Starting phenix.real_space_refine on Wed Mar 4 23:10:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rz8_24754/03_2026/7rz8_24754.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rz8_24754/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7rz8_24754/03_2026/7rz8_24754.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rz8_24754/03_2026/7rz8_24754.map" model { file = "/net/cci-nas-00/data/ceres_data/7rz8_24754/03_2026/7rz8_24754.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rz8_24754/03_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 157 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: 64 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: 157 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: 64 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: 4.06, per 1000 atoms: 0.24 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: 1.52 Conformation dependent library (CDL) restraints added in 580.1 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: 0.53 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: 2.77 Time building geometry restraints manager: 1.90 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: 9844 35.75 - 71.50: 356 71.50 - 107.25: 32 107.25 - 143.00: 6 143.00 - 178.75: 8 Dihedral angle restraints: 10246 sinusoidal: 4380 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 10243 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: 0.03 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: 3.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.370 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 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 : 17.557 178.748 6488 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 covalent geometry : bond 0.01047 (17048) covalent geometry : angle 1.29172 (22878) SS BOND : bond 0.00910 ( 6) SS BOND : angle 0.63470 ( 12) hydrogen bonds : bond 0.29436 ( 824) hydrogen bonds : angle 8.44921 ( 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 : 0.500 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: 0.1251 time to fit residues: 118.1999 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 : 0.601 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 791 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.125550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.097868 restraints weight = 43238.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.100861 restraints weight = 25252.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.103454 restraints weight = 16911.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.104039 restraints weight = 12008.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.104043 restraints weight = 11562.648| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 17054 Z= 0.144 Angle : 0.673 8.660 22890 Z= 0.353 Chirality : 0.044 0.209 2494 Planarity : 0.006 0.077 2778 Dihedral : 19.271 179.011 2802 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.23 % Allowed : 3.83 % Favored : 95.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 6.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.17), residues: 2020 helix: 0.11 (0.14), residues: 1094 sheet: -1.89 (0.31), residues: 236 loop : -2.10 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 594 TYR 0.024 0.002 TYR B 768 PHE 0.030 0.002 PHE C 901 TRP 0.045 0.002 TRP D 766 HIS 0.003 0.001 HIS A 883 Details of bonding type rmsd covalent geometry : bond 0.00312 (17048) covalent geometry : angle 0.67087 (22878) SS BOND : bond 0.01139 ( 6) SS BOND : angle 2.41431 ( 12) hydrogen bonds : bond 0.05338 ( 824) hydrogen bonds : angle 4.37161 ( 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 492 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 488 time to evaluate : 0.440 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: 0.7801 (m-40) cc_final: 0.7356 (m-40) REVERT: A 669 LYS cc_start: 0.9451 (ttpt) cc_final: 0.9046 (tttt) REVERT: A 835 LYS cc_start: 0.8473 (tppt) cc_final: 0.8040 (mmtt) REVERT: A 844 PHE cc_start: 0.8467 (m-80) cc_final: 0.8207 (m-80) REVERT: A 851 LEU cc_start: 0.8122 (tp) cc_final: 0.7845 (tp) REVERT: A 880 MET cc_start: 0.8204 (tmm) cc_final: 0.7605 (tmm) REVERT: A 937 PHE cc_start: 0.8674 (t80) cc_final: 0.8088 (t80) REVERT: A 947 ASN cc_start: 0.8336 (m110) cc_final: 0.8016 (m-40) REVERT: A 985 ASN cc_start: 0.8836 (m-40) cc_final: 0.8522 (m-40) REVERT: A 1023 MET cc_start: 0.8832 (mtp) cc_final: 0.8540 (mtp) REVERT: B 407 MET cc_start: 0.4713 (mtm) cc_final: 0.4504 (mmp) REVERT: B 411 ASN cc_start: 0.8217 (m-40) cc_final: 0.7820 (m-40) REVERT: B 418 ASN cc_start: 0.7461 (p0) cc_final: 0.6933 (p0) REVERT: B 503 MET cc_start: 0.8082 (ttt) cc_final: 0.7809 (ttp) REVERT: B 702 TYR cc_start: 0.7812 (t80) cc_final: 0.7271 (t80) REVERT: B 714 GLN cc_start: 0.8133 (mm-40) cc_final: 0.7580 (tt0) REVERT: B 813 GLU cc_start: 0.8287 (mt-10) cc_final: 0.8032 (mt-10) REVERT: C 502 ILE cc_start: 0.9454 (mp) cc_final: 0.9229 (mt) REVERT: C 527 MET cc_start: 0.8462 (ttm) cc_final: 0.8190 (ttm) REVERT: C 569 ASN cc_start: 0.7890 (t0) cc_final: 0.7043 (m-40) REVERT: C 573 ILE cc_start: 0.9024 (tp) cc_final: 0.8761 (tp) REVERT: C 577 LEU cc_start: 0.9378 (mm) cc_final: 0.9055 (mm) REVERT: C 616 TYR cc_start: 0.9119 (t80) cc_final: 0.8909 (t80) REVERT: C 655 THR cc_start: 0.9089 (m) cc_final: 0.8794 (p) REVERT: C 675 ARG cc_start: 0.7831 (ptm160) cc_final: 0.7423 (ptm160) REVERT: C 835 LYS cc_start: 0.8496 (tppt) cc_final: 0.8215 (ttpt) REVERT: C 866 GLU cc_start: 0.6826 (tp30) cc_final: 0.5952 (tt0) REVERT: C 880 MET cc_start: 0.8279 (tmm) cc_final: 0.7673 (tmm) REVERT: C 920 ASN cc_start: 0.8037 (t0) cc_final: 0.7732 (t0) REVERT: C 924 MET cc_start: 0.8109 (mmt) cc_final: 0.7471 (mmt) REVERT: C 950 HIS cc_start: 0.6380 (m-70) cc_final: 0.5909 (t-90) REVERT: C 1023 MET cc_start: 0.8393 (mtp) cc_final: 0.7913 (mtp) REVERT: C 1031 ARG cc_start: 0.6479 (ttp-110) cc_final: 0.6058 (mtp85) REVERT: D 411 ASN cc_start: 0.8083 (m-40) cc_final: 0.7527 (m110) REVERT: D 418 ASN cc_start: 0.7348 (p0) cc_final: 0.6497 (p0) REVERT: D 501 SER cc_start: 0.9297 (t) cc_final: 0.9001 (p) REVERT: D 503 MET cc_start: 0.8358 (ttt) cc_final: 0.7880 (ttt) REVERT: D 524 GLU cc_start: 0.8693 (pm20) cc_final: 0.8388 (pm20) REVERT: D 537 SER cc_start: 0.9349 (p) cc_final: 0.9000 (t) REVERT: D 570 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7687 (mm-30) REVERT: D 702 TYR cc_start: 0.7928 (t80) cc_final: 0.7059 (t80) REVERT: D 710 GLU cc_start: 0.8363 (tm-30) cc_final: 0.7985 (tm-30) REVERT: D 763 LYS cc_start: 0.9123 (tttt) cc_final: 0.8605 (tptt) REVERT: D 798 ILE cc_start: 0.9458 (mt) cc_final: 0.9152 (tp) REVERT: D 799 LEU cc_start: 0.9449 (tp) cc_final: 0.9017 (tt) REVERT: D 813 GLU cc_start: 0.8354 (mt-10) cc_final: 0.8083 (mp0) outliers start: 4 outliers final: 0 residues processed: 491 average time/residue: 0.1143 time to fit residues: 87.8566 Evaluate side-chains 333 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 333 time to evaluate : 0.590 ------------------------------------------------------------------------------- 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: 1.9990 chunk 74 optimal weight: 3.9990 chunk 163 optimal weight: 7.9990 chunk 171 optimal weight: 2.9990 chunk 127 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 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: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 HIS A 587 GLN B 586 GLN B 764 ASN C 411 ASN C 587 GLN C 619 ASN C 714 GLN D 461 ASN D 508 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.120480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.093370 restraints weight = 44372.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.095716 restraints weight = 28701.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.097099 restraints weight = 19057.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.097633 restraints weight = 15861.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.097782 restraints weight = 14545.140| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.4233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 17054 Z= 0.186 Angle : 0.687 9.736 22890 Z= 0.356 Chirality : 0.044 0.208 2494 Planarity : 0.005 0.073 2778 Dihedral : 18.226 172.223 2802 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.29 % Allowed : 4.06 % Favored : 95.65 % 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: -0.37 (0.19), residues: 2020 helix: 1.07 (0.15), residues: 1102 sheet: -1.76 (0.33), residues: 232 loop : -1.86 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 991 TYR 0.022 0.002 TYR C 905 PHE 0.028 0.002 PHE C 844 TRP 0.028 0.002 TRP C 767 HIS 0.003 0.001 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00416 (17048) covalent geometry : angle 0.68480 (22878) SS BOND : bond 0.01817 ( 6) SS BOND : angle 2.35588 ( 12) hydrogen bonds : bond 0.04347 ( 824) hydrogen bonds : angle 4.32423 ( 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 422 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 417 time to evaluate : 0.735 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: A 418 ASN cc_start: 0.8022 (m-40) cc_final: 0.7431 (m110) REVERT: A 419 GLU cc_start: 0.8514 (tp30) cc_final: 0.8094 (tp30) REVERT: A 425 CYS cc_start: 0.8753 (m) cc_final: 0.8440 (m) REVERT: A 537 SER cc_start: 0.9284 (m) cc_final: 0.8779 (t) REVERT: A 596 LEU cc_start: 0.8752 (tt) cc_final: 0.8238 (tt) REVERT: A 669 LYS cc_start: 0.9435 (ttpt) cc_final: 0.9174 (ttpt) REVERT: A 835 LYS cc_start: 0.8567 (tppt) cc_final: 0.8196 (mmtt) REVERT: A 851 LEU cc_start: 0.8045 (tp) cc_final: 0.7793 (tp) REVERT: A 880 MET cc_start: 0.8381 (tmm) cc_final: 0.7365 (tmm) REVERT: A 892 LEU cc_start: 0.7698 (tp) cc_final: 0.7462 (tp) REVERT: A 937 PHE cc_start: 0.8722 (t80) cc_final: 0.8324 (t80) REVERT: A 1023 MET cc_start: 0.8828 (mtp) cc_final: 0.8318 (mtp) REVERT: B 411 ASN cc_start: 0.8135 (m-40) cc_final: 0.7713 (m-40) REVERT: B 418 ASN cc_start: 0.7481 (p0) cc_final: 0.6702 (p0) REVERT: B 527 MET cc_start: 0.7778 (tpp) cc_final: 0.7370 (mmt) REVERT: B 531 PHE cc_start: 0.8589 (m-10) cc_final: 0.8329 (m-80) REVERT: B 604 VAL cc_start: 0.9778 (m) cc_final: 0.9554 (p) REVERT: B 710 GLU cc_start: 0.8708 (tp30) cc_final: 0.8464 (tp30) REVERT: B 714 GLN cc_start: 0.8208 (mm-40) cc_final: 0.7635 (tt0) REVERT: B 789 LEU cc_start: 0.9521 (tp) cc_final: 0.9228 (tp) REVERT: B 813 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7890 (mt-10) REVERT: C 527 MET cc_start: 0.8635 (ttm) cc_final: 0.8400 (ttm) REVERT: C 569 ASN cc_start: 0.8008 (t0) cc_final: 0.7110 (m-40) REVERT: C 596 LEU cc_start: 0.8910 (tt) cc_final: 0.8694 (tp) REVERT: C 616 TYR cc_start: 0.9440 (t80) cc_final: 0.9190 (t80) REVERT: C 655 THR cc_start: 0.9166 (m) cc_final: 0.8829 (p) REVERT: C 756 GLN cc_start: 0.8444 (tm-30) cc_final: 0.8049 (tm-30) REVERT: C 815 CYS cc_start: 0.7444 (m) cc_final: 0.6506 (p) REVERT: C 835 LYS cc_start: 0.8648 (tppt) cc_final: 0.8428 (ttpt) REVERT: C 866 GLU cc_start: 0.6887 (tp30) cc_final: 0.6219 (tp30) REVERT: C 880 MET cc_start: 0.8401 (tmm) cc_final: 0.7744 (tmm) REVERT: C 950 HIS cc_start: 0.6562 (m-70) cc_final: 0.5781 (t-90) REVERT: C 1013 SER cc_start: 0.9135 (t) cc_final: 0.8785 (p) REVERT: C 1023 MET cc_start: 0.8411 (mtp) cc_final: 0.8144 (mtp) REVERT: D 411 ASN cc_start: 0.7842 (m-40) cc_final: 0.7398 (m-40) REVERT: D 503 MET cc_start: 0.8683 (ttt) cc_final: 0.7625 (ttt) REVERT: D 537 SER cc_start: 0.9354 (p) cc_final: 0.9011 (t) REVERT: D 570 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7655 (mm-30) REVERT: D 710 GLU cc_start: 0.8367 (tm-30) cc_final: 0.8090 (tm-30) REVERT: D 799 LEU cc_start: 0.9490 (tp) cc_final: 0.9141 (tt) REVERT: D 813 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7791 (mt-10) outliers start: 5 outliers final: 0 residues processed: 419 average time/residue: 0.1098 time to fit residues: 72.7608 Evaluate side-chains 301 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 301 time to evaluate : 0.589 ------------------------------------------------------------------------------- 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: 2.9990 chunk 173 optimal weight: 1.9990 chunk 116 optimal weight: 6.9990 chunk 181 optimal weight: 1.9990 chunk 107 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 HIS A 726 ASN A 947 ASN C 587 GLN C 619 ASN C 726 ASN ** 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 = 0.3695 r_free = 0.3695 target = 0.116207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.088094 restraints weight = 45439.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.090495 restraints weight = 26912.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.092069 restraints weight = 19490.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.093034 restraints weight = 15997.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.093534 restraints weight = 14203.201| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.4947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 17054 Z= 0.275 Angle : 0.779 21.015 22890 Z= 0.402 Chirality : 0.047 0.337 2494 Planarity : 0.005 0.075 2778 Dihedral : 18.105 159.271 2802 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.17 % Allowed : 4.58 % Favored : 95.24 % Cbeta Deviations : 0.00 % 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: -0.37 (0.19), residues: 2020 helix: 1.19 (0.16), residues: 1082 sheet: -2.24 (0.34), residues: 184 loop : -1.86 (0.23), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 715 TYR 0.020 0.002 TYR B 768 PHE 0.030 0.002 PHE A 901 TRP 0.024 0.002 TRP C 861 HIS 0.005 0.001 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00609 (17048) covalent geometry : angle 0.77680 (22878) SS BOND : bond 0.00905 ( 6) SS BOND : angle 2.81554 ( 12) hydrogen bonds : bond 0.04459 ( 824) hydrogen bonds : angle 4.72051 ( 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 364 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 361 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 ASN cc_start: 0.8181 (m-40) cc_final: 0.7692 (m110) REVERT: A 419 GLU cc_start: 0.8514 (tp30) cc_final: 0.8164 (tp30) REVERT: A 519 ASP cc_start: 0.7821 (m-30) cc_final: 0.7583 (m-30) REVERT: A 537 SER cc_start: 0.9325 (m) cc_final: 0.8825 (t) REVERT: A 669 LYS cc_start: 0.9490 (ttpt) cc_final: 0.9194 (tttt) REVERT: A 808 LEU cc_start: 0.8995 (tt) cc_final: 0.8642 (mp) REVERT: A 835 LYS cc_start: 0.8536 (tppt) cc_final: 0.8171 (mmtt) REVERT: A 851 LEU cc_start: 0.7983 (tp) cc_final: 0.7776 (tp) REVERT: A 937 PHE cc_start: 0.8787 (t80) cc_final: 0.8340 (t80) REVERT: A 947 ASN cc_start: 0.8403 (m110) cc_final: 0.8185 (m110) REVERT: A 1023 MET cc_start: 0.8749 (mtp) cc_final: 0.8365 (mtp) REVERT: B 411 ASN cc_start: 0.7896 (m-40) cc_final: 0.7481 (m-40) REVERT: B 503 MET cc_start: 0.8953 (ttt) cc_final: 0.8554 (ttt) REVERT: B 524 GLU cc_start: 0.8548 (pm20) cc_final: 0.8244 (pm20) REVERT: B 528 CYS cc_start: 0.8621 (m) cc_final: 0.8295 (m) REVERT: B 670 MET cc_start: 0.9146 (mmp) cc_final: 0.8613 (mmm) REVERT: B 710 GLU cc_start: 0.8684 (tp30) cc_final: 0.8454 (tp30) REVERT: B 714 GLN cc_start: 0.8288 (mm-40) cc_final: 0.7509 (tt0) REVERT: B 747 ASN cc_start: 0.8686 (m-40) cc_final: 0.8463 (m110) REVERT: B 813 GLU cc_start: 0.8378 (mt-10) cc_final: 0.7753 (mt-10) REVERT: C 569 ASN cc_start: 0.8238 (t0) cc_final: 0.7389 (m-40) REVERT: C 756 GLN cc_start: 0.8555 (tm-30) cc_final: 0.8108 (tm-30) REVERT: C 813 GLU cc_start: 0.8974 (pp20) cc_final: 0.8359 (tt0) REVERT: C 815 CYS cc_start: 0.7712 (m) cc_final: 0.6790 (p) REVERT: C 840 LEU cc_start: 0.8168 (tp) cc_final: 0.7774 (tp) REVERT: C 844 PHE cc_start: 0.7868 (m-80) cc_final: 0.7585 (m-80) REVERT: C 880 MET cc_start: 0.8273 (tmm) cc_final: 0.7832 (tmm) REVERT: C 924 MET cc_start: 0.8259 (mmt) cc_final: 0.7400 (mmt) REVERT: C 950 HIS cc_start: 0.6544 (m-70) cc_final: 0.5769 (m-70) REVERT: C 1013 SER cc_start: 0.9209 (t) cc_final: 0.8961 (p) REVERT: C 1023 MET cc_start: 0.8556 (mtp) cc_final: 0.7967 (mtt) REVERT: C 1029 MET cc_start: 0.8913 (mtp) cc_final: 0.8335 (mpp) REVERT: D 411 ASN cc_start: 0.7860 (m-40) cc_final: 0.7461 (m-40) REVERT: D 503 MET cc_start: 0.8526 (ttt) cc_final: 0.7652 (ttp) REVERT: D 533 TYR cc_start: 0.9289 (t80) cc_final: 0.9055 (t80) REVERT: D 537 SER cc_start: 0.9409 (p) cc_final: 0.9059 (t) REVERT: D 710 GLU cc_start: 0.8345 (tm-30) cc_final: 0.8143 (tm-30) REVERT: D 742 LEU cc_start: 0.9377 (pp) cc_final: 0.9175 (pp) REVERT: D 813 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7728 (mt-10) outliers start: 3 outliers final: 0 residues processed: 364 average time/residue: 0.1070 time to fit residues: 62.5923 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 : 0.624 ------------------------------------------------------------------------------- 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: 7.9990 chunk 7 optimal weight: 0.9990 chunk 129 optimal weight: 0.8980 chunk 143 optimal weight: 5.9990 chunk 87 optimal weight: 0.0980 chunk 8 optimal weight: 3.9990 chunk 154 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 192 optimal weight: 8.9990 chunk 163 optimal weight: 7.9990 chunk 103 optimal weight: 6.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 HIS A 947 ASN B 726 ASN B 764 ASN C 587 GLN C 619 ASN ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 619 ASN ** 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 = 0.3745 r_free = 0.3745 target = 0.119524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.091784 restraints weight = 44548.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.094568 restraints weight = 27360.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.096347 restraints weight = 18574.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.097036 restraints weight = 14256.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.097080 restraints weight = 13641.639| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.5206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17054 Z= 0.154 Angle : 0.687 23.618 22890 Z= 0.352 Chirality : 0.045 0.403 2494 Planarity : 0.005 0.074 2778 Dihedral : 17.240 158.079 2802 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.17 % Allowed : 3.07 % Favored : 96.75 % 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: 0.02 (0.19), residues: 2020 helix: 1.49 (0.16), residues: 1096 sheet: -1.96 (0.35), residues: 176 loop : -1.76 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 715 TYR 0.016 0.001 TYR B 732 PHE 0.041 0.002 PHE A 901 TRP 0.017 0.001 TRP C 861 HIS 0.003 0.001 HIS C 954 Details of bonding type rmsd covalent geometry : bond 0.00346 (17048) covalent geometry : angle 0.68196 (22878) SS BOND : bond 0.01499 ( 6) SS BOND : angle 3.68505 ( 12) hydrogen bonds : bond 0.03940 ( 824) hydrogen bonds : angle 4.28464 ( 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 381 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 378 time to evaluate : 0.798 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: 0.8130 (m-40) cc_final: 0.7656 (m110) REVERT: A 419 GLU cc_start: 0.8526 (tp30) cc_final: 0.8257 (tp30) REVERT: A 425 CYS cc_start: 0.8650 (m) cc_final: 0.8428 (m) REVERT: A 427 ASP cc_start: 0.8869 (m-30) cc_final: 0.8664 (m-30) REVERT: A 537 SER cc_start: 0.9377 (m) cc_final: 0.9019 (m) REVERT: A 808 LEU cc_start: 0.8893 (tt) cc_final: 0.8513 (mp) REVERT: A 835 LYS cc_start: 0.8437 (tppt) cc_final: 0.8101 (mmtt) REVERT: A 844 PHE cc_start: 0.8428 (m-80) cc_final: 0.8171 (m-80) REVERT: A 851 LEU cc_start: 0.7931 (tp) cc_final: 0.7687 (tp) REVERT: A 874 GLN cc_start: 0.7145 (pt0) cc_final: 0.6861 (pt0) REVERT: A 880 MET cc_start: 0.8223 (tmm) cc_final: 0.7756 (tmm) REVERT: A 937 PHE cc_start: 0.8747 (t80) cc_final: 0.8361 (t80) REVERT: A 947 ASN cc_start: 0.8367 (m-40) cc_final: 0.8102 (m-40) REVERT: A 1023 MET cc_start: 0.8782 (mtp) cc_final: 0.8191 (mtp) REVERT: B 411 ASN cc_start: 0.7934 (m-40) cc_final: 0.7395 (m-40) REVERT: B 463 MET cc_start: 0.7727 (mmm) cc_final: 0.7216 (mmt) REVERT: B 503 MET cc_start: 0.8917 (ttt) cc_final: 0.8613 (ttt) REVERT: B 544 SER cc_start: 0.9041 (m) cc_final: 0.8810 (t) REVERT: B 670 MET cc_start: 0.9197 (mmp) cc_final: 0.8808 (mmm) REVERT: B 710 GLU cc_start: 0.8638 (tp30) cc_final: 0.8393 (tp30) REVERT: B 714 GLN cc_start: 0.8169 (mm-40) cc_final: 0.7601 (tt0) REVERT: B 726 ASN cc_start: 0.8649 (m-40) cc_final: 0.8338 (m110) REVERT: B 813 GLU cc_start: 0.8355 (mt-10) cc_final: 0.7733 (mt-10) REVERT: C 573 ILE cc_start: 0.9414 (tp) cc_final: 0.9199 (tp) REVERT: C 708 MET cc_start: 0.9019 (mpp) cc_final: 0.8451 (mtm) REVERT: C 756 GLN cc_start: 0.8645 (tm-30) cc_final: 0.8411 (tm-30) REVERT: C 813 GLU cc_start: 0.8956 (pp20) cc_final: 0.8567 (tt0) REVERT: C 815 CYS cc_start: 0.7756 (m) cc_final: 0.6442 (p) REVERT: C 840 LEU cc_start: 0.8032 (tp) cc_final: 0.7668 (tp) REVERT: C 844 PHE cc_start: 0.7856 (m-80) cc_final: 0.7540 (m-80) REVERT: C 874 GLN cc_start: 0.7194 (pt0) cc_final: 0.5394 (mm110) REVERT: C 924 MET cc_start: 0.8008 (mmt) cc_final: 0.7750 (mmt) REVERT: C 950 HIS cc_start: 0.6610 (m-70) cc_final: 0.6147 (m-70) REVERT: C 955 ARG cc_start: 0.4992 (mmm-85) cc_final: 0.3226 (ptt-90) REVERT: C 1023 MET cc_start: 0.8551 (mtp) cc_final: 0.8017 (mtp) REVERT: C 1029 MET cc_start: 0.8766 (mtp) cc_final: 0.8110 (tpp) REVERT: D 407 MET cc_start: 0.6284 (mtp) cc_final: 0.6009 (mtm) REVERT: D 411 ASN cc_start: 0.7868 (m-40) cc_final: 0.7446 (m-40) REVERT: D 460 TRP cc_start: 0.6433 (m100) cc_final: 0.6082 (m100) REVERT: D 503 MET cc_start: 0.8822 (ttt) cc_final: 0.8182 (ttt) REVERT: D 533 TYR cc_start: 0.9303 (t80) cc_final: 0.8846 (t80) REVERT: D 537 SER cc_start: 0.9329 (p) cc_final: 0.8991 (t) REVERT: D 673 TYR cc_start: 0.7997 (t80) cc_final: 0.7625 (t80) REVERT: D 709 ASN cc_start: 0.8551 (t0) cc_final: 0.8142 (m-40) REVERT: D 710 GLU cc_start: 0.8222 (tm-30) cc_final: 0.8018 (tm-30) REVERT: D 813 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7719 (mt-10) outliers start: 3 outliers final: 0 residues processed: 380 average time/residue: 0.1068 time to fit residues: 65.5635 Evaluate side-chains 284 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 284 time to evaluate : 0.582 ------------------------------------------------------------------------------- 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: 7.9990 chunk 174 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 61 optimal weight: 8.9990 chunk 192 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 chunk 169 optimal weight: 9.9990 chunk 130 optimal weight: 0.8980 chunk 40 optimal weight: 6.9990 chunk 94 optimal weight: 10.0000 chunk 151 optimal weight: 4.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 947 ASN B 764 ASN C 587 GLN C 619 ASN ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 764 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.116061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.089813 restraints weight = 44863.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.092026 restraints weight = 28082.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.093671 restraints weight = 18841.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.094011 restraints weight = 15465.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.094112 restraints weight = 14488.026| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.5598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 17054 Z= 0.257 Angle : 0.773 19.644 22890 Z= 0.398 Chirality : 0.047 0.317 2494 Planarity : 0.005 0.077 2778 Dihedral : 17.345 159.920 2802 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.06 % Allowed : 3.02 % Favored : 96.93 % 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: -0.29 (0.19), residues: 2020 helix: 1.27 (0.16), residues: 1096 sheet: -2.51 (0.32), residues: 194 loop : -1.79 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1031 TYR 0.019 0.002 TYR D 732 PHE 0.051 0.002 PHE A 938 TRP 0.032 0.002 TRP C 861 HIS 0.004 0.001 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00573 (17048) covalent geometry : angle 0.76867 (22878) SS BOND : bond 0.01285 ( 6) SS BOND : angle 3.50354 ( 12) hydrogen bonds : bond 0.04343 ( 824) hydrogen bonds : angle 4.70642 ( 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 336 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 335 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 ASN cc_start: 0.8131 (m-40) cc_final: 0.7691 (m110) REVERT: A 419 GLU cc_start: 0.8586 (tp30) cc_final: 0.8188 (tp30) REVERT: A 537 SER cc_start: 0.9279 (m) cc_final: 0.8858 (t) REVERT: A 596 LEU cc_start: 0.8950 (tt) cc_final: 0.8481 (tt) REVERT: A 808 LEU cc_start: 0.8895 (tt) cc_final: 0.8529 (mp) REVERT: A 851 LEU cc_start: 0.8040 (tp) cc_final: 0.7835 (tp) REVERT: A 880 MET cc_start: 0.8463 (tmm) cc_final: 0.7993 (tmm) REVERT: A 924 MET cc_start: 0.8079 (mmm) cc_final: 0.7363 (mmt) REVERT: A 937 PHE cc_start: 0.8747 (t80) cc_final: 0.8287 (t80) REVERT: A 947 ASN cc_start: 0.8467 (m110) cc_final: 0.8133 (m110) REVERT: A 1023 MET cc_start: 0.8712 (mtp) cc_final: 0.8343 (mtp) REVERT: B 399 THR cc_start: 0.7740 (m) cc_final: 0.7254 (p) REVERT: B 411 ASN cc_start: 0.8029 (m-40) cc_final: 0.7511 (m-40) REVERT: B 463 MET cc_start: 0.7732 (mmm) cc_final: 0.7204 (mmt) REVERT: B 503 MET cc_start: 0.8971 (ttt) cc_final: 0.8548 (ttt) REVERT: B 528 CYS cc_start: 0.8734 (m) cc_final: 0.8475 (m) REVERT: B 537 SER cc_start: 0.9371 (p) cc_final: 0.9046 (t) REVERT: B 544 SER cc_start: 0.9110 (m) cc_final: 0.8890 (t) REVERT: B 710 GLU cc_start: 0.8631 (tp30) cc_final: 0.8400 (tp30) REVERT: B 714 GLN cc_start: 0.8251 (mm-40) cc_final: 0.7574 (tt0) REVERT: B 726 ASN cc_start: 0.9055 (m-40) cc_final: 0.8825 (m-40) REVERT: B 734 ILE cc_start: 0.8455 (mm) cc_final: 0.8207 (mm) REVERT: B 747 ASN cc_start: 0.8768 (m110) cc_final: 0.8465 (m110) REVERT: B 813 GLU cc_start: 0.8331 (mt-10) cc_final: 0.7677 (mt-10) REVERT: C 503 MET cc_start: 0.8636 (tmm) cc_final: 0.8068 (tmm) REVERT: C 504 ILE cc_start: 0.9239 (mt) cc_final: 0.9014 (mt) REVERT: C 537 SER cc_start: 0.9149 (m) cc_final: 0.8668 (t) REVERT: C 574 PHE cc_start: 0.8824 (t80) cc_final: 0.8601 (t80) REVERT: C 596 LEU cc_start: 0.8915 (tt) cc_final: 0.8499 (tt) REVERT: C 756 GLN cc_start: 0.8680 (tm-30) cc_final: 0.8371 (tm-30) REVERT: C 759 LEU cc_start: 0.8681 (tt) cc_final: 0.8293 (tt) REVERT: C 767 TRP cc_start: 0.8532 (m-90) cc_final: 0.8323 (m-90) REVERT: C 807 MET cc_start: 0.8848 (mmm) cc_final: 0.8509 (mmm) REVERT: C 813 GLU cc_start: 0.8891 (pp20) cc_final: 0.8662 (tt0) REVERT: C 815 CYS cc_start: 0.7979 (m) cc_final: 0.6700 (p) REVERT: C 840 LEU cc_start: 0.8312 (tp) cc_final: 0.7820 (tp) REVERT: C 844 PHE cc_start: 0.7972 (m-80) cc_final: 0.7493 (m-80) REVERT: C 924 MET cc_start: 0.8158 (mmt) cc_final: 0.7744 (mmt) REVERT: C 955 ARG cc_start: 0.5070 (mmm-85) cc_final: 0.3071 (ptt-90) REVERT: C 1023 MET cc_start: 0.8664 (mtp) cc_final: 0.8080 (mtp) REVERT: C 1029 MET cc_start: 0.8838 (mtp) cc_final: 0.8041 (tpp) REVERT: D 411 ASN cc_start: 0.7746 (m-40) cc_final: 0.7186 (m-40) REVERT: D 503 MET cc_start: 0.8926 (ttt) cc_final: 0.8301 (ttt) REVERT: D 537 SER cc_start: 0.9413 (p) cc_final: 0.9021 (t) REVERT: D 649 THR cc_start: 0.8418 (p) cc_final: 0.8205 (p) REVERT: D 709 ASN cc_start: 0.8492 (t0) cc_final: 0.7986 (m-40) REVERT: D 747 ASN cc_start: 0.8777 (m110) cc_final: 0.8488 (m110) REVERT: D 764 ASN cc_start: 0.8673 (m-40) cc_final: 0.8387 (m110) REVERT: D 813 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7530 (mt-10) outliers start: 1 outliers final: 0 residues processed: 336 average time/residue: 0.1053 time to fit residues: 57.5742 Evaluate side-chains 266 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 0.624 ------------------------------------------------------------------------------- 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: 0.9980 chunk 82 optimal weight: 1.9990 chunk 146 optimal weight: 0.7980 chunk 121 optimal weight: 0.5980 chunk 148 optimal weight: 7.9990 chunk 191 optimal weight: 0.9990 chunk 144 optimal weight: 7.9990 chunk 2 optimal weight: 0.9980 chunk 135 optimal weight: 2.9990 chunk 27 optimal weight: 0.0470 chunk 184 optimal weight: 9.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 HIS A 947 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 Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.120856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.093426 restraints weight = 44067.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.096093 restraints weight = 26994.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.098298 restraints weight = 18341.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.098821 restraints weight = 13606.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.098828 restraints weight = 13255.048| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.5748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17054 Z= 0.126 Angle : 0.671 18.193 22890 Z= 0.342 Chirality : 0.044 0.344 2494 Planarity : 0.005 0.076 2778 Dihedral : 16.208 163.647 2802 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % 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: 0.11 (0.20), residues: 2020 helix: 1.59 (0.16), residues: 1098 sheet: -2.27 (0.33), residues: 194 loop : -1.65 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1031 TYR 0.029 0.001 TYR D 732 PHE 0.056 0.002 PHE A 901 TRP 0.016 0.001 TRP C 887 HIS 0.003 0.001 HIS A 883 Details of bonding type rmsd covalent geometry : bond 0.00276 (17048) covalent geometry : angle 0.66511 (22878) SS BOND : bond 0.01317 ( 6) SS BOND : angle 3.83278 ( 12) hydrogen bonds : bond 0.03829 ( 824) hydrogen bonds : angle 4.15890 ( 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 368 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 368 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 ASN cc_start: 0.8097 (m-40) cc_final: 0.7539 (m110) REVERT: A 419 GLU cc_start: 0.8582 (tp30) cc_final: 0.7977 (tp30) REVERT: A 434 LYS cc_start: 0.9004 (mmmt) cc_final: 0.8122 (ptmt) REVERT: A 537 SER cc_start: 0.9326 (m) cc_final: 0.8923 (t) REVERT: A 708 MET cc_start: 0.8946 (mpp) cc_final: 0.8508 (mtm) REVERT: A 714 GLN cc_start: 0.8790 (mp10) cc_final: 0.8514 (mm-40) REVERT: A 808 LEU cc_start: 0.8771 (tt) cc_final: 0.8434 (mp) REVERT: A 880 MET cc_start: 0.8265 (tmm) cc_final: 0.7944 (tmm) REVERT: A 920 ASN cc_start: 0.8290 (m110) cc_final: 0.7981 (m110) REVERT: A 924 MET cc_start: 0.8085 (mmm) cc_final: 0.7428 (mmt) REVERT: A 937 PHE cc_start: 0.8575 (t80) cc_final: 0.8106 (t80) REVERT: A 947 ASN cc_start: 0.8368 (m-40) cc_final: 0.8138 (m-40) REVERT: A 1023 MET cc_start: 0.8747 (mtp) cc_final: 0.8208 (mtp) REVERT: B 411 ASN cc_start: 0.8022 (m-40) cc_final: 0.7451 (m-40) REVERT: B 501 SER cc_start: 0.9288 (t) cc_final: 0.8987 (p) REVERT: B 503 MET cc_start: 0.8911 (ttt) cc_final: 0.8663 (ttt) REVERT: B 533 TYR cc_start: 0.9276 (t80) cc_final: 0.8954 (t80) REVERT: B 537 SER cc_start: 0.9315 (p) cc_final: 0.9026 (t) REVERT: B 710 GLU cc_start: 0.8670 (tp30) cc_final: 0.8379 (tp30) REVERT: B 714 GLN cc_start: 0.8006 (mm-40) cc_final: 0.7402 (tt0) REVERT: B 726 ASN cc_start: 0.8972 (m-40) cc_final: 0.8712 (m-40) REVERT: B 747 ASN cc_start: 0.8776 (m110) cc_final: 0.8435 (m110) REVERT: B 813 GLU cc_start: 0.8345 (mt-10) cc_final: 0.7708 (mt-10) REVERT: C 596 LEU cc_start: 0.8873 (tt) cc_final: 0.8651 (tt) REVERT: C 616 TYR cc_start: 0.9447 (t80) cc_final: 0.9182 (t80) REVERT: C 807 MET cc_start: 0.8813 (mmm) cc_final: 0.8439 (mmm) REVERT: C 813 GLU cc_start: 0.8899 (pp20) cc_final: 0.8672 (tt0) REVERT: C 815 CYS cc_start: 0.7700 (m) cc_final: 0.6412 (p) REVERT: C 840 LEU cc_start: 0.8104 (tp) cc_final: 0.7759 (tp) REVERT: C 844 PHE cc_start: 0.7890 (m-80) cc_final: 0.7467 (m-80) REVERT: C 874 GLN cc_start: 0.7239 (pt0) cc_final: 0.6941 (pt0) REVERT: C 924 MET cc_start: 0.8010 (mmt) cc_final: 0.7723 (mmt) REVERT: C 937 PHE cc_start: 0.8485 (t80) cc_final: 0.7995 (t80) REVERT: C 950 HIS cc_start: 0.6779 (m-70) cc_final: 0.6129 (m90) REVERT: C 955 ARG cc_start: 0.4828 (mmm-85) cc_final: 0.3033 (ptt-90) REVERT: C 1009 PHE cc_start: 0.8425 (m-10) cc_final: 0.8220 (m-10) REVERT: C 1023 MET cc_start: 0.8501 (mtp) cc_final: 0.7867 (mtp) REVERT: C 1029 MET cc_start: 0.8843 (mtp) cc_final: 0.8329 (tpp) REVERT: D 407 MET cc_start: 0.6052 (mtp) cc_final: 0.5776 (mtm) REVERT: D 411 ASN cc_start: 0.7733 (m-40) cc_final: 0.7170 (m-40) REVERT: D 503 MET cc_start: 0.8900 (ttt) cc_final: 0.8354 (ttt) REVERT: D 529 ILE cc_start: 0.9712 (mp) cc_final: 0.9480 (mp) REVERT: D 533 TYR cc_start: 0.9344 (t80) cc_final: 0.8955 (t80) REVERT: D 537 SER cc_start: 0.9359 (p) cc_final: 0.9028 (t) REVERT: D 700 TYR cc_start: 0.6584 (t80) cc_final: 0.6332 (t80) REVERT: D 709 ASN cc_start: 0.8689 (t0) cc_final: 0.8133 (m-40) REVERT: D 747 ASN cc_start: 0.8785 (m110) cc_final: 0.8520 (m110) REVERT: D 764 ASN cc_start: 0.8818 (m-40) cc_final: 0.8530 (m110) REVERT: D 813 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7692 (mt-10) outliers start: 0 outliers final: 0 residues processed: 368 average time/residue: 0.1083 time to fit residues: 64.1614 Evaluate side-chains 281 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 281 time to evaluate : 0.621 ------------------------------------------------------------------------------- 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: 3.9990 chunk 201 optimal weight: 0.9980 chunk 61 optimal weight: 7.9990 chunk 114 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 chunk 145 optimal weight: 10.0000 chunk 147 optimal weight: 0.9980 chunk 116 optimal weight: 0.5980 chunk 37 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 HIS B 619 ASN B 764 ASN C 619 ASN C 747 ASN C 947 ASN ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 619 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.119532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.092479 restraints weight = 44747.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.094997 restraints weight = 28233.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.096749 restraints weight = 18341.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.097149 restraints weight = 14962.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.097277 restraints weight = 13947.896| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.5939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 17054 Z= 0.162 Angle : 0.684 14.211 22890 Z= 0.351 Chirality : 0.045 0.302 2494 Planarity : 0.005 0.079 2778 Dihedral : 15.865 167.561 2802 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % 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: 0.00 (0.19), residues: 2020 helix: 1.48 (0.16), residues: 1104 sheet: -2.29 (0.33), residues: 198 loop : -1.67 (0.24), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 897 TYR 0.020 0.002 TYR C 732 PHE 0.048 0.002 PHE A 938 TRP 0.017 0.002 TRP C 861 HIS 0.004 0.001 HIS A 883 Details of bonding type rmsd covalent geometry : bond 0.00368 (17048) covalent geometry : angle 0.67965 (22878) SS BOND : bond 0.01899 ( 6) SS BOND : angle 3.44698 ( 12) hydrogen bonds : bond 0.03851 ( 824) hydrogen bonds : angle 4.27448 ( 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 338 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 338 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 ASN cc_start: 0.8081 (m-40) cc_final: 0.7496 (m-40) REVERT: A 434 LYS cc_start: 0.8957 (mmmt) cc_final: 0.8042 (ptmt) REVERT: A 537 SER cc_start: 0.9316 (m) cc_final: 0.8915 (t) REVERT: A 708 MET cc_start: 0.9061 (mpp) cc_final: 0.8466 (mtm) REVERT: A 807 MET cc_start: 0.8885 (mmm) cc_final: 0.8550 (mmm) REVERT: A 808 LEU cc_start: 0.8812 (tt) cc_final: 0.8442 (mp) REVERT: A 880 MET cc_start: 0.8302 (tmm) cc_final: 0.8083 (tmm) REVERT: A 920 ASN cc_start: 0.8242 (m110) cc_final: 0.7934 (m110) REVERT: A 924 MET cc_start: 0.8104 (mmm) cc_final: 0.7422 (mmt) REVERT: A 937 PHE cc_start: 0.8643 (t80) cc_final: 0.8135 (t80) REVERT: A 947 ASN cc_start: 0.8471 (m-40) cc_final: 0.8176 (m-40) REVERT: A 1023 MET cc_start: 0.8648 (mtp) cc_final: 0.8135 (mtp) REVERT: B 411 ASN cc_start: 0.7839 (m-40) cc_final: 0.7252 (m-40) REVERT: B 496 MET cc_start: 0.7426 (ptp) cc_final: 0.6957 (pmm) REVERT: B 503 MET cc_start: 0.8979 (ttt) cc_final: 0.8674 (ttt) REVERT: B 537 SER cc_start: 0.9317 (p) cc_final: 0.9067 (t) REVERT: B 710 GLU cc_start: 0.8632 (tp30) cc_final: 0.8412 (tp30) REVERT: B 714 GLN cc_start: 0.7970 (mm-40) cc_final: 0.7357 (tt0) REVERT: B 726 ASN cc_start: 0.8984 (m-40) cc_final: 0.8757 (m-40) REVERT: B 744 THR cc_start: 0.7906 (m) cc_final: 0.7675 (m) REVERT: B 747 ASN cc_start: 0.8794 (m110) cc_final: 0.8429 (m110) REVERT: B 813 GLU cc_start: 0.8369 (mt-10) cc_final: 0.7707 (mt-10) REVERT: C 503 MET cc_start: 0.8846 (tmm) cc_final: 0.8162 (tmm) REVERT: C 585 MET cc_start: 0.9226 (mmm) cc_final: 0.8799 (mmm) REVERT: C 596 LEU cc_start: 0.8923 (tt) cc_final: 0.8708 (tt) REVERT: C 708 MET cc_start: 0.8985 (mpp) cc_final: 0.8396 (mtm) REVERT: C 807 MET cc_start: 0.8767 (mmm) cc_final: 0.8382 (mmm) REVERT: C 813 GLU cc_start: 0.8890 (pp20) cc_final: 0.8687 (tt0) REVERT: C 815 CYS cc_start: 0.7795 (m) cc_final: 0.6509 (p) REVERT: C 840 LEU cc_start: 0.8218 (tp) cc_final: 0.7917 (tp) REVERT: C 874 GLN cc_start: 0.7153 (pt0) cc_final: 0.5418 (mm-40) REVERT: C 892 LEU cc_start: 0.7749 (tp) cc_final: 0.7478 (tp) REVERT: C 924 MET cc_start: 0.8103 (mmt) cc_final: 0.7707 (mmt) REVERT: C 955 ARG cc_start: 0.5051 (mmm-85) cc_final: 0.3152 (ptt-90) REVERT: C 1009 PHE cc_start: 0.8433 (m-10) cc_final: 0.8093 (m-10) REVERT: C 1023 MET cc_start: 0.8620 (mtp) cc_final: 0.8136 (mtp) REVERT: C 1029 MET cc_start: 0.8823 (mtp) cc_final: 0.8285 (tpp) REVERT: D 411 ASN cc_start: 0.7778 (m-40) cc_final: 0.7226 (m-40) REVERT: D 503 MET cc_start: 0.8899 (ttt) cc_final: 0.8331 (ttt) REVERT: D 529 ILE cc_start: 0.9702 (mp) cc_final: 0.9480 (mp) REVERT: D 533 TYR cc_start: 0.9349 (t80) cc_final: 0.8896 (t80) REVERT: D 537 SER cc_start: 0.9355 (p) cc_final: 0.9042 (t) REVERT: D 700 TYR cc_start: 0.6652 (t80) cc_final: 0.6352 (t80) REVERT: D 709 ASN cc_start: 0.8609 (t0) cc_final: 0.7992 (m-40) REVERT: D 747 ASN cc_start: 0.8778 (m110) cc_final: 0.8483 (m110) REVERT: D 764 ASN cc_start: 0.8829 (m-40) cc_final: 0.8551 (m110) REVERT: D 813 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7756 (mt-10) outliers start: 0 outliers final: 0 residues processed: 338 average time/residue: 0.1065 time to fit residues: 58.3808 Evaluate side-chains 271 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 0.627 ------------------------------------------------------------------------------- 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: 0.9990 chunk 109 optimal weight: 2.9990 chunk 94 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 176 optimal weight: 0.3980 chunk 168 optimal weight: 1.9990 chunk 172 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 152 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 overall best weight: 1.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 HIS B 764 ASN C 619 ASN C 714 GLN ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 619 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.120791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.093509 restraints weight = 44509.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.096141 restraints weight = 28152.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.097882 restraints weight = 18107.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.098266 restraints weight = 14808.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.098271 restraints weight = 13986.062| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.6080 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= 0.140 Angle : 0.676 16.706 22890 Z= 0.346 Chirality : 0.044 0.313 2494 Planarity : 0.005 0.079 2778 Dihedral : 15.399 170.557 2802 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Cbeta Deviations : 0.00 % 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: -0.00 (0.19), residues: 2020 helix: 1.44 (0.16), residues: 1112 sheet: -2.30 (0.33), residues: 194 loop : -1.65 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C1031 TYR 0.023 0.001 TYR A1026 PHE 0.046 0.002 PHE A 901 TRP 0.021 0.002 TRP B 460 HIS 0.006 0.001 HIS C 883 Details of bonding type rmsd covalent geometry : bond 0.00318 (17048) covalent geometry : angle 0.67213 (22878) SS BOND : bond 0.01326 ( 6) SS BOND : angle 3.34870 ( 12) hydrogen bonds : bond 0.03733 ( 824) hydrogen bonds : angle 4.17390 ( 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 349 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 349 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 418 ASN cc_start: 0.8000 (m-40) cc_final: 0.7625 (m-40) REVERT: A 434 LYS cc_start: 0.8955 (mmmt) cc_final: 0.8051 (ptmt) REVERT: A 442 LEU cc_start: 0.8787 (mt) cc_final: 0.8298 (mt) REVERT: A 537 SER cc_start: 0.9285 (m) cc_final: 0.8851 (t) REVERT: A 585 MET cc_start: 0.9131 (mmm) cc_final: 0.8446 (mmm) REVERT: A 708 MET cc_start: 0.9046 (mpp) cc_final: 0.8452 (mtm) REVERT: A 710 GLU cc_start: 0.8960 (mt-10) cc_final: 0.8512 (mt-10) REVERT: A 807 MET cc_start: 0.8745 (mmm) cc_final: 0.8395 (mmm) REVERT: A 808 LEU cc_start: 0.8784 (tt) cc_final: 0.8450 (mp) REVERT: A 880 MET cc_start: 0.8389 (tmm) cc_final: 0.8100 (tmm) REVERT: A 892 LEU cc_start: 0.7367 (tp) cc_final: 0.6959 (tp) REVERT: A 920 ASN cc_start: 0.8235 (m110) cc_final: 0.7968 (m110) REVERT: A 924 MET cc_start: 0.8041 (mmm) cc_final: 0.7391 (mmt) REVERT: A 937 PHE cc_start: 0.8621 (t80) cc_final: 0.8090 (t80) REVERT: A 947 ASN cc_start: 0.8286 (m-40) cc_final: 0.8020 (m-40) REVERT: B 496 MET cc_start: 0.7045 (ptp) cc_final: 0.6661 (pmm) REVERT: B 503 MET cc_start: 0.8907 (ttt) cc_final: 0.8579 (ttt) REVERT: B 533 TYR cc_start: 0.9262 (t80) cc_final: 0.8952 (t80) REVERT: B 537 SER cc_start: 0.9209 (p) cc_final: 0.8965 (t) REVERT: B 710 GLU cc_start: 0.8569 (tp30) cc_final: 0.8040 (tp30) REVERT: B 726 ASN cc_start: 0.8929 (m-40) cc_final: 0.8700 (m-40) REVERT: B 744 THR cc_start: 0.7829 (m) cc_final: 0.7593 (m) REVERT: B 747 ASN cc_start: 0.8671 (m110) cc_final: 0.8326 (m110) REVERT: B 813 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7642 (mt-10) REVERT: C 503 MET cc_start: 0.8649 (tmm) cc_final: 0.8118 (tmm) REVERT: C 504 ILE cc_start: 0.9301 (mt) cc_final: 0.8904 (mt) REVERT: C 585 MET cc_start: 0.9181 (mmm) cc_final: 0.8767 (mmm) REVERT: C 596 LEU cc_start: 0.8837 (tt) cc_final: 0.8623 (tt) REVERT: C 616 TYR cc_start: 0.9397 (t80) cc_final: 0.9154 (t80) REVERT: C 708 MET cc_start: 0.8966 (mpp) cc_final: 0.8401 (mtm) REVERT: C 807 MET cc_start: 0.8680 (mmm) cc_final: 0.8306 (mmm) REVERT: C 813 GLU cc_start: 0.8834 (pp20) cc_final: 0.8613 (tt0) REVERT: C 815 CYS cc_start: 0.7880 (m) cc_final: 0.6548 (p) REVERT: C 874 GLN cc_start: 0.7211 (pt0) cc_final: 0.5426 (mm110) REVERT: C 924 MET cc_start: 0.8120 (mmt) cc_final: 0.7724 (mmt) REVERT: C 937 PHE cc_start: 0.8520 (t80) cc_final: 0.8055 (t80) REVERT: C 1009 PHE cc_start: 0.8452 (m-10) cc_final: 0.8091 (m-10) REVERT: C 1023 MET cc_start: 0.8568 (mtp) cc_final: 0.8004 (mtp) REVERT: C 1029 MET cc_start: 0.8887 (mtp) cc_final: 0.8280 (tpp) REVERT: C 1031 ARG cc_start: 0.7869 (ttm110) cc_final: 0.7645 (mtm110) REVERT: D 503 MET cc_start: 0.8866 (ttt) cc_final: 0.8262 (ttt) REVERT: D 533 TYR cc_start: 0.9304 (t80) cc_final: 0.8924 (t80) REVERT: D 537 SER cc_start: 0.9282 (p) cc_final: 0.8935 (t) REVERT: D 700 TYR cc_start: 0.6471 (t80) cc_final: 0.6186 (t80) REVERT: D 709 ASN cc_start: 0.8569 (t0) cc_final: 0.7935 (m-40) REVERT: D 747 ASN cc_start: 0.8743 (m110) cc_final: 0.8431 (m110) REVERT: D 764 ASN cc_start: 0.8755 (m-40) cc_final: 0.8476 (m110) REVERT: D 813 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7660 (mt-10) outliers start: 0 outliers final: 0 residues processed: 349 average time/residue: 0.1098 time to fit residues: 61.7871 Evaluate side-chains 274 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 274 time to evaluate : 0.636 ------------------------------------------------------------------------------- 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: 3.9990 chunk 17 optimal weight: 0.9990 chunk 183 optimal weight: 0.0870 chunk 39 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 195 optimal weight: 2.9990 chunk 60 optimal weight: 9.9990 chunk 102 optimal weight: 0.0970 chunk 71 optimal weight: 0.8980 chunk 189 optimal weight: 6.9990 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 714 GLN A 874 GLN A1000 ASN B 764 ASN C 619 ASN ** C 747 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 587 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 619 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.121479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.094893 restraints weight = 44509.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.097297 restraints weight = 28778.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.098729 restraints weight = 18966.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.099274 restraints weight = 15849.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.099268 restraints weight = 14856.105| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.6207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 17054 Z= 0.131 Angle : 0.668 14.666 22890 Z= 0.341 Chirality : 0.043 0.269 2494 Planarity : 0.005 0.079 2778 Dihedral : 14.894 174.048 2802 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % 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 : 0.10 % 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: 0.12 (0.19), residues: 2020 helix: 1.49 (0.16), residues: 1108 sheet: -1.97 (0.37), residues: 164 loop : -1.61 (0.24), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 888 TYR 0.023 0.001 TYR A 424 PHE 0.056 0.002 PHE A 938 TRP 0.024 0.002 TRP D 460 HIS 0.003 0.001 HIS A 883 Details of bonding type rmsd covalent geometry : bond 0.00296 (17048) covalent geometry : angle 0.66386 (22878) SS BOND : bond 0.01144 ( 6) SS BOND : angle 3.15840 ( 12) hydrogen bonds : bond 0.03696 ( 824) hydrogen bonds : angle 4.08755 ( 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 351 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 351 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 418 ASN cc_start: 0.7886 (m-40) cc_final: 0.7506 (m-40) REVERT: A 434 LYS cc_start: 0.8837 (mmmt) cc_final: 0.7930 (ptmt) REVERT: A 442 LEU cc_start: 0.8917 (mt) cc_final: 0.8460 (mt) REVERT: A 537 SER cc_start: 0.9286 (m) cc_final: 0.8870 (t) REVERT: A 585 MET cc_start: 0.9152 (mmm) cc_final: 0.8399 (mmm) REVERT: A 708 MET cc_start: 0.8924 (mpp) cc_final: 0.8408 (mtm) REVERT: A 710 GLU cc_start: 0.9036 (mt-10) cc_final: 0.8534 (mt-10) REVERT: A 807 MET cc_start: 0.8792 (mmm) cc_final: 0.8436 (mmm) REVERT: A 808 LEU cc_start: 0.8695 (tt) cc_final: 0.8428 (mp) REVERT: A 880 MET cc_start: 0.8300 (tmm) cc_final: 0.8046 (tmm) REVERT: A 920 ASN cc_start: 0.8204 (m110) cc_final: 0.7948 (m110) REVERT: A 924 MET cc_start: 0.8035 (mmm) cc_final: 0.7368 (mmt) REVERT: A 937 PHE cc_start: 0.8586 (t80) cc_final: 0.8062 (t80) REVERT: A 947 ASN cc_start: 0.8337 (m-40) cc_final: 0.8080 (m-40) REVERT: A 1023 MET cc_start: 0.8634 (mtp) cc_final: 0.8374 (mtp) REVERT: B 493 LYS cc_start: 0.7068 (mmmt) cc_final: 0.6828 (mmmt) REVERT: B 496 MET cc_start: 0.7054 (ptp) cc_final: 0.6712 (pmm) REVERT: B 533 TYR cc_start: 0.9298 (t80) cc_final: 0.8990 (t80) REVERT: B 537 SER cc_start: 0.9241 (p) cc_final: 0.9013 (t) REVERT: B 710 GLU cc_start: 0.8614 (tp30) cc_final: 0.8073 (tp30) REVERT: B 726 ASN cc_start: 0.8891 (m-40) cc_final: 0.8663 (m-40) REVERT: B 744 THR cc_start: 0.7798 (m) cc_final: 0.7569 (m) REVERT: B 747 ASN cc_start: 0.8647 (m110) cc_final: 0.8328 (m110) REVERT: B 764 ASN cc_start: 0.8139 (m-40) cc_final: 0.7917 (m110) REVERT: B 813 GLU cc_start: 0.8260 (mt-10) cc_final: 0.7676 (mt-10) REVERT: B 819 ARG cc_start: 0.7378 (mmp80) cc_final: 0.5922 (tpp80) REVERT: C 434 LYS cc_start: 0.8900 (mmmm) cc_final: 0.8153 (mtpt) REVERT: C 503 MET cc_start: 0.8673 (tmm) cc_final: 0.8143 (tmm) REVERT: C 504 ILE cc_start: 0.9323 (mt) cc_final: 0.8972 (mt) REVERT: C 585 MET cc_start: 0.9133 (mmm) cc_final: 0.8836 (mmm) REVERT: C 596 LEU cc_start: 0.8790 (tt) cc_final: 0.8406 (tt) REVERT: C 616 TYR cc_start: 0.9442 (t80) cc_final: 0.9213 (t80) REVERT: C 708 MET cc_start: 0.9019 (mpp) cc_final: 0.8390 (mtm) REVERT: C 807 MET cc_start: 0.8714 (mmm) cc_final: 0.8320 (mmm) REVERT: C 815 CYS cc_start: 0.7857 (m) cc_final: 0.6557 (p) REVERT: C 844 PHE cc_start: 0.8132 (m-10) cc_final: 0.7900 (m-80) REVERT: C 874 GLN cc_start: 0.7162 (pt0) cc_final: 0.5398 (mm110) REVERT: C 937 PHE cc_start: 0.8488 (t80) cc_final: 0.7983 (t80) REVERT: C 955 ARG cc_start: 0.5119 (mmm-85) cc_final: 0.3113 (ptt90) REVERT: C 1009 PHE cc_start: 0.8559 (m-10) cc_final: 0.8170 (m-10) REVERT: C 1023 MET cc_start: 0.8607 (mtp) cc_final: 0.7977 (mtt) REVERT: D 533 TYR cc_start: 0.9313 (t80) cc_final: 0.8877 (t80) REVERT: D 537 SER cc_start: 0.9308 (p) cc_final: 0.8924 (t) REVERT: D 700 TYR cc_start: 0.6513 (t80) cc_final: 0.6170 (t80) REVERT: D 747 ASN cc_start: 0.8710 (m110) cc_final: 0.8395 (m110) REVERT: D 813 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7417 (mt-10) outliers start: 0 outliers final: 0 residues processed: 351 average time/residue: 0.1142 time to fit residues: 63.8631 Evaluate side-chains 278 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 0.601 ------------------------------------------------------------------------------- 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: 0.9980 chunk 94 optimal weight: 7.9990 chunk 181 optimal weight: 0.8980 chunk 41 optimal weight: 10.0000 chunk 31 optimal weight: 0.9980 chunk 163 optimal weight: 7.9990 chunk 190 optimal weight: 0.9980 chunk 36 optimal weight: 9.9990 chunk 84 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1000 ASN C 619 ASN C 747 ASN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.120196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.093401 restraints weight = 44619.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.095553 restraints weight = 30135.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.097417 restraints weight = 19549.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.097688 restraints weight = 15866.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.097781 restraints weight = 15023.354| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.6306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 17054 Z= 0.155 Angle : 0.698 14.921 22890 Z= 0.356 Chirality : 0.044 0.266 2494 Planarity : 0.005 0.079 2778 Dihedral : 14.853 176.220 2802 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.20 % 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: 0.12 (0.20), residues: 2020 helix: 1.56 (0.16), residues: 1100 sheet: -2.19 (0.36), residues: 174 loop : -1.63 (0.23), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 888 TYR 0.018 0.001 TYR C 732 PHE 0.055 0.002 PHE C 938 TRP 0.028 0.002 TRP D 460 HIS 0.003 0.001 HIS C 883 Details of bonding type rmsd covalent geometry : bond 0.00353 (17048) covalent geometry : angle 0.69398 (22878) SS BOND : bond 0.01392 ( 6) SS BOND : angle 3.44790 ( 12) hydrogen bonds : bond 0.03743 ( 824) hydrogen bonds : angle 4.19276 ( 2412) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2686.19 seconds wall clock time: 47 minutes 17.26 seconds (2837.26 seconds total)