Starting phenix.real_space_refine on Sat Mar 7 04:52:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vh6_31988/03_2026/7vh6_31988.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vh6_31988/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7vh6_31988/03_2026/7vh6_31988.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vh6_31988/03_2026/7vh6_31988.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vh6_31988/03_2026/7vh6_31988.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vh6_31988/03_2026/7vh6_31988.map" } 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-5986/lib/python3.9/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: 9.31, per 1000 atoms: 0.24 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: 4.05 Conformation dependent library (CDL) restraints added in 1.7 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: 1.42 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: 9.07 Time building geometry restraints manager: 5.12 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: 20617 21.68 - 43.36: 2211 43.36 - 65.05: 543 65.05 - 86.73: 145 86.73 - 108.41: 43 Dihedral angle restraints: 23559 sinusoidal: 10479 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 23556 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: 1.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.560 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 37.410 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6312 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 : 19.286 108.411 15171 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 covalent geometry : bond 0.01255 (38859) covalent geometry : angle 1.59054 (52227) hydrogen bonds : bond 0.27991 ( 2095) hydrogen bonds : angle 8.97313 ( 6177) Misc. bond : bond 0.37578 ( 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 : 1.288 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: 0.2330 time to fit residues: 371.1663 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 : 1.470 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 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 = 0.4531 r_free = 0.4531 target = 0.164122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.153744 restraints weight = 59282.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.150801 restraints weight = 33218.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.149683 restraints weight = 37667.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.149018 restraints weight = 32549.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.148566 restraints weight = 32198.812| |-----------------------------------------------------------------------------| r_work (final): 0.4385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6121 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 38872 Z= 0.147 Angle : 0.675 10.713 52227 Z= 0.345 Chirality : 0.044 0.189 5823 Planarity : 0.006 0.079 6309 Dihedral : 18.450 96.290 7316 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.36 % Allowed : 10.83 % Favored : 86.82 % 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: 0.57 (0.10), residues: 2550 sheet: -0.82 (0.22), residues: 474 loop : -1.02 (0.15), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 253 TYR 0.025 0.002 TYR F 694 PHE 0.030 0.002 PHE B 448 TRP 0.039 0.001 TRP A 805 HIS 0.007 0.001 HIS E 614 Details of bonding type rmsd covalent geometry : bond 0.00324 (38859) covalent geometry : angle 0.67495 (52227) hydrogen bonds : bond 0.05056 ( 2095) hydrogen bonds : angle 5.19328 ( 6177) Misc. bond : bond 0.00057 ( 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 665 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 577 time to evaluate : 1.284 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: 0.5621 (mt-10) cc_final: 0.5411 (tm-30) REVERT: A 700 LEU cc_start: 0.8975 (tt) cc_final: 0.8732 (tp) REVERT: A 722 ILE cc_start: 0.8430 (mm) cc_final: 0.8221 (mm) REVERT: B 314 TYR cc_start: 0.8779 (m-80) cc_final: 0.8527 (m-80) REVERT: B 798 GLN cc_start: 0.8334 (tm-30) cc_final: 0.8089 (tm-30) REVERT: B 803 GLU cc_start: 0.6585 (mt-10) cc_final: 0.6168 (mt-10) REVERT: C 656 ASP cc_start: 0.5474 (OUTLIER) cc_final: 0.5015 (t0) REVERT: D 190 GLU cc_start: 0.3286 (tt0) cc_final: 0.1789 (mp0) REVERT: D 258 MET cc_start: 0.3168 (ppp) cc_final: 0.2267 (ppp) REVERT: D 322 ILE cc_start: 0.7301 (mt) cc_final: 0.7080 (mp) REVERT: D 486 GLU cc_start: 0.5659 (pm20) cc_final: 0.4898 (pm20) REVERT: D 883 ASP cc_start: 0.5820 (t0) cc_final: 0.5586 (t70) REVERT: E 694 TYR cc_start: 0.8268 (t80) cc_final: 0.7929 (t80) REVERT: E 698 LEU cc_start: 0.8434 (mt) cc_final: 0.7282 (mt) REVERT: E 736 ILE cc_start: 0.7188 (mt) cc_final: 0.6926 (mt) REVERT: E 883 ASP cc_start: 0.5814 (OUTLIER) cc_final: 0.5263 (m-30) REVERT: F 228 SER cc_start: 0.7286 (m) cc_final: 0.6779 (t) REVERT: F 449 HIS cc_start: 0.3842 (OUTLIER) cc_final: 0.3602 (t70) REVERT: F 631 MET cc_start: 0.7074 (ppp) cc_final: 0.6657 (ppp) outliers start: 88 outliers final: 43 residues processed: 635 average time/residue: 0.2102 time to fit residues: 230.3847 Evaluate side-chains 466 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 420 time to evaluate : 1.294 ------------------------------------------------------------------------------- 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 674 ILE Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain B residue 119 PHE Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 209 VAL 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 720 ASP 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 251 VAL 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 345 THR Chi-restraints excluded: chain C residue 376 CYS 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 415 optimal weight: 10.0000 chunk 36 optimal weight: 0.2980 chunk 212 optimal weight: 0.9990 chunk 159 optimal weight: 6.9990 chunk 349 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 12 optimal weight: 20.0000 chunk 244 optimal weight: 10.0000 chunk 435 optimal weight: 2.9990 chunk 279 optimal weight: 20.0000 chunk 184 optimal weight: 0.0060 overall best weight: 1.8602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4486 r_free = 0.4486 target = 0.160117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.149961 restraints weight = 59983.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.142037 restraints weight = 28149.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.141110 restraints weight = 71566.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 75)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.139974 restraints weight = 45863.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 70)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.137895 restraints weight = 47710.395| |-----------------------------------------------------------------------------| r_work (final): 0.4234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6451 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 38872 Z= 0.164 Angle : 0.644 10.668 52227 Z= 0.326 Chirality : 0.044 0.181 5823 Planarity : 0.004 0.056 6309 Dihedral : 17.433 89.864 7312 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.14 % Allowed : 14.79 % Favored : 82.07 % 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: 0.04 (0.12), residues: 4560 helix: 0.86 (0.10), residues: 2538 sheet: -0.78 (0.20), residues: 564 loop : -0.97 (0.15), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 625 TYR 0.022 0.002 TYR F 691 PHE 0.032 0.002 PHE E 830 TRP 0.015 0.001 TRP A 805 HIS 0.022 0.001 HIS A 495 Details of bonding type rmsd covalent geometry : bond 0.00376 (38859) covalent geometry : angle 0.64431 (52227) hydrogen bonds : bond 0.04450 ( 2095) hydrogen bonds : angle 4.82991 ( 6177) Misc. bond : bond 0.00052 ( 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 560 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 443 time to evaluate : 1.268 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 353 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7518 (mt) REVERT: A 700 LEU cc_start: 0.9085 (tt) cc_final: 0.8857 (tp) REVERT: B 830 PHE cc_start: 0.7507 (m-10) cc_final: 0.7292 (m-80) REVERT: C 758 MET cc_start: 0.8015 (mtp) cc_final: 0.7748 (mtm) REVERT: C 886 MET cc_start: 0.7418 (mmm) cc_final: 0.7167 (mmm) REVERT: D 190 GLU cc_start: 0.3287 (tt0) cc_final: 0.1713 (mp0) REVERT: D 258 MET cc_start: 0.3102 (ppp) cc_final: 0.2312 (ppp) REVERT: D 486 GLU cc_start: 0.5626 (pm20) cc_final: 0.4823 (pm20) REVERT: E 118 MET cc_start: 0.6815 (ttm) cc_final: 0.6501 (ttt) REVERT: E 627 TYR cc_start: 0.6808 (m-80) cc_final: 0.6346 (m-80) REVERT: E 694 TYR cc_start: 0.8238 (t80) cc_final: 0.7953 (t80) REVERT: F 228 SER cc_start: 0.7563 (m) cc_final: 0.7073 (t) REVERT: F 449 HIS cc_start: 0.3894 (t70) cc_final: 0.3300 (t70) REVERT: F 801 LEU cc_start: 0.8440 (tp) cc_final: 0.8017 (tt) outliers start: 117 outliers final: 62 residues processed: 526 average time/residue: 0.1964 time to fit residues: 180.4837 Evaluate side-chains 445 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 382 time to evaluate : 1.149 ------------------------------------------------------------------------------- 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 353 LEU 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 748 VAL 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 133 ILE Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 250 THR 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 620 GLU 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 133 ILE Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 251 VAL 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 329 ILE Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 353 LEU 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 749 LYS Chi-restraints excluded: chain C residue 766 LEU Chi-restraints excluded: chain D residue 212 THR Chi-restraints excluded: chain D residue 485 GLU 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 863 ILE 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 538 ASP Chi-restraints excluded: chain E residue 621 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 380 THR Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 675 ILE Chi-restraints excluded: chain F residue 676 ASP Chi-restraints excluded: chain F residue 752 LEU Chi-restraints excluded: chain F residue 850 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 387 optimal weight: 3.9990 chunk 31 optimal weight: 8.9990 chunk 177 optimal weight: 0.9980 chunk 174 optimal weight: 0.8980 chunk 337 optimal weight: 0.8980 chunk 267 optimal weight: 6.9990 chunk 184 optimal weight: 0.8980 chunk 405 optimal weight: 1.9990 chunk 143 optimal weight: 0.8980 chunk 260 optimal weight: 8.9990 chunk 381 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 500 ASN A 614 HIS ** A 701 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 GLN B 542 GLN ** B 701 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 798 GLN ** 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 125 GLN ** E 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 449 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.161236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.151167 restraints weight = 59682.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.144390 restraints weight = 29800.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.144294 restraints weight = 60952.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.144043 restraints weight = 43671.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.143329 restraints weight = 36331.522| |-----------------------------------------------------------------------------| r_work (final): 0.4316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6290 moved from start: 0.4436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 38872 Z= 0.123 Angle : 0.586 9.042 52227 Z= 0.297 Chirality : 0.042 0.167 5823 Planarity : 0.004 0.043 6309 Dihedral : 16.299 88.520 7312 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.79 % Allowed : 17.36 % Favored : 79.85 % 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: 0.29 (0.12), residues: 4560 helix: 1.19 (0.10), residues: 2484 sheet: -0.95 (0.19), residues: 612 loop : -0.91 (0.15), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 625 TYR 0.025 0.001 TYR D 691 PHE 0.024 0.001 PHE D 426 TRP 0.015 0.001 TRP A 805 HIS 0.026 0.001 HIS A 549 Details of bonding type rmsd covalent geometry : bond 0.00274 (38859) covalent geometry : angle 0.58645 (52227) hydrogen bonds : bond 0.03987 ( 2095) hydrogen bonds : angle 4.56890 ( 6177) Misc. bond : bond 0.00028 ( 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 564 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 460 time to evaluate : 1.365 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: A 700 LEU cc_start: 0.9032 (tt) cc_final: 0.8777 (tp) REVERT: A 722 ILE cc_start: 0.8178 (mm) cc_final: 0.7704 (mm) REVERT: B 133 ILE cc_start: 0.7995 (OUTLIER) cc_final: 0.7779 (pt) REVERT: B 314 TYR cc_start: 0.8778 (m-80) cc_final: 0.8380 (m-80) REVERT: C 258 MET cc_start: 0.3412 (mpp) cc_final: 0.1817 (mpp) REVERT: C 758 MET cc_start: 0.8020 (mtp) cc_final: 0.7785 (mtm) REVERT: C 795 MET cc_start: 0.8425 (mmm) cc_final: 0.7502 (tmm) REVERT: D 190 GLU cc_start: 0.3268 (tt0) cc_final: 0.1758 (mp0) REVERT: D 258 MET cc_start: 0.3203 (ppp) cc_final: 0.2338 (ppp) REVERT: E 118 MET cc_start: 0.6941 (ttm) cc_final: 0.6651 (ttt) REVERT: E 627 TYR cc_start: 0.6074 (m-80) cc_final: 0.5793 (m-80) REVERT: E 694 TYR cc_start: 0.8127 (t80) cc_final: 0.7927 (t80) REVERT: F 228 SER cc_start: 0.7363 (m) cc_final: 0.6840 (t) REVERT: F 449 HIS cc_start: 0.3808 (OUTLIER) cc_final: 0.3396 (t-170) REVERT: F 597 LEU cc_start: 0.4260 (OUTLIER) cc_final: 0.3965 (tp) outliers start: 104 outliers final: 54 residues processed: 530 average time/residue: 0.1910 time to fit residues: 178.3667 Evaluate side-chains 462 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 405 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 PHE Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 733 THR Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 867 CYS 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 251 VAL Chi-restraints excluded: chain B residue 366 ILE 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 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 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 306 LEU 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 399 VAL Chi-restraints excluded: chain C residue 596 GLU Chi-restraints excluded: chain C residue 620 GLU Chi-restraints excluded: chain C residue 766 LEU 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 684 ILE Chi-restraints excluded: chain E residue 258 MET Chi-restraints excluded: chain E residue 538 ASP Chi-restraints excluded: chain E residue 621 ILE Chi-restraints excluded: chain E residue 646 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 380 THR Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 449 HIS Chi-restraints excluded: chain F residue 597 LEU Chi-restraints excluded: chain F residue 631 MET Chi-restraints excluded: chain F residue 676 ASP Chi-restraints excluded: chain F residue 734 LEU Chi-restraints excluded: chain F residue 766 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 145 optimal weight: 8.9990 chunk 336 optimal weight: 6.9990 chunk 400 optimal weight: 2.9990 chunk 167 optimal weight: 4.9990 chunk 344 optimal weight: 20.0000 chunk 99 optimal weight: 1.9990 chunk 421 optimal weight: 8.9990 chunk 51 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 296 optimal weight: 5.9990 chunk 454 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 549 HIS A 613 GLN ** 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 ** B 701 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 542 GLN ** D 701 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 792 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN E 740 ASN ** E 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.154783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.144865 restraints weight = 60426.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.139420 restraints weight = 30708.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.138538 restraints weight = 52408.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.138375 restraints weight = 38678.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.138133 restraints weight = 32799.301| |-----------------------------------------------------------------------------| r_work (final): 0.4244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6472 moved from start: 0.5147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 38872 Z= 0.234 Angle : 0.733 10.054 52227 Z= 0.366 Chirality : 0.046 0.244 5823 Planarity : 0.005 0.054 6309 Dihedral : 17.657 99.829 7312 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.78 % Allowed : 17.95 % Favored : 78.27 % 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: -0.00 (0.12), residues: 4560 helix: 0.87 (0.10), residues: 2496 sheet: -0.48 (0.19), residues: 624 loop : -1.21 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 617 TYR 0.040 0.002 TYR F 691 PHE 0.029 0.002 PHE F 451 TRP 0.076 0.002 TRP F 805 HIS 0.008 0.002 HIS F 285 Details of bonding type rmsd covalent geometry : bond 0.00536 (38859) covalent geometry : angle 0.73325 (52227) hydrogen bonds : bond 0.04660 ( 2095) hydrogen bonds : angle 4.92368 ( 6177) Misc. bond : bond 0.00079 ( 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 533 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 392 time to evaluate : 1.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 GLU cc_start: 0.6146 (mt-10) cc_final: 0.5902 (mt-10) REVERT: A 848 ASN cc_start: 0.5157 (p0) cc_final: 0.4330 (t0) REVERT: A 884 ARG cc_start: 0.6935 (tmt170) cc_final: 0.6377 (tmt170) REVERT: B 367 GLU cc_start: 0.6704 (pp20) cc_final: 0.6039 (tm-30) REVERT: C 306 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8590 (mt) REVERT: D 152 MET cc_start: 0.5043 (mtt) cc_final: 0.4665 (tpp) REVERT: D 190 GLU cc_start: 0.3143 (tt0) cc_final: 0.1698 (mp0) REVERT: D 258 MET cc_start: 0.3232 (ppp) cc_final: 0.2520 (ppp) REVERT: D 609 GLU cc_start: 0.5617 (OUTLIER) cc_final: 0.5375 (tm-30) REVERT: E 118 MET cc_start: 0.6643 (ttm) cc_final: 0.6349 (ttt) REVERT: F 228 SER cc_start: 0.7287 (m) cc_final: 0.6854 (t) REVERT: F 597 LEU cc_start: 0.4431 (OUTLIER) cc_final: 0.4177 (tp) outliers start: 141 outliers final: 90 residues processed: 503 average time/residue: 0.2020 time to fit residues: 177.0868 Evaluate side-chains 444 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 351 time to evaluate : 1.341 ------------------------------------------------------------------------------- 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 300 LEU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 736 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 A residue 868 VAL 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 251 VAL Chi-restraints excluded: chain B residue 258 MET Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 366 ILE 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 597 LEU 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 690 SER Chi-restraints excluded: chain B residue 701 HIS Chi-restraints excluded: chain B residue 702 LEU 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 212 THR Chi-restraints excluded: chain C residue 230 ILE Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 306 LEU 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 382 THR Chi-restraints excluded: chain C residue 399 VAL Chi-restraints excluded: chain C residue 564 ILE Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 596 GLU Chi-restraints excluded: chain C residue 620 GLU Chi-restraints excluded: chain C residue 766 LEU Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 334 VAL 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 597 LEU Chi-restraints excluded: chain D residue 609 GLU 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 765 VAL Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 258 MET Chi-restraints excluded: chain E residue 268 PHE 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 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 319 ILE 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 631 MET 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 739 ASP Chi-restraints excluded: chain F residue 758 MET Chi-restraints excluded: chain F residue 766 LEU Chi-restraints excluded: chain F residue 840 THR Chi-restraints excluded: chain F residue 850 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 9 optimal weight: 7.9990 chunk 71 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 159 optimal weight: 7.9990 chunk 365 optimal weight: 0.9990 chunk 141 optimal weight: 2.9990 chunk 271 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 138 optimal weight: 8.9990 chunk 67 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ** B 701 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 542 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.157007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.144297 restraints weight = 60213.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.132791 restraints weight = 40974.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.131069 restraints weight = 65820.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.131317 restraints weight = 51385.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.131017 restraints weight = 42096.726| |-----------------------------------------------------------------------------| r_work (final): 0.4133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6658 moved from start: 0.5323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 38872 Z= 0.138 Angle : 0.614 12.071 52227 Z= 0.308 Chirality : 0.043 0.321 5823 Planarity : 0.004 0.047 6309 Dihedral : 16.222 89.982 7312 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.05 % Allowed : 20.12 % Favored : 76.82 % 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: 0.25 (0.12), residues: 4560 helix: 1.14 (0.10), residues: 2484 sheet: -0.72 (0.20), residues: 576 loop : -1.04 (0.15), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 625 TYR 0.038 0.002 TYR F 694 PHE 0.021 0.001 PHE C 144 TRP 0.030 0.001 TRP F 805 HIS 0.007 0.001 HIS A 701 Details of bonding type rmsd covalent geometry : bond 0.00315 (38859) covalent geometry : angle 0.61408 (52227) hydrogen bonds : bond 0.04022 ( 2095) hydrogen bonds : angle 4.65206 ( 6177) Misc. bond : bond 0.00031 ( 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 535 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 421 time to evaluate : 1.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 700 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8717 (tp) REVERT: A 722 ILE cc_start: 0.8302 (mm) cc_final: 0.8027 (mm) REVERT: B 244 GLN cc_start: 0.3236 (tp40) cc_final: 0.2911 (tp40) REVERT: B 346 MET cc_start: 0.7663 (mmm) cc_final: 0.7286 (mmm) REVERT: B 367 GLU cc_start: 0.6702 (pp20) cc_final: 0.6165 (tm-30) REVERT: C 230 ILE cc_start: 0.7307 (OUTLIER) cc_final: 0.7105 (mp) REVERT: C 306 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8559 (mp) REVERT: C 684 ILE cc_start: 0.8680 (OUTLIER) cc_final: 0.8416 (tp) REVERT: D 152 MET cc_start: 0.5056 (mtt) cc_final: 0.4162 (tpp) REVERT: D 190 GLU cc_start: 0.3191 (tt0) cc_final: 0.1498 (mp0) REVERT: D 253 ARG cc_start: 0.6679 (OUTLIER) cc_final: 0.6027 (mtm110) REVERT: D 258 MET cc_start: 0.3084 (ppp) cc_final: 0.2184 (ppp) REVERT: D 322 ILE cc_start: 0.6283 (mm) cc_final: 0.6077 (mm) REVERT: D 609 GLU cc_start: 0.5788 (OUTLIER) cc_final: 0.5518 (tm-30) REVERT: D 678 LEU cc_start: 0.7974 (tt) cc_final: 0.7652 (tp) REVERT: E 118 MET cc_start: 0.5714 (OUTLIER) cc_final: 0.5344 (ttt) REVERT: E 883 ASP cc_start: 0.7877 (m-30) cc_final: 0.7534 (m-30) REVERT: F 228 SER cc_start: 0.7605 (m) cc_final: 0.7143 (t) REVERT: F 258 MET cc_start: 0.5149 (mpp) cc_final: 0.4428 (ttp) outliers start: 114 outliers final: 73 residues processed: 503 average time/residue: 0.2029 time to fit residues: 179.3118 Evaluate side-chains 451 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 371 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 PHE 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 700 LEU Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 714 ASP Chi-restraints excluded: chain A residue 748 VAL 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 113 VAL 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 251 VAL Chi-restraints excluded: chain B residue 258 MET Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 366 ILE 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 622 LEU 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 287 THR Chi-restraints excluded: chain C residue 306 LEU 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 596 GLU Chi-restraints excluded: chain C residue 620 GLU 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 320 VAL Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 485 GLU Chi-restraints excluded: chain D residue 529 VAL Chi-restraints excluded: chain D residue 609 GLU Chi-restraints excluded: chain D residue 620 GLU Chi-restraints excluded: chain D residue 720 ASP 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 268 PHE 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 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 380 THR Chi-restraints excluded: chain F residue 623 GLN Chi-restraints excluded: chain F residue 631 MET Chi-restraints excluded: chain F residue 675 ILE 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 766 LEU Chi-restraints excluded: chain F residue 878 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 23 optimal weight: 8.9990 chunk 310 optimal weight: 8.9990 chunk 346 optimal weight: 3.9990 chunk 246 optimal weight: 1.9990 chunk 430 optimal weight: 0.8980 chunk 38 optimal weight: 9.9990 chunk 18 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 422 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 chunk 328 optimal weight: 10.0000 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 391 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 ** 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 = 0.4463 r_free = 0.4463 target = 0.157766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.147804 restraints weight = 60041.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.141785 restraints weight = 26857.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.140814 restraints weight = 58052.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.140440 restraints weight = 41884.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.140126 restraints weight = 31692.396| |-----------------------------------------------------------------------------| r_work (final): 0.4272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6405 moved from start: 0.5491 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= 0.132 Angle : 0.611 15.963 52227 Z= 0.305 Chirality : 0.043 0.308 5823 Planarity : 0.004 0.044 6309 Dihedral : 15.581 89.378 7312 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.11 % Allowed : 21.20 % Favored : 75.70 % 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: 0.28 (0.12), residues: 4560 helix: 1.19 (0.10), residues: 2484 sheet: -0.63 (0.20), residues: 576 loop : -1.12 (0.15), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 754 TYR 0.046 0.002 TYR E 694 PHE 0.021 0.001 PHE D 842 TRP 0.020 0.001 TRP F 805 HIS 0.006 0.001 HIS A 701 Details of bonding type rmsd covalent geometry : bond 0.00299 (38859) covalent geometry : angle 0.61081 (52227) hydrogen bonds : bond 0.03930 ( 2095) hydrogen bonds : angle 4.60032 ( 6177) Misc. bond : bond 0.00027 ( 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 522 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 406 time to evaluate : 1.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 694 TYR cc_start: 0.8533 (OUTLIER) cc_final: 0.8276 (t80) REVERT: A 722 ILE cc_start: 0.8304 (mm) cc_final: 0.8035 (mm) REVERT: B 244 GLN cc_start: 0.2957 (tp40) cc_final: 0.2640 (tp40) REVERT: B 314 TYR cc_start: 0.8906 (m-80) cc_final: 0.8653 (m-80) REVERT: B 346 MET cc_start: 0.7851 (mmm) cc_final: 0.7447 (mmm) REVERT: B 367 GLU cc_start: 0.6656 (pp20) cc_final: 0.6167 (tm-30) REVERT: C 258 MET cc_start: 0.2735 (mpp) cc_final: 0.2177 (mpp) REVERT: C 306 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8557 (mp) REVERT: C 517 ARG cc_start: 0.5866 (OUTLIER) cc_final: 0.5516 (ttt180) REVERT: C 684 ILE cc_start: 0.8599 (OUTLIER) cc_final: 0.8366 (tp) REVERT: C 803 GLU cc_start: 0.6370 (mt-10) cc_final: 0.5803 (mt-10) REVERT: D 152 MET cc_start: 0.4834 (mtt) cc_final: 0.4020 (tpp) REVERT: D 190 GLU cc_start: 0.3100 (tt0) cc_final: 0.1628 (mp0) REVERT: D 253 ARG cc_start: 0.6639 (OUTLIER) cc_final: 0.6028 (mtm110) REVERT: D 258 MET cc_start: 0.2942 (ppp) cc_final: 0.2061 (ppp) REVERT: D 322 ILE cc_start: 0.6276 (mm) cc_final: 0.6053 (mm) REVERT: D 397 GLU cc_start: 0.5382 (pm20) cc_final: 0.5003 (tt0) REVERT: D 609 GLU cc_start: 0.5648 (OUTLIER) cc_final: 0.5407 (tm-30) REVERT: D 678 LEU cc_start: 0.7840 (tt) cc_final: 0.7532 (tp) REVERT: E 118 MET cc_start: 0.6214 (ttm) cc_final: 0.5790 (ttt) REVERT: E 708 LEU cc_start: 0.8275 (mt) cc_final: 0.8003 (mt) REVERT: F 228 SER cc_start: 0.7484 (m) cc_final: 0.6997 (t) REVERT: F 258 MET cc_start: 0.4700 (mpp) cc_final: 0.4330 (ttp) REVERT: F 847 GLU cc_start: 0.5082 (mp0) cc_final: 0.4302 (mt-10) outliers start: 116 outliers final: 82 residues processed: 487 average time/residue: 0.2049 time to fit residues: 174.5610 Evaluate side-chains 460 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 372 time to evaluate : 1.350 ------------------------------------------------------------------------------- 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 332 ILE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 342 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 694 TYR Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 791 MET Chi-restraints excluded: chain A residue 853 VAL Chi-restraints excluded: chain A residue 867 CYS Chi-restraints excluded: chain B residue 118 MET 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 240 HIS Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 258 MET Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 366 ILE 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 622 LEU 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 113 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 285 HIS Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 306 LEU 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 596 GLU Chi-restraints excluded: chain C residue 620 GLU 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 320 VAL 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 609 GLU Chi-restraints excluded: chain D residue 620 GLU Chi-restraints excluded: chain D residue 720 ASP Chi-restraints excluded: chain D residue 750 TRP Chi-restraints excluded: chain D residue 766 LEU Chi-restraints excluded: chain E residue 258 MET Chi-restraints excluded: chain E residue 268 PHE 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 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 360 VAL Chi-restraints excluded: chain F residue 380 THR Chi-restraints excluded: chain F residue 552 LEU Chi-restraints excluded: chain F residue 623 GLN Chi-restraints excluded: chain F residue 631 MET 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 766 LEU Chi-restraints excluded: chain F residue 779 LEU Chi-restraints excluded: chain F residue 878 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 20 optimal weight: 0.9990 chunk 219 optimal weight: 4.9990 chunk 443 optimal weight: 0.9980 chunk 325 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 378 optimal weight: 0.5980 chunk 104 optimal weight: 0.9980 chunk 194 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 337 optimal weight: 0.9980 chunk 106 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 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 = 0.4472 r_free = 0.4472 target = 0.158385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.148377 restraints weight = 59857.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.140801 restraints weight = 32249.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.140069 restraints weight = 82900.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.140172 restraints weight = 54405.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.139799 restraints weight = 39839.210| |-----------------------------------------------------------------------------| r_work (final): 0.4268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6408 moved from start: 0.5654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 38872 Z= 0.123 Angle : 0.601 13.243 52227 Z= 0.299 Chirality : 0.043 0.290 5823 Planarity : 0.004 0.043 6309 Dihedral : 14.990 89.343 7312 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.92 % Allowed : 21.33 % Favored : 75.75 % 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: 0.28 (0.12), residues: 4560 helix: 1.23 (0.10), residues: 2496 sheet: -0.56 (0.20), residues: 570 loop : -1.24 (0.15), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 682 TYR 0.026 0.001 TYR D 691 PHE 0.047 0.001 PHE E 830 TRP 0.025 0.001 TRP C 524 HIS 0.008 0.001 HIS C 549 Details of bonding type rmsd covalent geometry : bond 0.00276 (38859) covalent geometry : angle 0.60118 (52227) hydrogen bonds : bond 0.03812 ( 2095) hydrogen bonds : angle 4.52846 ( 6177) Misc. bond : bond 0.00024 ( 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 523 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 414 time to evaluate : 1.336 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: 0.5072 (OUTLIER) cc_final: 0.4841 (mm) REVERT: A 694 TYR cc_start: 0.8495 (OUTLIER) cc_final: 0.8216 (t80) REVERT: A 722 ILE cc_start: 0.8361 (mm) cc_final: 0.8088 (mm) REVERT: A 766 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8519 (mp) REVERT: B 244 GLN cc_start: 0.3037 (tp40) cc_final: 0.2726 (tp40) REVERT: B 314 TYR cc_start: 0.8917 (m-80) cc_final: 0.8654 (m-80) REVERT: B 346 MET cc_start: 0.7807 (mmm) cc_final: 0.7353 (mmm) REVERT: B 367 GLU cc_start: 0.6598 (pp20) cc_final: 0.6202 (tm-30) REVERT: B 781 LYS cc_start: 0.6147 (mtmt) cc_final: 0.5305 (mttp) REVERT: C 258 MET cc_start: 0.2751 (mpp) cc_final: 0.2313 (mpp) REVERT: C 306 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8564 (mp) REVERT: C 517 ARG cc_start: 0.5703 (OUTLIER) cc_final: 0.5307 (ttt180) REVERT: C 803 GLU cc_start: 0.6031 (mt-10) cc_final: 0.5611 (mt-10) REVERT: D 190 GLU cc_start: 0.3107 (tt0) cc_final: 0.1576 (mp0) REVERT: D 253 ARG cc_start: 0.6628 (OUTLIER) cc_final: 0.6038 (mtm110) REVERT: D 258 MET cc_start: 0.2790 (ppp) cc_final: 0.1848 (ppp) REVERT: D 322 ILE cc_start: 0.6161 (mm) cc_final: 0.5939 (mm) REVERT: D 397 GLU cc_start: 0.5224 (pm20) cc_final: 0.4968 (tt0) REVERT: D 678 LEU cc_start: 0.7846 (tt) cc_final: 0.7514 (tp) REVERT: E 118 MET cc_start: 0.6230 (ttm) cc_final: 0.5763 (ttt) REVERT: F 228 SER cc_start: 0.7517 (m) cc_final: 0.7003 (t) REVERT: F 258 MET cc_start: 0.4731 (mpp) cc_final: 0.4342 (ttp) REVERT: F 597 LEU cc_start: 0.4463 (OUTLIER) cc_final: 0.4243 (tp) REVERT: F 847 GLU cc_start: 0.5163 (mp0) cc_final: 0.4511 (mt-10) outliers start: 109 outliers final: 75 residues processed: 491 average time/residue: 0.2013 time to fit residues: 174.5161 Evaluate side-chains 469 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 387 time to evaluate : 1.292 ------------------------------------------------------------------------------- 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 332 ILE 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 374 ILE 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 748 VAL Chi-restraints excluded: chain A residue 766 LEU Chi-restraints excluded: chain A residue 791 MET Chi-restraints excluded: chain A residue 867 CYS 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 189 VAL Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 258 MET Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 366 ILE 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 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 285 HIS Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 329 ILE 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 596 GLU Chi-restraints excluded: chain C residue 620 GLU Chi-restraints excluded: chain C residue 628 LEU 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 320 VAL Chi-restraints excluded: chain D residue 334 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 720 ASP Chi-restraints excluded: chain D residue 750 TRP Chi-restraints excluded: chain D residue 766 LEU Chi-restraints excluded: chain E residue 258 MET Chi-restraints excluded: chain E residue 268 PHE 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 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 360 VAL Chi-restraints excluded: chain F residue 380 THR Chi-restraints excluded: chain F residue 552 LEU Chi-restraints excluded: chain F residue 597 LEU Chi-restraints excluded: chain F residue 631 MET 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 779 LEU Chi-restraints excluded: chain F residue 840 THR 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: 0.8980 chunk 403 optimal weight: 0.6980 chunk 48 optimal weight: 9.9990 chunk 46 optimal weight: 0.9980 chunk 172 optimal weight: 2.9990 chunk 430 optimal weight: 5.9990 chunk 253 optimal weight: 7.9990 chunk 125 optimal weight: 20.0000 chunk 258 optimal weight: 0.0470 chunk 231 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4481 r_free = 0.4481 target = 0.159129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.149258 restraints weight = 60175.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.148739 restraints weight = 44432.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.147919 restraints weight = 32292.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.147516 restraints weight = 35511.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.147350 restraints weight = 28232.507| |-----------------------------------------------------------------------------| r_work (final): 0.4371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6217 moved from start: 0.5807 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= 0.120 Angle : 0.603 13.000 52227 Z= 0.301 Chirality : 0.042 0.291 5823 Planarity : 0.004 0.042 6309 Dihedral : 14.388 89.793 7312 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.60 % Allowed : 22.13 % 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: 0.30 (0.12), residues: 4560 helix: 1.26 (0.10), residues: 2496 sheet: -0.68 (0.22), residues: 498 loop : -1.20 (0.15), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 695 TYR 0.025 0.001 TYR F 691 PHE 0.027 0.001 PHE B 600 TRP 0.016 0.001 TRP C 524 HIS 0.015 0.001 HIS F 549 Details of bonding type rmsd covalent geometry : bond 0.00266 (38859) covalent geometry : angle 0.60314 (52227) hydrogen bonds : bond 0.03798 ( 2095) hydrogen bonds : angle 4.50841 ( 6177) Misc. bond : bond 0.00025 ( 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 515 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 418 time to evaluate : 1.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 430 LEU cc_start: 0.5117 (OUTLIER) cc_final: 0.4857 (mm) REVERT: A 694 TYR cc_start: 0.8447 (OUTLIER) cc_final: 0.8177 (t80) REVERT: A 701 HIS cc_start: 0.8190 (OUTLIER) cc_final: 0.7895 (t-170) REVERT: B 244 GLN cc_start: 0.2802 (tp40) cc_final: 0.2529 (tp40) REVERT: B 314 TYR cc_start: 0.8921 (m-80) cc_final: 0.8633 (m-80) REVERT: B 346 MET cc_start: 0.7787 (mmm) cc_final: 0.7314 (mmm) REVERT: B 367 GLU cc_start: 0.6165 (OUTLIER) cc_final: 0.5821 (tm-30) REVERT: B 781 LYS cc_start: 0.6318 (mtmt) cc_final: 0.5547 (mttp) REVERT: C 258 MET cc_start: 0.2587 (mpp) cc_final: 0.2193 (mpp) REVERT: C 306 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8587 (mp) REVERT: C 517 ARG cc_start: 0.5611 (OUTLIER) cc_final: 0.5257 (ttt180) REVERT: D 141 TRP cc_start: 0.5334 (m100) cc_final: 0.4985 (m100) REVERT: D 253 ARG cc_start: 0.6529 (OUTLIER) cc_final: 0.5978 (mtm110) REVERT: D 258 MET cc_start: 0.2809 (ppp) cc_final: 0.1897 (ppp) REVERT: D 322 ILE cc_start: 0.6108 (mm) cc_final: 0.5876 (mm) REVERT: D 397 GLU cc_start: 0.5036 (pm20) cc_final: 0.4733 (tt0) REVERT: D 678 LEU cc_start: 0.7914 (tt) cc_final: 0.7554 (tp) REVERT: E 118 MET cc_start: 0.6337 (ttm) cc_final: 0.5898 (ttt) REVERT: E 620 GLU cc_start: 0.5677 (mm-30) cc_final: 0.4486 (mt-10) REVERT: E 698 LEU cc_start: 0.8341 (mt) cc_final: 0.8121 (mt) REVERT: F 228 SER cc_start: 0.7338 (m) cc_final: 0.6810 (t) REVERT: F 258 MET cc_start: 0.4524 (mpp) cc_final: 0.4269 (ttp) REVERT: F 700 LEU cc_start: 0.8481 (mt) cc_final: 0.8044 (mt) REVERT: F 847 GLU cc_start: 0.5276 (mp0) cc_final: 0.4417 (mt-10) outliers start: 97 outliers final: 71 residues processed: 488 average time/residue: 0.2051 time to fit residues: 176.1188 Evaluate side-chains 463 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 385 time to evaluate : 1.503 ------------------------------------------------------------------------------- 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 332 ILE Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 374 ILE 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 748 VAL Chi-restraints excluded: chain A residue 791 MET 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 148 CYS Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 258 MET Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 367 GLU 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 620 GLU Chi-restraints excluded: chain B residue 622 LEU 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 285 HIS Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 306 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 596 GLU Chi-restraints excluded: chain C residue 620 GLU Chi-restraints excluded: chain C residue 628 LEU Chi-restraints excluded: chain C residue 750 TRP Chi-restraints excluded: chain C residue 766 LEU Chi-restraints excluded: chain C residue 777 MET Chi-restraints excluded: chain D residue 253 ARG Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 334 VAL Chi-restraints excluded: chain D residue 529 VAL Chi-restraints excluded: chain D residue 620 GLU Chi-restraints excluded: chain D residue 720 ASP Chi-restraints excluded: chain D residue 750 TRP Chi-restraints excluded: chain D residue 839 PHE Chi-restraints excluded: chain E residue 258 MET Chi-restraints excluded: chain E residue 268 PHE 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 202 LEU Chi-restraints excluded: chain F residue 230 ILE Chi-restraints excluded: chain F residue 240 HIS Chi-restraints excluded: chain F residue 305 LEU Chi-restraints excluded: chain F residue 319 ILE Chi-restraints excluded: chain F residue 360 VAL Chi-restraints excluded: chain F residue 380 THR Chi-restraints excluded: chain F residue 549 HIS Chi-restraints excluded: chain F residue 552 LEU Chi-restraints excluded: chain F residue 631 MET Chi-restraints excluded: chain F residue 734 LEU Chi-restraints excluded: chain F residue 766 LEU Chi-restraints excluded: chain F residue 779 LEU Chi-restraints excluded: chain F residue 840 THR 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: 10.0000 chunk 383 optimal weight: 1.9990 chunk 411 optimal weight: 6.9990 chunk 305 optimal weight: 5.9990 chunk 419 optimal weight: 20.0000 chunk 42 optimal weight: 0.1980 chunk 451 optimal weight: 0.9980 chunk 191 optimal weight: 20.0000 chunk 337 optimal weight: 0.7980 chunk 8 optimal weight: 6.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 523 HIS ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 HIS ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 792 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 285 HIS ** E 887 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 549 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.156321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.146452 restraints weight = 60264.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.140391 restraints weight = 31013.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.139885 restraints weight = 63029.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.139661 restraints weight = 43203.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.139608 restraints weight = 34218.247| |-----------------------------------------------------------------------------| r_work (final): 0.4268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6425 moved from start: 0.5959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 38872 Z= 0.164 Angle : 0.660 12.226 52227 Z= 0.327 Chirality : 0.044 0.303 5823 Planarity : 0.004 0.048 6309 Dihedral : 15.008 89.188 7312 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.36 % Allowed : 22.83 % Favored : 74.81 % 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: 0.27 (0.12), residues: 4560 helix: 1.18 (0.10), residues: 2484 sheet: -0.45 (0.21), residues: 528 loop : -1.17 (0.15), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 508 TYR 0.042 0.002 TYR F 691 PHE 0.050 0.002 PHE E 830 TRP 0.014 0.001 TRP D 756 HIS 0.018 0.001 HIS F 549 Details of bonding type rmsd covalent geometry : bond 0.00379 (38859) covalent geometry : angle 0.65967 (52227) hydrogen bonds : bond 0.04044 ( 2095) hydrogen bonds : angle 4.63463 ( 6177) Misc. bond : bond 0.00046 ( 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 473 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 385 time to evaluate : 1.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 694 TYR cc_start: 0.8559 (OUTLIER) cc_final: 0.8342 (t80) REVERT: B 346 MET cc_start: 0.7827 (mmm) cc_final: 0.7364 (mmm) REVERT: B 781 LYS cc_start: 0.6410 (mtmt) cc_final: 0.5567 (mttp) REVERT: C 258 MET cc_start: 0.3316 (mpp) cc_final: 0.2991 (mpp) REVERT: C 306 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8578 (mp) REVERT: C 517 ARG cc_start: 0.5712 (OUTLIER) cc_final: 0.5329 (ttt180) REVERT: D 141 TRP cc_start: 0.5473 (m100) cc_final: 0.5180 (m100) REVERT: D 190 GLU cc_start: 0.3006 (tt0) cc_final: 0.1466 (mp0) REVERT: D 253 ARG cc_start: 0.6684 (OUTLIER) cc_final: 0.6113 (mtm110) REVERT: D 258 MET cc_start: 0.2875 (ppp) cc_final: 0.1938 (ppp) REVERT: D 322 ILE cc_start: 0.6214 (mm) cc_final: 0.5959 (mm) REVERT: D 397 GLU cc_start: 0.5264 (pm20) cc_final: 0.4866 (tt0) REVERT: D 426 PHE cc_start: 0.3992 (m-80) cc_final: 0.3769 (m-80) REVERT: D 678 LEU cc_start: 0.8061 (tt) cc_final: 0.7681 (tp) REVERT: E 118 MET cc_start: 0.6178 (ttm) cc_final: 0.5892 (ttt) REVERT: E 620 GLU cc_start: 0.5935 (mm-30) cc_final: 0.4606 (mt-10) REVERT: F 129 GLU cc_start: 0.7916 (mp0) cc_final: 0.7387 (mp0) REVERT: F 228 SER cc_start: 0.7460 (m) cc_final: 0.6997 (t) REVERT: F 258 MET cc_start: 0.4615 (mpp) cc_final: 0.4282 (ttp) REVERT: F 299 VAL cc_start: 0.9072 (t) cc_final: 0.8817 (t) REVERT: F 706 LEU cc_start: 0.8496 (mp) cc_final: 0.8276 (mt) REVERT: F 847 GLU cc_start: 0.5371 (mp0) cc_final: 0.4754 (mt-10) outliers start: 88 outliers final: 68 residues processed: 444 average time/residue: 0.2016 time to fit residues: 158.1667 Evaluate side-chains 444 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 372 time to evaluate : 1.350 ------------------------------------------------------------------------------- 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 374 ILE 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 703 GLU Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 791 MET Chi-restraints excluded: chain A residue 867 CYS 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 189 VAL Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 258 MET Chi-restraints excluded: chain B residue 353 LEU 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 620 GLU Chi-restraints excluded: chain B residue 622 LEU 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 133 ILE Chi-restraints excluded: chain C residue 285 HIS Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 329 ILE 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 596 GLU Chi-restraints excluded: chain C residue 620 GLU Chi-restraints excluded: chain C residue 628 LEU Chi-restraints excluded: chain C residue 750 TRP Chi-restraints excluded: chain C residue 766 LEU Chi-restraints excluded: chain C residue 777 MET Chi-restraints excluded: chain D residue 253 ARG Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 529 VAL 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 839 PHE Chi-restraints excluded: chain E residue 258 MET Chi-restraints excluded: chain E residue 268 PHE Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 497 ASN 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 319 ILE Chi-restraints excluded: chain F residue 360 VAL Chi-restraints excluded: chain F residue 380 THR Chi-restraints excluded: chain F residue 552 LEU Chi-restraints excluded: chain F residue 623 GLN Chi-restraints excluded: chain F residue 631 MET 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 878 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 327 optimal weight: 4.9990 chunk 346 optimal weight: 0.6980 chunk 124 optimal weight: 0.5980 chunk 448 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 141 optimal weight: 2.9990 chunk 221 optimal weight: 0.6980 chunk 116 optimal weight: 7.9990 chunk 396 optimal weight: 9.9990 chunk 117 optimal weight: 9.9990 chunk 267 optimal weight: 20.0000 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 GLN C 804 ASN ** D 701 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 792 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN E 887 ASN F 549 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.157197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.147020 restraints weight = 60498.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.139253 restraints weight = 31731.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.138285 restraints weight = 73668.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.138163 restraints weight = 47515.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.137421 restraints weight = 41860.997| |-----------------------------------------------------------------------------| r_work (final): 0.4234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6476 moved from start: 0.6074 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= 0.140 Angle : 0.634 13.229 52227 Z= 0.316 Chirality : 0.043 0.306 5823 Planarity : 0.004 0.044 6309 Dihedral : 14.658 89.880 7312 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.25 % Allowed : 22.96 % Favored : 74.79 % 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: 0.19 (0.12), residues: 4560 helix: 1.15 (0.10), residues: 2496 sheet: -0.66 (0.22), residues: 498 loop : -1.23 (0.15), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 695 TYR 0.035 0.001 TYR F 691 PHE 0.037 0.001 PHE E 119 TRP 0.011 0.001 TRP F 141 HIS 0.009 0.001 HIS F 549 Details of bonding type rmsd covalent geometry : bond 0.00320 (38859) covalent geometry : angle 0.63442 (52227) hydrogen bonds : bond 0.03977 ( 2095) hydrogen bonds : angle 4.59885 ( 6177) Misc. bond : bond 0.00035 ( 13) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6194.03 seconds wall clock time: 108 minutes 34.24 seconds (6514.24 seconds total)