Starting phenix.real_space_refine on Fri Mar 6 03:56:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f57_31460/03_2026/7f57_31460_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f57_31460/03_2026/7f57_31460.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7f57_31460/03_2026/7f57_31460.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f57_31460/03_2026/7f57_31460.map" model { file = "/net/cci-nas-00/data/ceres_data/7f57_31460/03_2026/7f57_31460_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f57_31460/03_2026/7f57_31460_neut.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.088 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: 4 Type Number sf(0) Gaussians S 157 5.16 5 C 17847 2.51 5 N 4605 2.21 5 O 5254 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27863 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 6614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 835, 6614 Classifications: {'peptide': 835} Link IDs: {'PTRANS': 33, 'TRANS': 801} Chain: "B" Number of atoms: 6611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 835, 6611 Classifications: {'peptide': 835} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 33, 'TRANS': 801} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "C" Number of atoms: 6611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 835, 6611 Classifications: {'peptide': 835} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 33, 'TRANS': 801} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 6467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 818, 6467 Classifications: {'peptide': 818} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 33, 'TRANS': 784} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1172 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 10, 'TRANS': 134} Chain breaks: 1 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.19, per 1000 atoms: 0.19 Number of scatterers: 27863 At special positions: 0 Unit cell: (138.6, 139.92, 205.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 157 16.00 O 5254 8.00 N 4605 7.00 C 17847 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS A 347 " distance=2.38 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 347 " distance=2.05 Simple disulfide: pdb=" SG CYS C 96 " - pdb=" SG CYS C 347 " distance=2.03 Simple disulfide: pdb=" SG CYS D 96 " - pdb=" SG CYS D 347 " distance=2.24 Simple disulfide: pdb=" SG CYS E 45 " - pdb=" SG CYS E 72 " distance=2.37 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " NAG-ASN " NAG A1001 " - " ASN A 423 " " NAG A1002 " - " ASN A 430 " " NAG A1003 " - " ASN A 751 " " NAG A1004 " - " ASN A 412 " " NAG B1001 " - " ASN B 275 " " NAG B1002 " - " ASN B 412 " " NAG C1001 " - " ASN C 412 " " NAG C1002 " - " ASN C 430 " " NAG C1003 " - " ASN C 751 " " NAG D1001 " - " ASN D 275 " " NAG D1002 " - " ASN D 412 " " NAG F 1 " - " ASN A 275 " " NAG G 1 " - " ASN A 378 " " NAG H 1 " - " ASN B 378 " " NAG I 1 " - " ASN C 275 " " NAG J 1 " - " ASN C 378 " " NAG K 1 " - " ASN D 378 " Time building additional restraints: 2.38 Conformation dependent library (CDL) restraints added in 1.1 seconds 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6464 Finding SS restraints... Secondary structure from input PDB file: 121 helices and 41 sheets defined 45.6% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 51 through 67 Processing helix chain 'A' and resid 87 through 102 Processing helix chain 'A' and resid 111 through 126 removed outlier: 3.547A pdb=" N ALA A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 168 Processing helix chain 'A' and resid 179 through 185 removed outlier: 4.252A pdb=" N ILE A 183 " --> pdb=" O SER A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 190 Processing helix chain 'A' and resid 191 through 194 Processing helix chain 'A' and resid 210 through 222 removed outlier: 4.676A pdb=" N LEU A 214 " --> pdb=" O ASP A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 245 removed outlier: 3.837A pdb=" N GLN A 241 " --> pdb=" O GLY A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 273 removed outlier: 4.263A pdb=" N SER A 272 " --> pdb=" O PRO A 268 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY A 273 " --> pdb=" O TYR A 269 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 268 through 273' Processing helix chain 'A' and resid 286 through 302 removed outlier: 3.793A pdb=" N GLN A 302 " --> pdb=" O MET A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 310 removed outlier: 3.693A pdb=" N GLY A 310 " --> pdb=" O PRO A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 335 removed outlier: 3.594A pdb=" N VAL A 327 " --> pdb=" O MET A 323 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N HIS A 328 " --> pdb=" O TYR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 365 removed outlier: 3.843A pdb=" N PHE A 359 " --> pdb=" O PHE A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 475 removed outlier: 3.578A pdb=" N GLU A 469 " --> pdb=" O ASP A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 507 removed outlier: 3.501A pdb=" N ARG A 503 " --> pdb=" O ASN A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 527 Processing helix chain 'A' and resid 560 through 584 removed outlier: 3.557A pdb=" N TRP A 564 " --> pdb=" O SER A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 620 removed outlier: 3.791A pdb=" N GLY A 615 " --> pdb=" O SER A 611 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N MET A 620 " --> pdb=" O VAL A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 664 removed outlier: 3.578A pdb=" N ILE A 635 " --> pdb=" O LEU A 631 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL A 636 " --> pdb=" O SER A 632 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY A 637 " --> pdb=" O THR A 633 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 659 " --> pdb=" O LEU A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 677 removed outlier: 3.786A pdb=" N LEU A 674 " --> pdb=" O SER A 670 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS A 676 " --> pdb=" O ASP A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 697 Processing helix chain 'A' and resid 699 through 713 removed outlier: 3.517A pdb=" N PHE A 708 " --> pdb=" O LYS A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 731 Processing helix chain 'A' and resid 739 through 749 removed outlier: 3.790A pdb=" N GLN A 747 " --> pdb=" O GLU A 743 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG A 748 " --> pdb=" O PHE A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 788 removed outlier: 3.866A pdb=" N LYS A 777 " --> pdb=" O PRO A 773 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU A 787 " --> pdb=" O LEU A 783 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU A 788 " --> pdb=" O GLN A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 799 Processing helix chain 'A' and resid 816 through 821 Processing helix chain 'A' and resid 821 through 850 removed outlier: 3.730A pdb=" N ILE A 825 " --> pdb=" O GLY A 821 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY A 830 " --> pdb=" O VAL A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 867 removed outlier: 3.688A pdb=" N ARG A 866 " --> pdb=" O VAL A 862 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 67 Processing helix chain 'B' and resid 87 through 102 Processing helix chain 'B' and resid 111 through 126 removed outlier: 3.586A pdb=" N ALA B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 167 Processing helix chain 'B' and resid 179 through 185 removed outlier: 4.240A pdb=" N ILE B 183 " --> pdb=" O SER B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 190 Processing helix chain 'B' and resid 191 through 194 Processing helix chain 'B' and resid 208 through 210 No H-bonds generated for 'chain 'B' and resid 208 through 210' Processing helix chain 'B' and resid 211 through 222 Processing helix chain 'B' and resid 231 through 245 removed outlier: 3.657A pdb=" N GLY B 237 " --> pdb=" O GLU B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 264 Processing helix chain 'B' and resid 269 through 273 removed outlier: 4.142A pdb=" N GLY B 273 " --> pdb=" O ARG B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 301 removed outlier: 3.657A pdb=" N GLU B 299 " --> pdb=" O LYS B 295 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 335 removed outlier: 3.627A pdb=" N VAL B 327 " --> pdb=" O MET B 323 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N HIS B 328 " --> pdb=" O TYR B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 365 removed outlier: 3.512A pdb=" N GLU B 365 " --> pdb=" O SER B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 419 removed outlier: 3.583A pdb=" N GLY B 419 " --> pdb=" O SER B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 474 Processing helix chain 'B' and resid 500 through 506 removed outlier: 4.223A pdb=" N GLU B 504 " --> pdb=" O GLY B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 527 removed outlier: 4.076A pdb=" N VAL B 526 " --> pdb=" O VAL B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 557 removed outlier: 3.825A pdb=" N PHE B 555 " --> pdb=" O GLY B 551 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LEU B 556 " --> pdb=" O VAL B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 584 removed outlier: 4.088A pdb=" N TRP B 564 " --> pdb=" O SER B 560 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N MET B 565 " --> pdb=" O PRO B 561 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL B 580 " --> pdb=" O CYS B 576 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE B 581 " --> pdb=" O VAL B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 620 removed outlier: 3.804A pdb=" N LEU B 619 " --> pdb=" O GLY B 615 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N MET B 620 " --> pdb=" O VAL B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 662 removed outlier: 4.554A pdb=" N VAL B 636 " --> pdb=" O SER B 632 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY B 637 " --> pdb=" O THR B 633 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR B 644 " --> pdb=" O TRP B 640 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE B 646 " --> pdb=" O PHE B 642 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL B 661 " --> pdb=" O ALA B 657 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU B 662 " --> pdb=" O PHE B 658 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 677 removed outlier: 3.975A pdb=" N GLN B 677 " --> pdb=" O ASP B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 695 Processing helix chain 'B' and resid 701 through 712 Processing helix chain 'B' and resid 720 through 731 removed outlier: 3.633A pdb=" N GLY B 724 " --> pdb=" O SER B 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 747 removed outlier: 3.905A pdb=" N PHE B 744 " --> pdb=" O THR B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 773 through 788 removed outlier: 3.793A pdb=" N ALA B 781 " --> pdb=" O LYS B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 799 removed outlier: 3.692A pdb=" N TRP B 798 " --> pdb=" O MET B 794 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 821 removed outlier: 3.775A pdb=" N ILE B 820 " --> pdb=" O GLY B 816 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 849 removed outlier: 3.609A pdb=" N ILE B 825 " --> pdb=" O GLY B 821 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY B 830 " --> pdb=" O VAL B 826 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL B 832 " --> pdb=" O ALA B 828 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL B 835 " --> pdb=" O LEU B 831 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE B 836 " --> pdb=" O VAL B 832 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN B 849 " --> pdb=" O LYS B 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 854 through 867 Processing helix chain 'C' and resid 51 through 67 removed outlier: 3.557A pdb=" N LEU C 55 " --> pdb=" O GLY C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 102 Processing helix chain 'C' and resid 111 through 126 removed outlier: 4.594A pdb=" N ALA C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 167 Processing helix chain 'C' and resid 180 through 190 removed outlier: 5.246A pdb=" N GLU C 187 " --> pdb=" O ILE C 183 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N LEU C 188 " --> pdb=" O ARG C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 194 Processing helix chain 'C' and resid 211 through 221 Processing helix chain 'C' and resid 231 through 245 removed outlier: 4.028A pdb=" N GLN C 241 " --> pdb=" O GLY C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 301 Processing helix chain 'C' and resid 317 through 335 removed outlier: 3.961A pdb=" N MET C 323 " --> pdb=" O ASP C 319 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N HIS C 328 " --> pdb=" O TYR C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 365 removed outlier: 3.535A pdb=" N SER C 361 " --> pdb=" O THR C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 457 Processing helix chain 'C' and resid 462 through 475 Processing helix chain 'C' and resid 499 through 507 Processing helix chain 'C' and resid 520 through 525 Processing helix chain 'C' and resid 553 through 557 Processing helix chain 'C' and resid 562 through 583 removed outlier: 3.551A pdb=" N LEU C 569 " --> pdb=" O MET C 565 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU C 572 " --> pdb=" O LEU C 568 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL C 577 " --> pdb=" O GLY C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 620 Processing helix chain 'C' and resid 630 through 665 removed outlier: 3.566A pdb=" N PHE C 642 " --> pdb=" O GLY C 638 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU C 665 " --> pdb=" O VAL C 661 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 677 removed outlier: 3.965A pdb=" N GLN C 677 " --> pdb=" O ASP C 673 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 697 removed outlier: 4.168A pdb=" N PHE C 694 " --> pdb=" O THR C 690 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS C 696 " --> pdb=" O THR C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 713 removed outlier: 3.600A pdb=" N MET C 709 " --> pdb=" O MET C 705 " (cutoff:3.500A) Processing helix chain 'C' and resid 720 through 731 removed outlier: 3.745A pdb=" N GLN C 726 " --> pdb=" O GLU C 722 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG C 727 " --> pdb=" O GLU C 723 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL C 728 " --> pdb=" O GLY C 724 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 747 Processing helix chain 'C' and resid 773 through 789 removed outlier: 3.727A pdb=" N LYS C 777 " --> pdb=" O PRO C 773 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE C 780 " --> pdb=" O ASP C 776 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA C 781 " --> pdb=" O LYS C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 800 Processing helix chain 'C' and resid 801 through 803 No H-bonds generated for 'chain 'C' and resid 801 through 803' Processing helix chain 'C' and resid 824 through 848 removed outlier: 4.316A pdb=" N SER C 846 " --> pdb=" O PHE C 842 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS C 847 " --> pdb=" O LEU C 843 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS C 848 " --> pdb=" O TYR C 844 " (cutoff:3.500A) Processing helix chain 'C' and resid 856 through 867 removed outlier: 3.594A pdb=" N ARG C 866 " --> pdb=" O VAL C 862 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N MET C 867 " --> pdb=" O GLU C 863 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 67 removed outlier: 3.891A pdb=" N ASN D 65 " --> pdb=" O VAL D 61 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN D 67 " --> pdb=" O THR D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 102 Processing helix chain 'D' and resid 111 through 126 removed outlier: 3.882A pdb=" N ALA D 117 " --> pdb=" O SER D 113 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL D 118 " --> pdb=" O SER D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 167 removed outlier: 3.564A pdb=" N LEU D 156 " --> pdb=" O ASP D 152 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ARG D 158 " --> pdb=" O SER D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 190 removed outlier: 4.377A pdb=" N ILE D 183 " --> pdb=" O SER D 179 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N GLU D 187 " --> pdb=" O ILE D 183 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LEU D 188 " --> pdb=" O ARG D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 194 Processing helix chain 'D' and resid 208 through 210 No H-bonds generated for 'chain 'D' and resid 208 through 210' Processing helix chain 'D' and resid 211 through 222 Processing helix chain 'D' and resid 231 through 245 removed outlier: 3.900A pdb=" N GLY D 237 " --> pdb=" O GLU D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 301 removed outlier: 3.649A pdb=" N GLU D 299 " --> pdb=" O LYS D 295 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU D 301 " --> pdb=" O SER D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 335 removed outlier: 3.775A pdb=" N MET D 323 " --> pdb=" O ASP D 319 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL D 327 " --> pdb=" O MET D 323 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N HIS D 328 " --> pdb=" O TYR D 324 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA D 333 " --> pdb=" O VAL D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 365 removed outlier: 3.589A pdb=" N SER D 361 " --> pdb=" O THR D 357 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU D 362 " --> pdb=" O ARG D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 417 No H-bonds generated for 'chain 'D' and resid 415 through 417' Processing helix chain 'D' and resid 461 through 475 removed outlier: 3.586A pdb=" N LEU D 466 " --> pdb=" O TYR D 462 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU D 467 " --> pdb=" O CYS D 463 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE D 473 " --> pdb=" O GLU D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 500 through 507 removed outlier: 4.304A pdb=" N GLU D 504 " --> pdb=" O GLY D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 525 Processing helix chain 'D' and resid 560 through 584 removed outlier: 4.259A pdb=" N LEU D 568 " --> pdb=" O TRP D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 609 through 620 Processing helix chain 'D' and resid 630 through 665 removed outlier: 4.337A pdb=" N VAL D 636 " --> pdb=" O SER D 632 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY D 637 " --> pdb=" O THR D 633 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE D 647 " --> pdb=" O PHE D 643 " (cutoff:3.500A) Processing helix chain 'D' and resid 670 through 675 removed outlier: 3.691A pdb=" N LEU D 674 " --> pdb=" O SER D 670 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 695 Processing helix chain 'D' and resid 701 through 712 removed outlier: 4.095A pdb=" N MET D 705 " --> pdb=" O THR D 701 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 731 removed outlier: 3.502A pdb=" N GLN D 726 " --> pdb=" O GLU D 722 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG D 727 " --> pdb=" O GLU D 723 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER D 731 " --> pdb=" O ARG D 727 " (cutoff:3.500A) Processing helix chain 'D' and resid 739 through 749 removed outlier: 3.707A pdb=" N PHE D 744 " --> pdb=" O THR D 740 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLN D 747 " --> pdb=" O GLU D 743 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ARG D 748 " --> pdb=" O PHE D 744 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN D 749 " --> pdb=" O VAL D 745 " (cutoff:3.500A) Processing helix chain 'D' and resid 773 through 788 removed outlier: 3.818A pdb=" N LYS D 777 " --> pdb=" O PRO D 773 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ILE D 780 " --> pdb=" O ASP D 776 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA D 781 " --> pdb=" O LYS D 777 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU D 788 " --> pdb=" O GLN D 784 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 799 Processing helix chain 'D' and resid 816 through 821 Processing helix chain 'D' and resid 821 through 850 removed outlier: 3.911A pdb=" N ILE D 825 " --> pdb=" O GLY D 821 " (cutoff:3.500A) Processing helix chain 'E' and resid 348 through 372 removed outlier: 4.334A pdb=" N VAL E 368 " --> pdb=" O ILE E 364 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 75 through 80 removed outlier: 5.975A pdb=" N LEU A 36 " --> pdb=" O THR A 77 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ASP A 79 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N PHE A 38 " --> pdb=" O ASP A 79 " (cutoff:3.500A) removed outlier: 8.990A pdb=" N LEU A 107 " --> pdb=" O ARG A 37 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N GLY A 39 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE A 106 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 173 through 176 removed outlier: 6.815A pdb=" N VAL A 174 " --> pdb=" O ARG A 202 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 226 through 228 removed outlier: 4.353A pdb=" N PHE A 279 " --> pdb=" O PHE A 256 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N MET A 276 " --> pdb=" O LEU A 394 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 368 through 370 removed outlier: 3.836A pdb=" N TRP A 368 " --> pdb=" O ILE A 375 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 432 through 437 Processing sheet with id=AA6, first strand: chain 'A' and resid 445 through 446 Processing sheet with id=AA7, first strand: chain 'A' and resid 528 through 529 Processing sheet with id=AA8, first strand: chain 'A' and resid 534 through 536 removed outlier: 4.158A pdb=" N MET A 534 " --> pdb=" O TYR A 764 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 736 through 738 removed outlier: 3.973A pdb=" N ILE A 540 " --> pdb=" O ILE A 755 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 35 through 38 removed outlier: 6.116A pdb=" N LEU B 36 " --> pdb=" O THR B 77 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 41 through 43 Processing sheet with id=AB3, first strand: chain 'B' and resid 106 through 107 removed outlier: 6.173A pdb=" N ILE B 106 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 199 through 203 removed outlier: 6.692A pdb=" N VAL B 172 " --> pdb=" O LYS B 200 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N ARG B 202 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N VAL B 174 " --> pdb=" O ARG B 202 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL B 226 " --> pdb=" O ILE B 255 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 369 through 370 Processing sheet with id=AB6, first strand: chain 'B' and resid 389 through 395 removed outlier: 3.734A pdb=" N GLY B 403 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N SER B 393 " --> pdb=" O LYS B 401 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N LYS B 401 " --> pdb=" O SER B 393 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LYS B 395 " --> pdb=" O LEU B 399 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N LEU B 399 " --> pdb=" O LYS B 395 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 445 through 446 Processing sheet with id=AB8, first strand: chain 'B' and resid 513 through 514 Processing sheet with id=AB9, first strand: chain 'B' and resid 534 through 535 removed outlier: 4.203A pdb=" N MET B 534 " --> pdb=" O TYR B 764 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 735 through 738 Processing sheet with id=AC2, first strand: chain 'B' and resid 684 through 685 removed outlier: 6.879A pdb=" N ALA B 684 " --> pdb=" O VAL B 718 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 74 through 81 removed outlier: 5.025A pdb=" N HIS C 34 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N THR C 77 " --> pdb=" O HIS C 34 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N LEU C 36 " --> pdb=" O THR C 77 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ASP C 79 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N PHE C 38 " --> pdb=" O ASP C 79 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N GLN C 81 " --> pdb=" O PHE C 38 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N GLY C 40 " --> pdb=" O GLN C 81 " (cutoff:3.500A) removed outlier: 8.631A pdb=" N LEU C 107 " --> pdb=" O ARG C 37 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N GLY C 39 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ILE C 106 " --> pdb=" O ILE C 130 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 198 through 203 removed outlier: 3.647A pdb=" N LYS C 200 " --> pdb=" O VAL C 172 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL C 174 " --> pdb=" O LYS C 200 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR C 176 " --> pdb=" O ARG C 202 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL C 226 " --> pdb=" O ILE C 255 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 277 through 280 removed outlier: 3.956A pdb=" N GLY C 403 " --> pdb=" O VAL C 391 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N SER C 393 " --> pdb=" O LYS C 401 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N LYS C 401 " --> pdb=" O SER C 393 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 368 through 370 removed outlier: 4.017A pdb=" N TRP C 368 " --> pdb=" O ILE C 375 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 478 through 482 removed outlier: 3.955A pdb=" N LEU C 512 " --> pdb=" O ILE C 434 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 444 through 446 Processing sheet with id=AC9, first strand: chain 'C' and resid 528 through 529 Processing sheet with id=AD1, first strand: chain 'C' and resid 534 through 536 removed outlier: 3.662A pdb=" N MET C 534 " --> pdb=" O TYR C 764 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR C 764 " --> pdb=" O MET C 534 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 737 through 738 removed outlier: 4.103A pdb=" N ILE C 540 " --> pdb=" O ILE C 755 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE C 755 " --> pdb=" O ILE C 540 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR C 542 " --> pdb=" O THR C 753 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 35 through 38 removed outlier: 5.909A pdb=" N LEU D 36 " --> pdb=" O THR D 77 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'D' and resid 41 through 43 removed outlier: 5.954A pdb=" N PHE D 42 " --> pdb=" O ILE D 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'D' and resid 106 through 107 removed outlier: 6.409A pdb=" N ILE D 106 " --> pdb=" O ILE D 130 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 200 through 203 removed outlier: 6.125A pdb=" N VAL D 174 " --> pdb=" O ARG D 202 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N THR D 173 " --> pdb=" O ILE D 227 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL D 226 " --> pdb=" O HIS D 253 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N TYR D 254 " --> pdb=" O THR D 277 " (cutoff:3.500A) removed outlier: 8.707A pdb=" N PHE D 279 " --> pdb=" O TYR D 254 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N PHE D 256 " --> pdb=" O PHE D 279 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY D 403 " --> pdb=" O VAL D 391 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N SER D 393 " --> pdb=" O LYS D 401 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N LYS D 401 " --> pdb=" O SER D 393 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LYS D 395 " --> pdb=" O LEU D 399 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N LEU D 399 " --> pdb=" O LYS D 395 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP D 406 " --> pdb=" O GLY D 410 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 369 through 370 Processing sheet with id=AD8, first strand: chain 'D' and resid 433 through 435 removed outlier: 6.105A pdb=" N GLU D 479 " --> pdb=" O VAL D 435 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'D' and resid 445 through 446 Processing sheet with id=AE1, first strand: chain 'D' and resid 528 through 529 Processing sheet with id=AE2, first strand: chain 'D' and resid 717 through 718 removed outlier: 6.737A pdb=" N ALA D 684 " --> pdb=" O VAL D 718 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLY D 683 " --> pdb=" O LEU D 736 " (cutoff:3.500A) removed outlier: 9.185A pdb=" N GLU D 738 " --> pdb=" O GLY D 683 " (cutoff:3.500A) removed outlier: 10.727A pdb=" N VAL D 685 " --> pdb=" O GLU D 738 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N MET D 737 " --> pdb=" O SER D 539 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER D 539 " --> pdb=" O MET D 737 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 717 through 718 removed outlier: 6.737A pdb=" N ALA D 684 " --> pdb=" O VAL D 718 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLY D 683 " --> pdb=" O LEU D 736 " (cutoff:3.500A) removed outlier: 9.185A pdb=" N GLU D 738 " --> pdb=" O GLY D 683 " (cutoff:3.500A) removed outlier: 10.727A pdb=" N VAL D 685 " --> pdb=" O GLU D 738 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N MET D 737 " --> pdb=" O SER D 539 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER D 539 " --> pdb=" O MET D 737 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N MET D 534 " --> pdb=" O TYR D 764 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 54 through 58 removed outlier: 3.740A pdb=" N ILE E 84 " --> pdb=" O SER E 132 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER E 132 " --> pdb=" O ILE E 84 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU E 86 " --> pdb=" O ILE E 130 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ILE E 130 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 72 through 77 removed outlier: 3.607A pdb=" N PHE E 141 " --> pdb=" O CYS E 72 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N MET E 137 " --> pdb=" O LEU E 76 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS E 140 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASP E 119 " --> pdb=" O VAL E 107 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ASP E 109 " --> pdb=" O LEU E 117 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N LEU E 117 " --> pdb=" O ASP E 109 " (cutoff:3.500A) 1120 hydrogen bonds defined for protein. 3246 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: 5.28 Time building geometry restraints manager: 3.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5031 1.32 - 1.45: 7347 1.45 - 1.57: 15843 1.57 - 1.69: 2 1.69 - 1.82: 267 Bond restraints: 28490 Sorted by residual: bond pdb=" CA ASP D 260 " pdb=" C ASP D 260 " ideal model delta sigma weight residual 1.526 1.455 0.071 1.28e-02 6.10e+03 3.11e+01 bond pdb=" CA SER C 272 " pdb=" CB SER C 272 " ideal model delta sigma weight residual 1.532 1.471 0.060 1.74e-02 3.30e+03 1.21e+01 bond pdb=" N ILE A 755 " pdb=" CA ILE A 755 " ideal model delta sigma weight residual 1.456 1.495 -0.040 1.23e-02 6.61e+03 1.04e+01 bond pdb=" N MET A 340 " pdb=" CA MET A 340 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.23e-02 6.61e+03 1.02e+01 bond pdb=" N MET C 276 " pdb=" CA MET C 276 " ideal model delta sigma weight residual 1.456 1.497 -0.040 1.27e-02 6.20e+03 1.01e+01 ... (remaining 28485 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 37635 2.78 - 5.55: 852 5.55 - 8.33: 79 8.33 - 11.10: 11 11.10 - 13.88: 3 Bond angle restraints: 38580 Sorted by residual: angle pdb=" C THR A 520 " pdb=" CA THR A 520 " pdb=" CB THR A 520 " ideal model delta sigma weight residual 116.54 102.66 13.88 1.15e+00 7.56e-01 1.46e+02 angle pdb=" C HIS B 350 " pdb=" CA HIS B 350 " pdb=" CB HIS B 350 " ideal model delta sigma weight residual 111.89 100.48 11.41 1.42e+00 4.96e-01 6.46e+01 angle pdb=" N ALA A 211 " pdb=" CA ALA A 211 " pdb=" C ALA A 211 " ideal model delta sigma weight residual 113.19 103.72 9.47 1.19e+00 7.06e-01 6.33e+01 angle pdb=" N ILE A 519 " pdb=" CA ILE A 519 " pdb=" C ILE A 519 " ideal model delta sigma weight residual 110.62 102.71 7.91 1.02e+00 9.61e-01 6.01e+01 angle pdb=" CA TYR A 521 " pdb=" C TYR A 521 " pdb=" O TYR A 521 " ideal model delta sigma weight residual 121.38 113.98 7.40 1.06e+00 8.90e-01 4.88e+01 ... (remaining 38575 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.32: 16217 21.32 - 42.64: 976 42.64 - 63.97: 113 63.97 - 85.29: 63 85.29 - 106.61: 27 Dihedral angle restraints: 17396 sinusoidal: 7343 harmonic: 10053 Sorted by residual: dihedral pdb=" CB CYS A 96 " pdb=" SG CYS A 96 " pdb=" SG CYS A 347 " pdb=" CB CYS A 347 " ideal model delta sinusoidal sigma weight residual 93.00 159.31 -66.31 1 1.00e+01 1.00e-02 5.74e+01 dihedral pdb=" CB CYS E 45 " pdb=" SG CYS E 45 " pdb=" SG CYS E 72 " pdb=" CB CYS E 72 " ideal model delta sinusoidal sigma weight residual 93.00 36.77 56.23 1 1.00e+01 1.00e-02 4.26e+01 dihedral pdb=" CA SER C 427 " pdb=" C SER C 427 " pdb=" N LEU C 428 " pdb=" CA LEU C 428 " ideal model delta harmonic sigma weight residual 180.00 152.02 27.98 0 5.00e+00 4.00e-02 3.13e+01 ... (remaining 17393 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.934: 4378 0.934 - 1.868: 1 1.868 - 2.802: 0 2.802 - 3.736: 0 3.736 - 4.670: 1 Chirality restraints: 4380 Sorted by residual: chirality pdb=" C1 BMA I 3 " pdb=" O4 NAG I 2 " pdb=" C2 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.40 2.27 -4.67 2.00e-02 2.50e+03 5.45e+04 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-02 2.50e+03 6.71e+02 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.52e+02 ... (remaining 4377 not shown) Planarity restraints: 4878 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1002 " -0.352 2.00e-02 2.50e+03 3.02e-01 1.14e+03 pdb=" C7 NAG A1002 " 0.087 2.00e-02 2.50e+03 pdb=" C8 NAG A1002 " -0.147 2.00e-02 2.50e+03 pdb=" N2 NAG A1002 " 0.537 2.00e-02 2.50e+03 pdb=" O7 NAG A1002 " -0.124 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 1 " 0.346 2.00e-02 2.50e+03 2.99e-01 1.11e+03 pdb=" C7 NAG F 1 " -0.080 2.00e-02 2.50e+03 pdb=" C8 NAG F 1 " 0.123 2.00e-02 2.50e+03 pdb=" N2 NAG F 1 " -0.533 2.00e-02 2.50e+03 pdb=" O7 NAG F 1 " 0.145 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 1 " 0.342 2.00e-02 2.50e+03 2.95e-01 1.09e+03 pdb=" C7 NAG G 1 " -0.079 2.00e-02 2.50e+03 pdb=" C8 NAG G 1 " 0.119 2.00e-02 2.50e+03 pdb=" N2 NAG G 1 " -0.527 2.00e-02 2.50e+03 pdb=" O7 NAG G 1 " 0.145 2.00e-02 2.50e+03 ... (remaining 4875 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 449 2.63 - 3.20: 27952 3.20 - 3.76: 42355 3.76 - 4.33: 57673 4.33 - 4.90: 90170 Nonbonded interactions: 218599 Sorted by model distance: nonbonded pdb=" O LEU D 482 " pdb=" CD1 LEU D 482 " model vdw 2.061 3.460 nonbonded pdb=" OD1 ASP B 177 " pdb=" N ASP B 178 " model vdw 2.151 3.120 nonbonded pdb=" O ASN A 819 " pdb=" OD1 ASN A 819 " model vdw 2.182 3.040 nonbonded pdb=" O ASP D 87 " pdb=" OG SER D 114 " model vdw 2.195 3.040 nonbonded pdb=" ND2 ASN B 123 " pdb=" OD1 ASP B 143 " model vdw 2.197 3.120 ... (remaining 218594 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 33 through 42 or (resid 43 and (name N or name CA or name \ C or name O or name CB )) or resid 44 through 142 or (resid 143 and (name N or n \ ame CA or name C or name O or name CB )) or resid 144 through 663 or (resid 664 \ and (name N or name CA or name C or name O or name CB )) or resid 665 through 85 \ 0)) selection = (chain 'B' and (resid 33 through 42 or (resid 43 and (name N or name CA or name \ C or name O or name CB )) or resid 44 through 142 or (resid 143 and (name N or n \ ame CA or name C or name O or name CB )) or resid 144 through 850)) selection = (chain 'C' and (resid 33 through 42 or (resid 43 and (name N or name CA or name \ C or name O or name CB )) or resid 44 through 663 or (resid 664 and (name N or n \ ame CA or name C or name O or name CB )) or resid 665 through 850)) selection = (chain 'D' and (resid 33 through 142 or (resid 143 and (name N or name CA or nam \ e C or name O or name CB )) or resid 144 through 850)) } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } 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: 1.080 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: 0.040 Extract box with map and model: 0.400 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 22.700 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.060 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 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 : 0.008 0.354 28524 Z= 0.418 Angle : 1.023 13.878 38677 Z= 0.616 Chirality : 0.096 4.670 4380 Planarity : 0.015 0.302 4861 Dihedral : 14.798 106.609 10917 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 0.60 % Allowed : 1.49 % Favored : 97.91 % Cbeta Deviations : 0.09 % 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: -2.23 (0.14), residues: 3456 helix: -0.20 (0.14), residues: 1361 sheet: -2.84 (0.24), residues: 401 loop : -2.22 (0.14), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 503 TYR 0.049 0.002 TYR C 44 PHE 0.022 0.002 PHE D 359 TRP 0.023 0.002 TRP D 353 HIS 0.017 0.002 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00739 (28490) covalent geometry : angle 0.99185 (38580) SS BOND : bond 0.23841 ( 5) SS BOND : angle 6.29269 ( 10) hydrogen bonds : bond 0.25338 ( 1118) hydrogen bonds : angle 8.53441 ( 3246) link_BETA1-4 : bond 0.00473 ( 12) link_BETA1-4 : angle 3.48134 ( 36) link_NAG-ASN : bond 0.01252 ( 17) link_NAG-ASN : angle 5.77721 ( 51) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 3016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 242 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 454 TYR cc_start: 0.6149 (m-80) cc_final: 0.5913 (m-80) REVERT: A 836 PHE cc_start: 0.8820 (t80) cc_final: 0.8289 (t80) REVERT: A 861 MET cc_start: 0.4757 (ppp) cc_final: 0.4506 (ppp) REVERT: B 501 MET cc_start: 0.7635 (mmm) cc_final: 0.7089 (mmm) REVERT: B 794 MET cc_start: 0.9164 (mtm) cc_final: 0.8961 (mtp) REVERT: C 709 MET cc_start: 0.7937 (mpp) cc_final: 0.7590 (mpp) REVERT: D 364 LYS cc_start: 0.9236 (OUTLIER) cc_final: 0.9008 (ttmt) REVERT: D 367 HIS cc_start: 0.8355 (OUTLIER) cc_final: 0.8142 (m-70) REVERT: D 415 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7497 (tp30) REVERT: D 590 TYR cc_start: 0.7889 (t80) cc_final: 0.7332 (t80) REVERT: D 705 MET cc_start: 0.7852 (mpp) cc_final: 0.6713 (mpp) REVERT: D 770 MET cc_start: 0.8191 (mmp) cc_final: 0.7949 (mmp) REVERT: D 793 MET cc_start: 0.8507 (mpp) cc_final: 0.8026 (mpp) REVERT: D 804 CYS cc_start: 0.7287 (t) cc_final: 0.6908 (p) REVERT: D 836 PHE cc_start: 0.8687 (m-80) cc_final: 0.8445 (m-80) outliers start: 18 outliers final: 2 residues processed: 259 average time/residue: 0.1643 time to fit residues: 70.2097 Evaluate side-chains 189 residues out of total 3016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 184 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain D residue 364 LYS Chi-restraints excluded: chain D residue 367 HIS Chi-restraints excluded: chain D residue 415 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 HIS ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 GLN ** B 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 ASN B 367 HIS B 417 GLN B 549 ASN ** B 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 754 GLN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 621 GLN ** D 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 747 GLN D 802 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.095936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.068376 restraints weight = 106877.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.069051 restraints weight = 65331.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.069434 restraints weight = 44784.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.069744 restraints weight = 42562.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.069811 restraints weight = 38573.189| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 28524 Z= 0.200 Angle : 0.762 13.593 38677 Z= 0.376 Chirality : 0.046 0.309 4380 Planarity : 0.005 0.067 4861 Dihedral : 9.710 73.076 4355 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 0.90 % Allowed : 8.20 % Favored : 90.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.64 (0.14), residues: 3456 helix: 0.53 (0.14), residues: 1414 sheet: -2.68 (0.24), residues: 409 loop : -2.14 (0.15), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 775 TYR 0.018 0.002 TYR C 44 PHE 0.023 0.002 PHE D 584 TRP 0.018 0.002 TRP D 798 HIS 0.011 0.002 HIS B 111 Details of bonding type rmsd covalent geometry : bond 0.00448 (28490) covalent geometry : angle 0.74173 (38580) SS BOND : bond 0.00735 ( 5) SS BOND : angle 1.19855 ( 10) hydrogen bonds : bond 0.06217 ( 1118) hydrogen bonds : angle 5.92328 ( 3246) link_BETA1-4 : bond 0.00966 ( 12) link_BETA1-4 : angle 3.97128 ( 36) link_NAG-ASN : bond 0.00472 ( 17) link_NAG-ASN : angle 3.56234 ( 51) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 3016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 206 time to evaluate : 1.049 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 627 MET cc_start: 0.7926 (mpp) cc_final: 0.7657 (mpp) REVERT: A 641 TRP cc_start: 0.8638 (m-10) cc_final: 0.8299 (m-10) REVERT: A 836 PHE cc_start: 0.8815 (t80) cc_final: 0.8406 (t80) REVERT: B 709 MET cc_start: 0.8176 (OUTLIER) cc_final: 0.7664 (ppp) REVERT: B 794 MET cc_start: 0.9308 (mtm) cc_final: 0.8991 (mtp) REVERT: C 301 LEU cc_start: 0.8491 (tt) cc_final: 0.8244 (mt) REVERT: C 576 CYS cc_start: 0.8974 (m) cc_final: 0.8727 (m) REVERT: C 620 MET cc_start: 0.9144 (mmm) cc_final: 0.8077 (mmm) REVERT: D 565 MET cc_start: 0.8638 (mtp) cc_final: 0.8143 (mtm) REVERT: D 590 TYR cc_start: 0.8003 (t80) cc_final: 0.7440 (t80) REVERT: D 691 MET cc_start: 0.8498 (mtt) cc_final: 0.8055 (mtt) REVERT: D 804 CYS cc_start: 0.7443 (t) cc_final: 0.7026 (p) outliers start: 27 outliers final: 18 residues processed: 222 average time/residue: 0.1469 time to fit residues: 55.9189 Evaluate side-chains 205 residues out of total 3016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 186 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 521 TYR Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 693 PHE Chi-restraints excluded: chain B residue 709 MET Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 576 CYS Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain E residue 119 ASP Chi-restraints excluded: chain E residue 129 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 162 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 186 optimal weight: 6.9990 chunk 251 optimal weight: 0.9980 chunk 147 optimal weight: 10.0000 chunk 191 optimal weight: 10.0000 chunk 308 optimal weight: 0.4980 chunk 200 optimal weight: 0.0670 chunk 173 optimal weight: 8.9990 chunk 232 optimal weight: 8.9990 chunk 271 optimal weight: 0.8980 overall best weight: 1.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 456 ASN ** D 654 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 = 0.3943 r_free = 0.3943 target = 0.096886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.069941 restraints weight = 106891.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.070065 restraints weight = 65455.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.070244 restraints weight = 49830.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.070549 restraints weight = 46131.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.070798 restraints weight = 40789.199| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 28524 Z= 0.147 Angle : 0.665 10.947 38677 Z= 0.326 Chirality : 0.043 0.226 4380 Planarity : 0.004 0.051 4861 Dihedral : 7.427 54.018 4346 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.29 % Allowed : 10.52 % Favored : 88.18 % 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: -1.28 (0.14), residues: 3456 helix: 0.86 (0.14), residues: 1422 sheet: -2.49 (0.24), residues: 403 loop : -2.01 (0.15), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 300 TYR 0.030 0.001 TYR A 454 PHE 0.022 0.001 PHE D 735 TRP 0.015 0.001 TRP C 613 HIS 0.010 0.001 HIS B 111 Details of bonding type rmsd covalent geometry : bond 0.00332 (28490) covalent geometry : angle 0.65047 (38580) SS BOND : bond 0.00132 ( 5) SS BOND : angle 0.74277 ( 10) hydrogen bonds : bond 0.04569 ( 1118) hydrogen bonds : angle 5.24907 ( 3246) link_BETA1-4 : bond 0.00784 ( 12) link_BETA1-4 : angle 3.14785 ( 36) link_NAG-ASN : bond 0.00324 ( 17) link_NAG-ASN : angle 2.81055 ( 51) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 3016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 212 time to evaluate : 1.003 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 627 MET cc_start: 0.7997 (mpp) cc_final: 0.7680 (mpp) REVERT: A 641 TRP cc_start: 0.8351 (m-10) cc_final: 0.7982 (m-10) REVERT: A 691 MET cc_start: 0.8303 (ttp) cc_final: 0.8086 (ptt) REVERT: A 836 PHE cc_start: 0.8768 (t80) cc_final: 0.8401 (t80) REVERT: B 578 LEU cc_start: 0.8447 (tt) cc_final: 0.8207 (tp) REVERT: B 635 ILE cc_start: 0.9235 (OUTLIER) cc_final: 0.8956 (tp) REVERT: B 691 MET cc_start: 0.8137 (ptt) cc_final: 0.7409 (ptt) REVERT: B 709 MET cc_start: 0.8053 (ptp) cc_final: 0.7617 (ppp) REVERT: C 301 LEU cc_start: 0.8533 (tt) cc_final: 0.8279 (mt) REVERT: C 413 MET cc_start: 0.8130 (mtp) cc_final: 0.7832 (mtp) REVERT: C 565 MET cc_start: 0.7805 (mmt) cc_final: 0.7589 (mmp) REVERT: C 742 ILE cc_start: 0.9334 (OUTLIER) cc_final: 0.8871 (mm) REVERT: D 565 MET cc_start: 0.8478 (mtp) cc_final: 0.7992 (mtm) REVERT: D 590 TYR cc_start: 0.8087 (t80) cc_final: 0.7695 (t80) REVERT: D 804 CYS cc_start: 0.7723 (t) cc_final: 0.7131 (p) outliers start: 39 outliers final: 20 residues processed: 238 average time/residue: 0.1534 time to fit residues: 61.9450 Evaluate side-chains 207 residues out of total 3016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 185 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 693 PHE Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 576 CYS Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain E residue 119 ASP Chi-restraints excluded: chain E residue 129 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 38 optimal weight: 9.9990 chunk 52 optimal weight: 10.0000 chunk 290 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 236 optimal weight: 7.9990 chunk 152 optimal weight: 6.9990 chunk 15 optimal weight: 0.6980 chunk 126 optimal weight: 9.9990 chunk 327 optimal weight: 6.9990 chunk 217 optimal weight: 10.0000 chunk 127 optimal weight: 6.9990 overall best weight: 5.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 430 ASN ** B 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 GLN ** C 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 654 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 = 0.3879 r_free = 0.3879 target = 0.093733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.066491 restraints weight = 107473.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.066588 restraints weight = 59373.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.066408 restraints weight = 48745.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.066750 restraints weight = 48717.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.067251 restraints weight = 41541.892| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 28524 Z= 0.313 Angle : 0.790 12.571 38677 Z= 0.392 Chirality : 0.046 0.311 4380 Planarity : 0.005 0.047 4861 Dihedral : 6.891 51.645 4346 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 2.12 % Allowed : 13.41 % Favored : 84.46 % 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: -1.57 (0.14), residues: 3456 helix: 0.65 (0.14), residues: 1430 sheet: -2.91 (0.23), residues: 415 loop : -2.12 (0.15), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 158 TYR 0.023 0.002 TYR B 682 PHE 0.021 0.002 PHE A 315 TRP 0.018 0.002 TRP C 353 HIS 0.016 0.002 HIS B 136 Details of bonding type rmsd covalent geometry : bond 0.00710 (28490) covalent geometry : angle 0.77756 (38580) SS BOND : bond 0.00329 ( 5) SS BOND : angle 1.04392 ( 10) hydrogen bonds : bond 0.04934 ( 1118) hydrogen bonds : angle 5.50693 ( 3246) link_BETA1-4 : bond 0.00750 ( 12) link_BETA1-4 : angle 3.05701 ( 36) link_NAG-ASN : bond 0.00679 ( 17) link_NAG-ASN : angle 3.09547 ( 51) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 3016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 186 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 619 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8888 (tp) REVERT: A 641 TRP cc_start: 0.8464 (m-10) cc_final: 0.8095 (m-10) REVERT: A 691 MET cc_start: 0.8468 (ttp) cc_final: 0.7998 (ptt) REVERT: A 793 MET cc_start: 0.9394 (mpp) cc_final: 0.9153 (mpp) REVERT: A 836 PHE cc_start: 0.8783 (t80) cc_final: 0.8391 (t80) REVERT: B 578 LEU cc_start: 0.8337 (tt) cc_final: 0.8017 (tp) REVERT: B 691 MET cc_start: 0.8058 (ptt) cc_final: 0.7476 (ptt) REVERT: B 705 MET cc_start: 0.8657 (tpp) cc_final: 0.8442 (tpt) REVERT: B 709 MET cc_start: 0.8104 (ptp) cc_final: 0.7826 (ptm) REVERT: B 793 MET cc_start: 0.9353 (mmm) cc_final: 0.9016 (ptt) REVERT: C 301 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8271 (mt) REVERT: C 316 MET cc_start: 0.8049 (ttt) cc_final: 0.7825 (ttt) REVERT: C 413 MET cc_start: 0.8341 (mtp) cc_final: 0.8094 (mtp) REVERT: C 565 MET cc_start: 0.7683 (mmt) cc_final: 0.7470 (mmp) REVERT: D 565 MET cc_start: 0.8474 (mtp) cc_final: 0.7974 (mtm) REVERT: D 590 TYR cc_start: 0.8045 (t80) cc_final: 0.7653 (t80) outliers start: 64 outliers final: 35 residues processed: 237 average time/residue: 0.1523 time to fit residues: 61.7469 Evaluate side-chains 218 residues out of total 3016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 181 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain A residue 576 CYS Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 652 THR Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 549 ASN Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 652 THR Chi-restraints excluded: chain B residue 693 PHE Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain D residue 103 VAL Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 487 LYS Chi-restraints excluded: chain D residue 576 CYS Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 729 LEU Chi-restraints excluded: chain E residue 119 ASP Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 361 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 133 optimal weight: 20.0000 chunk 18 optimal weight: 3.9990 chunk 251 optimal weight: 1.9990 chunk 339 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 295 optimal weight: 0.1980 chunk 59 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 78 optimal weight: 0.9990 chunk 321 optimal weight: 0.9980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 ASN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 HIS ** D 654 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 = 0.3933 r_free = 0.3933 target = 0.096330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.069919 restraints weight = 105771.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.070525 restraints weight = 55770.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.070711 restraints weight = 42874.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.071030 restraints weight = 41118.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.071252 restraints weight = 36807.597| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 28524 Z= 0.123 Angle : 0.630 10.440 38677 Z= 0.311 Chirality : 0.042 0.248 4380 Planarity : 0.004 0.051 4861 Dihedral : 6.279 53.802 4345 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.53 % Allowed : 14.87 % Favored : 83.60 % 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: -1.11 (0.14), residues: 3456 helix: 1.06 (0.14), residues: 1433 sheet: -2.52 (0.24), residues: 411 loop : -1.95 (0.15), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 50 TYR 0.024 0.001 TYR B 682 PHE 0.011 0.001 PHE D 735 TRP 0.013 0.001 TRP C 613 HIS 0.006 0.001 HIS B 111 Details of bonding type rmsd covalent geometry : bond 0.00275 (28490) covalent geometry : angle 0.61910 (38580) SS BOND : bond 0.00107 ( 5) SS BOND : angle 0.59986 ( 10) hydrogen bonds : bond 0.03976 ( 1118) hydrogen bonds : angle 4.94024 ( 3246) link_BETA1-4 : bond 0.00602 ( 12) link_BETA1-4 : angle 2.60111 ( 36) link_NAG-ASN : bond 0.00307 ( 17) link_NAG-ASN : angle 2.52241 ( 51) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 3016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 197 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 641 TRP cc_start: 0.8251 (m-10) cc_final: 0.7937 (m-10) REVERT: A 691 MET cc_start: 0.8469 (ttp) cc_final: 0.7977 (ptt) REVERT: A 836 PHE cc_start: 0.8778 (t80) cc_final: 0.8406 (t80) REVERT: B 578 LEU cc_start: 0.8313 (tt) cc_final: 0.8011 (tp) REVERT: B 629 LYS cc_start: 0.7366 (ptpt) cc_final: 0.6935 (tptm) REVERT: B 691 MET cc_start: 0.8298 (ptt) cc_final: 0.7694 (ptt) REVERT: B 793 MET cc_start: 0.9343 (mmm) cc_final: 0.9074 (ptt) REVERT: C 301 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8301 (mt) REVERT: C 800 ARG cc_start: 0.7688 (mmp-170) cc_final: 0.7278 (mmp80) REVERT: D 565 MET cc_start: 0.8350 (mtp) cc_final: 0.7876 (mtm) REVERT: D 590 TYR cc_start: 0.8036 (t80) cc_final: 0.7665 (t80) outliers start: 46 outliers final: 27 residues processed: 229 average time/residue: 0.1503 time to fit residues: 59.3114 Evaluate side-chains 212 residues out of total 3016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 184 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 693 PHE Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 685 VAL Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 576 CYS Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 729 LEU Chi-restraints excluded: chain E residue 102 PHE Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 361 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 111 optimal weight: 0.9990 chunk 197 optimal weight: 1.9990 chunk 260 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 125 optimal weight: 30.0000 chunk 191 optimal weight: 9.9990 chunk 295 optimal weight: 6.9990 chunk 100 optimal weight: 1.9990 chunk 325 optimal weight: 20.0000 chunk 269 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 GLN ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 654 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 = 0.3934 r_free = 0.3934 target = 0.096537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.069478 restraints weight = 106740.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.069602 restraints weight = 64290.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.069881 restraints weight = 49488.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.070428 restraints weight = 44840.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.070580 restraints weight = 39128.291| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 28524 Z= 0.129 Angle : 0.620 10.984 38677 Z= 0.304 Chirality : 0.041 0.298 4380 Planarity : 0.004 0.050 4861 Dihedral : 6.018 54.159 4345 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.53 % Favored : 94.44 % Rotamer: Outliers : 1.86 % Allowed : 15.44 % Favored : 82.70 % 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: -0.92 (0.15), residues: 3456 helix: 1.23 (0.14), residues: 1434 sheet: -2.31 (0.24), residues: 413 loop : -1.90 (0.15), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 503 TYR 0.026 0.001 TYR B 682 PHE 0.014 0.001 PHE C 579 TRP 0.015 0.001 TRP C 613 HIS 0.007 0.001 HIS B 111 Details of bonding type rmsd covalent geometry : bond 0.00294 (28490) covalent geometry : angle 0.60946 (38580) SS BOND : bond 0.00142 ( 5) SS BOND : angle 0.63746 ( 10) hydrogen bonds : bond 0.03848 ( 1118) hydrogen bonds : angle 4.78078 ( 3246) link_BETA1-4 : bond 0.00633 ( 12) link_BETA1-4 : angle 2.43993 ( 36) link_NAG-ASN : bond 0.00285 ( 17) link_NAG-ASN : angle 2.41326 ( 51) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 3016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 194 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 641 TRP cc_start: 0.8239 (m-10) cc_final: 0.7538 (m-10) REVERT: A 836 PHE cc_start: 0.8790 (t80) cc_final: 0.8451 (t80) REVERT: B 360 MET cc_start: 0.8587 (tpt) cc_final: 0.8302 (tpt) REVERT: B 578 LEU cc_start: 0.8326 (tt) cc_final: 0.8037 (tp) REVERT: B 629 LYS cc_start: 0.7373 (ptpt) cc_final: 0.7000 (tptm) REVERT: B 691 MET cc_start: 0.8510 (ptt) cc_final: 0.7958 (ptt) REVERT: B 793 MET cc_start: 0.9391 (mmm) cc_final: 0.9152 (ptt) REVERT: C 184 ARG cc_start: 0.8938 (OUTLIER) cc_final: 0.8623 (ttp-110) REVERT: C 620 MET cc_start: 0.9205 (mmm) cc_final: 0.7203 (mmm) REVERT: C 742 ILE cc_start: 0.9383 (OUTLIER) cc_final: 0.8991 (mm) REVERT: C 794 MET cc_start: 0.9357 (mpp) cc_final: 0.9114 (mpp) REVERT: C 800 ARG cc_start: 0.7581 (mmp-170) cc_final: 0.7124 (mmp80) REVERT: D 360 MET cc_start: 0.8442 (tpp) cc_final: 0.8213 (tpp) REVERT: D 565 MET cc_start: 0.8396 (mtp) cc_final: 0.7969 (mtm) REVERT: D 590 TYR cc_start: 0.8094 (t80) cc_final: 0.7719 (t80) REVERT: D 705 MET cc_start: 0.7800 (mpp) cc_final: 0.6682 (mpp) REVERT: D 794 MET cc_start: 0.8449 (mtt) cc_final: 0.8219 (mmp) outliers start: 56 outliers final: 36 residues processed: 237 average time/residue: 0.1553 time to fit residues: 62.5054 Evaluate side-chains 225 residues out of total 3016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 187 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 693 PHE Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 184 ARG Chi-restraints excluded: chain C residue 209 LYS Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 350 HIS Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 559 LEU Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 685 VAL Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 576 CYS Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 729 LEU Chi-restraints excluded: chain E residue 102 PHE Chi-restraints excluded: chain E residue 114 PHE Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 361 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 337 optimal weight: 30.0000 chunk 144 optimal weight: 5.9990 chunk 288 optimal weight: 30.0000 chunk 82 optimal weight: 0.8980 chunk 41 optimal weight: 9.9990 chunk 214 optimal weight: 0.0970 chunk 85 optimal weight: 4.9990 chunk 38 optimal weight: 20.0000 chunk 101 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 314 optimal weight: 20.0000 overall best weight: 3.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 346 GLN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 654 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 = 0.3911 r_free = 0.3911 target = 0.095360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.068572 restraints weight = 106461.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.069073 restraints weight = 55999.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.068927 restraints weight = 44221.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.069321 restraints weight = 44524.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.069991 restraints weight = 38386.273| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 28524 Z= 0.193 Angle : 0.654 13.374 38677 Z= 0.323 Chirality : 0.042 0.263 4380 Planarity : 0.004 0.048 4861 Dihedral : 6.082 52.687 4345 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.02 % Favored : 93.95 % Rotamer: Outliers : 1.99 % Allowed : 15.87 % Favored : 82.14 % 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: -0.94 (0.15), residues: 3456 helix: 1.23 (0.14), residues: 1437 sheet: -2.48 (0.23), residues: 443 loop : -1.85 (0.15), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 120 TYR 0.015 0.001 TYR A 254 PHE 0.017 0.001 PHE D 555 TRP 0.019 0.002 TRP E 138 HIS 0.008 0.001 HIS B 136 Details of bonding type rmsd covalent geometry : bond 0.00441 (28490) covalent geometry : angle 0.64389 (38580) SS BOND : bond 0.00222 ( 5) SS BOND : angle 0.82862 ( 10) hydrogen bonds : bond 0.03920 ( 1118) hydrogen bonds : angle 4.89166 ( 3246) link_BETA1-4 : bond 0.00606 ( 12) link_BETA1-4 : angle 2.37568 ( 36) link_NAG-ASN : bond 0.00399 ( 17) link_NAG-ASN : angle 2.49436 ( 51) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 3016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 183 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 PHE cc_start: 0.8869 (OUTLIER) cc_final: 0.8103 (m-80) REVERT: A 130 ILE cc_start: 0.9137 (OUTLIER) cc_final: 0.8853 (mm) REVERT: A 641 TRP cc_start: 0.8289 (m-10) cc_final: 0.7478 (m-10) REVERT: A 836 PHE cc_start: 0.8812 (t80) cc_final: 0.8431 (t80) REVERT: B 629 LYS cc_start: 0.7327 (ptpt) cc_final: 0.6957 (tptm) REVERT: B 691 MET cc_start: 0.8434 (ptt) cc_final: 0.7956 (ptt) REVERT: B 705 MET cc_start: 0.8374 (tpt) cc_final: 0.8074 (tpt) REVERT: C 620 MET cc_start: 0.9303 (mmm) cc_final: 0.7258 (mmm) REVERT: C 709 MET cc_start: 0.7993 (mtm) cc_final: 0.7741 (mpp) REVERT: C 742 ILE cc_start: 0.9371 (OUTLIER) cc_final: 0.8976 (mm) REVERT: C 783 LEU cc_start: 0.9444 (OUTLIER) cc_final: 0.9180 (mm) REVERT: C 800 ARG cc_start: 0.7378 (mmp-170) cc_final: 0.6970 (mmp80) REVERT: D 501 MET cc_start: 0.8610 (mmt) cc_final: 0.8254 (mmt) REVERT: D 565 MET cc_start: 0.8323 (mtp) cc_final: 0.7921 (mtm) REVERT: D 590 TYR cc_start: 0.7986 (t80) cc_final: 0.7622 (t80) REVERT: D 705 MET cc_start: 0.7813 (mpp) cc_final: 0.7359 (mpp) REVERT: D 709 MET cc_start: 0.8832 (mpp) cc_final: 0.8377 (mpp) outliers start: 60 outliers final: 42 residues processed: 235 average time/residue: 0.1555 time to fit residues: 62.2254 Evaluate side-chains 224 residues out of total 3016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 178 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 PHE Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 693 PHE Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 209 LYS Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 350 HIS Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 685 VAL Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain D residue 487 LYS Chi-restraints excluded: chain D residue 512 LEU Chi-restraints excluded: chain D residue 576 CYS Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 631 LEU Chi-restraints excluded: chain D residue 729 LEU Chi-restraints excluded: chain E residue 102 PHE Chi-restraints excluded: chain E residue 114 PHE Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 361 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 105 optimal weight: 4.9990 chunk 111 optimal weight: 0.4980 chunk 334 optimal weight: 7.9990 chunk 195 optimal weight: 0.9990 chunk 66 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 233 optimal weight: 8.9990 chunk 65 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 158 optimal weight: 20.0000 chunk 121 optimal weight: 10.0000 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 491 GLN ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 654 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.090378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.062203 restraints weight = 102484.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.062033 restraints weight = 68413.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.062264 restraints weight = 53693.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.062490 restraints weight = 50170.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.062615 restraints weight = 46709.176| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 28524 Z= 0.178 Angle : 0.647 12.260 38677 Z= 0.320 Chirality : 0.042 0.337 4380 Planarity : 0.004 0.048 4861 Dihedral : 6.100 52.590 4343 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.02 % Favored : 93.95 % Rotamer: Outliers : 1.93 % Allowed : 16.40 % Favored : 81.67 % 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: -0.86 (0.14), residues: 3456 helix: 1.27 (0.14), residues: 1436 sheet: -2.39 (0.24), residues: 409 loop : -1.83 (0.15), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 503 TYR 0.027 0.001 TYR E 121 PHE 0.021 0.001 PHE C 555 TRP 0.013 0.001 TRP D 706 HIS 0.007 0.001 HIS B 111 Details of bonding type rmsd covalent geometry : bond 0.00408 (28490) covalent geometry : angle 0.63601 (38580) SS BOND : bond 0.00191 ( 5) SS BOND : angle 0.73492 ( 10) hydrogen bonds : bond 0.03818 ( 1118) hydrogen bonds : angle 4.85232 ( 3246) link_BETA1-4 : bond 0.00572 ( 12) link_BETA1-4 : angle 2.27816 ( 36) link_NAG-ASN : bond 0.00356 ( 17) link_NAG-ASN : angle 2.70430 ( 51) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 3016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 185 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 PHE cc_start: 0.8740 (OUTLIER) cc_final: 0.8140 (m-80) REVERT: A 130 ILE cc_start: 0.9107 (OUTLIER) cc_final: 0.8857 (mm) REVERT: A 641 TRP cc_start: 0.8262 (m-10) cc_final: 0.7435 (m-10) REVERT: A 705 MET cc_start: 0.8975 (ptp) cc_final: 0.8572 (ptp) REVERT: A 836 PHE cc_start: 0.8789 (t80) cc_final: 0.8425 (t80) REVERT: B 629 LYS cc_start: 0.7414 (ptpt) cc_final: 0.7083 (tptm) REVERT: B 691 MET cc_start: 0.8576 (ptt) cc_final: 0.8143 (ptt) REVERT: B 694 PHE cc_start: 0.8680 (OUTLIER) cc_final: 0.7990 (t80) REVERT: B 705 MET cc_start: 0.8301 (tpt) cc_final: 0.7948 (tpt) REVERT: B 737 MET cc_start: 0.8652 (ppp) cc_final: 0.8425 (ppp) REVERT: C 620 MET cc_start: 0.9267 (mmm) cc_final: 0.8124 (mmm) REVERT: C 668 ILE cc_start: 0.9490 (OUTLIER) cc_final: 0.9196 (mm) REVERT: C 709 MET cc_start: 0.8010 (mtm) cc_final: 0.7694 (mpp) REVERT: C 742 ILE cc_start: 0.9364 (OUTLIER) cc_final: 0.8964 (mm) REVERT: C 783 LEU cc_start: 0.9432 (OUTLIER) cc_final: 0.9172 (mm) REVERT: D 565 MET cc_start: 0.8297 (mtp) cc_final: 0.7896 (mtm) REVERT: D 590 TYR cc_start: 0.7922 (t80) cc_final: 0.7557 (t80) REVERT: D 705 MET cc_start: 0.7651 (mpp) cc_final: 0.7279 (mpp) REVERT: D 709 MET cc_start: 0.8614 (mpp) cc_final: 0.8033 (mpp) outliers start: 58 outliers final: 43 residues processed: 234 average time/residue: 0.1498 time to fit residues: 59.7657 Evaluate side-chains 229 residues out of total 3016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 180 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 PHE Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 693 PHE Chi-restraints excluded: chain B residue 694 PHE Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 209 LYS Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 350 HIS Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 668 ILE Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 685 VAL Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 820 ILE Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 487 LYS Chi-restraints excluded: chain D residue 512 LEU Chi-restraints excluded: chain D residue 576 CYS Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 729 LEU Chi-restraints excluded: chain E residue 102 PHE Chi-restraints excluded: chain E residue 114 PHE Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 361 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 148 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 86 optimal weight: 9.9990 chunk 15 optimal weight: 0.9990 chunk 154 optimal weight: 0.0570 chunk 276 optimal weight: 20.0000 chunk 181 optimal weight: 0.9990 chunk 53 optimal weight: 10.0000 chunk 306 optimal weight: 7.9990 chunk 308 optimal weight: 4.9990 chunk 239 optimal weight: 2.9990 overall best weight: 1.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.091204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.063624 restraints weight = 101287.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.063048 restraints weight = 65496.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.063281 restraints weight = 55616.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.063527 restraints weight = 50414.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.063659 restraints weight = 46637.418| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28524 Z= 0.129 Angle : 0.620 12.065 38677 Z= 0.306 Chirality : 0.041 0.320 4380 Planarity : 0.004 0.049 4861 Dihedral : 6.023 54.257 4343 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.50 % Favored : 94.47 % Rotamer: Outliers : 1.79 % Allowed : 16.60 % Favored : 81.61 % 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: -0.75 (0.15), residues: 3456 helix: 1.35 (0.14), residues: 1442 sheet: -2.28 (0.24), residues: 411 loop : -1.78 (0.15), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 800 TYR 0.024 0.001 TYR E 121 PHE 0.013 0.001 PHE C 59 TRP 0.013 0.001 TRP C 613 HIS 0.005 0.001 HIS B 111 Details of bonding type rmsd covalent geometry : bond 0.00296 (28490) covalent geometry : angle 0.61024 (38580) SS BOND : bond 0.00142 ( 5) SS BOND : angle 0.64874 ( 10) hydrogen bonds : bond 0.03609 ( 1118) hydrogen bonds : angle 4.71856 ( 3246) link_BETA1-4 : bond 0.00581 ( 12) link_BETA1-4 : angle 2.19052 ( 36) link_NAG-ASN : bond 0.00292 ( 17) link_NAG-ASN : angle 2.51079 ( 51) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 3016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 192 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ILE cc_start: 0.9161 (OUTLIER) cc_final: 0.8895 (mm) REVERT: A 641 TRP cc_start: 0.8202 (m-10) cc_final: 0.7375 (m-10) REVERT: A 664 MET cc_start: 0.7822 (pmm) cc_final: 0.7584 (pmm) REVERT: A 836 PHE cc_start: 0.8822 (t80) cc_final: 0.8433 (t80) REVERT: B 629 LYS cc_start: 0.7375 (ptpt) cc_final: 0.7092 (tptm) REVERT: B 691 MET cc_start: 0.8628 (ptt) cc_final: 0.8170 (ptt) REVERT: B 694 PHE cc_start: 0.8751 (OUTLIER) cc_final: 0.8148 (t80) REVERT: B 705 MET cc_start: 0.8301 (tpt) cc_final: 0.7874 (tpt) REVERT: B 737 MET cc_start: 0.8604 (ppp) cc_final: 0.8346 (ppp) REVERT: C 620 MET cc_start: 0.9190 (mmm) cc_final: 0.8013 (mmm) REVERT: C 668 ILE cc_start: 0.9485 (OUTLIER) cc_final: 0.9184 (mm) REVERT: C 709 MET cc_start: 0.7994 (mtm) cc_final: 0.7778 (mpp) REVERT: C 713 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.7059 (tpt170) REVERT: D 565 MET cc_start: 0.8268 (mtp) cc_final: 0.8019 (mtm) REVERT: D 590 TYR cc_start: 0.8012 (t80) cc_final: 0.7657 (t80) REVERT: D 705 MET cc_start: 0.7611 (mpp) cc_final: 0.7073 (mpp) REVERT: D 709 MET cc_start: 0.8636 (mpp) cc_final: 0.8360 (mpp) outliers start: 54 outliers final: 40 residues processed: 235 average time/residue: 0.1587 time to fit residues: 63.1819 Evaluate side-chains 225 residues out of total 3016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 181 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 693 PHE Chi-restraints excluded: chain B residue 694 PHE Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 209 LYS Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 350 HIS Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 668 ILE Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 685 VAL Chi-restraints excluded: chain C residue 713 ARG Chi-restraints excluded: chain C residue 820 ILE Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 487 LYS Chi-restraints excluded: chain D residue 512 LEU Chi-restraints excluded: chain D residue 576 CYS Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 729 LEU Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain E residue 102 PHE Chi-restraints excluded: chain E residue 114 PHE Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 361 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 87 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 31 optimal weight: 8.9990 chunk 264 optimal weight: 3.9990 chunk 238 optimal weight: 5.9990 chunk 313 optimal weight: 0.9990 chunk 1 optimal weight: 0.0770 chunk 266 optimal weight: 1.9990 chunk 284 optimal weight: 0.9980 chunk 114 optimal weight: 9.9990 chunk 223 optimal weight: 0.0670 overall best weight: 0.8280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 GLN ** D 98 GLN ** 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 = 0.3792 r_free = 0.3792 target = 0.092089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.063927 restraints weight = 101826.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.063969 restraints weight = 64028.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.064104 restraints weight = 51896.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.064358 restraints weight = 49011.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.064484 restraints weight = 45155.525| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 28524 Z= 0.110 Angle : 0.623 12.003 38677 Z= 0.305 Chirality : 0.041 0.312 4380 Planarity : 0.004 0.050 4861 Dihedral : 5.915 56.332 4343 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.27 % Favored : 94.70 % Rotamer: Outliers : 1.69 % Allowed : 16.93 % Favored : 81.37 % 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: -0.67 (0.15), residues: 3456 helix: 1.36 (0.14), residues: 1445 sheet: -2.11 (0.25), residues: 411 loop : -1.72 (0.15), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 133 TYR 0.022 0.001 TYR E 121 PHE 0.012 0.001 PHE D 359 TRP 0.015 0.001 TRP C 613 HIS 0.005 0.001 HIS A 253 Details of bonding type rmsd covalent geometry : bond 0.00248 (28490) covalent geometry : angle 0.61408 (38580) SS BOND : bond 0.00120 ( 5) SS BOND : angle 0.59911 ( 10) hydrogen bonds : bond 0.03459 ( 1118) hydrogen bonds : angle 4.62002 ( 3246) link_BETA1-4 : bond 0.00578 ( 12) link_BETA1-4 : angle 2.09259 ( 36) link_NAG-ASN : bond 0.00270 ( 17) link_NAG-ASN : angle 2.34501 ( 51) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 3016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 202 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 PHE cc_start: 0.8532 (OUTLIER) cc_final: 0.8141 (m-80) REVERT: A 130 ILE cc_start: 0.9174 (OUTLIER) cc_final: 0.8884 (mm) REVERT: A 323 MET cc_start: 0.8596 (tmm) cc_final: 0.7672 (tmm) REVERT: A 641 TRP cc_start: 0.8114 (m-10) cc_final: 0.7286 (m-10) REVERT: A 836 PHE cc_start: 0.8805 (t80) cc_final: 0.8434 (t80) REVERT: B 289 VAL cc_start: 0.8859 (t) cc_final: 0.8634 (t) REVERT: B 691 MET cc_start: 0.8625 (ptt) cc_final: 0.8182 (ptt) REVERT: B 694 PHE cc_start: 0.8756 (OUTLIER) cc_final: 0.8211 (t80) REVERT: B 705 MET cc_start: 0.8286 (tpt) cc_final: 0.7877 (tpt) REVERT: B 737 MET cc_start: 0.8611 (ppp) cc_final: 0.8324 (ppp) REVERT: C 620 MET cc_start: 0.9120 (mmm) cc_final: 0.7868 (mmm) REVERT: C 668 ILE cc_start: 0.9446 (OUTLIER) cc_final: 0.9155 (mm) REVERT: C 709 MET cc_start: 0.7948 (mtm) cc_final: 0.7736 (mtm) REVERT: C 713 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.6957 (tpt170) REVERT: D 262 PHE cc_start: 0.8293 (OUTLIER) cc_final: 0.7798 (t80) REVERT: D 383 LEU cc_start: 0.8509 (mp) cc_final: 0.8290 (tp) REVERT: D 501 MET cc_start: 0.8459 (mmt) cc_final: 0.8201 (mmt) REVERT: D 521 TYR cc_start: 0.9313 (t80) cc_final: 0.8815 (t80) REVERT: D 565 MET cc_start: 0.8257 (mtp) cc_final: 0.8009 (mtm) REVERT: D 590 TYR cc_start: 0.7974 (t80) cc_final: 0.7634 (t80) REVERT: D 705 MET cc_start: 0.7638 (mpp) cc_final: 0.7102 (mpp) REVERT: D 836 PHE cc_start: 0.8723 (m-80) cc_final: 0.8495 (m-80) outliers start: 51 outliers final: 34 residues processed: 244 average time/residue: 0.1569 time to fit residues: 63.8882 Evaluate side-chains 232 residues out of total 3016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 192 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 PHE Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 257 THR Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 636 VAL Chi-restraints excluded: chain B residue 694 PHE Chi-restraints excluded: chain B residue 768 THR Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 209 LYS Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 350 HIS Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 514 VAL Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 578 LEU Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 668 ILE Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 685 VAL Chi-restraints excluded: chain C residue 713 ARG Chi-restraints excluded: chain C residue 820 ILE Chi-restraints excluded: chain D residue 262 PHE Chi-restraints excluded: chain D residue 512 LEU Chi-restraints excluded: chain D residue 576 CYS Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 729 LEU Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain E residue 102 PHE Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 361 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 201 optimal weight: 4.9990 chunk 322 optimal weight: 6.9990 chunk 106 optimal weight: 0.7980 chunk 213 optimal weight: 0.0020 chunk 195 optimal weight: 0.8980 chunk 142 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 206 optimal weight: 6.9990 chunk 76 optimal weight: 8.9990 chunk 241 optimal weight: 4.9990 chunk 55 optimal weight: 30.0000 overall best weight: 2.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN ** A 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 ASN ** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 HIS ** 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 = 0.3779 r_free = 0.3779 target = 0.091407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.064027 restraints weight = 101324.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.063491 restraints weight = 69522.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.063755 restraints weight = 56276.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.064257 restraints weight = 50683.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.064315 restraints weight = 44470.332| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 28524 Z= 0.144 Angle : 0.642 17.470 38677 Z= 0.315 Chirality : 0.042 0.313 4380 Planarity : 0.004 0.049 4861 Dihedral : 5.887 53.371 4343 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.38 % Favored : 94.59 % Rotamer: Outliers : 1.43 % Allowed : 17.43 % Favored : 81.14 % 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: -0.64 (0.15), residues: 3456 helix: 1.39 (0.14), residues: 1455 sheet: -2.14 (0.24), residues: 411 loop : -1.71 (0.15), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 300 TYR 0.021 0.001 TYR E 121 PHE 0.014 0.001 PHE B 693 TRP 0.015 0.001 TRP C 613 HIS 0.008 0.001 HIS C 111 Details of bonding type rmsd covalent geometry : bond 0.00333 (28490) covalent geometry : angle 0.63404 (38580) SS BOND : bond 0.00174 ( 5) SS BOND : angle 0.66514 ( 10) hydrogen bonds : bond 0.03505 ( 1118) hydrogen bonds : angle 4.65929 ( 3246) link_BETA1-4 : bond 0.00567 ( 12) link_BETA1-4 : angle 2.13260 ( 36) link_NAG-ASN : bond 0.00296 ( 17) link_NAG-ASN : angle 2.35999 ( 51) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3995.94 seconds wall clock time: 70 minutes 15.21 seconds (4215.21 seconds total)