.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.096142 restraints weight = 19663.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.096659 restraints weight = 16158.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.096745 restraints weight = 15285.921| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.5986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 17054 Z= 0.176 Angle : 0.696 13.554 22890 Z= 0.357 Chirality : 0.044 0.282 2494 Planarity : 0.005 0.080 2778 Dihedral : 14.358 149.349 2662 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.19), residues: 2020 helix: 1.51 (0.16), residues: 1096 sheet: -2.28 (0.33), residues: 194 loop : -1.59 (0.24), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C1031 TYR 0.021 0.002 TYR C1026 PHE 0.055 0.002 PHE A 938 TRP 0.028 0.002 TRP A 767 HIS 0.004 0.001 HIS A 883 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.18 (17048) covalent geometry : angle 0.69239 / 0.36 (22878) SS BOND : bond 0.01081 / 0.54 ( 6) SS BOND : angle 3.32853 / 1.91 ( 12) hydrogen bonds : bond 0.03919 / 2.56 ( 824) hydrogen bonds : angle 4.31156 / 3.00 ( 2412) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 346 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 ASN cc_start: 0.8075 (m-40) cc_final: 0.7563 (m-40) REVERT: A 419 GLU cc_start: 0.8559 (tp30) cc_final: 0.7925 (tp30) REVERT: A 434 LYS cc_start: 0.8928 (mmmt) cc_final: 0.8016 (ptmt) REVERT: A 537 SER cc_start: 0.9294 (m) cc_final: 0.8900 (t) REVERT: A 585 MET cc_start: 0.9245 (mmm) cc_final: 0.8596 (mmm) REVERT: A 708 MET cc_start: 0.8905 (mpp) cc_final: 0.8564 (mtm) REVERT: A 714 GLN cc_start: 0.8853 (mp10) cc_final: 0.8478 (mm-40) REVERT: A 807 MET cc_start: 0.8906 (mmm) cc_final: 0.8592 (mmm) REVERT: A 808 LEU cc_start: 0.8735 (tt) cc_final: 0.8397 (mp) REVERT: A 881 SER cc_start: 0.8136 (t) cc_final: 0.7865 (m) REVERT: A 937 PHE cc_start: 0.8654 (t80) cc_final: 0.8151 (t80) REVERT: A 947 ASN cc_start: 0.8512 (m110) cc_final: 0.8229 (m110) REVERT: A 1023 MET cc_start: 0.8640 (mtp) cc_final: 0.8157 (mtp) REVERT: B 411 ASN cc_start: 0.7943 (m-40) cc_final: 0.7355 (m-40) REVERT: B 496 MET cc_start: 0.7726 (pmm) cc_final: 0.7312 (pmm) REVERT: B 537 SER cc_start: 0.9324 (p) cc_final: 0.9053 (t) REVERT: B 726 ASN cc_start: 0.9000 (m-40) cc_final: 0.8763 (m-40) REVERT: B 764 ASN cc_start: 0.8190 (m-40) cc_final: 0.7977 (m110) REVERT: B 813 GLU cc_start: 0.8348 (mt-10) cc_final: 0.7709 (mt-10) REVERT: C 537 SER cc_start: 0.9180 (m) cc_final: 0.8738 (t) REVERT: C 585 MET cc_start: 0.9156 (mmm) cc_final: 0.8630 (mmm) REVERT: C 596 LEU cc_start: 0.8869 (tt) cc_final: 0.8512 (tt) REVERT: C 708 MET cc_start: 0.8908 (mpp) cc_final: 0.7618 (mtm) REVERT: C 807 MET cc_start: 0.8823 (mmm) cc_final: 0.8478 (mmm) REVERT: C 813 GLU cc_start: 0.8868 (pp20) cc_final: 0.8606 (tt0) REVERT: C 815 CYS cc_start: 0.7933 (m) cc_final: 0.6574 (p) REVERT: C 874 GLN cc_start: 0.7225 (pt0) cc_final: 0.5489 (mm110) REVERT: C 937 PHE cc_start: 0.8394 (t80) cc_final: 0.8011 (t80) REVERT: C 955 ARG cc_start: 0.4970 (mmm-85) cc_final: 0.2824 (ttp80) REVERT: C 1009 PHE cc_start: 0.8470 (m-10) cc_final: 0.8241 (m-10) REVERT: C 1023 MET cc_start: 0.8636 (mtp) cc_final: 0.8223 (mtp) REVERT: C 1029 MET cc_start: 0.8224 (mtp) cc_final: 0.7580 (tpp) REVERT: D 408 MET cc_start: 0.4644 (mmm) cc_final: 0.4015 (mmm) REVERT: D 503 MET cc_start: 0.8860 (ttt) cc_final: 0.8317 (ttt) REVERT: D 533 TYR cc_start: 0.9307 (t80) cc_final: 0.8877 (t80) REVERT: D 537 SER cc_start: 0.9345 (p) cc_final: 0.9051 (t) REVERT: D 709 ASN cc_start: 0.8544 (t0) cc_final: 0.7940 (m-40) REVERT: D 710 GLU cc_start: 0.8196 (pp20) cc_final: 0.7985 (tm-30) REVERT: D 714 GLN cc_start: 0.8072 (mm-40) cc_final: 0.7365 (mm-40) REVERT: D 747 ASN cc_start: 0.8780 (m110) cc_final: 0.8508 (m-40) REVERT: D 764 ASN cc_start: 0.8786 (m-40) cc_final: 0.8523 (m110) REVERT: D 813 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7456 (mt-10) outliers start: 0 outliers final: 0 residues processed: 346 average time/residue: 0.1120 time to fit residues: 62.1586 Evaluate side-chains 275 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 6 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 183 optimal weight: 0.0040 chunk 39 optimal weight: 4.9990 chunk 49 optimal weight: 10.0000 chunk 195 optimal weight: 6.9990 chunk 60 optimal weight: 10.0000 chunk 102 optimal weight: 0.9980 chunk 71 optimal weight: 0.0870 chunk 189 optimal weight: 10.0000 overall best weight: 0.8174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 435 HIS A 947 ASN ** B 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 619 ASN C 747 ASN ** D 587 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 = 0.3788 r_free = 0.3788 target = 0.121503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.094295 restraints weight = 44144.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.096906 restraints weight = 27963.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.098623 restraints weight = 17894.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.099112 restraints weight = 14516.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.099317 restraints weight = 13620.141| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.6143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 17054 Z= 0.132 Angle : 0.690 16.649 22890 Z= 0.352 Chirality : 0.044 0.294 2494 Planarity : 0.005 0.079 2778 Dihedral : 13.936 148.409 2662 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.15 % 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: 0.20 (0.20), residues: 2020 helix: 1.56 (0.16), residues: 1100 sheet: -2.06 (0.37), residues: 174 loop : -1.51 (0.24), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG C1031 TYR 0.016 0.001 TYR C 616 PHE 0.052 0.002 PHE C 938 TRP 0.024 0.002 TRP A 767 HIS 0.003 0.001 HIS A 883 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (17048) covalent geometry : angle 0.68615 / 0.35 (22878) SS BOND : bond 0.01393 / 0.77 ( 6) SS BOND : angle 3.43301 / 2.06 ( 12) hydrogen bonds : bond 0.03767 / 2.45 ( 824) hydrogen bonds : angle 4.14550 / 2.89 ( 2412) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4040 Ramachandran restraints generated. 2020 Oldfield, 0 Emsley, 2020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 359 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 ASN cc_start: 0.7967 (m-40) cc_final: 0.7474 (m-40) REVERT: A 434 LYS cc_start: 0.8882 (mmmt) cc_final: 0.7966 (ptmt) REVERT: A 537 SER cc_start: 0.9273 (m) cc_final: 0.8887 (t) REVERT: A 585 MET cc_start: 0.9160 (mmm) cc_final: 0.8736 (mmm) REVERT: A 708 MET cc_start: 0.8773 (mpp) cc_final: 0.8476 (mtm) REVERT: A 710 GLU cc_start: 0.9002 (mt-10) cc_final: 0.8759 (mt-10) REVERT: A 714 GLN cc_start: 0.8845 (mp10) cc_final: 0.8466 (mm-40) REVERT: A 807 MET cc_start: 0.8777 (mmm) cc_final: 0.8453 (mmm) REVERT: A 808 LEU cc_start: 0.8692 (tt) cc_final: 0.8431 (mp) REVERT: A 937 PHE cc_start: 0.8611 (t80) cc_final: 0.8104 (t80) REVERT: A 947 ASN cc_start: 0.8440 (m-40) cc_final: 0.8200 (m-40) REVERT: A 1023 MET cc_start: 0.8589 (mtp) cc_final: 0.8144 (mtp) REVERT: B 408 MET cc_start: 0.5403 (mmt) cc_final: 0.4977 (mmm) REVERT: B 411 ASN cc_start: 0.7885 (m-40) cc_final: 0.7258 (m-40) REVERT: B 496 MET cc_start: 0.7742 (pmm) cc_final: 0.7161 (pmm) REVERT: B 533 TYR cc_start: 0.9277 (t80) cc_final: 0.8965 (t80) REVERT: B 537 SER cc_start: 0.9226 (p) cc_final: 0.8971 (t) REVERT: B 700 TYR cc_start: 0.7009 (t80) cc_final: 0.6769 (t80) REVERT: B 726 ASN cc_start: 0.8922 (m-40) cc_final: 0.8708 (m-40) REVERT: B 744 THR cc_start: 0.7804 (m) cc_final: 0.7594 (m) REVERT: B 747 ASN cc_start: 0.8702 (m110) cc_final: 0.8392 (m110) REVERT: B 764 ASN cc_start: 0.8271 (m-40) cc_final: 0.7916 (m-40) REVERT: B 813 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7629 (mt-10) REVERT: B 815 CYS cc_start: 0.8851 (t) cc_final: 0.8650 (t) REVERT: C 503 MET cc_start: 0.9123 (tpt) cc_final: 0.8840 (tpt) REVERT: C 585 MET cc_start: 0.8990 (mmm) cc_final: 0.8589 (mmm) REVERT: C 596 LEU cc_start: 0.8831 (tt) cc_final: 0.8629 (tt) REVERT: C 705 GLU cc_start: 0.8054 (pm20) cc_final: 0.7504 (mp0) REVERT: C 807 MET cc_start: 0.8745 (mmm) cc_final: 0.8393 (mmm) REVERT: C 815 CYS cc_start: 0.7842 (m) cc_final: 0.6508 (p) REVERT: C 874 GLN cc_start: 0.7206 (pt0) cc_final: 0.5518 (mm110) REVERT: C 880 MET cc_start: 0.8278 (tmm) cc_final: 0.8071 (tmm) REVERT: C 924 MET cc_start: 0.8326 (mmt) cc_final: 0.7826 (mmt) REVERT: C 937 PHE cc_start: 0.8345 (t80) cc_final: 0.7921 (t80) REVERT: C 955 ARG cc_start: 0.5098 (mmm-85) cc_final: 0.2898 (ttp80) REVERT: C 1009 PHE cc_start: 0.8430 (m-10) cc_final: 0.8134 (m-10) REVERT: C 1023 MET cc_start: 0.8540 (mtp) cc_final: 0.8129 (mtp) REVERT: C 1029 MET cc_start: 0.8173 (mtp) cc_final: 0.7581 (tpp) REVERT: D 460 TRP cc_start: 0.6564 (m100) cc_final: 0.6227 (m100) REVERT: D 503 MET cc_start: 0.8809 (ttt) cc_final: 0.8309 (ttt) REVERT: D 531 PHE cc_start: 0.8852 (m-80) cc_final: 0.8575 (m-10) REVERT: D 533 TYR cc_start: 0.9256 (t80) cc_final: 0.8759 (t80) REVERT: D 537 SER cc_start: 0.9327 (p) cc_final: 0.8958 (t) REVERT: D 709 ASN cc_start: 0.8490 (t0) cc_final: 0.7863 (m-40) REVERT: D 714 GLN cc_start: 0.7977 (mm-40) cc_final: 0.7434 (mm-40) REVERT: D 747 ASN cc_start: 0.8791 (m110) cc_final: 0.8525 (m-40) REVERT: D 764 ASN cc_start: 0.8710 (m-40) cc_final: 0.8431 (m110) REVERT: D 813 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7628 (mt-10) outliers start: 0 outliers final: 0 residues processed: 359 average time/residue: 0.1059 time to fit residues: 61.1081 Evaluate side-chains 282 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 282 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 67 optimal weight: 0.8980 chunk 94 optimal weight: 8.9990 chunk 181 optimal weight: 0.8980 chunk 41 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 163 optimal weight: 9.9990 chunk 190 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 84 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 chunk 91 optimal weight: 0.0020 overall best weight: 0.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 435 HIS B 461 ASN ** B 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 619 ASN C 714 GLN ** D 587 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 = 0.3795 r_free = 0.3795 target = 0.121998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.094662 restraints weight = 44663.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.097043 restraints weight = 29380.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.099073 restraints weight = 18865.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.099432 restraints weight = 14925.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.099475 restraints weight = 14242.445| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.6267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 17054 Z= 0.130 Angle : 0.682 15.595 22890 Z= 0.347 Chirality : 0.044 0.278 2494 Planarity : 0.005 0.078 2778 Dihedral : 13.638 148.243 2662 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.15 % 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: 0.22 (0.19), residues: 2020 helix: 1.54 (0.16), residues: 1096 sheet: -2.05 (0.38), residues: 164 loop : -1.43 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1031 TYR 0.016 0.001 TYR C1026 PHE 0.067 0.002 PHE A1009 TRP 0.023 0.001 TRP A 767 HIS 0.002 0.001 HIS A 883 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (17048) covalent geometry : angle 0.67802 / 0.35 (22878) SS BOND : bond 0.01268 / 0.71 ( 6) SS BOND : angle 3.43463 / 2.08 ( 12) hydrogen bonds : bond 0.03754 / 2.45 ( 824) hydrogen bonds : angle 4.12808 / 2.87 ( 2412) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2711.69 seconds wall clock time: 47 minutes 51.43 seconds (2871.43 seconds total)