Starting phenix.real_space_refine on Mon Jul 6 18:53:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7vh6_31988/07_2026/7vh6_31988.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vh6_31988/07_2026/7vh6_31988.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vh6_31988/07_2026/7vh6_31988.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vh6_31988/07_2026/7vh6_31988.map" model { file = "/net/cci-nas-00/data/ceres_data/7vh6_31988/07_2026/7vh6_31988.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vh6_31988/07_2026/7vh6_31988.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7vh6_31988/07_2026/7vh6_31988.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7vh6_31988/07_2026/7vh6_31988.cif" } resolution = 3.8 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: 7 Type Number sf(0) Gaussians P 57 5.49 5 S 162 5.16 5 Be 6 3.05 5 C 25206 2.51 5 N 5859 2.21 5 O 6894 1.98 5 F 18 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 162 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 38202 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 768, 5869 Classifications: {'peptide': 768} Link IDs: {'PTRANS': 28, 'TRANS': 739} Chain breaks: 3 Chain: "B" Number of atoms: 5869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 768, 5869 Classifications: {'peptide': 768} Link IDs: {'PTRANS': 28, 'TRANS': 739} Chain breaks: 3 Chain: "C" Number of atoms: 5869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 768, 5869 Classifications: {'peptide': 768} Link IDs: {'PTRANS': 28, 'TRANS': 739} Chain breaks: 3 Chain: "D" Number of atoms: 5869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 768, 5869 Classifications: {'peptide': 768} Link IDs: {'PTRANS': 28, 'TRANS': 739} Chain breaks: 3 Chain: "E" Number of atoms: 5869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 768, 5869 Classifications: {'peptide': 768} Link IDs: {'PTRANS': 28, 'TRANS': 739} Chain breaks: 3 Chain: "F" Number of atoms: 5869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 768, 5869 Classifications: {'peptide': 768} Link IDs: {'PTRANS': 28, 'TRANS': 739} Chain breaks: 3 Chain: "A" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 576 Unusual residues: {'BEF': 1, 'POV': 11} Classifications: {'undetermined': 12} Link IDs: {None: 11} Chain: "B" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 472 Unusual residues: {'BEF': 1, 'POV': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "C" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 472 Unusual residues: {'BEF': 1, 'POV': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "D" Number of atoms: 524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 524 Unusual residues: {'BEF': 1, 'POV': 10} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "E" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 472 Unusual residues: {'BEF': 1, 'POV': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "F" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 472 Unusual residues: {'BEF': 1, 'POV': 9} Classifications: {'undetermined': 10} Link IDs: {None: 9} Time building chain proxies: 8.35, per 1000 atoms: 0.22 Number of scatterers: 38202 At special positions: 0 Unit cell: (139.36, 189.28, 193.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 162 16.00 P 57 15.00 F 18 9.00 O 6894 8.00 N 5859 7.00 C 25206 6.00 Be 6 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=13, symmetry=0 Number of additional bonds: simple=13, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.42 Conformation dependent library (CDL) restraints added in 1.6 seconds 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8388 Finding SS restraints... Secondary structure from input PDB file: 174 helices and 30 sheets defined 58.5% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 110 through 121 removed outlier: 3.541A pdb=" N MET A 118 " --> pdb=" O VAL A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 138 removed outlier: 3.666A pdb=" N VAL A 127 " --> pdb=" O PRO A 123 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N MET A 128 " --> pdb=" O ILE A 124 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU A 129 " --> pdb=" O GLN A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 173 removed outlier: 3.788A pdb=" N ILE A 147 " --> pdb=" O ASP A 143 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN A 161 " --> pdb=" O VAL A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 279 Processing helix chain 'A' and resid 284 through 315 removed outlier: 3.636A pdb=" N LEU A 307 " --> pdb=" O ALA A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 334 removed outlier: 3.782A pdb=" N ILE A 332 " --> pdb=" O GLY A 328 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL A 334 " --> pdb=" O THR A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 355 removed outlier: 3.611A pdb=" N THR A 343 " --> pdb=" O PRO A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 372 removed outlier: 4.376A pdb=" N GLU A 367 " --> pdb=" O LEU A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 411 Processing helix chain 'A' and resid 420 through 428 removed outlier: 3.517A pdb=" N ALA A 425 " --> pdb=" O ALA A 421 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A 427 " --> pdb=" O ASP A 423 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS A 428 " --> pdb=" O LYS A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 439 removed outlier: 4.001A pdb=" N ALA A 439 " --> pdb=" O LYS A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 482 Processing helix chain 'A' and resid 490 through 508 Processing helix chain 'A' and resid 537 through 550 removed outlier: 3.807A pdb=" N ALA A 541 " --> pdb=" O ARG A 537 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLN A 542 " --> pdb=" O ASP A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 573 removed outlier: 3.566A pdb=" N THR A 568 " --> pdb=" O ILE A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 585 Processing helix chain 'A' and resid 595 through 604 Processing helix chain 'A' and resid 611 through 626 removed outlier: 3.541A pdb=" N LEU A 622 " --> pdb=" O VAL A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 645 Processing helix chain 'A' and resid 655 through 662 Processing helix chain 'A' and resid 672 through 714 removed outlier: 3.985A pdb=" N ASP A 676 " --> pdb=" O SER A 672 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA A 697 " --> pdb=" O VAL A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 734 removed outlier: 3.552A pdb=" N VAL A 723 " --> pdb=" O ILE A 719 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE A 724 " --> pdb=" O ASP A 720 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR A 733 " --> pdb=" O ALA A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 737 No H-bonds generated for 'chain 'A' and resid 735 through 737' Processing helix chain 'A' and resid 751 through 777 removed outlier: 3.712A pdb=" N MET A 777 " --> pdb=" O THR A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 805 removed outlier: 3.579A pdb=" N MET A 795 " --> pdb=" O MET A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 811 removed outlier: 3.954A pdb=" N ILE A 809 " --> pdb=" O TRP A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 842 removed outlier: 3.732A pdb=" N THR A 840 " --> pdb=" O ALA A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 878 removed outlier: 3.521A pdb=" N THR A 878 " --> pdb=" O TYR A 874 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 888 removed outlier: 3.905A pdb=" N ASP A 883 " --> pdb=" O SER A 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 121 removed outlier: 3.541A pdb=" N MET B 118 " --> pdb=" O VAL B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 138 removed outlier: 3.666A pdb=" N VAL B 127 " --> pdb=" O PRO B 123 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N MET B 128 " --> pdb=" O ILE B 124 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU B 129 " --> pdb=" O GLN B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 173 removed outlier: 3.788A pdb=" N ILE B 147 " --> pdb=" O ASP B 143 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN B 161 " --> pdb=" O VAL B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 279 Processing helix chain 'B' and resid 284 through 315 removed outlier: 3.636A pdb=" N LEU B 307 " --> pdb=" O ALA B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 334 removed outlier: 3.781A pdb=" N ILE B 332 " --> pdb=" O GLY B 328 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL B 334 " --> pdb=" O THR B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 355 removed outlier: 3.610A pdb=" N THR B 343 " --> pdb=" O PRO B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 372 removed outlier: 4.376A pdb=" N GLU B 367 " --> pdb=" O LEU B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 411 Processing helix chain 'B' and resid 420 through 428 removed outlier: 3.517A pdb=" N ALA B 425 " --> pdb=" O ALA B 421 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU B 427 " --> pdb=" O ASP B 423 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS B 428 " --> pdb=" O LYS B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 439 removed outlier: 4.020A pdb=" N ALA B 439 " --> pdb=" O LYS B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 482 Processing helix chain 'B' and resid 490 through 508 Processing helix chain 'B' and resid 537 through 550 removed outlier: 3.807A pdb=" N ALA B 541 " --> pdb=" O ARG B 537 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLN B 542 " --> pdb=" O ASP B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 573 removed outlier: 3.566A pdb=" N THR B 568 " --> pdb=" O ILE B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 585 Processing helix chain 'B' and resid 595 through 604 Processing helix chain 'B' and resid 611 through 626 removed outlier: 3.541A pdb=" N LEU B 622 " --> pdb=" O VAL B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 645 Processing helix chain 'B' and resid 655 through 662 Processing helix chain 'B' and resid 672 through 714 removed outlier: 3.986A pdb=" N ASP B 676 " --> pdb=" O SER B 672 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA B 697 " --> pdb=" O VAL B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 734 removed outlier: 3.553A pdb=" N VAL B 723 " --> pdb=" O ILE B 719 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N PHE B 724 " --> pdb=" O ASP B 720 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR B 733 " --> pdb=" O ALA B 729 " (cutoff:3.500A) Processing helix chain 'B' and resid 735 through 737 No H-bonds generated for 'chain 'B' and resid 735 through 737' Processing helix chain 'B' and resid 751 through 777 removed outlier: 3.712A pdb=" N MET B 777 " --> pdb=" O THR B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 790 through 805 removed outlier: 3.580A pdb=" N MET B 795 " --> pdb=" O MET B 791 " (cutoff:3.500A) Processing helix chain 'B' and resid 805 through 811 removed outlier: 3.954A pdb=" N ILE B 809 " --> pdb=" O TRP B 805 " (cutoff:3.500A) Processing helix chain 'B' and resid 822 through 842 removed outlier: 3.732A pdb=" N THR B 840 " --> pdb=" O ALA B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 851 through 878 removed outlier: 3.520A pdb=" N THR B 878 " --> pdb=" O TYR B 874 " (cutoff:3.500A) Processing helix chain 'B' and resid 879 through 888 removed outlier: 3.905A pdb=" N ASP B 883 " --> pdb=" O SER B 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 121 removed outlier: 3.541A pdb=" N MET C 118 " --> pdb=" O VAL C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 138 removed outlier: 3.666A pdb=" N VAL C 127 " --> pdb=" O PRO C 123 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N MET C 128 " --> pdb=" O ILE C 124 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU C 129 " --> pdb=" O GLN C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 173 removed outlier: 3.789A pdb=" N ILE C 147 " --> pdb=" O ASP C 143 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN C 161 " --> pdb=" O VAL C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 279 Processing helix chain 'C' and resid 284 through 315 removed outlier: 3.637A pdb=" N LEU C 307 " --> pdb=" O ALA C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 334 removed outlier: 3.781A pdb=" N ILE C 332 " --> pdb=" O GLY C 328 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL C 334 " --> pdb=" O THR C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 355 removed outlier: 3.610A pdb=" N THR C 343 " --> pdb=" O PRO C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 372 removed outlier: 4.376A pdb=" N GLU C 367 " --> pdb=" O LEU C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 411 Processing helix chain 'C' and resid 420 through 428 removed outlier: 3.517A pdb=" N ALA C 425 " --> pdb=" O ALA C 421 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU C 427 " --> pdb=" O ASP C 423 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS C 428 " --> pdb=" O LYS C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 434 through 439 removed outlier: 4.024A pdb=" N ALA C 439 " --> pdb=" O LYS C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 482 Processing helix chain 'C' and resid 490 through 508 Processing helix chain 'C' and resid 537 through 550 removed outlier: 3.807A pdb=" N ALA C 541 " --> pdb=" O ARG C 537 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLN C 542 " --> pdb=" O ASP C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 561 through 573 removed outlier: 3.566A pdb=" N THR C 568 " --> pdb=" O ILE C 564 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 585 Processing helix chain 'C' and resid 595 through 604 Processing helix chain 'C' and resid 611 through 626 removed outlier: 3.542A pdb=" N LEU C 622 " --> pdb=" O VAL C 618 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 645 Processing helix chain 'C' and resid 655 through 662 Processing helix chain 'C' and resid 672 through 714 removed outlier: 3.985A pdb=" N ASP C 676 " --> pdb=" O SER C 672 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA C 697 " --> pdb=" O VAL C 693 " (cutoff:3.500A) Processing helix chain 'C' and resid 718 through 734 removed outlier: 3.553A pdb=" N VAL C 723 " --> pdb=" O ILE C 719 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE C 724 " --> pdb=" O ASP C 720 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR C 733 " --> pdb=" O ALA C 729 " (cutoff:3.500A) Processing helix chain 'C' and resid 735 through 737 No H-bonds generated for 'chain 'C' and resid 735 through 737' Processing helix chain 'C' and resid 751 through 777 removed outlier: 3.711A pdb=" N MET C 777 " --> pdb=" O THR C 773 " (cutoff:3.500A) Processing helix chain 'C' and resid 790 through 805 removed outlier: 3.579A pdb=" N MET C 795 " --> pdb=" O MET C 791 " (cutoff:3.500A) Processing helix chain 'C' and resid 805 through 811 removed outlier: 3.954A pdb=" N ILE C 809 " --> pdb=" O TRP C 805 " (cutoff:3.500A) Processing helix chain 'C' and resid 822 through 842 removed outlier: 3.732A pdb=" N THR C 840 " --> pdb=" O ALA C 836 " (cutoff:3.500A) Processing helix chain 'C' and resid 851 through 878 removed outlier: 3.521A pdb=" N THR C 878 " --> pdb=" O TYR C 874 " (cutoff:3.500A) Processing helix chain 'C' and resid 879 through 888 removed outlier: 3.905A pdb=" N ASP C 883 " --> pdb=" O SER C 879 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 121 removed outlier: 3.541A pdb=" N MET D 118 " --> pdb=" O VAL D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 138 removed outlier: 3.665A pdb=" N VAL D 127 " --> pdb=" O PRO D 123 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N MET D 128 " --> pdb=" O ILE D 124 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU D 129 " --> pdb=" O GLN D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 173 removed outlier: 3.788A pdb=" N ILE D 147 " --> pdb=" O ASP D 143 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN D 161 " --> pdb=" O VAL D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 279 Processing helix chain 'D' and resid 284 through 315 removed outlier: 3.636A pdb=" N LEU D 307 " --> pdb=" O ALA D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 334 removed outlier: 3.781A pdb=" N ILE D 332 " --> pdb=" O GLY D 328 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL D 334 " --> pdb=" O THR D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 355 removed outlier: 3.611A pdb=" N THR D 343 " --> pdb=" O PRO D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 372 removed outlier: 4.376A pdb=" N GLU D 367 " --> pdb=" O LEU D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 411 Processing helix chain 'D' and resid 420 through 428 removed outlier: 3.517A pdb=" N ALA D 425 " --> pdb=" O ALA D 421 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU D 427 " --> pdb=" O ASP D 423 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS D 428 " --> pdb=" O LYS D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 434 through 439 removed outlier: 4.011A pdb=" N ALA D 439 " --> pdb=" O LYS D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 482 Processing helix chain 'D' and resid 490 through 508 Processing helix chain 'D' and resid 537 through 550 removed outlier: 3.806A pdb=" N ALA D 541 " --> pdb=" O ARG D 537 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLN D 542 " --> pdb=" O ASP D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 561 through 573 removed outlier: 3.566A pdb=" N THR D 568 " --> pdb=" O ILE D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 585 Processing helix chain 'D' and resid 595 through 604 Processing helix chain 'D' and resid 611 through 626 removed outlier: 3.541A pdb=" N LEU D 622 " --> pdb=" O VAL D 618 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 645 Processing helix chain 'D' and resid 655 through 662 Processing helix chain 'D' and resid 672 through 714 removed outlier: 3.986A pdb=" N ASP D 676 " --> pdb=" O SER D 672 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA D 697 " --> pdb=" O VAL D 693 " (cutoff:3.500A) Processing helix chain 'D' and resid 718 through 734 removed outlier: 3.552A pdb=" N VAL D 723 " --> pdb=" O ILE D 719 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE D 724 " --> pdb=" O ASP D 720 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR D 733 " --> pdb=" O ALA D 729 " (cutoff:3.500A) Processing helix chain 'D' and resid 735 through 737 No H-bonds generated for 'chain 'D' and resid 735 through 737' Processing helix chain 'D' and resid 751 through 777 removed outlier: 3.712A pdb=" N MET D 777 " --> pdb=" O THR D 773 " (cutoff:3.500A) Processing helix chain 'D' and resid 790 through 805 removed outlier: 3.579A pdb=" N MET D 795 " --> pdb=" O MET D 791 " (cutoff:3.500A) Processing helix chain 'D' and resid 805 through 811 removed outlier: 3.955A pdb=" N ILE D 809 " --> pdb=" O TRP D 805 " (cutoff:3.500A) Processing helix chain 'D' and resid 822 through 842 removed outlier: 3.731A pdb=" N THR D 840 " --> pdb=" O ALA D 836 " (cutoff:3.500A) Processing helix chain 'D' and resid 851 through 878 removed outlier: 3.521A pdb=" N THR D 878 " --> pdb=" O TYR D 874 " (cutoff:3.500A) Processing helix chain 'D' and resid 879 through 888 removed outlier: 3.906A pdb=" N ASP D 883 " --> pdb=" O SER D 879 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 121 removed outlier: 3.541A pdb=" N MET E 118 " --> pdb=" O VAL E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 138 removed outlier: 3.667A pdb=" N VAL E 127 " --> pdb=" O PRO E 123 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N MET E 128 " --> pdb=" O ILE E 124 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU E 129 " --> pdb=" O GLN E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 173 removed outlier: 3.788A pdb=" N ILE E 147 " --> pdb=" O ASP E 143 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN E 161 " --> pdb=" O VAL E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 279 Processing helix chain 'E' and resid 284 through 315 removed outlier: 3.636A pdb=" N LEU E 307 " --> pdb=" O ALA E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 334 removed outlier: 3.782A pdb=" N ILE E 332 " --> pdb=" O GLY E 328 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL E 334 " --> pdb=" O THR E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 355 removed outlier: 3.610A pdb=" N THR E 343 " --> pdb=" O PRO E 339 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 372 removed outlier: 4.376A pdb=" N GLU E 367 " --> pdb=" O LEU E 363 " (cutoff:3.500A) Processing helix chain 'E' and resid 402 through 411 Processing helix chain 'E' and resid 420 through 428 removed outlier: 3.517A pdb=" N ALA E 425 " --> pdb=" O ALA E 421 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU E 427 " --> pdb=" O ASP E 423 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS E 428 " --> pdb=" O LYS E 424 " (cutoff:3.500A) Processing helix chain 'E' and resid 434 through 439 removed outlier: 4.021A pdb=" N ALA E 439 " --> pdb=" O LYS E 435 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 482 Processing helix chain 'E' and resid 490 through 508 Processing helix chain 'E' and resid 537 through 550 removed outlier: 3.807A pdb=" N ALA E 541 " --> pdb=" O ARG E 537 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLN E 542 " --> pdb=" O ASP E 538 " (cutoff:3.500A) Processing helix chain 'E' and resid 561 through 573 removed outlier: 3.566A pdb=" N THR E 568 " --> pdb=" O ILE E 564 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 585 Processing helix chain 'E' and resid 595 through 604 Processing helix chain 'E' and resid 611 through 626 removed outlier: 3.542A pdb=" N LEU E 622 " --> pdb=" O VAL E 618 " (cutoff:3.500A) Processing helix chain 'E' and resid 638 through 645 Processing helix chain 'E' and resid 655 through 662 Processing helix chain 'E' and resid 672 through 714 removed outlier: 3.985A pdb=" N ASP E 676 " --> pdb=" O SER E 672 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA E 697 " --> pdb=" O VAL E 693 " (cutoff:3.500A) Processing helix chain 'E' and resid 718 through 734 removed outlier: 3.553A pdb=" N VAL E 723 " --> pdb=" O ILE E 719 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N PHE E 724 " --> pdb=" O ASP E 720 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR E 733 " --> pdb=" O ALA E 729 " (cutoff:3.500A) Processing helix chain 'E' and resid 735 through 737 No H-bonds generated for 'chain 'E' and resid 735 through 737' Processing helix chain 'E' and resid 751 through 777 removed outlier: 3.712A pdb=" N MET E 777 " --> pdb=" O THR E 773 " (cutoff:3.500A) Processing helix chain 'E' and resid 790 through 805 removed outlier: 3.580A pdb=" N MET E 795 " --> pdb=" O MET E 791 " (cutoff:3.500A) Processing helix chain 'E' and resid 805 through 811 removed outlier: 3.954A pdb=" N ILE E 809 " --> pdb=" O TRP E 805 " (cutoff:3.500A) Processing helix chain 'E' and resid 822 through 842 removed outlier: 3.732A pdb=" N THR E 840 " --> pdb=" O ALA E 836 " (cutoff:3.500A) Processing helix chain 'E' and resid 851 through 878 removed outlier: 3.522A pdb=" N THR E 878 " --> pdb=" O TYR E 874 " (cutoff:3.500A) Processing helix chain 'E' and resid 879 through 888 removed outlier: 3.905A pdb=" N ASP E 883 " --> pdb=" O SER E 879 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 121 removed outlier: 3.541A pdb=" N MET F 118 " --> pdb=" O VAL F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 138 removed outlier: 3.666A pdb=" N VAL F 127 " --> pdb=" O PRO F 123 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N MET F 128 " --> pdb=" O ILE F 124 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU F 129 " --> pdb=" O GLN F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 173 removed outlier: 3.788A pdb=" N ILE F 147 " --> pdb=" O ASP F 143 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN F 161 " --> pdb=" O VAL F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 279 Processing helix chain 'F' and resid 284 through 315 removed outlier: 3.636A pdb=" N LEU F 307 " --> pdb=" O ALA F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 334 removed outlier: 3.782A pdb=" N ILE F 332 " --> pdb=" O GLY F 328 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL F 334 " --> pdb=" O THR F 330 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 355 removed outlier: 3.610A pdb=" N THR F 343 " --> pdb=" O PRO F 339 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 372 removed outlier: 4.376A pdb=" N GLU F 367 " --> pdb=" O LEU F 363 " (cutoff:3.500A) Processing helix chain 'F' and resid 402 through 411 Processing helix chain 'F' and resid 420 through 428 removed outlier: 3.517A pdb=" N ALA F 425 " --> pdb=" O ALA F 421 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU F 427 " --> pdb=" O ASP F 423 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS F 428 " --> pdb=" O LYS F 424 " (cutoff:3.500A) Processing helix chain 'F' and resid 434 through 439 removed outlier: 4.019A pdb=" N ALA F 439 " --> pdb=" O LYS F 435 " (cutoff:3.500A) Processing helix chain 'F' and resid 476 through 482 Processing helix chain 'F' and resid 490 through 508 Processing helix chain 'F' and resid 537 through 550 removed outlier: 3.807A pdb=" N ALA F 541 " --> pdb=" O ARG F 537 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLN F 542 " --> pdb=" O ASP F 538 " (cutoff:3.500A) Processing helix chain 'F' and resid 561 through 573 removed outlier: 3.566A pdb=" N THR F 568 " --> pdb=" O ILE F 564 " (cutoff:3.500A) Processing helix chain 'F' and resid 581 through 585 Processing helix chain 'F' and resid 595 through 604 Processing helix chain 'F' and resid 611 through 626 removed outlier: 3.541A pdb=" N LEU F 622 " --> pdb=" O VAL F 618 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 645 Processing helix chain 'F' and resid 655 through 662 Processing helix chain 'F' and resid 672 through 714 removed outlier: 3.985A pdb=" N ASP F 676 " --> pdb=" O SER F 672 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA F 697 " --> pdb=" O VAL F 693 " (cutoff:3.500A) Processing helix chain 'F' and resid 718 through 734 removed outlier: 3.552A pdb=" N VAL F 723 " --> pdb=" O ILE F 719 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE F 724 " --> pdb=" O ASP F 720 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR F 733 " --> pdb=" O ALA F 729 " (cutoff:3.500A) Processing helix chain 'F' and resid 735 through 737 No H-bonds generated for 'chain 'F' and resid 735 through 737' Processing helix chain 'F' and resid 751 through 777 removed outlier: 3.713A pdb=" N MET F 777 " --> pdb=" O THR F 773 " (cutoff:3.500A) Processing helix chain 'F' and resid 790 through 805 removed outlier: 3.580A pdb=" N MET F 795 " --> pdb=" O MET F 791 " (cutoff:3.500A) Processing helix chain 'F' and resid 805 through 811 removed outlier: 3.954A pdb=" N ILE F 809 " --> pdb=" O TRP F 805 " (cutoff:3.500A) Processing helix chain 'F' and resid 822 through 842 removed outlier: 3.732A pdb=" N THR F 840 " --> pdb=" O ALA F 836 " (cutoff:3.500A) Processing helix chain 'F' and resid 851 through 878 removed outlier: 3.521A pdb=" N THR F 878 " --> pdb=" O TYR F 874 " (cutoff:3.500A) Processing helix chain 'F' and resid 879 through 888 removed outlier: 3.905A pdb=" N ASP F 883 " --> pdb=" O SER F 879 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 179 through 184 Processing sheet with id=AA2, first strand: chain 'A' and resid 201 through 204 Processing sheet with id=AA3, first strand: chain 'A' and resid 233 through 239 removed outlier: 7.364A pdb=" N LEU A 235 " --> pdb=" O GLN A 227 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N GLN A 227 " --> pdb=" O LEU A 235 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE A 225 " --> pdb=" O VAL A 237 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N GLN A 224 " --> pdb=" O LYS A 252 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR A 250 " --> pdb=" O ASP A 226 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 358 through 360 removed outlier: 5.910A pdb=" N GLY A 648 " --> pdb=" O ILE A 664 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N PHE A 666 " --> pdb=" O GLY A 648 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA A 650 " --> pdb=" O PHE A 666 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N VAL A 629 " --> pdb=" O THR A 647 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ILE A 649 " --> pdb=" O VAL A 629 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N MET A 631 " --> pdb=" O ILE A 649 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N LEU A 375 " --> pdb=" O LYS A 555 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N LEU A 557 " --> pdb=" O LEU A 375 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N SER A 377 " --> pdb=" O LEU A 557 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N PHE A 607 " --> pdb=" O VAL A 554 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N MET A 556 " --> pdb=" O PHE A 607 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N TYR A 579 " --> pdb=" O ALA A 608 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 445 through 449 removed outlier: 6.370A pdb=" N VAL A 445 " --> pdb=" O GLU A 463 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLU A 463 " --> pdb=" O VAL A 445 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU A 447 " --> pdb=" O VAL A 461 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR A 459 " --> pdb=" O HIS A 449 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA A 516 " --> pdb=" O VAL A 473 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ARG A 517 " --> pdb=" O ILE A 526 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ILE A 526 " --> pdb=" O ARG A 517 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 179 through 184 Processing sheet with id=AA7, first strand: chain 'B' and resid 201 through 204 Processing sheet with id=AA8, first strand: chain 'B' and resid 233 through 239 removed outlier: 7.365A pdb=" N LEU B 235 " --> pdb=" O GLN B 227 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N GLN B 227 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE B 225 " --> pdb=" O VAL B 237 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N GLN B 224 " --> pdb=" O LYS B 252 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR B 250 " --> pdb=" O ASP B 226 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 358 through 360 removed outlier: 5.910A pdb=" N GLY B 648 " --> pdb=" O ILE B 664 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N PHE B 666 " --> pdb=" O GLY B 648 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA B 650 " --> pdb=" O PHE B 666 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N VAL B 629 " --> pdb=" O THR B 647 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ILE B 649 " --> pdb=" O VAL B 629 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N MET B 631 " --> pdb=" O ILE B 649 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N LEU B 375 " --> pdb=" O LYS B 555 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N LEU B 557 " --> pdb=" O LEU B 375 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N SER B 377 " --> pdb=" O LEU B 557 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N PHE B 607 " --> pdb=" O VAL B 554 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N MET B 556 " --> pdb=" O PHE B 607 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N TYR B 579 " --> pdb=" O ALA B 608 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 445 through 449 removed outlier: 6.370A pdb=" N VAL B 445 " --> pdb=" O GLU B 463 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N GLU B 463 " --> pdb=" O VAL B 445 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU B 447 " --> pdb=" O VAL B 461 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR B 459 " --> pdb=" O HIS B 449 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA B 516 " --> pdb=" O VAL B 473 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ARG B 517 " --> pdb=" O ILE B 526 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ILE B 526 " --> pdb=" O ARG B 517 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 179 through 184 Processing sheet with id=AB3, first strand: chain 'C' and resid 201 through 204 Processing sheet with id=AB4, first strand: chain 'C' and resid 233 through 239 removed outlier: 7.364A pdb=" N LEU C 235 " --> pdb=" O GLN C 227 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N GLN C 227 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE C 225 " --> pdb=" O VAL C 237 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N GLN C 224 " --> pdb=" O LYS C 252 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR C 250 " --> pdb=" O ASP C 226 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 358 through 360 removed outlier: 5.910A pdb=" N GLY C 648 " --> pdb=" O ILE C 664 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N PHE C 666 " --> pdb=" O GLY C 648 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA C 650 " --> pdb=" O PHE C 666 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N VAL C 629 " --> pdb=" O THR C 647 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ILE C 649 " --> pdb=" O VAL C 629 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N MET C 631 " --> pdb=" O ILE C 649 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N LEU C 375 " --> pdb=" O LYS C 555 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N LEU C 557 " --> pdb=" O LEU C 375 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N SER C 377 " --> pdb=" O LEU C 557 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N PHE C 607 " --> pdb=" O VAL C 554 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N MET C 556 " --> pdb=" O PHE C 607 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N TYR C 579 " --> pdb=" O ALA C 608 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 445 through 449 removed outlier: 6.370A pdb=" N VAL C 445 " --> pdb=" O GLU C 463 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLU C 463 " --> pdb=" O VAL C 445 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU C 447 " --> pdb=" O VAL C 461 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR C 459 " --> pdb=" O HIS C 449 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA C 516 " --> pdb=" O VAL C 473 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ARG C 517 " --> pdb=" O ILE C 526 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ILE C 526 " --> pdb=" O ARG C 517 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 179 through 184 Processing sheet with id=AB8, first strand: chain 'D' and resid 201 through 204 Processing sheet with id=AB9, first strand: chain 'D' and resid 233 through 239 removed outlier: 7.365A pdb=" N LEU D 235 " --> pdb=" O GLN D 227 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N GLN D 227 " --> pdb=" O LEU D 235 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE D 225 " --> pdb=" O VAL D 237 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N GLN D 224 " --> pdb=" O LYS D 252 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR D 250 " --> pdb=" O ASP D 226 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 358 through 360 removed outlier: 5.910A pdb=" N GLY D 648 " --> pdb=" O ILE D 664 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N PHE D 666 " --> pdb=" O GLY D 648 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA D 650 " --> pdb=" O PHE D 666 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N VAL D 629 " --> pdb=" O THR D 647 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N ILE D 649 " --> pdb=" O VAL D 629 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N MET D 631 " --> pdb=" O ILE D 649 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N LEU D 375 " --> pdb=" O LYS D 555 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LEU D 557 " --> pdb=" O LEU D 375 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N SER D 377 " --> pdb=" O LEU D 557 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N PHE D 607 " --> pdb=" O VAL D 554 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N MET D 556 " --> pdb=" O PHE D 607 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N TYR D 579 " --> pdb=" O ALA D 608 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 445 through 449 removed outlier: 6.370A pdb=" N VAL D 445 " --> pdb=" O GLU D 463 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLU D 463 " --> pdb=" O VAL D 445 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU D 447 " --> pdb=" O VAL D 461 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR D 459 " --> pdb=" O HIS D 449 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA D 516 " --> pdb=" O VAL D 473 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ARG D 517 " --> pdb=" O ILE D 526 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ILE D 526 " --> pdb=" O ARG D 517 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 179 through 184 Processing sheet with id=AC4, first strand: chain 'E' and resid 201 through 204 Processing sheet with id=AC5, first strand: chain 'E' and resid 233 through 239 removed outlier: 7.365A pdb=" N LEU E 235 " --> pdb=" O GLN E 227 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N GLN E 227 " --> pdb=" O LEU E 235 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE E 225 " --> pdb=" O VAL E 237 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N GLN E 224 " --> pdb=" O LYS E 252 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR E 250 " --> pdb=" O ASP E 226 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 358 through 360 removed outlier: 5.910A pdb=" N GLY E 648 " --> pdb=" O ILE E 664 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N PHE E 666 " --> pdb=" O GLY E 648 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA E 650 " --> pdb=" O PHE E 666 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N VAL E 629 " --> pdb=" O THR E 647 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N ILE E 649 " --> pdb=" O VAL E 629 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N MET E 631 " --> pdb=" O ILE E 649 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N LEU E 375 " --> pdb=" O LYS E 555 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LEU E 557 " --> pdb=" O LEU E 375 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N SER E 377 " --> pdb=" O LEU E 557 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N PHE E 607 " --> pdb=" O VAL E 554 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N MET E 556 " --> pdb=" O PHE E 607 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N TYR E 579 " --> pdb=" O ALA E 608 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 445 through 449 removed outlier: 6.371A pdb=" N VAL E 445 " --> pdb=" O GLU E 463 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N GLU E 463 " --> pdb=" O VAL E 445 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU E 447 " --> pdb=" O VAL E 461 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR E 459 " --> pdb=" O HIS E 449 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA E 516 " --> pdb=" O VAL E 473 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ARG E 517 " --> pdb=" O ILE E 526 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N ILE E 526 " --> pdb=" O ARG E 517 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 179 through 184 Processing sheet with id=AC9, first strand: chain 'F' and resid 201 through 204 Processing sheet with id=AD1, first strand: chain 'F' and resid 233 through 239 removed outlier: 7.364A pdb=" N LEU F 235 " --> pdb=" O GLN F 227 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N GLN F 227 " --> pdb=" O LEU F 235 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE F 225 " --> pdb=" O VAL F 237 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N GLN F 224 " --> pdb=" O LYS F 252 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR F 250 " --> pdb=" O ASP F 226 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 358 through 360 removed outlier: 5.910A pdb=" N GLY F 648 " --> pdb=" O ILE F 664 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N PHE F 666 " --> pdb=" O GLY F 648 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ALA F 650 " --> pdb=" O PHE F 666 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N VAL F 629 " --> pdb=" O THR F 647 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ILE F 649 " --> pdb=" O VAL F 629 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N MET F 631 " --> pdb=" O ILE F 649 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N LEU F 375 " --> pdb=" O LYS F 555 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LEU F 557 " --> pdb=" O LEU F 375 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N SER F 377 " --> pdb=" O LEU F 557 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N PHE F 607 " --> pdb=" O VAL F 554 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N MET F 556 " --> pdb=" O PHE F 607 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N TYR F 579 " --> pdb=" O ALA F 608 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 445 through 449 removed outlier: 6.370A pdb=" N VAL F 445 " --> pdb=" O GLU F 463 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLU F 463 " --> pdb=" O VAL F 445 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU F 447 " --> pdb=" O VAL F 461 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR F 459 " --> pdb=" O HIS F 449 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA F 516 " --> pdb=" O VAL F 473 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ARG F 517 " --> pdb=" O ILE F 526 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ILE F 526 " --> pdb=" O ARG F 517 " (cutoff:3.500A) 2095 hydrogen bonds defined for protein. 6177 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: 8.02 Time building geometry restraints manager: 4.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 5940 1.27 - 1.40: 8562 1.40 - 1.54: 22118 1.54 - 1.68: 1912 1.68 - 1.81: 327 Bond restraints: 38859 Sorted by residual: bond pdb=" CG PRO B 198 " pdb=" CD PRO B 198 " ideal model delta sigma weight residual 1.503 1.132 0.371 3.40e-02 8.65e+02 1.19e+02 bond pdb=" CG PRO F 198 " pdb=" CD PRO F 198 " ideal model delta sigma weight residual 1.503 1.132 0.371 3.40e-02 8.65e+02 1.19e+02 bond pdb=" CG PRO D 198 " pdb=" CD PRO D 198 " ideal model delta sigma weight residual 1.503 1.132 0.371 3.40e-02 8.65e+02 1.19e+02 bond pdb=" CG PRO E 198 " pdb=" CD PRO E 198 " ideal model delta sigma weight residual 1.503 1.133 0.370 3.40e-02 8.65e+02 1.19e+02 bond pdb=" CG PRO A 198 " pdb=" CD PRO A 198 " ideal model delta sigma weight residual 1.503 1.133 0.370 3.40e-02 8.65e+02 1.19e+02 ... (remaining 38854 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.85: 49818 3.85 - 7.70: 1969 7.70 - 11.55: 364 11.55 - 15.39: 70 15.39 - 19.24: 6 Bond angle restraints: 52227 Sorted by residual: angle pdb=" N PRO C 198 " pdb=" CD PRO C 198 " pdb=" CG PRO C 198 " ideal model delta sigma weight residual 103.20 83.96 19.24 1.50e+00 4.44e-01 1.65e+02 angle pdb=" N PRO A 198 " pdb=" CD PRO A 198 " pdb=" CG PRO A 198 " ideal model delta sigma weight residual 103.20 83.97 19.23 1.50e+00 4.44e-01 1.64e+02 angle pdb=" N PRO F 198 " pdb=" CD PRO F 198 " pdb=" CG PRO F 198 " ideal model delta sigma weight residual 103.20 83.98 19.22 1.50e+00 4.44e-01 1.64e+02 angle pdb=" N PRO E 198 " pdb=" CD PRO E 198 " pdb=" CG PRO E 198 " ideal model delta sigma weight residual 103.20 83.99 19.21 1.50e+00 4.44e-01 1.64e+02 angle pdb=" N PRO B 198 " pdb=" CD PRO B 198 " pdb=" CG PRO B 198 " ideal model delta sigma weight residual 103.20 83.99 19.21 1.50e+00 4.44e-01 1.64e+02 ... (remaining 52222 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.68: 20445 21.68 - 43.36: 2113 43.36 - 65.05: 490 65.05 - 86.73: 132 86.73 - 108.41: 37 Dihedral angle restraints: 23217 sinusoidal: 10137 harmonic: 13080 Sorted by residual: dihedral pdb=" CA GLU E 847 " pdb=" C GLU E 847 " pdb=" N ASN E 848 " pdb=" CA ASN E 848 " ideal model delta harmonic sigma weight residual -180.00 -154.85 -25.15 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA GLU A 847 " pdb=" C GLU A 847 " pdb=" N ASN A 848 " pdb=" CA ASN A 848 " ideal model delta harmonic sigma weight residual -180.00 -154.87 -25.13 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA GLU D 847 " pdb=" C GLU D 847 " pdb=" N ASN D 848 " pdb=" CA ASN D 848 " ideal model delta harmonic sigma weight residual -180.00 -154.89 -25.11 0 5.00e+00 4.00e-02 2.52e+01 ... (remaining 23214 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 4246 0.054 - 0.108: 1263 0.108 - 0.163: 268 0.163 - 0.217: 34 0.217 - 0.271: 12 Chirality restraints: 5823 Sorted by residual: chirality pdb=" CA ASN E 386 " pdb=" N ASN E 386 " pdb=" C ASN E 386 " pdb=" CB ASN E 386 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CA ASN F 386 " pdb=" N ASN F 386 " pdb=" C ASN F 386 " pdb=" CB ASN F 386 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CA ASN B 386 " pdb=" N ASN B 386 " pdb=" C ASN B 386 " pdb=" CB ASN B 386 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.81e+00 ... (remaining 5820 not shown) Planarity restraints: 6309 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 210 " -0.111 5.00e-02 4.00e+02 1.61e-01 4.13e+01 pdb=" N PRO B 211 " 0.278 5.00e-02 4.00e+02 pdb=" CA PRO B 211 " -0.086 5.00e-02 4.00e+02 pdb=" CD PRO B 211 " -0.081 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE F 210 " -0.111 5.00e-02 4.00e+02 1.61e-01 4.13e+01 pdb=" N PRO F 211 " 0.278 5.00e-02 4.00e+02 pdb=" CA PRO F 211 " -0.085 5.00e-02 4.00e+02 pdb=" CD PRO F 211 " -0.081 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 210 " -0.111 5.00e-02 4.00e+02 1.61e-01 4.13e+01 pdb=" N PRO C 211 " 0.277 5.00e-02 4.00e+02 pdb=" CA PRO C 211 " -0.085 5.00e-02 4.00e+02 pdb=" CD PRO C 211 " -0.081 5.00e-02 4.00e+02 ... (remaining 6306 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 317 2.51 - 3.11: 27342 3.11 - 3.70: 58864 3.70 - 4.30: 86178 4.30 - 4.90: 142620 Nonbonded interactions: 315321 Sorted by model distance: nonbonded pdb=" O PHE E 313 " pdb=" O GLY F 783 " model vdw 1.910 3.040 nonbonded pdb=" O GLY A 783 " pdb=" O PHE F 313 " model vdw 1.972 3.040 nonbonded pdb=" O PHE C 313 " pdb=" O GLY D 783 " model vdw 1.993 3.040 nonbonded pdb=" O PHE B 313 " pdb=" O GLY C 783 " model vdw 2.011 3.040 nonbonded pdb=" OD1 ASP E 634 " pdb=" F3 BEF E1001 " model vdw 2.032 2.990 ... (remaining 315316 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 110 through 1010) selection = chain 'B' selection = chain 'C' selection = (chain 'D' and resid 110 through 1010) selection = chain 'E' selection = chain 'F' } 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: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.570 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 33.070 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6326 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 : 0.014 0.752 38872 Z= 0.901 Angle : 1.591 19.243 52227 Z= 0.671 Chirality : 0.054 0.271 5823 Planarity : 0.008 0.161 6309 Dihedral : 18.854 108.411 14829 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.72 % Allowed : 0.54 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.18 (0.11), residues: 4560 helix: -0.60 (0.09), residues: 2322 sheet: -0.21 (0.24), residues: 414 loop : -0.97 (0.14), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 570 TYR 0.020 0.003 TYR D 691 PHE 0.032 0.002 PHE B 126 TRP 0.036 0.003 TRP D 805 HIS 0.005 0.002 HIS E 614 Details of bonding type rmsd/Z covalent geometry : bond 0.01255 / 0.58 (38859) covalent geometry : angle 1.59054 / 0.67 (52227) hydrogen bonds : bond 0.27991 / 18.80 ( 2095) hydrogen bonds : angle 8.97313 / 6.35 ( 6177) Misc. bond : bond 0.37578 / 21.50 ( 13) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 960 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 933 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 700 LEU cc_start: 0.9014 (tt) cc_final: 0.8770 (tp) REVERT: B 154 ASN cc_start: 0.6397 (t0) cc_final: 0.6000 (m-40) REVERT: B 721 LEU cc_start: 0.7879 (mp) cc_final: 0.7554 (mp) REVERT: B 733 THR cc_start: 0.7382 (p) cc_final: 0.7051 (t) REVERT: B 802 THR cc_start: 0.8409 (p) cc_final: 0.8161 (p) REVERT: C 543 THR cc_start: 0.8149 (m) cc_final: 0.7794 (p) REVERT: D 405 MET cc_start: 0.0848 (ttp) cc_final: 0.0396 (ptp) REVERT: E 786 GLN cc_start: 0.5459 (tt0) cc_final: 0.5222 (tt0) REVERT: F 228 SER cc_start: 0.7399 (m) cc_final: 0.6990 (t) REVERT: F 848 ASN cc_start: 0.4236 (p0) cc_final: 0.4008 (t0) outliers start: 27 outliers final: 4 residues processed: 958 average time/residue: 0.2090 time to fit residues: 333.0812 Evaluate side-chains 447 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 443 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 386 ASN Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain D residue 400 SER Chi-restraints excluded: chain E residue 400 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 432 optimal weight: 1.9990 chunk 197 optimal weight: 8.9990 chunk 388 optimal weight: 0.0050 chunk 455 optimal weight: 0.4980 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.9990 chunk 401 optimal weight: 0.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 495 HIS A 549 HIS ** A 701 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 792 ASN B 449 HIS ** B 798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 HIS C 391 HIS C 432 GLN C 542 GLN C 571 GLN ** C 701 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 203 GLN ** D 701 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 285 HIS E 614 HIS ** E 701 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 449 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.163947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.153553 restraints weight = 59348.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 90)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.147776 restraints weight = 32363.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.145673 restraints weight = 55207.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.145340 restraints weight = 45233.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.144176 restraints weight = 42980.127| |-----------------------------------------------------------------------------| r_work (final): 0.4325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6254 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 38872 Z= 0.150 Angle : 0.671 10.625 52227 Z= 0.345 Chirality : 0.044 0.189 5823 Planarity : 0.006 0.080 6309 Dihedral : 17.863 96.837 6974 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.14 % Allowed : 11.15 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.12), residues: 4560 helix: 0.56 (0.09), residues: 2550 sheet: -0.82 (0.22), residues: 474 loop : -1.01 (0.15), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 253 TYR 0.026 0.002 TYR F 694 PHE 0.029 0.002 PHE B 448 TRP 0.039 0.001 TRP F 805 HIS 0.006 0.001 HIS B 523 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (38859) covalent geometry : angle 0.67122 / 0.35 (52227) hydrogen bonds : bond 0.05210 / 3.48 ( 2095) hydrogen bonds : angle 5.24801 / 3.74 ( 6177) Misc. bond : bond 0.00115 / 0.05 ( 13) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 572 time to evaluate : 0.935 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 504 GLU cc_start: 0.5695 (mt-10) cc_final: 0.5441 (tm-30) REVERT: A 700 LEU cc_start: 0.8981 (tt) cc_final: 0.8708 (tp) REVERT: B 314 TYR cc_start: 0.8791 (m-80) cc_final: 0.8540 (m-80) REVERT: B 798 GLN cc_start: 0.8283 (tm-30) cc_final: 0.8057 (tm-30) REVERT: B 803 GLU cc_start: 0.6509 (mt-10) cc_final: 0.6097 (mt-10) REVERT: C 127 VAL cc_start: 0.8962 (m) cc_final: 0.8758 (t) REVERT: C 223 LEU cc_start: 0.5532 (mt) cc_final: 0.5182 (tp) REVERT: C 405 MET cc_start: 0.2863 (ttt) cc_final: 0.2566 (ttt) REVERT: C 656 ASP cc_start: 0.5587 (OUTLIER) cc_final: 0.5198 (t0) REVERT: D 190 GLU cc_start: 0.3334 (tt0) cc_final: 0.1791 (mp0) REVERT: D 258 MET cc_start: 0.3053 (ppp) cc_final: 0.2157 (ppp) REVERT: D 883 ASP cc_start: 0.5936 (t0) cc_final: 0.5688 (t70) REVERT: E 694 TYR cc_start: 0.8271 (t80) cc_final: 0.7945 (t80) REVERT: E 698 LEU cc_start: 0.8393 (mt) cc_final: 0.7233 (mt) REVERT: E 736 ILE cc_start: 0.7235 (mt) cc_final: 0.6985 (mt) REVERT: E 883 ASP cc_start: 0.5875 (OUTLIER) cc_final: 0.5267 (m-30) REVERT: F 228 SER cc_start: 0.7357 (m) cc_final: 0.6826 (t) REVERT: F 449 HIS cc_start: 0.3978 (OUTLIER) cc_final: 0.3640 (t70) REVERT: F 631 MET cc_start: 0.7096 (ppp) cc_final: 0.6620 (ppp) outliers start: 80 outliers final: 39 residues processed: 623 average time/residue: 0.1988 time to fit residues: 213.4290 Evaluate side-chains 460 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 418 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 495 HIS Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 500 ASN Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 569 CYS Chi-restraints excluded: chain B residue 578 ILE Chi-restraints excluded: chain B residue 853 VAL Chi-restraints excluded: chain C residue 119 PHE Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 596 GLU Chi-restraints excluded: chain C residue 656 ASP Chi-restraints excluded: chain C residue 749 LYS Chi-restraints excluded: chain C residue 766 LEU Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 684 ILE Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 725 ILE Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 621 ILE Chi-restraints excluded: chain E residue 646 ASP Chi-restraints excluded: chain E residue 883 ASP Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain F residue 240 HIS Chi-restraints excluded: chain F residue 380 THR Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 445 VAL Chi-restraints excluded: chain F residue 449 HIS Chi-restraints excluded: chain F residue 752 LEU Chi-restraints excluded: chain F residue 868 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 415 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 212 optimal weight: 0.8980 chunk 159 optimal weight: 0.9990 chunk 349 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 12 optimal weight: 10.0000 chunk 244 optimal weight: 9.9990 chunk 435 optimal weight: 5.9990 chunk 279 optimal weight: 20.0000 chunk 184 optimal weight: 9.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 549 HIS ** A 701 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 GLN D 624 ASN D 686 HIS ** D 701 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 792 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 580 ASN E 614 HIS E 686 HIS ** E 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.156026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.145904 restraints weight = 60858.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.138384 restraints weight = 27570.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.137585 restraints weight = 63389.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.137269 restraints weight = 48705.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.136711 restraints weight = 37380.558| |-----------------------------------------------------------------------------| r_work (final): 0.4219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6517 moved from start: 0.4438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 38872 Z= 0.252 Angle : 0.765 11.146 52227 Z= 0.383 Chirality : 0.047 0.194 5823 Planarity : 0.005 0.100 6309 Dihedral : 18.124 98.455 6970 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.72 % Allowed : 15.19 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.12), residues: 4560 helix: 0.60 (0.10), residues: 2514 sheet: -0.87 (0.19), residues: 582 loop : -0.99 (0.15), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 315 TYR 0.035 0.003 TYR D 314 PHE 0.028 0.002 PHE D 808 TRP 0.017 0.002 TRP A 805 HIS 0.022 0.002 HIS F 449 Details of bonding type rmsd/Z covalent geometry : bond 0.00572 / 0.25 (38859) covalent geometry : angle 0.76468 / 0.38 (52227) hydrogen bonds : bond 0.04958 / 3.32 ( 2095) hydrogen bonds : angle 5.13257 / 3.64 ( 6177) Misc. bond : bond 0.00085 / 0.04 ( 13) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 403 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 GLU cc_start: 0.6118 (mt-10) cc_final: 0.5850 (mt-10) REVERT: B 405 MET cc_start: 0.6123 (tpt) cc_final: 0.5893 (tpt) REVERT: B 712 ILE cc_start: 0.8909 (OUTLIER) cc_final: 0.8668 (mp) REVERT: C 187 GLN cc_start: 0.6744 (tm-30) cc_final: 0.6416 (tm-30) REVERT: C 258 MET cc_start: 0.3289 (mpp) cc_final: 0.2773 (mpp) REVERT: C 684 ILE cc_start: 0.8528 (OUTLIER) cc_final: 0.8287 (tp) REVERT: D 128 MET cc_start: 0.5239 (mmt) cc_final: 0.4906 (mmt) REVERT: D 152 MET cc_start: 0.5044 (mtt) cc_final: 0.4783 (tpp) REVERT: D 258 MET cc_start: 0.3097 (ppp) cc_final: 0.2233 (ppp) REVERT: D 268 PHE cc_start: 0.0107 (OUTLIER) cc_final: -0.0503 (m-80) REVERT: E 118 MET cc_start: 0.6974 (ttm) cc_final: 0.6696 (ttt) REVERT: E 285 HIS cc_start: 0.6588 (OUTLIER) cc_final: 0.6356 (t-90) REVERT: E 582 GLU cc_start: 0.4648 (mm-30) cc_final: 0.4091 (mt-10) REVERT: E 678 LEU cc_start: 0.6751 (tp) cc_final: 0.6497 (tt) REVERT: F 228 SER cc_start: 0.7281 (m) cc_final: 0.6830 (t) REVERT: F 597 LEU cc_start: 0.4392 (OUTLIER) cc_final: 0.4140 (tp) outliers start: 139 outliers final: 83 residues processed: 507 average time/residue: 0.1919 time to fit residues: 168.7414 Evaluate side-chains 428 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 340 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 495 HIS Chi-restraints excluded: chain A residue 549 HIS Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 719 ILE Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 792 ASN Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 867 CYS Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 119 PHE Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 500 ASN Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 569 CYS Chi-restraints excluded: chain B residue 578 ILE Chi-restraints excluded: chain B residue 614 HIS Chi-restraints excluded: chain B residue 620 GLU Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 760 ILE Chi-restraints excluded: chain B residue 853 VAL Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 119 PHE Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 391 HIS Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 596 GLU Chi-restraints excluded: chain C residue 620 GLU Chi-restraints excluded: chain C residue 684 ILE Chi-restraints excluded: chain C residue 749 LYS Chi-restraints excluded: chain C residue 766 LEU Chi-restraints excluded: chain C residue 875 GLU Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain D residue 268 PHE Chi-restraints excluded: chain D residue 485 GLU Chi-restraints excluded: chain D residue 597 LEU Chi-restraints excluded: chain D residue 620 GLU Chi-restraints excluded: chain D residue 684 ILE Chi-restraints excluded: chain D residue 693 VAL Chi-restraints excluded: chain D residue 760 ILE Chi-restraints excluded: chain E residue 258 MET Chi-restraints excluded: chain E residue 268 PHE Chi-restraints excluded: chain E residue 285 HIS Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 538 ASP Chi-restraints excluded: chain E residue 823 TRP Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain F residue 230 ILE Chi-restraints excluded: chain F residue 240 HIS Chi-restraints excluded: chain F residue 319 ILE Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 360 VAL Chi-restraints excluded: chain F residue 380 THR Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 597 LEU Chi-restraints excluded: chain F residue 675 ILE Chi-restraints excluded: chain F residue 676 ASP Chi-restraints excluded: chain F residue 739 ASP Chi-restraints excluded: chain F residue 752 LEU Chi-restraints excluded: chain F residue 758 MET Chi-restraints excluded: chain F residue 766 LEU Chi-restraints excluded: chain F residue 850 THR Chi-restraints excluded: chain F residue 868 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 387 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 chunk 177 optimal weight: 7.9990 chunk 174 optimal weight: 7.9990 chunk 337 optimal weight: 0.1980 chunk 267 optimal weight: 20.0000 chunk 184 optimal weight: 8.9990 chunk 405 optimal weight: 1.9990 chunk 143 optimal weight: 0.8980 chunk 260 optimal weight: 6.9990 chunk 381 optimal weight: 0.7980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 500 ASN A 549 HIS ** A 701 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 GLN B 542 GLN ** B 701 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 HIS ** D 701 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 792 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 449 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.159011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.148633 restraints weight = 60187.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.140792 restraints weight = 28731.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.139880 restraints weight = 69413.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.139764 restraints weight = 46796.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.139156 restraints weight = 34931.370| |-----------------------------------------------------------------------------| r_work (final): 0.4253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6439 moved from start: 0.4676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 38872 Z= 0.128 Angle : 0.595 11.887 52227 Z= 0.303 Chirality : 0.042 0.216 5823 Planarity : 0.004 0.046 6309 Dihedral : 16.204 89.162 6970 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.05 % Allowed : 17.63 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.12), residues: 4560 helix: 1.05 (0.10), residues: 2490 sheet: -0.76 (0.20), residues: 576 loop : -1.04 (0.15), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 253 TYR 0.022 0.001 TYR C 691 PHE 0.023 0.001 PHE C 144 TRP 0.019 0.001 TRP A 805 HIS 0.018 0.001 HIS A 549 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (38859) covalent geometry : angle 0.59488 / 0.30 (52227) hydrogen bonds : bond 0.04115 / 2.76 ( 2095) hydrogen bonds : angle 4.69736 / 3.34 ( 6177) Misc. bond : bond 0.00028 / 0.02 ( 13) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 434 time to evaluate : 1.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 700 LEU cc_start: 0.8986 (tt) cc_final: 0.8724 (tp) REVERT: A 848 ASN cc_start: 0.4861 (p0) cc_final: 0.4447 (t0) REVERT: B 314 TYR cc_start: 0.8860 (m-80) cc_final: 0.8592 (m-80) REVERT: B 681 SER cc_start: 0.7482 (OUTLIER) cc_final: 0.7196 (p) REVERT: B 712 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.8482 (mt) REVERT: C 684 ILE cc_start: 0.8566 (OUTLIER) cc_final: 0.8304 (tp) REVERT: D 152 MET cc_start: 0.4939 (mtt) cc_final: 0.4593 (tpp) REVERT: D 258 MET cc_start: 0.3032 (ppp) cc_final: 0.2159 (ppp) REVERT: D 268 PHE cc_start: -0.0117 (OUTLIER) cc_final: -0.0695 (m-80) REVERT: D 312 CYS cc_start: 0.7152 (p) cc_final: 0.6792 (m) REVERT: D 486 GLU cc_start: 0.5674 (pm20) cc_final: 0.5003 (pm20) REVERT: E 118 MET cc_start: 0.6511 (OUTLIER) cc_final: 0.6159 (ttt) REVERT: E 582 GLU cc_start: 0.4650 (mm-30) cc_final: 0.4174 (mt-10) REVERT: F 228 SER cc_start: 0.7375 (m) cc_final: 0.6902 (t) REVERT: F 449 HIS cc_start: 0.3904 (OUTLIER) cc_final: 0.3605 (t70) REVERT: F 627 TYR cc_start: 0.6685 (m-80) cc_final: 0.6458 (m-80) outliers start: 114 outliers final: 57 residues processed: 515 average time/residue: 0.1827 time to fit residues: 164.3527 Evaluate side-chains 437 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 374 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 119 PHE Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 500 ASN Chi-restraints excluded: chain B residue 569 CYS Chi-restraints excluded: chain B residue 620 GLU Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 681 SER Chi-restraints excluded: chain B residue 690 SER Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 760 ILE Chi-restraints excluded: chain B residue 853 VAL Chi-restraints excluded: chain C residue 119 PHE Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 620 GLU Chi-restraints excluded: chain C residue 684 ILE Chi-restraints excluded: chain C residue 766 LEU Chi-restraints excluded: chain D residue 268 PHE Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 485 GLU Chi-restraints excluded: chain D residue 529 VAL Chi-restraints excluded: chain D residue 620 GLU Chi-restraints excluded: chain D residue 684 ILE Chi-restraints excluded: chain D residue 750 TRP Chi-restraints excluded: chain E residue 118 MET Chi-restraints excluded: chain E residue 258 MET Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 538 ASP Chi-restraints excluded: chain E residue 712 ILE Chi-restraints excluded: chain E residue 823 TRP Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain F residue 230 ILE Chi-restraints excluded: chain F residue 240 HIS Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 360 VAL Chi-restraints excluded: chain F residue 380 THR Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 449 HIS Chi-restraints excluded: chain F residue 676 ASP Chi-restraints excluded: chain F residue 766 LEU Chi-restraints excluded: chain F residue 868 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 145 optimal weight: 1.9990 chunk 336 optimal weight: 1.9990 chunk 400 optimal weight: 0.9980 chunk 167 optimal weight: 5.9990 chunk 344 optimal weight: 8.9990 chunk 99 optimal weight: 4.9990 chunk 421 optimal weight: 8.9990 chunk 51 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 chunk 296 optimal weight: 0.9980 chunk 454 optimal weight: 0.9980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 701 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 GLN ** B 701 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 701 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 792 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN ** E 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.158032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.148394 restraints weight = 59919.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.145558 restraints weight = 31629.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.144347 restraints weight = 40731.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.144233 restraints weight = 37211.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.143829 restraints weight = 28609.231| |-----------------------------------------------------------------------------| r_work (final): 0.4324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6301 moved from start: 0.4976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 38872 Z= 0.139 Angle : 0.601 12.478 52227 Z= 0.304 Chirality : 0.043 0.323 5823 Planarity : 0.004 0.045 6309 Dihedral : 15.634 89.586 6970 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.19 % Allowed : 19.24 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.12), residues: 4560 helix: 1.20 (0.10), residues: 2490 sheet: -0.61 (0.20), residues: 570 loop : -1.07 (0.15), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 625 TYR 0.026 0.002 TYR E 694 PHE 0.020 0.001 PHE C 144 TRP 0.014 0.001 TRP A 805 HIS 0.006 0.001 HIS F 701 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (38859) covalent geometry : angle 0.60102 / 0.30 (52227) hydrogen bonds : bond 0.04057 / 2.72 ( 2095) hydrogen bonds : angle 4.62218 / 3.29 ( 6177) Misc. bond : bond 0.00030 / 0.02 ( 13) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 403 time to evaluate : 1.362 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 766 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8464 (mp) REVERT: A 848 ASN cc_start: 0.4787 (p0) cc_final: 0.4273 (t0) REVERT: B 314 TYR cc_start: 0.8893 (m-80) cc_final: 0.8654 (m-80) REVERT: B 681 SER cc_start: 0.7513 (OUTLIER) cc_final: 0.7247 (p) REVERT: C 631 MET cc_start: 0.4859 (tmm) cc_final: 0.4539 (tmm) REVERT: C 684 ILE cc_start: 0.8537 (OUTLIER) cc_final: 0.8308 (tp) REVERT: D 152 MET cc_start: 0.5002 (mtt) cc_final: 0.4635 (tpp) REVERT: D 253 ARG cc_start: 0.6580 (OUTLIER) cc_final: 0.5974 (mtm110) REVERT: D 258 MET cc_start: 0.3123 (ppp) cc_final: 0.2161 (ppp) REVERT: D 268 PHE cc_start: -0.0230 (OUTLIER) cc_final: -0.0712 (m-80) REVERT: D 486 GLU cc_start: 0.5533 (pm20) cc_final: 0.4658 (pm20) REVERT: E 118 MET cc_start: 0.6800 (ttm) cc_final: 0.6506 (ttt) REVERT: E 127 VAL cc_start: 0.7719 (OUTLIER) cc_final: 0.7260 (t) REVERT: E 582 GLU cc_start: 0.4563 (mm-30) cc_final: 0.4243 (mt-10) REVERT: E 627 TYR cc_start: 0.6231 (m-80) cc_final: 0.5992 (m-80) REVERT: E 698 LEU cc_start: 0.8360 (mt) cc_final: 0.7995 (mt) REVERT: E 803 GLU cc_start: 0.6544 (mt-10) cc_final: 0.6179 (mt-10) REVERT: F 228 SER cc_start: 0.7284 (m) cc_final: 0.6805 (t) REVERT: F 258 MET cc_start: 0.4628 (mpp) cc_final: 0.4392 (ttp) outliers start: 119 outliers final: 79 residues processed: 493 average time/residue: 0.1832 time to fit residues: 157.9648 Evaluate side-chains 450 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 365 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 867 CYS Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 878 THR Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 119 PHE Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain B residue 500 ASN Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 569 CYS Chi-restraints excluded: chain B residue 620 GLU Chi-restraints excluded: chain B residue 622 LEU Chi-restraints excluded: chain B residue 681 SER Chi-restraints excluded: chain B residue 690 SER Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 760 ILE Chi-restraints excluded: chain B residue 853 VAL Chi-restraints excluded: chain C residue 119 PHE Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 285 HIS Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 620 GLU Chi-restraints excluded: chain C residue 628 LEU Chi-restraints excluded: chain C residue 684 ILE Chi-restraints excluded: chain C residue 766 LEU Chi-restraints excluded: chain D residue 233 GLU Chi-restraints excluded: chain D residue 253 ARG Chi-restraints excluded: chain D residue 268 PHE Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 485 GLU Chi-restraints excluded: chain D residue 505 LEU Chi-restraints excluded: chain D residue 529 VAL Chi-restraints excluded: chain D residue 620 GLU Chi-restraints excluded: chain D residue 684 ILE Chi-restraints excluded: chain D residue 750 TRP Chi-restraints excluded: chain D residue 760 ILE Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 161 GLN Chi-restraints excluded: chain E residue 258 MET Chi-restraints excluded: chain E residue 268 PHE Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 538 ASP Chi-restraints excluded: chain E residue 823 TRP Chi-restraints excluded: chain E residue 832 VAL Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 230 ILE Chi-restraints excluded: chain F residue 240 HIS Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 380 THR Chi-restraints excluded: chain F residue 505 LEU Chi-restraints excluded: chain F residue 676 ASP Chi-restraints excluded: chain F residue 723 VAL Chi-restraints excluded: chain F residue 734 LEU Chi-restraints excluded: chain F residue 758 MET Chi-restraints excluded: chain F residue 766 LEU Chi-restraints excluded: chain F residue 868 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 9 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 159 optimal weight: 3.9990 chunk 365 optimal weight: 3.9990 chunk 141 optimal weight: 4.9990 chunk 271 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 138 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 101 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 GLN ** B 701 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 701 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 792 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.158870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.148262 restraints weight = 60182.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.144395 restraints weight = 31925.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 155)---------------| | r_work = 0.4170 r_free = 0.4170 target = 0.131416 restraints weight = 37746.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.131342 restraints weight = 72123.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.130991 restraints weight = 63022.262| |-----------------------------------------------------------------------------| r_work (final): 0.4128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6676 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 0.064 38872 Z= 0.120 Angle : 0.582 12.454 52227 Z= 0.294 Chirality : 0.042 0.222 5823 Planarity : 0.004 0.042 6309 Dihedral : 14.793 89.208 6970 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.30 % Allowed : 19.96 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.12), residues: 4560 helix: 1.33 (0.10), residues: 2472 sheet: -0.57 (0.20), residues: 570 loop : -1.07 (0.15), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 625 TYR 0.022 0.001 TYR C 691 PHE 0.034 0.001 PHE E 119 TRP 0.013 0.001 TRP A 805 HIS 0.011 0.001 HIS A 701 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (38859) covalent geometry : angle 0.58217 / 0.29 (52227) hydrogen bonds : bond 0.03890 / 2.62 ( 2095) hydrogen bonds : angle 4.53415 / 3.22 ( 6177) Misc. bond : bond 0.00024 / 0.01 ( 13) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 433 time to evaluate : 1.219 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 346 MET cc_start: 0.7107 (mtm) cc_final: 0.6902 (mtm) REVERT: A 700 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8693 (tp) REVERT: A 701 HIS cc_start: 0.8308 (OUTLIER) cc_final: 0.8053 (t70) REVERT: A 722 ILE cc_start: 0.7963 (mm) cc_final: 0.7575 (mm) REVERT: A 766 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8293 (mp) REVERT: A 848 ASN cc_start: 0.4700 (p0) cc_final: 0.4373 (t0) REVERT: B 314 TYR cc_start: 0.8757 (m-80) cc_final: 0.8477 (m-80) REVERT: B 367 GLU cc_start: 0.6294 (OUTLIER) cc_final: 0.5946 (tm-30) REVERT: B 681 SER cc_start: 0.7456 (OUTLIER) cc_final: 0.7147 (p) REVERT: C 346 MET cc_start: 0.6722 (mtm) cc_final: 0.6391 (mtm) REVERT: C 405 MET cc_start: 0.2694 (mtp) cc_final: 0.2169 (mmm) REVERT: C 684 ILE cc_start: 0.8602 (OUTLIER) cc_final: 0.8390 (tp) REVERT: C 795 MET cc_start: 0.8263 (tpt) cc_final: 0.8034 (mmm) REVERT: D 118 MET cc_start: 0.4067 (mtp) cc_final: 0.3824 (mtp) REVERT: D 152 MET cc_start: 0.4787 (mtt) cc_final: 0.3969 (tpp) REVERT: D 253 ARG cc_start: 0.6629 (OUTLIER) cc_final: 0.5961 (mtm110) REVERT: D 258 MET cc_start: 0.2805 (ppp) cc_final: 0.1740 (ppp) REVERT: D 268 PHE cc_start: -0.0019 (OUTLIER) cc_final: -0.0440 (m-80) REVERT: D 312 CYS cc_start: 0.7002 (p) cc_final: 0.6679 (m) REVERT: D 426 PHE cc_start: 0.4436 (m-80) cc_final: 0.4223 (m-80) REVERT: D 631 MET cc_start: 0.6917 (tpp) cc_final: 0.6691 (tpt) REVERT: D 840 THR cc_start: 0.7863 (t) cc_final: 0.7654 (t) REVERT: E 127 VAL cc_start: 0.7817 (OUTLIER) cc_final: 0.7499 (t) REVERT: E 582 GLU cc_start: 0.5160 (mm-30) cc_final: 0.4710 (mt-10) REVERT: F 228 SER cc_start: 0.7699 (m) cc_final: 0.7215 (t) REVERT: F 258 MET cc_start: 0.5197 (mpp) cc_final: 0.4421 (ttp) REVERT: F 847 GLU cc_start: 0.4862 (mp0) cc_final: 0.4234 (mt-10) outliers start: 123 outliers final: 77 residues processed: 526 average time/residue: 0.1827 time to fit residues: 168.3465 Evaluate side-chains 470 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 384 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 700 LEU Chi-restraints excluded: chain A residue 701 HIS Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 867 CYS Chi-restraints excluded: chain A residue 878 THR Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 119 PHE Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 367 GLU Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain B residue 500 ASN Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 569 CYS Chi-restraints excluded: chain B residue 614 HIS Chi-restraints excluded: chain B residue 620 GLU Chi-restraints excluded: chain B residue 681 SER Chi-restraints excluded: chain B residue 690 SER Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 760 ILE Chi-restraints excluded: chain B residue 853 VAL Chi-restraints excluded: chain C residue 119 PHE Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 285 HIS Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 620 GLU Chi-restraints excluded: chain C residue 628 LEU Chi-restraints excluded: chain C residue 684 ILE Chi-restraints excluded: chain C residue 750 TRP Chi-restraints excluded: chain C residue 766 LEU Chi-restraints excluded: chain D residue 253 ARG Chi-restraints excluded: chain D residue 268 PHE Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 485 GLU Chi-restraints excluded: chain D residue 529 VAL Chi-restraints excluded: chain D residue 620 GLU Chi-restraints excluded: chain D residue 750 TRP Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 161 GLN Chi-restraints excluded: chain E residue 258 MET Chi-restraints excluded: chain E residue 268 PHE Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 538 ASP Chi-restraints excluded: chain E residue 823 TRP Chi-restraints excluded: chain E residue 832 VAL Chi-restraints excluded: chain E residue 868 VAL Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 230 ILE Chi-restraints excluded: chain F residue 240 HIS Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 380 THR Chi-restraints excluded: chain F residue 505 LEU Chi-restraints excluded: chain F residue 663 ASP Chi-restraints excluded: chain F residue 676 ASP Chi-restraints excluded: chain F residue 766 LEU Chi-restraints excluded: chain F residue 840 THR Chi-restraints excluded: chain F residue 868 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 23 optimal weight: 0.5980 chunk 310 optimal weight: 0.2980 chunk 346 optimal weight: 0.0670 chunk 246 optimal weight: 4.9990 chunk 430 optimal weight: 8.9990 chunk 38 optimal weight: 10.0000 chunk 18 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 422 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 328 optimal weight: 9.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 391 HIS ** A 701 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 542 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.160203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.150290 restraints weight = 59858.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.145970 restraints weight = 42786.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.144154 restraints weight = 67533.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.143935 restraints weight = 56505.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.143839 restraints weight = 44257.088| |-----------------------------------------------------------------------------| r_work (final): 0.4318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6305 moved from start: 0.5394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 38872 Z= 0.112 Angle : 0.578 16.213 52227 Z= 0.292 Chirality : 0.042 0.241 5823 Planarity : 0.004 0.041 6309 Dihedral : 13.977 89.063 6970 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.81 % Allowed : 20.93 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.12), residues: 4560 helix: 1.34 (0.10), residues: 2502 sheet: -0.54 (0.20), residues: 582 loop : -1.19 (0.15), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 625 TYR 0.033 0.001 TYR F 694 PHE 0.021 0.001 PHE A 611 TRP 0.013 0.001 TRP D 845 HIS 0.012 0.001 HIS A 701 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (38859) covalent geometry : angle 0.57768 / 0.29 (52227) hydrogen bonds : bond 0.03750 / 2.52 ( 2095) hydrogen bonds : angle 4.47568 / 3.18 ( 6177) Misc. bond : bond 0.00020 / 0.01 ( 13) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 444 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 430 LEU cc_start: 0.5118 (OUTLIER) cc_final: 0.4857 (mm) REVERT: A 701 HIS cc_start: 0.8335 (OUTLIER) cc_final: 0.8034 (t70) REVERT: A 722 ILE cc_start: 0.8130 (mm) cc_final: 0.7778 (mm) REVERT: A 766 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8337 (mp) REVERT: A 848 ASN cc_start: 0.4912 (p0) cc_final: 0.4497 (t0) REVERT: B 314 TYR cc_start: 0.8734 (m-80) cc_final: 0.8470 (m-80) REVERT: B 681 SER cc_start: 0.7406 (OUTLIER) cc_final: 0.7100 (p) REVERT: B 781 LYS cc_start: 0.6134 (mtmt) cc_final: 0.5186 (mttp) REVERT: C 405 MET cc_start: 0.2326 (mtp) cc_final: 0.1965 (mmm) REVERT: C 517 ARG cc_start: 0.5818 (OUTLIER) cc_final: 0.5546 (ttt180) REVERT: C 684 ILE cc_start: 0.8628 (OUTLIER) cc_final: 0.8427 (tp) REVERT: C 703 GLU cc_start: 0.7572 (mt-10) cc_final: 0.7149 (tm-30) REVERT: D 152 MET cc_start: 0.4649 (mtt) cc_final: 0.3746 (tpp) REVERT: D 253 ARG cc_start: 0.6531 (OUTLIER) cc_final: 0.5939 (mtm110) REVERT: D 258 MET cc_start: 0.2897 (ppp) cc_final: 0.1890 (ppp) REVERT: D 530 MET cc_start: 0.1724 (ttt) cc_final: 0.1100 (mmm) REVERT: D 739 ASP cc_start: 0.5014 (OUTLIER) cc_final: 0.4684 (m-30) REVERT: D 839 PHE cc_start: 0.6823 (OUTLIER) cc_final: 0.6262 (m-80) REVERT: E 127 VAL cc_start: 0.7789 (OUTLIER) cc_final: 0.7350 (t) REVERT: E 582 GLU cc_start: 0.4674 (mm-30) cc_final: 0.4255 (mt-10) REVERT: E 866 PHE cc_start: 0.8572 (t80) cc_final: 0.8273 (t80) REVERT: F 228 SER cc_start: 0.7430 (m) cc_final: 0.6852 (t) REVERT: F 258 MET cc_start: 0.4766 (mpp) cc_final: 0.4276 (ttp) REVERT: F 847 GLU cc_start: 0.4771 (mp0) cc_final: 0.4117 (mt-10) outliers start: 105 outliers final: 67 residues processed: 522 average time/residue: 0.1844 time to fit residues: 167.8860 Evaluate side-chains 461 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 384 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 701 HIS Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 867 CYS Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain B residue 119 PHE Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain B residue 500 ASN Chi-restraints excluded: chain B residue 569 CYS Chi-restraints excluded: chain B residue 681 SER Chi-restraints excluded: chain B residue 690 SER Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 760 ILE Chi-restraints excluded: chain C residue 119 PHE Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 517 ARG Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 620 GLU Chi-restraints excluded: chain C residue 628 LEU Chi-restraints excluded: chain C residue 684 ILE Chi-restraints excluded: chain C residue 750 TRP Chi-restraints excluded: chain C residue 766 LEU Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain D residue 253 ARG Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 485 GLU Chi-restraints excluded: chain D residue 529 VAL Chi-restraints excluded: chain D residue 620 GLU Chi-restraints excluded: chain D residue 739 ASP Chi-restraints excluded: chain D residue 750 TRP Chi-restraints excluded: chain D residue 839 PHE Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 161 GLN Chi-restraints excluded: chain E residue 258 MET Chi-restraints excluded: chain E residue 268 PHE Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 538 ASP Chi-restraints excluded: chain E residue 823 TRP Chi-restraints excluded: chain E residue 868 VAL Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 230 ILE Chi-restraints excluded: chain F residue 240 HIS Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 380 THR Chi-restraints excluded: chain F residue 505 LEU Chi-restraints excluded: chain F residue 663 ASP Chi-restraints excluded: chain F residue 676 ASP Chi-restraints excluded: chain F residue 766 LEU Chi-restraints excluded: chain F residue 868 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 20 optimal weight: 4.9990 chunk 219 optimal weight: 5.9990 chunk 443 optimal weight: 0.9980 chunk 325 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 378 optimal weight: 0.7980 chunk 104 optimal weight: 0.6980 chunk 194 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 337 optimal weight: 10.0000 chunk 106 optimal weight: 6.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 701 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 GLN ** D 701 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 549 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.159662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.152702 restraints weight = 59806.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.152332 restraints weight = 34158.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.152025 restraints weight = 26167.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.152046 restraints weight = 21383.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.152110 restraints weight = 17707.994| |-----------------------------------------------------------------------------| r_work (final): 0.4423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6108 moved from start: 0.5578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 38872 Z= 0.120 Angle : 0.595 12.631 52227 Z= 0.297 Chirality : 0.042 0.228 5823 Planarity : 0.004 0.045 6309 Dihedral : 13.765 89.986 6970 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.05 % Allowed : 21.68 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.12), residues: 4560 helix: 1.40 (0.10), residues: 2472 sheet: -0.36 (0.21), residues: 528 loop : -1.01 (0.15), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 625 TYR 0.035 0.001 TYR E 694 PHE 0.033 0.001 PHE B 600 TRP 0.012 0.001 TRP D 845 HIS 0.011 0.001 HIS A 701 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (38859) covalent geometry : angle 0.59534 / 0.30 (52227) hydrogen bonds : bond 0.03782 / 2.55 ( 2095) hydrogen bonds : angle 4.49893 / 3.18 ( 6177) Misc. bond : bond 0.00025 / 0.01 ( 13) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 425 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 430 LEU cc_start: 0.5058 (OUTLIER) cc_final: 0.4854 (mm) REVERT: A 694 TYR cc_start: 0.8525 (OUTLIER) cc_final: 0.8230 (t80) REVERT: A 701 HIS cc_start: 0.8297 (OUTLIER) cc_final: 0.8035 (t70) REVERT: A 722 ILE cc_start: 0.8103 (mm) cc_final: 0.7746 (mm) REVERT: A 766 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8525 (mp) REVERT: B 314 TYR cc_start: 0.8818 (m-80) cc_final: 0.8479 (m-80) REVERT: B 367 GLU cc_start: 0.6301 (OUTLIER) cc_final: 0.5867 (tm-30) REVERT: B 781 LYS cc_start: 0.6170 (mtmt) cc_final: 0.5301 (mttp) REVERT: C 405 MET cc_start: 0.1891 (mtp) cc_final: 0.1512 (mmm) REVERT: C 517 ARG cc_start: 0.5760 (OUTLIER) cc_final: 0.5429 (ttt180) REVERT: C 684 ILE cc_start: 0.8602 (OUTLIER) cc_final: 0.8387 (tp) REVERT: C 703 GLU cc_start: 0.7543 (mt-10) cc_final: 0.7144 (tm-30) REVERT: D 141 TRP cc_start: 0.5438 (m100) cc_final: 0.5072 (m100) REVERT: D 253 ARG cc_start: 0.6321 (OUTLIER) cc_final: 0.5756 (mtm110) REVERT: D 258 MET cc_start: 0.3032 (ppp) cc_final: 0.1956 (ppp) REVERT: D 268 PHE cc_start: -0.0243 (OUTLIER) cc_final: -0.0774 (m-80) REVERT: D 530 MET cc_start: 0.1607 (ttt) cc_final: 0.1085 (mmm) REVERT: D 839 PHE cc_start: 0.6842 (OUTLIER) cc_final: 0.6241 (m-80) REVERT: E 127 VAL cc_start: 0.7765 (OUTLIER) cc_final: 0.7428 (t) REVERT: E 582 GLU cc_start: 0.4540 (mm-30) cc_final: 0.4067 (mt-10) REVERT: F 129 GLU cc_start: 0.7694 (mp0) cc_final: 0.7367 (mp0) REVERT: F 228 SER cc_start: 0.7185 (m) cc_final: 0.6678 (t) REVERT: F 258 MET cc_start: 0.4499 (mpp) cc_final: 0.4152 (ttp) REVERT: F 847 GLU cc_start: 0.4679 (mp0) cc_final: 0.4166 (mt-10) outliers start: 114 outliers final: 73 residues processed: 510 average time/residue: 0.1852 time to fit residues: 165.8069 Evaluate side-chains 472 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 388 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 694 TYR Chi-restraints excluded: chain A residue 701 HIS Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 867 CYS Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 878 THR Chi-restraints excluded: chain B residue 119 PHE Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 367 GLU Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 500 ASN Chi-restraints excluded: chain B residue 569 CYS Chi-restraints excluded: chain B residue 614 HIS Chi-restraints excluded: chain B residue 690 SER Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 760 ILE Chi-restraints excluded: chain C residue 119 PHE Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 517 ARG Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 620 GLU Chi-restraints excluded: chain C residue 628 LEU Chi-restraints excluded: chain C residue 684 ILE Chi-restraints excluded: chain C residue 750 TRP Chi-restraints excluded: chain C residue 766 LEU Chi-restraints excluded: chain D residue 253 ARG Chi-restraints excluded: chain D residue 268 PHE Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 485 GLU Chi-restraints excluded: chain D residue 620 GLU Chi-restraints excluded: chain D residue 720 ASP Chi-restraints excluded: chain D residue 744 SER Chi-restraints excluded: chain D residue 750 TRP Chi-restraints excluded: chain D residue 760 ILE Chi-restraints excluded: chain D residue 839 PHE Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 258 MET Chi-restraints excluded: chain E residue 268 PHE Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 538 ASP Chi-restraints excluded: chain E residue 823 TRP Chi-restraints excluded: chain E residue 868 VAL Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain F residue 230 ILE Chi-restraints excluded: chain F residue 240 HIS Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 380 THR Chi-restraints excluded: chain F residue 505 LEU Chi-restraints excluded: chain F residue 552 LEU Chi-restraints excluded: chain F residue 676 ASP Chi-restraints excluded: chain F residue 734 LEU Chi-restraints excluded: chain F residue 766 LEU Chi-restraints excluded: chain F residue 840 THR Chi-restraints excluded: chain F residue 868 VAL Chi-restraints excluded: chain F residue 878 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 94 optimal weight: 0.6980 chunk 403 optimal weight: 0.7980 chunk 48 optimal weight: 9.9990 chunk 46 optimal weight: 7.9990 chunk 172 optimal weight: 0.7980 chunk 430 optimal weight: 9.9990 chunk 253 optimal weight: 8.9990 chunk 125 optimal weight: 20.0000 chunk 258 optimal weight: 0.9980 chunk 231 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 701 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 GLN ** C 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 701 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 792 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 549 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.158701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.149589 restraints weight = 60439.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.147222 restraints weight = 32143.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.147021 restraints weight = 35354.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 71)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.143612 restraints weight = 32296.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.143510 restraints weight = 48724.336| |-----------------------------------------------------------------------------| r_work (final): 0.4318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6311 moved from start: 0.5721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 38872 Z= 0.133 Angle : 0.617 12.870 52227 Z= 0.307 Chirality : 0.043 0.275 5823 Planarity : 0.004 0.042 6309 Dihedral : 13.833 88.699 6970 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.97 % Allowed : 21.86 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.12), residues: 4560 helix: 1.30 (0.10), residues: 2496 sheet: -0.60 (0.22), residues: 504 loop : -1.12 (0.15), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 625 TYR 0.037 0.001 TYR F 691 PHE 0.028 0.001 PHE B 600 TRP 0.014 0.001 TRP D 845 HIS 0.017 0.001 HIS F 549 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 (38859) covalent geometry : angle 0.61747 / 0.31 (52227) hydrogen bonds : bond 0.03839 / 2.59 ( 2095) hydrogen bonds : angle 4.51958 / 3.19 ( 6177) Misc. bond : bond 0.00029 / 0.02 ( 13) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 405 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 430 LEU cc_start: 0.5100 (OUTLIER) cc_final: 0.4845 (mm) REVERT: A 694 TYR cc_start: 0.8526 (OUTLIER) cc_final: 0.8212 (t80) REVERT: A 701 HIS cc_start: 0.8350 (OUTLIER) cc_final: 0.8138 (t70) REVERT: A 722 ILE cc_start: 0.8098 (mm) cc_final: 0.7746 (mm) REVERT: A 766 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8580 (mp) REVERT: B 367 GLU cc_start: 0.6240 (pp20) cc_final: 0.5938 (tm-30) REVERT: B 781 LYS cc_start: 0.6227 (mtmt) cc_final: 0.5409 (mttp) REVERT: C 405 MET cc_start: 0.1947 (mtp) cc_final: 0.0943 (mmm) REVERT: C 517 ARG cc_start: 0.5838 (OUTLIER) cc_final: 0.5507 (ttt180) REVERT: C 684 ILE cc_start: 0.8606 (OUTLIER) cc_final: 0.8391 (tp) REVERT: C 703 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7260 (tm-30) REVERT: D 141 TRP cc_start: 0.5495 (m100) cc_final: 0.5160 (m100) REVERT: D 253 ARG cc_start: 0.6377 (OUTLIER) cc_final: 0.5819 (mtm110) REVERT: D 258 MET cc_start: 0.2876 (ppp) cc_final: 0.1831 (ppp) REVERT: D 268 PHE cc_start: -0.0572 (OUTLIER) cc_final: -0.0903 (m-80) REVERT: D 397 GLU cc_start: 0.5158 (pm20) cc_final: 0.4844 (tt0) REVERT: D 839 PHE cc_start: 0.6870 (OUTLIER) cc_final: 0.6287 (m-80) REVERT: E 127 VAL cc_start: 0.7860 (OUTLIER) cc_final: 0.7178 (t) REVERT: E 582 GLU cc_start: 0.4749 (mm-30) cc_final: 0.4408 (mt-10) REVERT: E 620 GLU cc_start: 0.5620 (mm-30) cc_final: 0.4374 (mt-10) REVERT: E 807 ILE cc_start: 0.8474 (tt) cc_final: 0.8256 (tp) REVERT: E 883 ASP cc_start: 0.7145 (m-30) cc_final: 0.6943 (m-30) REVERT: F 129 GLU cc_start: 0.7737 (mp0) cc_final: 0.7386 (mp0) REVERT: F 228 SER cc_start: 0.7271 (m) cc_final: 0.6764 (t) REVERT: F 258 MET cc_start: 0.4608 (mpp) cc_final: 0.4271 (ttp) REVERT: F 299 VAL cc_start: 0.9012 (t) cc_final: 0.8796 (t) REVERT: F 706 LEU cc_start: 0.8423 (mp) cc_final: 0.8205 (mt) REVERT: F 847 GLU cc_start: 0.4812 (mp0) cc_final: 0.4291 (mt-10) outliers start: 111 outliers final: 80 residues processed: 485 average time/residue: 0.1770 time to fit residues: 151.1460 Evaluate side-chains 471 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 381 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 694 TYR Chi-restraints excluded: chain A residue 701 HIS Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 867 CYS Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 878 THR Chi-restraints excluded: chain B residue 119 PHE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 366 ILE Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 500 ASN Chi-restraints excluded: chain B residue 569 CYS Chi-restraints excluded: chain B residue 614 HIS Chi-restraints excluded: chain B residue 690 SER Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 750 TRP Chi-restraints excluded: chain B residue 760 ILE Chi-restraints excluded: chain B residue 853 VAL Chi-restraints excluded: chain C residue 119 PHE Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 517 ARG Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 620 GLU Chi-restraints excluded: chain C residue 628 LEU Chi-restraints excluded: chain C residue 684 ILE Chi-restraints excluded: chain C residue 750 TRP Chi-restraints excluded: chain C residue 766 LEU Chi-restraints excluded: chain C residue 803 GLU Chi-restraints excluded: chain D residue 253 ARG Chi-restraints excluded: chain D residue 268 PHE Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 319 ILE Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 485 GLU Chi-restraints excluded: chain D residue 529 VAL Chi-restraints excluded: chain D residue 720 ASP Chi-restraints excluded: chain D residue 744 SER Chi-restraints excluded: chain D residue 750 TRP Chi-restraints excluded: chain D residue 760 ILE Chi-restraints excluded: chain D residue 839 PHE Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 258 MET Chi-restraints excluded: chain E residue 268 PHE Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 538 ASP Chi-restraints excluded: chain E residue 823 TRP Chi-restraints excluded: chain E residue 868 VAL Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain F residue 230 ILE Chi-restraints excluded: chain F residue 240 HIS Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 380 THR Chi-restraints excluded: chain F residue 505 LEU Chi-restraints excluded: chain F residue 549 HIS Chi-restraints excluded: chain F residue 552 LEU Chi-restraints excluded: chain F residue 734 LEU Chi-restraints excluded: chain F residue 766 LEU Chi-restraints excluded: chain F residue 840 THR Chi-restraints excluded: chain F residue 868 VAL Chi-restraints excluded: chain F residue 878 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 355 optimal weight: 8.9990 chunk 343 optimal weight: 9.9990 chunk 383 optimal weight: 0.8980 chunk 411 optimal weight: 10.0000 chunk 305 optimal weight: 0.9980 chunk 419 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 451 optimal weight: 2.9990 chunk 191 optimal weight: 8.9990 chunk 337 optimal weight: 0.1980 chunk 8 optimal weight: 0.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 701 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 HIS B 542 GLN ** C 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 792 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 701 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 549 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.158354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.150949 restraints weight = 60458.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.150815 restraints weight = 40261.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.150512 restraints weight = 27711.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.150213 restraints weight = 25835.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.150045 restraints weight = 24555.914| |-----------------------------------------------------------------------------| r_work (final): 0.4396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6157 moved from start: 0.5867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 38872 Z= 0.132 Angle : 0.627 11.984 52227 Z= 0.311 Chirality : 0.043 0.290 5823 Planarity : 0.004 0.042 6309 Dihedral : 13.753 89.967 6970 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.73 % Allowed : 22.59 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.12), residues: 4560 helix: 1.31 (0.10), residues: 2472 sheet: -0.56 (0.22), residues: 504 loop : -1.09 (0.15), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 548 TYR 0.035 0.001 TYR F 691 PHE 0.027 0.001 PHE B 600 TRP 0.018 0.001 TRP D 845 HIS 0.013 0.001 HIS A 701 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (38859) covalent geometry : angle 0.62679 / 0.31 (52227) hydrogen bonds : bond 0.03849 / 2.59 ( 2095) hydrogen bonds : angle 4.53924 / 3.20 ( 6177) Misc. bond : bond 0.00034 / 0.02 ( 13) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9120 Ramachandran restraints generated. 4560 Oldfield, 0 Emsley, 4560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 414 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 524 TRP cc_start: 0.2522 (m100) cc_final: 0.2296 (m100) REVERT: A 694 TYR cc_start: 0.8536 (OUTLIER) cc_final: 0.8203 (t80) REVERT: A 722 ILE cc_start: 0.8134 (mm) cc_final: 0.7769 (mm) REVERT: A 766 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8600 (mp) REVERT: B 367 GLU cc_start: 0.6361 (OUTLIER) cc_final: 0.5985 (tm-30) REVERT: B 781 LYS cc_start: 0.6279 (mtmt) cc_final: 0.5479 (mttp) REVERT: C 258 MET cc_start: 0.2571 (mpp) cc_final: 0.2366 (mpp) REVERT: C 405 MET cc_start: 0.1431 (mtp) cc_final: -0.0273 (mmp) REVERT: C 517 ARG cc_start: 0.5809 (OUTLIER) cc_final: 0.5478 (ttt180) REVERT: C 684 ILE cc_start: 0.8624 (OUTLIER) cc_final: 0.8422 (tp) REVERT: C 703 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7196 (tm-30) REVERT: C 795 MET cc_start: 0.8475 (tpt) cc_final: 0.8063 (mmm) REVERT: D 141 TRP cc_start: 0.5328 (m100) cc_final: 0.4949 (m100) REVERT: D 253 ARG cc_start: 0.6370 (OUTLIER) cc_final: 0.5845 (mtm110) REVERT: D 258 MET cc_start: 0.2858 (ppp) cc_final: 0.2052 (ppp) REVERT: D 268 PHE cc_start: -0.0549 (OUTLIER) cc_final: -0.1003 (m-80) REVERT: D 397 GLU cc_start: 0.4985 (pm20) cc_final: 0.4677 (tt0) REVERT: D 839 PHE cc_start: 0.6902 (OUTLIER) cc_final: 0.6337 (m-80) REVERT: E 127 VAL cc_start: 0.7749 (OUTLIER) cc_final: 0.7358 (t) REVERT: E 498 TYR cc_start: 0.4090 (m-80) cc_final: 0.3878 (m-80) REVERT: E 582 GLU cc_start: 0.4855 (mm-30) cc_final: 0.4440 (mt-10) REVERT: E 620 GLU cc_start: 0.5488 (mm-30) cc_final: 0.4438 (mt-10) REVERT: E 807 ILE cc_start: 0.8550 (tt) cc_final: 0.8286 (tp) REVERT: E 883 ASP cc_start: 0.7126 (m-30) cc_final: 0.6908 (m-30) REVERT: F 129 GLU cc_start: 0.7725 (mp0) cc_final: 0.7501 (mp0) REVERT: F 228 SER cc_start: 0.7043 (m) cc_final: 0.6475 (t) REVERT: F 258 MET cc_start: 0.4463 (mpp) cc_final: 0.4200 (ttp) REVERT: F 299 VAL cc_start: 0.9038 (t) cc_final: 0.8815 (t) REVERT: F 847 GLU cc_start: 0.4891 (mp0) cc_final: 0.4457 (mt-10) outliers start: 102 outliers final: 71 residues processed: 490 average time/residue: 0.1816 time to fit residues: 156.7677 Evaluate side-chains 469 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 389 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 694 TYR Chi-restraints excluded: chain A residue 723 VAL Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 867 CYS Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain B residue 119 PHE Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 367 GLU Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 406 LEU Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 500 ASN Chi-restraints excluded: chain B residue 614 HIS Chi-restraints excluded: chain B residue 690 SER Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 750 TRP Chi-restraints excluded: chain B residue 760 ILE Chi-restraints excluded: chain B residue 853 VAL Chi-restraints excluded: chain C residue 119 PHE Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 517 ARG Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 620 GLU Chi-restraints excluded: chain C residue 628 LEU Chi-restraints excluded: chain C residue 684 ILE Chi-restraints excluded: chain C residue 750 TRP Chi-restraints excluded: chain C residue 766 LEU Chi-restraints excluded: chain D residue 253 ARG Chi-restraints excluded: chain D residue 268 PHE Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 377 SER Chi-restraints excluded: chain D residue 529 VAL Chi-restraints excluded: chain D residue 720 ASP Chi-restraints excluded: chain D residue 725 ILE Chi-restraints excluded: chain D residue 744 SER Chi-restraints excluded: chain D residue 750 TRP Chi-restraints excluded: chain D residue 760 ILE Chi-restraints excluded: chain D residue 839 PHE Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 258 MET Chi-restraints excluded: chain E residue 268 PHE Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 538 ASP Chi-restraints excluded: chain E residue 823 TRP Chi-restraints excluded: chain E residue 868 VAL Chi-restraints excluded: chain F residue 202 LEU Chi-restraints excluded: chain F residue 230 ILE Chi-restraints excluded: chain F residue 240 HIS Chi-restraints excluded: chain F residue 306 LEU Chi-restraints excluded: chain F residue 336 VAL Chi-restraints excluded: chain F residue 380 THR Chi-restraints excluded: chain F residue 505 LEU Chi-restraints excluded: chain F residue 552 LEU Chi-restraints excluded: chain F residue 766 LEU Chi-restraints excluded: chain F residue 840 THR Chi-restraints excluded: chain F residue 868 VAL Chi-restraints excluded: chain F residue 878 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 327 optimal weight: 5.9990 chunk 346 optimal weight: 2.9990 chunk 124 optimal weight: 9.9990 chunk 448 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 141 optimal weight: 1.9990 chunk 221 optimal weight: 6.9990 chunk 116 optimal weight: 2.9990 chunk 396 optimal weight: 4.9990 chunk 117 optimal weight: 0.5980 chunk 267 optimal weight: 10.0000 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 GLN C 542 GLN ** C 804 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 701 HIS ** D 792 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN ** E 614 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 549 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.156452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.149207 restraints weight = 60934.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.149081 restraints weight = 36600.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.148760 restraints weight = 26456.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.148316 restraints weight = 24854.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.148150 restraints weight = 23365.179| |-----------------------------------------------------------------------------| r_work (final): 0.4370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6217 moved from start: 0.6017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 38872 Z= 0.160 Angle : 0.661 14.563 52227 Z= 0.327 Chirality : 0.045 0.324 5823 Planarity : 0.004 0.048 6309 Dihedral : 14.217 89.711 6970 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.52 % Allowed : 22.75 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.12), residues: 4560 helix: 1.26 (0.10), residues: 2454 sheet: -0.56 (0.21), residues: 558 loop : -1.02 (0.16), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 625 TYR 0.036 0.002 TYR F 691 PHE 0.028 0.002 PHE E 144 TRP 0.017 0.001 TRP D 845 HIS 0.016 0.001 HIS A 701 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (38859) covalent geometry : angle 0.66091 / 0.33 (52227) hydrogen bonds : bond 0.04028 / 2.71 ( 2095) hydrogen bonds : angle 4.61893 / 3.25 ( 6177) Misc. bond : bond 0.00042 / 0.02 ( 13) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5600.16 seconds wall clock time: 98 minutes 10.70 seconds (5890.70 seconds total)