Starting phenix.real_space_refine on Fri Aug 7 13:19:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ikz_60663/08_2026/9ikz_60663.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ikz_60663/08_2026/9ikz_60663.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ikz_60663/08_2026/9ikz_60663.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ikz_60663/08_2026/9ikz_60663.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ikz_60663/08_2026/9ikz_60663.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ikz_60663/08_2026/9ikz_60663.map" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.049 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 32 atoms to isotropic. 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: 9 Type Number sf(0) Gaussians Zn 8 6.06 5 P 54 5.49 5 Mg 1 5.21 5 S 158 5.16 5 Be 1 3.05 5 C 13729 2.51 5 N 3690 2.21 5 O 4300 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21944 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 931, 7492 Classifications: {'peptide': 931} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 30, 'TRANS': 900} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 1396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1396 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 6, 'TRANS': 180} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'TYR:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "C" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 600 Classifications: {'peptide': 78} Link IDs: {'TRANS': 77} Chain: "D" Number of atoms: 1422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1422 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 6, 'TRANS': 180} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "E" Number of atoms: 4513 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 586, 4505 Classifications: {'peptide': 586} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 555} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 5, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 35 Conformer: "B" Number of residues, atoms: 586, 4505 Classifications: {'peptide': 586} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 555} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 5, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 35 bond proxies already assigned to first conformer: 4598 Chain: "F" Number of atoms: 4502 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 585, 4494 Classifications: {'peptide': 585} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'CIS': 1, 'PTRANS': 30, 'TRANS': 553} Chain breaks: 3 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 5, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 35 Conformer: "B" Number of residues, atoms: 585, 4494 Classifications: {'peptide': 585} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'CIS': 1, 'PTRANS': 30, 'TRANS': 553} Chain breaks: 3 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 5, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 35 bond proxies already assigned to first conformer: 4586 Chain: "G" Number of atoms: 868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 868 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 6, 'TRANS': 106} Chain: "I" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 545 Classifications: {'RNA': 25} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 16, 'rna3p_pyr': 8} Link IDs: {'rna3p': 24} Chain: "J" Number of atoms: 565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 565 Classifications: {'RNA': 27} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 9, 'rna3p_pyr': 17} Link IDs: {'rna2p': 1, 'rna3p': 25} Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 35 Unusual residues: {' MG': 1, ' ZN': 2, 'BEF': 1, 'GDP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2465 SG CYS A 301 80.792 79.928 122.181 1.00 38.16 S ATOM 2506 SG CYS A 306 80.720 78.081 125.483 1.00 43.46 S ATOM 2538 SG CYS A 310 79.471 81.680 125.311 1.00 34.97 S ATOM 11019 SG CYS E 16 91.875 60.979 63.841 1.00 85.92 S ATOM 10958 SG CYS E 8 83.194 64.760 53.777 1.00142.78 S ATOM 11308 SG CYS E 55 91.902 47.833 81.209 1.00128.66 S ATOM 15547 SG CYS F 19 50.965 73.693 49.269 1.00105.83 S ATOM 15450 SG CYS F 5 40.569 68.734 51.061 1.00131.57 S ATOM 15471 SG CYS F 8 38.509 66.120 48.357 1.00141.33 S ATOM 15954 SG CYS F 72 64.001 56.772 62.752 1.00120.76 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AMET E 474 " occ=0.78 ... (14 atoms not shown) pdb=" CE BMET E 474 " occ=0.22 residue: pdb=" N AMET F 474 " occ=0.42 ... (14 atoms not shown) pdb=" CE BMET F 474 " occ=0.58 Time building chain proxies: 5.25, per 1000 atoms: 0.24 Number of scatterers: 21944 At special positions: 0 Unit cell: (155.8, 136.12, 186.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 8 29.99 S 158 16.00 P 54 15.00 Mg 1 11.99 F 3 9.00 O 4300 8.00 N 3690 7.00 C 13729 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS E 50 " - pdb=" SG CYS E 72 " distance=2.68 Simple disulfide: pdb=" SG CYS F 50 " - pdb=" SG CYS F 55 " distance=2.01 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.35 Conformation dependent library (CDL) restraints added in 850.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb=" ZN E 701 " pdb="ZN ZN E 701 " - pdb=" NE2 HIS E 33 " pdb="ZN ZN E 701 " - pdb=" ND1 HIS E 39 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 16 " pdb=" ZN E 702 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 8 " pdb=" ZN E 703 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 55 " pdb=" ZN F 701 " pdb="ZN ZN F 701 " - pdb=" SG CYS F 19 " pdb="ZN ZN F 701 " - pdb=" NE2 HIS F 33 " pdb=" ZN F 702 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 5 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 8 " pdb=" ZN F 703 " pdb="ZN ZN F 703 " - pdb=" SG CYS F 72 " Number of angles added : 3 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5092 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 23 sheets defined 34.2% alpha, 10.5% beta 6 base pairs and 32 stacking pairs defined. Time for finding SS restraints: 1.87 Creating SS restraints... Processing helix chain 'A' and resid 4 through 12 removed outlier: 3.527A pdb=" N LEU A 8 " --> pdb=" O ALA A 4 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N CYS A 12 " --> pdb=" O LEU A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 83 removed outlier: 3.861A pdb=" N TYR A 80 " --> pdb=" O THR A 76 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN A 81 " --> pdb=" O PHE A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 133 removed outlier: 3.640A pdb=" N LEU A 127 " --> pdb=" O THR A 123 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU A 131 " --> pdb=" O LEU A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 149 removed outlier: 3.594A pdb=" N ILE A 145 " --> pdb=" O THR A 141 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N VAL A 147 " --> pdb=" O LYS A 143 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TYR A 149 " --> pdb=" O ILE A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 175 Processing helix chain 'A' and resid 178 through 184 Processing helix chain 'A' and resid 186 through 199 removed outlier: 3.783A pdb=" N VAL A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA A 199 " --> pdb=" O ALA A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 242 Processing helix chain 'A' and resid 243 through 248 removed outlier: 3.741A pdb=" N LEU A 247 " --> pdb=" O PRO A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 253 removed outlier: 3.817A pdb=" N THR A 252 " --> pdb=" O ARG A 249 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ALA A 253 " --> pdb=" O ALA A 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 249 through 253' Processing helix chain 'A' and resid 278 through 287 removed outlier: 3.691A pdb=" N ASP A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR A 286 " --> pdb=" O LEU A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 removed outlier: 3.684A pdb=" N CYS A 301 " --> pdb=" O CYS A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.675A pdb=" N LEU A 308 " --> pdb=" O ASP A 304 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N HIS A 309 " --> pdb=" O ARG A 305 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN A 312 " --> pdb=" O LEU A 308 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN A 314 " --> pdb=" O CYS A 310 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 326 removed outlier: 3.992A pdb=" N PHE A 326 " --> pdb=" O PRO A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 376 removed outlier: 3.632A pdb=" N ALA A 376 " --> pdb=" O LEU A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 382 removed outlier: 4.469A pdb=" N HIS A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 425 Processing helix chain 'A' and resid 447 through 454 removed outlier: 3.789A pdb=" N SER A 451 " --> pdb=" O ASN A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 459 removed outlier: 3.902A pdb=" N TYR A 458 " --> pdb=" O TYR A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 477 removed outlier: 3.962A pdb=" N PHE A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 519 removed outlier: 3.859A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N MET A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 531 removed outlier: 3.511A pdb=" N THR A 531 " --> pdb=" O LEU A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 577 removed outlier: 3.605A pdb=" N THR A 565 " --> pdb=" O SER A 561 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE A 571 " --> pdb=" O THR A 567 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 606 removed outlier: 3.591A pdb=" N TYR A 606 " --> pdb=" O LEU A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 626 Processing helix chain 'A' and resid 631 through 639 removed outlier: 3.616A pdb=" N SER A 635 " --> pdb=" O ARG A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 642 No H-bonds generated for 'chain 'A' and resid 640 through 642' Processing helix chain 'A' and resid 652 through 663 removed outlier: 3.977A pdb=" N GLU A 658 " --> pdb=" O ARG A 654 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN A 661 " --> pdb=" O ASN A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 708 removed outlier: 3.656A pdb=" N VAL A 693 " --> pdb=" O TYR A 689 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA A 699 " --> pdb=" O ASN A 695 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA A 702 " --> pdb=" O GLN A 698 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ASN A 703 " --> pdb=" O ALA A 699 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU A 707 " --> pdb=" O ASN A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 733 removed outlier: 3.647A pdb=" N ASN A 722 " --> pdb=" O LYS A 718 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLN A 724 " --> pdb=" O VAL A 720 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS A 725 " --> pdb=" O ARG A 721 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A 727 " --> pdb=" O LEU A 723 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TYR A 728 " --> pdb=" O GLN A 724 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU A 729 " --> pdb=" O HIS A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 752 removed outlier: 3.515A pdb=" N ALA A 747 " --> pdb=" O ASN A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 789 removed outlier: 3.555A pdb=" N SER A 784 " --> pdb=" O LYS A 780 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL A 785 " --> pdb=" O ASN A 781 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TYR A 787 " --> pdb=" O LYS A 783 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR A 788 " --> pdb=" O SER A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 808 removed outlier: 3.681A pdb=" N GLY A 808 " --> pdb=" O LEU A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 842 removed outlier: 3.843A pdb=" N GLY A 841 " --> pdb=" O ILE A 837 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS A 842 " --> pdb=" O LEU A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 855 removed outlier: 3.637A pdb=" N LEU A 854 " --> pdb=" O ASP A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 864 Processing helix chain 'A' and resid 866 through 872 removed outlier: 3.721A pdb=" N LYS A 871 " --> pdb=" O PRO A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 899 removed outlier: 4.068A pdb=" N HIS A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG A 889 " --> pdb=" O LEU A 885 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A 895 " --> pdb=" O LEU A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 917 removed outlier: 3.552A pdb=" N TRP A 916 " --> pdb=" O SER A 913 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU A 917 " --> pdb=" O ARG A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 925 removed outlier: 3.543A pdb=" N TYR A 925 " --> pdb=" O GLU A 922 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 24 removed outlier: 4.062A pdb=" N PHE B 15 " --> pdb=" O SER B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 40 removed outlier: 4.268A pdb=" N LYS B 37 " --> pdb=" O VAL B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 55 removed outlier: 3.529A pdb=" N MET B 55 " --> pdb=" O ARG B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 64 Processing helix chain 'B' and resid 70 through 84 removed outlier: 3.718A pdb=" N GLU B 77 " --> pdb=" O GLN B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 91 removed outlier: 3.546A pdb=" N THR B 89 " --> pdb=" O SER B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 134 through 140 removed outlier: 3.696A pdb=" N ASN B 140 " --> pdb=" O ASN B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 180 Processing helix chain 'C' and resid 2 through 17 removed outlier: 3.548A pdb=" N VAL C 6 " --> pdb=" O LYS C 2 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS C 7 " --> pdb=" O MET C 3 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N CYS C 8 " --> pdb=" O SER C 4 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL C 11 " --> pdb=" O LYS C 7 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL C 12 " --> pdb=" O CYS C 8 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU C 14 " --> pdb=" O SER C 10 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER C 15 " --> pdb=" O VAL C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 37 removed outlier: 3.895A pdb=" N GLN C 34 " --> pdb=" O ALA C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 61 removed outlier: 3.903A pdb=" N SER C 54 " --> pdb=" O GLU C 50 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 66 removed outlier: 3.588A pdb=" N ALA C 65 " --> pdb=" O MET C 62 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL C 66 " --> pdb=" O GLN C 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 62 through 66' Processing helix chain 'C' and resid 67 through 73 Processing helix chain 'D' and resid 16 through 29 removed outlier: 4.275A pdb=" N VAL D 26 " --> pdb=" O TYR D 22 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N ALA D 27 " --> pdb=" O GLU D 23 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASN D 28 " --> pdb=" O GLN D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 43 Processing helix chain 'D' and resid 48 through 53 removed outlier: 3.691A pdb=" N ASP D 52 " --> pdb=" O GLU D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 76 removed outlier: 3.912A pdb=" N LYS D 61 " --> pdb=" O ARG D 57 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP D 64 " --> pdb=" O GLU D 60 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N THR D 68 " --> pdb=" O ASP D 64 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N TYR D 71 " --> pdb=" O MET D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 98 removed outlier: 3.816A pdb=" N THR D 89 " --> pdb=" O SER D 85 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS D 97 " --> pdb=" O THR D 93 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU D 98 " --> pdb=" O MET D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 113 removed outlier: 3.561A pdb=" N ILE D 107 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASN D 108 " --> pdb=" O ASN D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 141 Processing helix chain 'D' and resid 168 through 172 removed outlier: 4.190A pdb=" N ILE D 172 " --> pdb=" O LEU D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 180 Processing helix chain 'E' and resid 27 through 36 removed outlier: 3.833A pdb=" N TYR E 31 " --> pdb=" O CYS E 27 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP E 32 " --> pdb=" O LYS E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 112 Processing helix chain 'E' and resid 116 through 124 removed outlier: 4.082A pdb=" N TYR E 120 " --> pdb=" O ASN E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 147 Processing helix chain 'E' and resid 264 through 273 Processing helix chain 'E' and resid 290 through 299 Processing helix chain 'E' and resid 315 through 325 removed outlier: 3.875A pdb=" N LYS E 320 " --> pdb=" O ALA E 316 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ALA E 321 " --> pdb=" O LEU E 317 " (cutoff:3.500A) Processing helix chain 'E' and resid 380 through 390 Processing helix chain 'E' and resid 419 through 423 removed outlier: 3.825A pdb=" N ASN E 423 " --> pdb=" O GLU E 420 " (cutoff:3.500A) Processing helix chain 'E' and resid 424 through 432 removed outlier: 4.811A pdb=" N LYS E 430 " --> pdb=" O CYS E 426 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE E 432 " --> pdb=" O LEU E 428 " (cutoff:3.500A) Processing helix chain 'E' and resid 446 through 456 Processing helix chain 'E' and resid 489 through 491 No H-bonds generated for 'chain 'E' and resid 489 through 491' Processing helix chain 'E' and resid 492 through 500 removed outlier: 3.556A pdb=" N VAL E 496 " --> pdb=" O GLN E 492 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG E 497 " --> pdb=" O ILE E 493 " (cutoff:3.500A) Processing helix chain 'E' and resid 503 through 507 removed outlier: 3.810A pdb=" N TRP E 506 " --> pdb=" O ASN E 503 " (cutoff:3.500A) Processing helix chain 'E' and resid 515 through 526 removed outlier: 3.511A pdb=" N ASN E 519 " --> pdb=" O TYR E 515 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 36 removed outlier: 3.951A pdb=" N ILE F 35 " --> pdb=" O TYR F 31 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER F 36 " --> pdb=" O ASP F 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 31 through 36' Processing helix chain 'F' and resid 105 through 110 Processing helix chain 'F' and resid 116 through 124 Processing helix chain 'F' and resid 127 through 147 removed outlier: 3.685A pdb=" N LEU F 147 " --> pdb=" O GLU F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 274 Processing helix chain 'F' and resid 290 through 299 Processing helix chain 'F' and resid 310 through 321 removed outlier: 3.661A pdb=" N VAL F 314 " --> pdb=" O SER F 310 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA F 316 " --> pdb=" O ALA F 312 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU F 317 " --> pdb=" O ALA F 313 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N LYS F 320 " --> pdb=" O ALA F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 330 removed outlier: 3.669A pdb=" N CYS F 330 " --> pdb=" O ILE F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 391 removed outlier: 4.411A pdb=" N LEU F 384 " --> pdb=" O THR F 380 " (cutoff:3.500A) Processing helix chain 'F' and resid 428 through 433 Processing helix chain 'F' and resid 445 through 456 removed outlier: 3.606A pdb=" N VAL F 449 " --> pdb=" O PRO F 445 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N THR F 451 " --> pdb=" O GLU F 447 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL F 456 " --> pdb=" O VAL F 452 " (cutoff:3.500A) Processing helix chain 'F' and resid 490 through 501 Processing helix chain 'F' and resid 515 through 523 removed outlier: 3.762A pdb=" N ASN F 519 " --> pdb=" O TYR F 515 " (cutoff:3.500A) Processing helix chain 'F' and resid 550 through 555 Processing helix chain 'F' and resid 562 through 566 Processing helix chain 'G' and resid 97 through 109 removed outlier: 3.581A pdb=" N THR G 109 " --> pdb=" O SER G 105 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 21 removed outlier: 5.166A pdb=" N ASN A 52 " --> pdb=" O ASP A 29 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ASP A 29 " --> pdb=" O ASN A 52 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 21 removed outlier: 5.836A pdb=" N ASN A 52 " --> pdb=" O ARG A 74 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N SER A 68 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N TYR A 69 " --> pdb=" O ARG A 118 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 223 through 224 removed outlier: 7.249A pdb=" N VAL A 233 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N GLY A 203 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 352 through 355 removed outlier: 6.120A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) removed outlier: 9.542A pdb=" N SER A 363 " --> pdb=" O LYS A 332 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N PHE A 334 " --> pdb=" O SER A 363 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 352 through 355 removed outlier: 6.120A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 556 through 559 removed outlier: 6.743A pdb=" N THR A 540 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA A 399 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N VAL A 398 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LEU A 388 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU A 387 " --> pdb=" O MET B 129 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N VAL B 131 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LEU A 389 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N LEU B 189 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N ILE B 156 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 414 through 415 removed outlier: 3.896A pdb=" N ASN A 414 " --> pdb=" O VAL A 844 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 753 through 757 Processing sheet with id=AA9, first strand: chain 'A' and resid 816 through 822 Processing sheet with id=AB1, first strand: chain 'D' and resid 128 through 130 removed outlier: 3.512A pdb=" N GLN D 158 " --> pdb=" O THR D 187 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU D 189 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N ILE D 156 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR D 146 " --> pdb=" O ASP D 143 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 3 through 4 Processing sheet with id=AB3, first strand: chain 'E' and resid 84 through 85 removed outlier: 3.746A pdb=" N ALA E 85 " --> pdb=" O GLN E 88 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 152 through 154 Processing sheet with id=AB5, first strand: chain 'E' and resid 182 through 187 removed outlier: 6.591A pdb=" N PHE E 182 " --> pdb=" O GLU E 197 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLU E 197 " --> pdb=" O PHE E 182 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N GLY E 184 " --> pdb=" O ILE E 195 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE E 195 " --> pdb=" O GLY E 184 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 347 through 348 removed outlier: 4.413A pdb=" N LYS E 347 " --> pdb=" O CYS E 330 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N SER E 331 " --> pdb=" O PHE E 357 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N THR E 359 " --> pdb=" O SER E 331 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL E 356 " --> pdb=" O ILE E 304 " (cutoff:3.500A) removed outlier: 8.550A pdb=" N THR E 367 " --> pdb=" O ALA E 393 " (cutoff:3.500A) removed outlier: 9.523A pdb=" N HIS E 395 " --> pdb=" O THR E 367 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N ASP E 369 " --> pdb=" O HIS E 395 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N VAL E 397 " --> pdb=" O ASP E 369 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL E 371 " --> pdb=" O VAL E 397 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 510 through 511 removed outlier: 6.731A pdb=" N VAL E 510 " --> pdb=" O ILE E 545 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU E 573 " --> pdb=" O VAL E 544 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 15 through 16 Processing sheet with id=AB9, first strand: chain 'F' and resid 69 through 71 removed outlier: 4.295A pdb=" N PHE F 81 " --> pdb=" O LEU F 65 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 152 through 153 Processing sheet with id=AC2, first strand: chain 'F' and resid 186 through 187 Processing sheet with id=AC3, first strand: chain 'F' and resid 277 through 279 removed outlier: 7.187A pdb=" N SER F 278 " --> pdb=" O TYR F 398 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N VAL F 371 " --> pdb=" O VAL F 397 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL F 305 " --> pdb=" O ILE F 370 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL F 372 " --> pdb=" O VAL F 305 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N THR F 307 " --> pdb=" O VAL F 372 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N CYS F 358 " --> pdb=" O ILE F 304 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N TYR F 306 " --> pdb=" O CYS F 358 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'G' and resid 12 through 13 removed outlier: 3.841A pdb=" N SER G 13 " --> pdb=" O ALA G 30 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA G 30 " --> pdb=" O SER G 13 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 73 through 75 removed outlier: 3.595A pdb=" N PHE G 75 " --> pdb=" O LYS G 86 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS G 86 " --> pdb=" O PHE G 75 " (cutoff:3.500A) 561 hydrogen bonds defined for protein. 1554 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 15 hydrogen bonds 30 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 32 stacking parallelities Total time for adding SS restraints: 3.01 Time building geometry restraints manager: 1.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3532 1.31 - 1.44: 6499 1.44 - 1.58: 12150 1.58 - 1.71: 111 1.71 - 1.85: 223 Bond restraints: 22515 Sorted by residual: bond pdb=" F2 BEF A1004 " pdb="BE BEF A1004 " ideal model delta sigma weight residual 1.476 1.708 -0.232 2.00e-02 2.50e+03 1.34e+02 bond pdb=" F1 BEF A1004 " pdb="BE BEF A1004 " ideal model delta sigma weight residual 1.476 1.706 -0.230 2.00e-02 2.50e+03 1.33e+02 bond pdb=" F3 BEF A1004 " pdb="BE BEF A1004 " ideal model delta sigma weight residual 1.476 1.698 -0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" CA VAL A 848 " pdb=" C VAL A 848 " ideal model delta sigma weight residual 1.523 1.418 0.105 1.27e-02 6.20e+03 6.87e+01 bond pdb=" CB VAL F 226 " pdb=" CG1 VAL F 226 " ideal model delta sigma weight residual 1.521 1.274 0.247 3.30e-02 9.18e+02 5.61e+01 ... (remaining 22510 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.96: 30631 4.96 - 9.92: 194 9.92 - 14.87: 26 14.87 - 19.83: 7 19.83 - 24.79: 2 Bond angle restraints: 30860 Sorted by residual: angle pdb=" N SER B 76 " pdb=" CA SER B 76 " pdb=" CB SER B 76 " ideal model delta sigma weight residual 110.40 90.88 19.52 1.63e+00 3.76e-01 1.43e+02 angle pdb=" N THR A 850 " pdb=" CA THR A 850 " pdb=" C THR A 850 " ideal model delta sigma weight residual 113.02 95.55 17.47 1.49e+00 4.50e-01 1.37e+02 angle pdb=" N THR G 34 " pdb=" CA THR G 34 " pdb=" C THR G 34 " ideal model delta sigma weight residual 111.71 98.82 12.89 1.15e+00 7.56e-01 1.26e+02 angle pdb=" C ILE A 106 " pdb=" CA ILE A 106 " pdb=" CB ILE A 106 " ideal model delta sigma weight residual 111.87 124.98 -13.11 1.29e+00 6.01e-01 1.03e+02 angle pdb=" N TYR A 217 " pdb=" CA TYR A 217 " pdb=" C TYR A 217 " ideal model delta sigma weight residual 110.80 131.02 -20.22 2.13e+00 2.20e-01 9.01e+01 ... (remaining 30855 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.68: 12925 35.68 - 71.36: 605 71.36 - 107.05: 28 107.05 - 142.73: 2 142.73 - 178.41: 1 Dihedral angle restraints: 13561 sinusoidal: 5670 harmonic: 7891 Sorted by residual: dihedral pdb=" C ARG B 75 " pdb=" N ARG B 75 " pdb=" CA ARG B 75 " pdb=" CB ARG B 75 " ideal model delta harmonic sigma weight residual -122.60 -161.57 38.97 0 2.50e+00 1.60e-01 2.43e+02 dihedral pdb=" N ARG B 75 " pdb=" C ARG B 75 " pdb=" CA ARG B 75 " pdb=" CB ARG B 75 " ideal model delta harmonic sigma weight residual 122.80 157.96 -35.16 0 2.50e+00 1.60e-01 1.98e+02 dihedral pdb=" O4' U J 31 " pdb=" C1' U J 31 " pdb=" N1 U J 31 " pdb=" C2 U J 31 " ideal model delta sinusoidal sigma weight residual 200.00 21.59 178.41 1 1.50e+01 4.44e-03 8.53e+01 ... (remaining 13558 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.326: 3572 0.326 - 0.651: 7 0.651 - 0.977: 0 0.977 - 1.302: 0 1.302 - 1.628: 1 Chirality restraints: 3580 Sorted by residual: chirality pdb=" CA ARG B 75 " pdb=" N ARG B 75 " pdb=" C ARG B 75 " pdb=" CB ARG B 75 " both_signs ideal model delta sigma weight residual False 2.51 0.88 1.63 2.00e-01 2.50e+01 6.63e+01 chirality pdb=" CA ALA G 16 " pdb=" N ALA G 16 " pdb=" C ALA G 16 " pdb=" CB ALA G 16 " both_signs ideal model delta sigma weight residual False 2.48 3.04 -0.56 2.00e-01 2.50e+01 7.71e+00 chirality pdb=" CA TYR A 217 " pdb=" N TYR A 217 " pdb=" C TYR A 217 " pdb=" CB TYR A 217 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.42e+00 ... (remaining 3577 not shown) Planarity restraints: 3745 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 504 " -0.125 5.00e-02 4.00e+02 1.85e-01 5.48e+01 pdb=" N PRO A 505 " 0.319 5.00e-02 4.00e+02 pdb=" CA PRO A 505 " -0.116 5.00e-02 4.00e+02 pdb=" CD PRO A 505 " -0.078 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN E 220 " 0.028 2.00e-02 2.50e+03 5.69e-02 3.24e+01 pdb=" C ASN E 220 " -0.098 2.00e-02 2.50e+03 pdb=" O ASN E 220 " 0.037 2.00e-02 2.50e+03 pdb=" N VAL E 221 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 149 " -0.003 2.00e-02 2.50e+03 3.92e-02 3.07e+01 pdb=" CG TYR F 149 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR F 149 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR F 149 " -0.039 2.00e-02 2.50e+03 pdb=" CE1 TYR F 149 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR F 149 " 0.070 2.00e-02 2.50e+03 pdb=" CZ TYR F 149 " 0.036 2.00e-02 2.50e+03 pdb=" OH TYR F 149 " -0.057 2.00e-02 2.50e+03 ... (remaining 3742 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.32: 43 2.32 - 2.97: 11025 2.97 - 3.61: 29943 3.61 - 4.26: 49009 4.26 - 4.90: 80046 Nonbonded interactions: 170066 Sorted by model distance: nonbonded pdb=" OD2 ASP A 218 " pdb=" F3 BEF A1004 " model vdw 1.680 2.990 nonbonded pdb=" OD2 ASP A 218 " pdb=" F1 BEF A1004 " model vdw 1.901 2.990 nonbonded pdb=" OD2 ASP A 218 " pdb="BE BEF A1004 " model vdw 1.982 2.420 nonbonded pdb=" OH TYR A 420 " pdb=" OG SER C 4 " model vdw 2.038 3.040 nonbonded pdb=" OD1 ASP A 218 " pdb=" F1 BEF A1004 " model vdw 2.054 2.990 ... (remaining 170061 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 'B' and ((resid 6 through 8 and (name N or name CA or name C or name O or \ name CB )) or resid 9 through 22 or (resid 23 through 28 and (name N or name CA \ or name C or name O or name CB )) or resid 29 through 192)) selection = (chain 'D' and (resid 6 through 21 or (resid 22 through 28 and (name N or name C \ A or name C or name O or name CB )) or resid 29 through 31 or (resid 32 and (nam \ e N or name CA or name C or name O or name CB )) or resid 33 through 34 or (resi \ d 35 through 37 and (name N or name CA or name C or name O or name CB )) or resi \ d 38 or (resid 39 through 40 and (name N or name CA or name C or name O or name \ CB )) or resid 41 through 42 or (resid 43 and (name N or name CA or name C or na \ me O or name CB )) or resid 44 through 46 or (resid 47 and (name N or name CA or \ name C or name O or name CB )) or resid 48 through 192)) } ncs_group { reference = (chain 'E' and (resid 1 through 172 or resid 174 through 473 or resid 475 throug \ h 703)) selection = (chain 'F' and (resid 1 through 473 or resid 475 through 703)) } 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=0.22 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 6.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 21.000 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 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 : 0.015 0.686 22534 Z= 0.766 Angle : 1.182 53.658 30867 Z= 0.719 Chirality : 0.063 1.628 3580 Planarity : 0.007 0.185 3745 Dihedral : 18.545 178.411 8463 Min Nonbonded Distance : 1.680 Molprobity Statistics. All-atom Clashscore : 19.06 Ramachandran Plot: Outliers : 1.63 % Allowed : 10.06 % Favored : 88.31 % Rotamer: Outliers : 3.29 % Allowed : 26.22 % Favored : 70.49 % Cbeta Deviations : 0.31 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % 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: -4.69 (0.13), residues: 2649 helix: -3.37 (0.13), residues: 896 sheet: -1.47 (0.34), residues: 210 loop : -3.33 (0.13), residues: 1543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG F 390 TYR 0.070 0.002 TYR F 149 PHE 0.035 0.002 PHE E 546 TRP 0.026 0.002 TRP F 506 HIS 0.053 0.002 HIS E 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00831 / 0.48 (22515) covalent geometry : angle 1.13903 / 0.70 (30860) SS BOND : bond 0.46182 / 24.30 ( 2) SS BOND : angle 27.40395 / 14.47 ( 4) hydrogen bonds : bond 0.25392 / 16.46 ( 565) hydrogen bonds : angle 9.86326 / 6.72 ( 1584) metal coordination : bond 0.46587 / 30.99 ( 14) metal coordination : angle 4.60225 / 2.33 ( 3) Misc. bond : bond 0.34946 / 17.39 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 383 time to evaluate : 0.674 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: C 67 ASP cc_start: 0.8082 (t0) cc_final: 0.7823 (t0) REVERT: D 135 TYR cc_start: 0.7956 (t80) cc_final: 0.7362 (t80) REVERT: D 176 ASN cc_start: 0.7705 (OUTLIER) cc_final: 0.7242 (p0) REVERT: E 21 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.7108 (mtt-85) REVERT: E 34 VAL cc_start: 0.8266 (OUTLIER) cc_final: 0.8034 (t) REVERT: E 190 ASN cc_start: 0.4548 (m110) cc_final: 0.4208 (t0) REVERT: E 194 GLN cc_start: 0.2055 (tp40) cc_final: 0.1815 (tt0) REVERT: E 344 ASP cc_start: 0.1142 (m-30) cc_final: 0.0665 (p0) REVERT: E 436 MET cc_start: -0.0489 (ptp) cc_final: -0.1025 (mtp) REVERT: F 141 THR cc_start: 0.5882 (t) cc_final: 0.5603 (t) REVERT: F 157 VAL cc_start: 0.3709 (t) cc_final: 0.3251 (p) REVERT: F 241 VAL cc_start: 0.0484 (m) cc_final: 0.0212 (p) REVERT: F 345 LYS cc_start: 0.3174 (ttmt) cc_final: 0.2864 (pttp) REVERT: F 488 ILE cc_start: 0.2371 (tp) cc_final: 0.1960 (mt) outliers start: 72 outliers final: 18 residues processed: 440 average time/residue: 0.1444 time to fit residues: 95.7060 Evaluate side-chains 213 residues out of total 2326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 192 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain D residue 87 MET Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 176 ASN Chi-restraints excluded: chain E residue 15 ARG Chi-restraints excluded: chain E residue 21 ARG Chi-restraints excluded: chain E residue 32 ASP Chi-restraints excluded: chain E residue 34 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain G residue 23 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 0.0020 chunk 111 optimal weight: 0.6980 overall best weight: 1.3192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 9 ASN A 210 GLN A 497 ASN A 568 ASN A 705 ASN D 43 ASN ** D 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 9 ASN E 11 GLN E 404 GLN E 482 HIS E 537 GLN ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 562 ASN F 46 ASN F 107 ASN ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 2 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.181041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.117152 restraints weight = 79235.806| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 5.81 r_work: 0.3048 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3042 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3042 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 22534 Z= 0.189 Angle : 0.766 16.342 30867 Z= 0.396 Chirality : 0.046 0.298 3580 Planarity : 0.006 0.161 3745 Dihedral : 13.291 171.974 3769 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.42 % Allowed : 8.89 % Favored : 90.69 % Rotamer: Outliers : 4.48 % Allowed : 24.15 % Favored : 71.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.07 (0.14), residues: 2649 helix: -2.65 (0.14), residues: 931 sheet: -1.26 (0.35), residues: 196 loop : -3.05 (0.14), residues: 1522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG D 96 TYR 0.023 0.002 TYR F 541 PHE 0.015 0.002 PHE D 92 TRP 0.016 0.001 TRP B 182 HIS 0.016 0.001 HIS F 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.19 (22515) covalent geometry : angle 0.76259 / 0.40 (30860) SS BOND : bond 0.01529 / 0.79 ( 2) SS BOND : angle 5.72570 / 3.00 ( 4) hydrogen bonds : bond 0.05521 / 3.62 ( 565) hydrogen bonds : angle 5.83655 / 3.99 ( 1584) metal coordination : bond 0.02572 / 1.75 ( 14) metal coordination : angle 1.99783 / 1.06 ( 3) Misc. bond : bond 0.01020 / 0.50 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 210 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.6914 (tm-30) cc_final: 0.6387 (tm-30) REVERT: A 18 ARG cc_start: 0.7785 (mtp180) cc_final: 0.7510 (mtp180) REVERT: A 902 MET cc_start: 0.6939 (ttt) cc_final: 0.6422 (tpp) REVERT: B 61 LYS cc_start: 0.7315 (mtpp) cc_final: 0.7106 (mmmt) REVERT: B 64 ASP cc_start: 0.7081 (t0) cc_final: 0.6784 (t0) REVERT: D 22 TYR cc_start: 0.6433 (t80) cc_final: 0.5991 (t80) REVERT: D 43 ASN cc_start: 0.8198 (OUTLIER) cc_final: 0.7939 (t0) REVERT: D 70 MET cc_start: 0.7325 (tpp) cc_final: 0.6885 (mtt) REVERT: D 77 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7470 (mt-10) REVERT: E 11 GLN cc_start: 0.8247 (OUTLIER) cc_final: 0.8023 (tp40) REVERT: E 190 ASN cc_start: 0.4581 (m110) cc_final: 0.3768 (t0) REVERT: E 334 ILE cc_start: 0.2998 (OUTLIER) cc_final: 0.2177 (tt) REVERT: E 344 ASP cc_start: 0.3521 (m-30) cc_final: 0.2667 (p0) REVERT: E 436 MET cc_start: 0.1458 (ptp) cc_final: 0.1220 (ptm) REVERT: F 76 LYS cc_start: 0.6161 (tppt) cc_final: 0.5228 (tppt) REVERT: F 303 ARG cc_start: 0.5766 (mtm-85) cc_final: 0.5207 (mmt-90) REVERT: F 488 ILE cc_start: 0.2447 (tp) cc_final: 0.2097 (mt) REVERT: G 33 ASN cc_start: 0.6544 (t0) cc_final: 0.6321 (t0) REVERT: G 55 ARG cc_start: 0.6794 (mtm110) cc_final: 0.6159 (tmt-80) REVERT: G 75 PHE cc_start: 0.5291 (OUTLIER) cc_final: 0.4973 (m-80) REVERT: G 87 TYR cc_start: 0.7840 (m-80) cc_final: 0.7583 (m-80) outliers start: 99 outliers final: 52 residues processed: 295 average time/residue: 0.1363 time to fit residues: 62.9399 Evaluate side-chains 243 residues out of total 2326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 187 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 487 CYS Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 645 CYS Chi-restraints excluded: chain A residue 646 CYS Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 157 GLN Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain D residue 43 ASN Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain E residue 11 GLN Chi-restraints excluded: chain E residue 15 ARG Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 32 ASP Chi-restraints excluded: chain E residue 50 CYS Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 75 HIS Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 334 ILE Chi-restraints excluded: chain E residue 340 VAL Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 35 ILE Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 133 PHE Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 376 ILE Chi-restraints excluded: chain F residue 511 PHE Chi-restraints excluded: chain F residue 517 SER Chi-restraints excluded: chain F residue 541 TYR Chi-restraints excluded: chain F residue 547 THR Chi-restraints excluded: chain G residue 2 ASN Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 75 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 224 optimal weight: 4.9990 chunk 223 optimal weight: 5.9990 chunk 201 optimal weight: 3.9990 chunk 166 optimal weight: 8.9990 chunk 140 optimal weight: 5.9990 chunk 80 optimal weight: 0.5980 chunk 149 optimal weight: 6.9990 chunk 141 optimal weight: 5.9990 chunk 264 optimal weight: 20.0000 chunk 108 optimal weight: 0.0470 chunk 150 optimal weight: 3.9990 overall best weight: 2.7284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 497 ASN D 43 ASN D 179 ASN E 9 ASN ** E 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 537 GLN ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 281 GLN ** F 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 492 GLN F 519 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.175875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.103863 restraints weight = 69224.589| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 5.47 r_work: 0.2970 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2976 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2976 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 22534 Z= 0.265 Angle : 0.749 16.391 30867 Z= 0.389 Chirality : 0.048 0.297 3580 Planarity : 0.006 0.159 3745 Dihedral : 12.974 168.557 3747 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.08 % Favored : 90.62 % Rotamer: Outliers : 4.57 % Allowed : 24.15 % Favored : 71.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.93 % Twisted General : 0.08 % 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: -3.71 (0.14), residues: 2649 helix: -2.26 (0.15), residues: 934 sheet: -1.13 (0.35), residues: 194 loop : -2.88 (0.14), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 427 TYR 0.024 0.002 TYR G 89 PHE 0.023 0.002 PHE F 145 TRP 0.017 0.002 TRP A 290 HIS 0.015 0.002 HIS E 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00624 / 0.26 (22515) covalent geometry : angle 0.74686 / 0.39 (30860) SS BOND : bond 0.01162 / 0.61 ( 2) SS BOND : angle 4.63632 / 2.44 ( 4) hydrogen bonds : bond 0.05239 / 3.44 ( 565) hydrogen bonds : angle 5.42725 / 3.74 ( 1584) metal coordination : bond 0.01771 / 1.05 ( 14) metal coordination : angle 2.78284 / 1.49 ( 3) Misc. bond : bond 0.00080 / 0.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 198 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLN cc_start: 0.6921 (tm-30) cc_final: 0.6159 (tm-30) REVERT: A 18 ARG cc_start: 0.7944 (mtp180) cc_final: 0.7700 (mtp180) REVERT: A 77 PHE cc_start: 0.8854 (t80) cc_final: 0.8371 (t80) REVERT: A 85 THR cc_start: 0.9015 (OUTLIER) cc_final: 0.8702 (p) REVERT: A 138 ASN cc_start: 0.8826 (t0) cc_final: 0.8308 (t0) REVERT: A 665 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.8169 (pt0) REVERT: A 876 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8512 (mt-10) REVERT: A 902 MET cc_start: 0.7006 (ttt) cc_final: 0.6515 (ptm) REVERT: B 64 ASP cc_start: 0.7600 (t0) cc_final: 0.7289 (t0) REVERT: B 69 GLN cc_start: 0.8611 (tm-30) cc_final: 0.8198 (tm-30) REVERT: C 3 MET cc_start: 0.8456 (tpp) cc_final: 0.8249 (tpp) REVERT: C 70 LYS cc_start: 0.8932 (pttt) cc_final: 0.8628 (pttp) REVERT: D 22 TYR cc_start: 0.6841 (t80) cc_final: 0.6513 (t80) REVERT: D 70 MET cc_start: 0.7631 (tpp) cc_final: 0.7188 (mtt) REVERT: D 77 GLU cc_start: 0.8287 (mm-30) cc_final: 0.7841 (mt-10) REVERT: D 157 GLN cc_start: 0.8154 (mt0) cc_final: 0.7923 (mt0) REVERT: E 190 ASN cc_start: 0.4638 (m110) cc_final: 0.3893 (t0) REVERT: E 344 ASP cc_start: 0.3354 (m-30) cc_final: 0.2088 (p0) REVERT: E 436 MET cc_start: 0.1487 (ptp) cc_final: 0.1078 (ptm) REVERT: E 461 LEU cc_start: -0.0281 (OUTLIER) cc_final: -0.1997 (mm) REVERT: F 157 VAL cc_start: 0.5293 (t) cc_final: 0.5058 (p) REVERT: F 270 GLN cc_start: 0.2218 (mm-40) cc_final: 0.2011 (tp-100) REVERT: F 274 MET cc_start: 0.6859 (ppp) cc_final: 0.6078 (tpp) REVERT: F 281 GLN cc_start: 0.5839 (OUTLIER) cc_final: 0.5397 (tt0) REVERT: F 303 ARG cc_start: 0.5926 (mtm-85) cc_final: 0.5333 (mmt-90) REVERT: F 488 ILE cc_start: 0.2609 (tp) cc_final: 0.2246 (mt) REVERT: F 590 LEU cc_start: 0.1744 (OUTLIER) cc_final: 0.0625 (mp) REVERT: G 12 MET cc_start: 0.7897 (tmm) cc_final: 0.7586 (ttm) REVERT: G 51 LEU cc_start: 0.3418 (OUTLIER) cc_final: 0.3168 (mt) outliers start: 102 outliers final: 56 residues processed: 279 average time/residue: 0.1410 time to fit residues: 61.7513 Evaluate side-chains 245 residues out of total 2326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 182 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 487 CYS Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 645 CYS Chi-restraints excluded: chain A residue 646 CYS Chi-restraints excluded: chain A residue 665 GLU Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 876 GLU Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain D residue 55 MET Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain E residue 16 CYS Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 75 HIS Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 340 VAL Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain F residue 6 VAL Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 133 PHE Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 281 GLN Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 399 ILE Chi-restraints excluded: chain F residue 479 VAL Chi-restraints excluded: chain F residue 511 PHE Chi-restraints excluded: chain F residue 547 THR Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 590 LEU Chi-restraints excluded: chain G residue 2 ASN Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 75 PHE Chi-restraints excluded: chain G residue 79 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 225 optimal weight: 1.9990 chunk 259 optimal weight: 20.0000 chunk 179 optimal weight: 30.0000 chunk 249 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 246 optimal weight: 7.9990 chunk 133 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 160 optimal weight: 0.0030 chunk 16 optimal weight: 0.6980 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 497 ASN D 179 ASN E 9 ASN ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 2 ASN ** G 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.178169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.107604 restraints weight = 71972.803| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 6.07 r_work: 0.2993 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3006 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3006 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 22534 Z= 0.118 Angle : 0.622 13.429 30867 Z= 0.320 Chirality : 0.042 0.271 3580 Planarity : 0.005 0.151 3745 Dihedral : 12.789 164.226 3739 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.53 % Favored : 92.17 % Rotamer: Outliers : 3.56 % Allowed : 25.16 % Favored : 71.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.93 % Twisted General : 0.04 % 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: -3.30 (0.15), residues: 2649 helix: -1.84 (0.16), residues: 937 sheet: -0.92 (0.35), residues: 194 loop : -2.70 (0.14), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 55 TYR 0.024 0.001 TYR F 541 PHE 0.019 0.001 PHE F 145 TRP 0.015 0.001 TRP B 182 HIS 0.017 0.001 HIS E 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (22515) covalent geometry : angle 0.62093 / 0.32 (30860) SS BOND : bond 0.00304 / 0.16 ( 2) SS BOND : angle 2.32155 / 1.34 ( 4) hydrogen bonds : bond 0.03761 / 2.50 ( 565) hydrogen bonds : angle 5.05421 / 3.50 ( 1584) metal coordination : bond 0.00978 / 0.56 ( 14) metal coordination : angle 2.30842 / 1.24 ( 3) Misc. bond : bond 0.00241 / 0.11 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 197 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 PHE cc_start: 0.8838 (t80) cc_final: 0.8349 (t80) REVERT: A 138 ASN cc_start: 0.8772 (t0) cc_final: 0.8277 (t0) REVERT: A 740 ASP cc_start: 0.8695 (OUTLIER) cc_final: 0.8401 (t0) REVERT: A 876 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.8488 (mt-10) REVERT: A 902 MET cc_start: 0.7052 (ttt) cc_final: 0.6567 (ptm) REVERT: B 48 GLU cc_start: 0.7332 (tp30) cc_final: 0.7073 (tp30) REVERT: B 58 LYS cc_start: 0.7622 (mttm) cc_final: 0.7337 (mtmm) REVERT: B 64 ASP cc_start: 0.7572 (t0) cc_final: 0.7290 (t0) REVERT: B 69 GLN cc_start: 0.8573 (tm-30) cc_final: 0.8298 (tm-30) REVERT: C 70 LYS cc_start: 0.8897 (pttt) cc_final: 0.8627 (pttp) REVERT: D 15 PHE cc_start: 0.7007 (OUTLIER) cc_final: 0.6038 (m-80) REVERT: D 70 MET cc_start: 0.7504 (tpp) cc_final: 0.7100 (mtt) REVERT: D 77 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7735 (mt-10) REVERT: D 94 MET cc_start: 0.8508 (mtp) cc_final: 0.8225 (mtp) REVERT: D 157 GLN cc_start: 0.8151 (mt0) cc_final: 0.7888 (mt0) REVERT: E 190 ASN cc_start: 0.4643 (m110) cc_final: 0.3877 (t0) REVERT: E 344 ASP cc_start: 0.3312 (m-30) cc_final: 0.2165 (p0) REVERT: E 436 MET cc_start: 0.1427 (ptp) cc_final: 0.0976 (ptm) REVERT: E 461 LEU cc_start: -0.0298 (OUTLIER) cc_final: -0.2006 (mm) REVERT: F 157 VAL cc_start: 0.5246 (t) cc_final: 0.4980 (p) REVERT: F 270 GLN cc_start: 0.2324 (mm-40) cc_final: 0.2104 (tp-100) REVERT: F 274 MET cc_start: 0.6925 (ppp) cc_final: 0.6177 (tpp) REVERT: F 277 TYR cc_start: -0.3049 (OUTLIER) cc_final: -0.3492 (p90) REVERT: F 303 ARG cc_start: 0.5942 (mtm-85) cc_final: 0.5341 (mmt-90) REVERT: F 488 ILE cc_start: 0.2528 (tp) cc_final: 0.2172 (mt) REVERT: F 590 LEU cc_start: 0.1599 (OUTLIER) cc_final: 0.0474 (mp) REVERT: G 12 MET cc_start: 0.7614 (tmm) cc_final: 0.7330 (ttt) REVERT: G 55 ARG cc_start: 0.6754 (mtm110) cc_final: 0.5681 (tmt-80) REVERT: G 87 TYR cc_start: 0.7702 (m-80) cc_final: 0.7098 (m-80) outliers start: 78 outliers final: 51 residues processed: 257 average time/residue: 0.1376 time to fit residues: 55.1728 Evaluate side-chains 238 residues out of total 2326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 181 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 487 CYS Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 645 CYS Chi-restraints excluded: chain A residue 646 CYS Chi-restraints excluded: chain A residue 665 GLU Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain A residue 798 LYS Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 876 GLU Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain D residue 15 PHE Chi-restraints excluded: chain D residue 55 MET Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 75 HIS Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 340 VAL Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 133 PHE Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 277 TYR Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 358 CYS Chi-restraints excluded: chain F residue 376 ILE Chi-restraints excluded: chain F residue 421 TYR Chi-restraints excluded: chain F residue 511 PHE Chi-restraints excluded: chain F residue 512 ILE Chi-restraints excluded: chain F residue 547 THR Chi-restraints excluded: chain F residue 590 LEU Chi-restraints excluded: chain G residue 2 ASN Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 75 PHE Chi-restraints excluded: chain G residue 79 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 221 optimal weight: 8.9990 chunk 96 optimal weight: 2.9990 chunk 164 optimal weight: 0.2980 chunk 87 optimal weight: 0.8980 chunk 265 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 140 optimal weight: 0.0770 chunk 237 optimal weight: 6.9990 chunk 155 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 103 optimal weight: 8.9990 overall best weight: 1.0340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 497 ASN A 552 ASN C 19 GLN E 9 ASN ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 2 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.177458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.107348 restraints weight = 69370.051| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 5.94 r_work: 0.2988 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2994 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2994 r_free = 0.2994 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2994 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22534 Z= 0.134 Angle : 0.600 12.520 30867 Z= 0.310 Chirality : 0.042 0.265 3580 Planarity : 0.005 0.148 3745 Dihedral : 12.679 165.184 3738 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.17 % Favored : 91.56 % Rotamer: Outliers : 3.78 % Allowed : 23.94 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.93 % Twisted General : 0.04 % 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: -3.05 (0.15), residues: 2649 helix: -1.59 (0.16), residues: 934 sheet: -0.77 (0.35), residues: 194 loop : -2.58 (0.14), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 105 TYR 0.015 0.001 TYR E 31 PHE 0.027 0.001 PHE F 145 TRP 0.066 0.002 TRP F 114 HIS 0.015 0.001 HIS E 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (22515) covalent geometry : angle 0.59869 / 0.31 (30860) SS BOND : bond 0.01295 / 0.68 ( 2) SS BOND : angle 2.66897 / 1.55 ( 4) hydrogen bonds : bond 0.03669 / 2.45 ( 565) hydrogen bonds : angle 4.89073 / 3.40 ( 1584) metal coordination : bond 0.00957 / 0.53 ( 14) metal coordination : angle 2.02237 / 1.09 ( 3) Misc. bond : bond 0.00028 / 0.01 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 183 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 PHE cc_start: 0.8825 (t80) cc_final: 0.8343 (t80) REVERT: A 138 ASN cc_start: 0.8783 (t0) cc_final: 0.8320 (t0) REVERT: A 876 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8497 (mt-10) REVERT: A 902 MET cc_start: 0.7094 (ttt) cc_final: 0.6645 (ptm) REVERT: B 48 GLU cc_start: 0.7465 (tp30) cc_final: 0.7239 (tp30) REVERT: B 58 LYS cc_start: 0.7592 (mttm) cc_final: 0.7296 (mtmm) REVERT: B 64 ASP cc_start: 0.7635 (t0) cc_final: 0.7340 (t70) REVERT: B 69 GLN cc_start: 0.8553 (tm-30) cc_final: 0.8186 (tm-30) REVERT: B 174 MET cc_start: 0.8895 (tpt) cc_final: 0.8672 (tpt) REVERT: C 70 LYS cc_start: 0.8867 (pttt) cc_final: 0.8609 (pttp) REVERT: D 15 PHE cc_start: 0.7113 (OUTLIER) cc_final: 0.6108 (m-80) REVERT: D 50 ASP cc_start: 0.8415 (m-30) cc_final: 0.8022 (p0) REVERT: D 70 MET cc_start: 0.7488 (tpp) cc_final: 0.7080 (mtt) REVERT: D 77 GLU cc_start: 0.8192 (mm-30) cc_final: 0.7727 (mt-10) REVERT: E 176 LEU cc_start: 0.1058 (OUTLIER) cc_final: 0.0854 (mm) REVERT: E 190 ASN cc_start: 0.4655 (m110) cc_final: 0.3910 (t0) REVERT: E 344 ASP cc_start: 0.3316 (m-30) cc_final: 0.2212 (p0) REVERT: E 436 MET cc_start: 0.1690 (ptp) cc_final: 0.1307 (ptm) REVERT: E 461 LEU cc_start: -0.0158 (OUTLIER) cc_final: -0.1902 (mm) REVERT: F 274 MET cc_start: 0.6805 (ppp) cc_final: 0.6185 (tpp) REVERT: F 277 TYR cc_start: -0.2997 (OUTLIER) cc_final: -0.3456 (p90) REVERT: F 303 ARG cc_start: 0.6079 (mtm-85) cc_final: 0.5470 (mmt-90) REVERT: F 488 ILE cc_start: 0.2548 (tp) cc_final: 0.2158 (mt) REVERT: F 537 GLN cc_start: 0.3460 (OUTLIER) cc_final: 0.3096 (pt0) REVERT: F 590 LEU cc_start: 0.1639 (OUTLIER) cc_final: 0.0520 (mp) REVERT: G 12 MET cc_start: 0.7603 (tmm) cc_final: 0.7347 (ttt) REVERT: G 74 ARG cc_start: 0.7712 (OUTLIER) cc_final: 0.7081 (ptm160) outliers start: 83 outliers final: 52 residues processed: 251 average time/residue: 0.1443 time to fit residues: 56.1495 Evaluate side-chains 233 residues out of total 2326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 173 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 487 CYS Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 645 CYS Chi-restraints excluded: chain A residue 646 CYS Chi-restraints excluded: chain A residue 665 GLU Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 697 CYS Chi-restraints excluded: chain A residue 798 LYS Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 876 GLU Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain D residue 15 PHE Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 55 MET Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 75 HIS Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 340 VAL Chi-restraints excluded: chain E residue 399 ILE Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 588 THR Chi-restraints excluded: chain F residue 35 ILE Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 133 PHE Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 243 GLN Chi-restraints excluded: chain F residue 277 TYR Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 358 CYS Chi-restraints excluded: chain F residue 479 VAL Chi-restraints excluded: chain F residue 511 PHE Chi-restraints excluded: chain F residue 512 ILE Chi-restraints excluded: chain F residue 537 GLN Chi-restraints excluded: chain F residue 547 THR Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 590 LEU Chi-restraints excluded: chain G residue 74 ARG Chi-restraints excluded: chain G residue 75 PHE Chi-restraints excluded: chain G residue 79 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 227 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 187 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 24 optimal weight: 0.2980 chunk 155 optimal weight: 0.9990 chunk 237 optimal weight: 20.0000 chunk 1 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 166 optimal weight: 20.0000 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 157 GLN E 9 ASN ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 381 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 = 0.4475 r_free = 0.4475 target = 0.177063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.097707 restraints weight = 89360.864| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 5.41 r_work: 0.3003 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3009 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3009 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22534 Z= 0.129 Angle : 0.588 11.691 30867 Z= 0.304 Chirality : 0.042 0.260 3580 Planarity : 0.005 0.146 3745 Dihedral : 12.589 164.854 3738 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.68 % Favored : 92.09 % Rotamer: Outliers : 3.51 % Allowed : 24.42 % Favored : 72.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.93 % Twisted General : 0.04 % 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: -2.77 (0.15), residues: 2649 helix: -1.30 (0.16), residues: 932 sheet: -0.64 (0.36), residues: 194 loop : -2.45 (0.15), residues: 1523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG G 55 TYR 0.015 0.001 TYR G 87 PHE 0.014 0.001 PHE D 92 TRP 0.048 0.002 TRP F 114 HIS 0.013 0.001 HIS E 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (22515) covalent geometry : angle 0.58726 / 0.30 (30860) SS BOND : bond 0.01064 / 0.56 ( 2) SS BOND : angle 2.32830 / 1.35 ( 4) hydrogen bonds : bond 0.03527 / 2.37 ( 565) hydrogen bonds : angle 4.79399 / 3.34 ( 1584) metal coordination : bond 0.00897 / 0.50 ( 14) metal coordination : angle 1.91842 / 1.03 ( 3) Misc. bond : bond 0.00071 / 0.03 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 188 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 ASN cc_start: 0.8786 (t0) cc_final: 0.8369 (t0) REVERT: A 365 ARG cc_start: 0.8015 (ttp-110) cc_final: 0.7790 (ttm-80) REVERT: A 740 ASP cc_start: 0.8751 (OUTLIER) cc_final: 0.8402 (t0) REVERT: A 876 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8547 (mt-10) REVERT: A 902 MET cc_start: 0.7097 (ttt) cc_final: 0.6852 (tpp) REVERT: B 64 ASP cc_start: 0.7669 (t0) cc_final: 0.7438 (t0) REVERT: B 69 GLN cc_start: 0.8505 (tm-30) cc_final: 0.8091 (tm-30) REVERT: B 174 MET cc_start: 0.8851 (tpt) cc_final: 0.8549 (tpt) REVERT: C 70 LYS cc_start: 0.8887 (pttt) cc_final: 0.8634 (pttp) REVERT: D 15 PHE cc_start: 0.7139 (OUTLIER) cc_final: 0.6178 (m-80) REVERT: D 50 ASP cc_start: 0.8355 (m-30) cc_final: 0.7909 (p0) REVERT: D 70 MET cc_start: 0.7478 (tpp) cc_final: 0.7136 (mtt) REVERT: D 77 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7874 (mt-10) REVERT: D 94 MET cc_start: 0.8607 (mtp) cc_final: 0.8366 (mtp) REVERT: E 190 ASN cc_start: 0.4678 (m110) cc_final: 0.3937 (t0) REVERT: E 344 ASP cc_start: 0.3460 (m-30) cc_final: 0.2391 (p0) REVERT: E 436 MET cc_start: 0.1619 (ptp) cc_final: 0.1385 (ptm) REVERT: E 461 LEU cc_start: -0.0106 (OUTLIER) cc_final: -0.1834 (mm) REVERT: F 274 MET cc_start: 0.6613 (ppp) cc_final: 0.5923 (tpp) REVERT: F 277 TYR cc_start: -0.2942 (OUTLIER) cc_final: -0.3419 (p90) REVERT: F 303 ARG cc_start: 0.6067 (mtm-85) cc_final: 0.5489 (mmt-90) REVERT: F 378 MET cc_start: 0.6539 (mmm) cc_final: 0.6322 (tpp) REVERT: F 488 ILE cc_start: 0.2548 (tp) cc_final: 0.2192 (mt) REVERT: F 537 GLN cc_start: 0.3609 (OUTLIER) cc_final: 0.3199 (pt0) REVERT: F 576 MET cc_start: -0.0027 (mtt) cc_final: -0.1373 (ttm) REVERT: F 590 LEU cc_start: 0.1803 (OUTLIER) cc_final: 0.0778 (mp) REVERT: G 12 MET cc_start: 0.7605 (tmm) cc_final: 0.7353 (ttp) REVERT: G 74 ARG cc_start: 0.7632 (OUTLIER) cc_final: 0.7074 (ptm160) REVERT: G 112 LEU cc_start: 0.6705 (OUTLIER) cc_final: 0.6303 (mp) outliers start: 77 outliers final: 53 residues processed: 248 average time/residue: 0.1426 time to fit residues: 55.3629 Evaluate side-chains 235 residues out of total 2326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 173 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 487 CYS Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 645 CYS Chi-restraints excluded: chain A residue 646 CYS Chi-restraints excluded: chain A residue 665 GLU Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 697 CYS Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 876 GLU Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 139 LYS Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain D residue 15 PHE Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 75 HIS Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 340 VAL Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 588 THR Chi-restraints excluded: chain F residue 35 ILE Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 133 PHE Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 243 GLN Chi-restraints excluded: chain F residue 277 TYR Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 479 VAL Chi-restraints excluded: chain F residue 511 PHE Chi-restraints excluded: chain F residue 512 ILE Chi-restraints excluded: chain F residue 537 GLN Chi-restraints excluded: chain F residue 547 THR Chi-restraints excluded: chain F residue 590 LEU Chi-restraints excluded: chain G residue 2 ASN Chi-restraints excluded: chain G residue 74 ARG Chi-restraints excluded: chain G residue 75 PHE Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 112 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 134 optimal weight: 0.1980 chunk 155 optimal weight: 0.9980 chunk 172 optimal weight: 2.9990 chunk 209 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 221 optimal weight: 0.0070 chunk 29 optimal weight: 1.9990 chunk 237 optimal weight: 4.9990 chunk 116 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 140 optimal weight: 0.9990 overall best weight: 0.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 GLN A 497 ASN E 9 ASN ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 HIS F 281 GLN ** F 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.177719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.105916 restraints weight = 71088.156| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 6.10 r_work: 0.2994 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3007 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3007 r_free = 0.3007 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3007 r_free = 0.3007 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3007 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 22534 Z= 0.107 Angle : 0.562 10.859 30867 Z= 0.290 Chirality : 0.041 0.252 3580 Planarity : 0.005 0.144 3745 Dihedral : 12.470 163.502 3737 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.38 % Favored : 92.40 % Rotamer: Outliers : 3.25 % Allowed : 24.99 % Favored : 71.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.93 % Twisted General : 0.04 % 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: -2.56 (0.15), residues: 2649 helix: -1.07 (0.17), residues: 936 sheet: -0.55 (0.36), residues: 194 loop : -2.36 (0.15), residues: 1519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 497 TYR 0.015 0.001 TYR G 89 PHE 0.024 0.001 PHE F 106 TRP 0.034 0.001 TRP F 114 HIS 0.011 0.001 HIS E 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (22515) covalent geometry : angle 0.56146 / 0.29 (30860) SS BOND : bond 0.00884 / 0.47 ( 2) SS BOND : angle 2.18314 / 1.27 ( 4) hydrogen bonds : bond 0.03285 / 2.21 ( 565) hydrogen bonds : angle 4.70167 / 3.28 ( 1584) metal coordination : bond 0.00992 / 0.63 ( 14) metal coordination : angle 1.72047 / 0.92 ( 3) Misc. bond : bond 0.00047 / 0.02 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 191 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.8351 (t) cc_final: 0.8102 (m) REVERT: A 138 ASN cc_start: 0.8781 (t0) cc_final: 0.8387 (t0) REVERT: A 155 ASP cc_start: 0.8824 (m-30) cc_final: 0.8525 (m-30) REVERT: A 365 ARG cc_start: 0.8004 (ttp-110) cc_final: 0.7777 (ttm-80) REVERT: A 740 ASP cc_start: 0.8787 (OUTLIER) cc_final: 0.8405 (t0) REVERT: A 876 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8521 (mt-10) REVERT: A 902 MET cc_start: 0.7110 (ttt) cc_final: 0.6859 (tpp) REVERT: B 48 GLU cc_start: 0.7471 (tp30) cc_final: 0.7253 (tp30) REVERT: B 64 ASP cc_start: 0.7681 (t0) cc_final: 0.7457 (t0) REVERT: B 69 GLN cc_start: 0.8498 (tm-30) cc_final: 0.8077 (tm-30) REVERT: C 70 LYS cc_start: 0.8869 (pttt) cc_final: 0.8609 (pttp) REVERT: D 15 PHE cc_start: 0.7145 (OUTLIER) cc_final: 0.6219 (m-80) REVERT: D 50 ASP cc_start: 0.8293 (m-30) cc_final: 0.7849 (p0) REVERT: D 70 MET cc_start: 0.7289 (tpp) cc_final: 0.6979 (mtt) REVERT: D 77 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7826 (mt-10) REVERT: D 94 MET cc_start: 0.8517 (mtp) cc_final: 0.8263 (mtp) REVERT: E 190 ASN cc_start: 0.4878 (m110) cc_final: 0.4179 (t0) REVERT: E 344 ASP cc_start: 0.3310 (m-30) cc_final: 0.2263 (p0) REVERT: E 436 MET cc_start: 0.1440 (ptp) cc_final: 0.1191 (ptm) REVERT: E 461 LEU cc_start: -0.0636 (OUTLIER) cc_final: -0.2299 (mm) REVERT: E 576 MET cc_start: 0.2306 (mmp) cc_final: 0.1988 (mmp) REVERT: F 274 MET cc_start: 0.6620 (ppp) cc_final: 0.6033 (tpp) REVERT: F 277 TYR cc_start: -0.2859 (OUTLIER) cc_final: -0.3389 (p90) REVERT: F 303 ARG cc_start: 0.6046 (mtm-85) cc_final: 0.5457 (mmt-90) REVERT: F 488 ILE cc_start: 0.2430 (tp) cc_final: 0.2045 (mt) REVERT: F 537 GLN cc_start: 0.3814 (OUTLIER) cc_final: 0.3411 (pt0) REVERT: F 590 LEU cc_start: 0.1520 (OUTLIER) cc_final: 0.0401 (mp) REVERT: G 12 MET cc_start: 0.7606 (tmm) cc_final: 0.7378 (ttp) REVERT: G 70 GLU cc_start: 0.6268 (pm20) cc_final: 0.6038 (pm20) REVERT: G 74 ARG cc_start: 0.7614 (OUTLIER) cc_final: 0.6987 (ptm160) REVERT: G 112 LEU cc_start: 0.6697 (OUTLIER) cc_final: 0.6338 (mp) outliers start: 71 outliers final: 48 residues processed: 248 average time/residue: 0.1514 time to fit residues: 58.1314 Evaluate side-chains 235 residues out of total 2326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 178 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 487 CYS Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 645 CYS Chi-restraints excluded: chain A residue 665 GLU Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 697 CYS Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 876 GLU Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 139 LYS Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain D residue 15 PHE Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 340 VAL Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 588 THR Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 35 ILE Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 133 PHE Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 243 GLN Chi-restraints excluded: chain F residue 277 TYR Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 479 VAL Chi-restraints excluded: chain F residue 511 PHE Chi-restraints excluded: chain F residue 512 ILE Chi-restraints excluded: chain F residue 537 GLN Chi-restraints excluded: chain F residue 547 THR Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 590 LEU Chi-restraints excluded: chain G residue 74 ARG Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 112 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 43 optimal weight: 0.2980 chunk 76 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 254 optimal weight: 7.9990 chunk 225 optimal weight: 5.9990 chunk 112 optimal weight: 0.7980 chunk 230 optimal weight: 0.0670 chunk 257 optimal weight: 9.9990 chunk 101 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 497 ASN E 9 ASN ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 519 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.177785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.107245 restraints weight = 68311.347| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 5.67 r_work: 0.3005 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3015 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3015 r_free = 0.3015 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3015 r_free = 0.3015 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3015 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.4123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 22534 Z= 0.104 Angle : 0.559 10.093 30867 Z= 0.288 Chirality : 0.041 0.241 3580 Planarity : 0.005 0.141 3745 Dihedral : 12.374 163.540 3735 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.00 % Favored : 92.77 % Rotamer: Outliers : 2.90 % Allowed : 25.08 % Favored : 72.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.93 % Twisted General : 0.04 % 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: -2.42 (0.15), residues: 2649 helix: -0.93 (0.17), residues: 943 sheet: -0.70 (0.36), residues: 200 loop : -2.26 (0.15), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 55 TYR 0.013 0.001 TYR E 269 PHE 0.015 0.001 PHE G 40 TRP 0.027 0.001 TRP F 114 HIS 0.009 0.001 HIS E 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 (22515) covalent geometry : angle 0.55851 / 0.29 (30860) SS BOND : bond 0.00804 / 0.42 ( 2) SS BOND : angle 1.99311 / 1.16 ( 4) hydrogen bonds : bond 0.03208 / 2.16 ( 565) hydrogen bonds : angle 4.63726 / 3.23 ( 1584) metal coordination : bond 0.00674 / 0.39 ( 14) metal coordination : angle 1.54071 / 0.82 ( 3) Misc. bond : bond 0.00051 / 0.02 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 183 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.8286 (t) cc_final: 0.8033 (m) REVERT: A 138 ASN cc_start: 0.8772 (t0) cc_final: 0.8387 (t0) REVERT: A 155 ASP cc_start: 0.8820 (m-30) cc_final: 0.8548 (m-30) REVERT: A 365 ARG cc_start: 0.8038 (ttp-110) cc_final: 0.7792 (ttm-80) REVERT: A 718 LYS cc_start: 0.8356 (tttm) cc_final: 0.8153 (mmtm) REVERT: A 740 ASP cc_start: 0.8707 (OUTLIER) cc_final: 0.8373 (t0) REVERT: A 876 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8519 (mt-10) REVERT: A 902 MET cc_start: 0.7147 (ttt) cc_final: 0.6890 (tpp) REVERT: B 55 MET cc_start: 0.7408 (ppp) cc_final: 0.7156 (tpt) REVERT: B 61 LYS cc_start: 0.7620 (mmmt) cc_final: 0.7107 (tptp) REVERT: B 64 ASP cc_start: 0.7656 (t0) cc_final: 0.7380 (t0) REVERT: B 69 GLN cc_start: 0.8401 (tm-30) cc_final: 0.7951 (tm-30) REVERT: C 70 LYS cc_start: 0.8845 (pttt) cc_final: 0.8622 (pttp) REVERT: D 15 PHE cc_start: 0.7184 (OUTLIER) cc_final: 0.6718 (m-80) REVERT: D 70 MET cc_start: 0.7147 (tpp) cc_final: 0.6874 (mtt) REVERT: D 77 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7806 (mt-10) REVERT: D 94 MET cc_start: 0.8508 (mtp) cc_final: 0.8240 (mtp) REVERT: E 190 ASN cc_start: 0.4857 (m110) cc_final: 0.4168 (t0) REVERT: E 194 GLN cc_start: 0.3427 (tt0) cc_final: 0.2852 (tp40) REVERT: E 344 ASP cc_start: 0.3392 (m-30) cc_final: 0.2377 (p0) REVERT: E 436 MET cc_start: 0.1602 (ptp) cc_final: 0.1180 (ptm) REVERT: E 461 LEU cc_start: -0.0616 (OUTLIER) cc_final: -0.2236 (mm) REVERT: E 576 MET cc_start: 0.2221 (mmp) cc_final: 0.1913 (mmp) REVERT: F 198 TYR cc_start: 0.1738 (m-80) cc_final: 0.1471 (m-10) REVERT: F 274 MET cc_start: 0.6631 (ppp) cc_final: 0.6069 (tpp) REVERT: F 277 TYR cc_start: -0.2850 (OUTLIER) cc_final: -0.3375 (p90) REVERT: F 303 ARG cc_start: 0.6054 (mtm-85) cc_final: 0.5472 (mmt-90) REVERT: F 488 ILE cc_start: 0.2442 (tp) cc_final: 0.2073 (mt) REVERT: F 537 GLN cc_start: 0.3664 (OUTLIER) cc_final: 0.3269 (pt0) REVERT: F 590 LEU cc_start: 0.1622 (OUTLIER) cc_final: 0.0506 (mp) REVERT: G 12 MET cc_start: 0.7559 (tmm) cc_final: 0.7219 (ttm) REVERT: G 70 GLU cc_start: 0.6374 (pm20) cc_final: 0.6145 (pm20) REVERT: G 74 ARG cc_start: 0.7606 (OUTLIER) cc_final: 0.7007 (ptm160) outliers start: 63 outliers final: 52 residues processed: 234 average time/residue: 0.1482 time to fit residues: 53.9392 Evaluate side-chains 236 residues out of total 2326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 176 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 487 CYS Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 645 CYS Chi-restraints excluded: chain A residue 665 GLU Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 697 CYS Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 876 GLU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 139 LYS Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain D residue 15 PHE Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 75 HIS Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 340 VAL Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 588 THR Chi-restraints excluded: chain F residue 35 ILE Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 133 PHE Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 277 TYR Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 479 VAL Chi-restraints excluded: chain F residue 511 PHE Chi-restraints excluded: chain F residue 512 ILE Chi-restraints excluded: chain F residue 519 ASN Chi-restraints excluded: chain F residue 537 GLN Chi-restraints excluded: chain F residue 547 THR Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 590 LEU Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 74 ARG Chi-restraints excluded: chain G residue 79 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 103 optimal weight: 0.4980 chunk 183 optimal weight: 3.9990 chunk 265 optimal weight: 10.0000 chunk 248 optimal weight: 8.9990 chunk 187 optimal weight: 30.0000 chunk 53 optimal weight: 0.3980 chunk 124 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 236 optimal weight: 20.0000 chunk 230 optimal weight: 10.0000 chunk 166 optimal weight: 6.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 497 ASN B 140 ASN E 9 ASN ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 519 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.177463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.097442 restraints weight = 93773.496| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 4.91 r_work: 0.3030 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3037 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3037 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.4129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.141 22534 Z= 0.177 Angle : 0.708 59.200 30867 Z= 0.401 Chirality : 0.044 0.648 3580 Planarity : 0.005 0.140 3745 Dihedral : 12.381 163.771 3735 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.19 % Favored : 92.58 % Rotamer: Outliers : 3.03 % Allowed : 24.86 % Favored : 72.11 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.93 % Twisted General : 0.04 % 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: -2.42 (0.15), residues: 2649 helix: -0.93 (0.17), residues: 942 sheet: -0.75 (0.36), residues: 206 loop : -2.25 (0.15), residues: 1501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 55 TYR 0.014 0.001 TYR E 269 PHE 0.011 0.001 PHE A 753 TRP 0.022 0.001 TRP F 114 HIS 0.009 0.001 HIS E 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.18 (22515) covalent geometry : angle 0.70726 / 0.40 (30860) SS BOND : bond 0.00878 / 0.46 ( 2) SS BOND : angle 1.98334 / 1.15 ( 4) hydrogen bonds : bond 0.03330 / 2.24 ( 565) hydrogen bonds : angle 4.64110 / 3.24 ( 1584) metal coordination : bond 0.00771 / 0.45 ( 14) metal coordination : angle 1.54228 / 0.82 ( 3) Misc. bond : bond 0.00081 / 0.04 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 176 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.8322 (t) cc_final: 0.8081 (m) REVERT: A 138 ASN cc_start: 0.8788 (t0) cc_final: 0.8405 (t0) REVERT: A 155 ASP cc_start: 0.8820 (m-30) cc_final: 0.8548 (m-30) REVERT: A 365 ARG cc_start: 0.7993 (ttp-110) cc_final: 0.7786 (ttm-80) REVERT: A 740 ASP cc_start: 0.8702 (OUTLIER) cc_final: 0.8357 (t0) REVERT: A 876 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8535 (mt-10) REVERT: A 902 MET cc_start: 0.7127 (ttt) cc_final: 0.6879 (tpp) REVERT: A 906 MET cc_start: 0.6339 (pmm) cc_final: 0.6107 (pmm) REVERT: B 55 MET cc_start: 0.7423 (ppp) cc_final: 0.7187 (tpt) REVERT: B 61 LYS cc_start: 0.7650 (mmmt) cc_final: 0.7132 (tptp) REVERT: B 64 ASP cc_start: 0.7682 (t0) cc_final: 0.7397 (t0) REVERT: B 69 GLN cc_start: 0.8408 (tm-30) cc_final: 0.7950 (tm-30) REVERT: C 67 ASP cc_start: 0.8169 (t70) cc_final: 0.7927 (t70) REVERT: C 70 LYS cc_start: 0.8870 (pttt) cc_final: 0.8654 (pttp) REVERT: D 15 PHE cc_start: 0.7128 (OUTLIER) cc_final: 0.6727 (m-80) REVERT: D 70 MET cc_start: 0.7215 (tpp) cc_final: 0.6936 (mtt) REVERT: D 77 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7832 (mt-10) REVERT: D 94 MET cc_start: 0.8572 (mtp) cc_final: 0.8303 (mtp) REVERT: E 190 ASN cc_start: 0.4863 (m110) cc_final: 0.4173 (t0) REVERT: E 194 GLN cc_start: 0.3434 (tt0) cc_final: 0.2840 (tp40) REVERT: E 344 ASP cc_start: 0.3343 (m-30) cc_final: 0.2328 (p0) REVERT: E 436 MET cc_start: 0.1529 (ptp) cc_final: 0.1100 (ptm) REVERT: E 461 LEU cc_start: -0.0695 (OUTLIER) cc_final: -0.2296 (mm) REVERT: E 576 MET cc_start: 0.2228 (mmp) cc_final: 0.1920 (mmp) REVERT: F 274 MET cc_start: 0.6626 (ppp) cc_final: 0.6064 (tpp) REVERT: F 277 TYR cc_start: -0.2838 (OUTLIER) cc_final: -0.3370 (p90) REVERT: F 303 ARG cc_start: 0.6047 (mtm-85) cc_final: 0.5467 (mmt-90) REVERT: F 488 ILE cc_start: 0.2447 (tp) cc_final: 0.2075 (mt) REVERT: F 537 GLN cc_start: 0.3685 (OUTLIER) cc_final: 0.3288 (pt0) REVERT: F 590 LEU cc_start: 0.1579 (OUTLIER) cc_final: 0.0453 (mp) REVERT: G 12 MET cc_start: 0.7540 (tmm) cc_final: 0.7192 (ttm) REVERT: G 70 GLU cc_start: 0.6387 (pm20) cc_final: 0.6164 (pm20) REVERT: G 74 ARG cc_start: 0.7621 (OUTLIER) cc_final: 0.7029 (ptm160) outliers start: 66 outliers final: 53 residues processed: 229 average time/residue: 0.1481 time to fit residues: 53.5780 Evaluate side-chains 236 residues out of total 2326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 175 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 487 CYS Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 645 CYS Chi-restraints excluded: chain A residue 665 GLU Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 697 CYS Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 876 GLU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain D residue 15 PHE Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 75 HIS Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 340 VAL Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 588 THR Chi-restraints excluded: chain F residue 35 ILE Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 133 PHE Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 243 GLN Chi-restraints excluded: chain F residue 277 TYR Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 479 VAL Chi-restraints excluded: chain F residue 511 PHE Chi-restraints excluded: chain F residue 512 ILE Chi-restraints excluded: chain F residue 519 ASN Chi-restraints excluded: chain F residue 537 GLN Chi-restraints excluded: chain F residue 547 THR Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 590 LEU Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 74 ARG Chi-restraints excluded: chain G residue 79 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 126 optimal weight: 1.9990 chunk 214 optimal weight: 0.2980 chunk 105 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 206 optimal weight: 0.1980 chunk 57 optimal weight: 0.5980 chunk 151 optimal weight: 6.9990 chunk 111 optimal weight: 0.9990 chunk 119 optimal weight: 8.9990 chunk 63 optimal weight: 0.9980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 497 ASN E 9 ASN ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 519 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 = 0.4480 r_free = 0.4480 target = 0.177447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.100476 restraints weight = 62326.677| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 4.69 r_work: 0.3049 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3051 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3051 r_free = 0.3051 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3051 r_free = 0.3051 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3051 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.141 22534 Z= 0.177 Angle : 0.706 57.818 30867 Z= 0.401 Chirality : 0.044 0.639 3580 Planarity : 0.005 0.140 3745 Dihedral : 12.381 163.771 3735 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.19 % Favored : 92.58 % Rotamer: Outliers : 2.85 % Allowed : 25.03 % Favored : 72.11 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.93 % Twisted General : 0.04 % 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: -2.42 (0.15), residues: 2649 helix: -0.93 (0.17), residues: 942 sheet: -0.75 (0.36), residues: 206 loop : -2.25 (0.15), residues: 1501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 55 TYR 0.014 0.001 TYR E 269 PHE 0.011 0.001 PHE A 753 TRP 0.022 0.001 TRP F 114 HIS 0.009 0.001 HIS E 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.18 (22515) covalent geometry : angle 0.70517 / 0.40 (30860) SS BOND : bond 0.00878 / 0.46 ( 2) SS BOND : angle 1.98334 / 1.15 ( 4) hydrogen bonds : bond 0.03330 / 2.24 ( 565) hydrogen bonds : angle 4.64110 / 3.24 ( 1584) metal coordination : bond 0.00909 / 0.57 ( 14) metal coordination : angle 1.54228 / 0.82 ( 3) Misc. bond : bond 0.00081 / 0.04 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 175 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 VAL cc_start: 0.8280 (t) cc_final: 0.8029 (m) REVERT: A 138 ASN cc_start: 0.8768 (t0) cc_final: 0.8379 (t0) REVERT: A 155 ASP cc_start: 0.8815 (m-30) cc_final: 0.8537 (m-30) REVERT: A 365 ARG cc_start: 0.7953 (ttp-110) cc_final: 0.7752 (ttm-80) REVERT: A 740 ASP cc_start: 0.8687 (OUTLIER) cc_final: 0.8336 (t0) REVERT: A 876 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8496 (mt-10) REVERT: A 902 MET cc_start: 0.7136 (ttt) cc_final: 0.6886 (tpp) REVERT: A 906 MET cc_start: 0.6326 (pmm) cc_final: 0.6092 (pmm) REVERT: B 55 MET cc_start: 0.7409 (ppp) cc_final: 0.7173 (tpt) REVERT: B 61 LYS cc_start: 0.7609 (mmmt) cc_final: 0.7096 (tptp) REVERT: B 64 ASP cc_start: 0.7658 (t0) cc_final: 0.7377 (t0) REVERT: B 69 GLN cc_start: 0.8373 (tm-30) cc_final: 0.7915 (tm-30) REVERT: C 67 ASP cc_start: 0.8165 (t70) cc_final: 0.7921 (t70) REVERT: C 70 LYS cc_start: 0.8879 (pttt) cc_final: 0.8657 (pttp) REVERT: D 15 PHE cc_start: 0.7109 (OUTLIER) cc_final: 0.6705 (m-80) REVERT: D 70 MET cc_start: 0.7128 (tpp) cc_final: 0.6848 (mtt) REVERT: D 77 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7787 (mt-10) REVERT: D 94 MET cc_start: 0.8501 (mtp) cc_final: 0.8226 (mtp) REVERT: E 190 ASN cc_start: 0.4855 (m110) cc_final: 0.4163 (t0) REVERT: E 194 GLN cc_start: 0.3436 (tt0) cc_final: 0.2852 (tp40) REVERT: E 344 ASP cc_start: 0.3350 (m-30) cc_final: 0.2329 (p0) REVERT: E 436 MET cc_start: 0.1526 (ptp) cc_final: 0.1094 (ptm) REVERT: E 461 LEU cc_start: -0.0720 (OUTLIER) cc_final: -0.2318 (mm) REVERT: E 576 MET cc_start: 0.2240 (mmp) cc_final: 0.1930 (mmp) REVERT: F 274 MET cc_start: 0.6632 (ppp) cc_final: 0.6068 (tpp) REVERT: F 277 TYR cc_start: -0.2840 (OUTLIER) cc_final: -0.3372 (p90) REVERT: F 303 ARG cc_start: 0.6044 (mtm-85) cc_final: 0.5452 (mmt-90) REVERT: F 488 ILE cc_start: 0.2439 (tp) cc_final: 0.2062 (mt) REVERT: F 537 GLN cc_start: 0.3700 (OUTLIER) cc_final: 0.3301 (pt0) REVERT: F 590 LEU cc_start: 0.1545 (OUTLIER) cc_final: 0.0406 (mp) REVERT: G 12 MET cc_start: 0.7568 (tmm) cc_final: 0.7230 (ttm) REVERT: G 70 GLU cc_start: 0.6362 (pm20) cc_final: 0.6132 (pm20) REVERT: G 74 ARG cc_start: 0.7612 (OUTLIER) cc_final: 0.7019 (ptm160) outliers start: 62 outliers final: 53 residues processed: 226 average time/residue: 0.1363 time to fit residues: 48.7470 Evaluate side-chains 235 residues out of total 2326 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 174 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 487 CYS Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 645 CYS Chi-restraints excluded: chain A residue 665 GLU Chi-restraints excluded: chain A residue 680 THR Chi-restraints excluded: chain A residue 697 CYS Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 857 GLU Chi-restraints excluded: chain A residue 876 GLU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain D residue 15 PHE Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 172 ILE Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 75 HIS Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 340 VAL Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 588 THR Chi-restraints excluded: chain F residue 35 ILE Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 133 PHE Chi-restraints excluded: chain F residue 181 VAL Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 243 GLN Chi-restraints excluded: chain F residue 277 TYR Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 348 VAL Chi-restraints excluded: chain F residue 479 VAL Chi-restraints excluded: chain F residue 511 PHE Chi-restraints excluded: chain F residue 512 ILE Chi-restraints excluded: chain F residue 519 ASN Chi-restraints excluded: chain F residue 537 GLN Chi-restraints excluded: chain F residue 547 THR Chi-restraints excluded: chain F residue 552 THR Chi-restraints excluded: chain F residue 590 LEU Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 74 ARG Chi-restraints excluded: chain G residue 79 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 115 optimal weight: 2.9990 chunk 119 optimal weight: 8.9990 chunk 245 optimal weight: 8.9990 chunk 208 optimal weight: 3.9990 chunk 220 optimal weight: 8.9990 chunk 15 optimal weight: 0.0270 chunk 194 optimal weight: 4.9990 chunk 145 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 184 optimal weight: 9.9990 chunk 180 optimal weight: 7.9990 overall best weight: 3.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 497 ASN E 9 ASN E 519 ASN E 537 GLN ** E 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 290 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 381 ASN F 519 ASN G 98 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.173090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.106122 restraints weight = 79917.939| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 6.03 r_work: 0.2891 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2899 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2899 r_free = 0.2899 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2899 r_free = 0.2899 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2899 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.4415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 22534 Z= 0.292 Angle : 0.700 9.751 30867 Z= 0.363 Chirality : 0.048 0.308 3580 Planarity : 0.006 0.135 3745 Dihedral : 12.561 171.969 3735 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.17 % Favored : 91.56 % Rotamer: Outliers : 2.85 % Allowed : 25.08 % Favored : 72.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.93 % Twisted General : 0.08 % 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: -2.71 (0.15), residues: 2649 helix: -1.33 (0.16), residues: 942 sheet: -1.01 (0.35), residues: 218 loop : -2.30 (0.15), residues: 1489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 55 TYR 0.023 0.002 TYR A 788 PHE 0.029 0.002 PHE G 56 TRP 0.015 0.002 TRP F 114 HIS 0.012 0.002 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00703 / 0.29 (22515) covalent geometry : angle 0.69942 / 0.36 (30860) SS BOND : bond 0.01060 / 0.56 ( 2) SS BOND : angle 2.09180 / 1.20 ( 4) hydrogen bonds : bond 0.04483 / 3.02 ( 565) hydrogen bonds : angle 4.95089 / 3.43 ( 1584) metal coordination : bond 0.01582 / 0.86 ( 14) metal coordination : angle 3.07007 / 1.70 ( 3) Misc. bond : bond 0.00053 / 0.03 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7528.07 seconds wall clock time: 128 minutes 49.69 seconds (7729.69 seconds total)