Starting phenix.real_space_refine on Sat Jul 4 16:02:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gwk_34314/07_2026/8gwk_34314.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gwk_34314/07_2026/8gwk_34314.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8gwk_34314/07_2026/8gwk_34314.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gwk_34314/07_2026/8gwk_34314.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gwk_34314/07_2026/8gwk_34314.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gwk_34314/07_2026/8gwk_34314.map" } resolution = 2.72 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= -0.001 sd= 0.079 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 8 6.06 5 P 55 5.49 5 Mg 1 5.21 5 S 158 5.16 5 C 13731 2.51 5 N 3695 2.21 5 O 4301 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21949 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 7496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 931, 7496 Classifications: {'peptide': 931} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 900} Chain: "B" Number of atoms: 1400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1400 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 6, 'TRANS': 180} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 47 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': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 586 Classifications: {'peptide': 76} Link IDs: {'TRANS': 75} Chain: "D" Number of atoms: 1418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1418 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 179} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 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: "I" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 545 Classifications: {'RNA': 25} Modifications used: {'rna3p_pur': 17, 'rna3p_pyr': 8} Link IDs: {'rna3p': 24} Chain: "J" Number of atoms: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 545 Classifications: {'RNA': 26} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 9, 'rna3p_pyr': 16} Link IDs: {'rna2p': 1, 'rna3p': 24} Chain: "E" Number of atoms: 4512 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 585, 4504 Classifications: {'peptide': 585} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 30, 'TRANS': 554} Chain breaks: 2 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 49 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, 4504 Classifications: {'peptide': 585} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 30, 'TRANS': 554} Chain breaks: 2 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 49 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: 4597 Chain: "F" Number of atoms: 4508 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 585, 4500 Classifications: {'peptide': 585} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 554} 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: 585, 4500 Classifications: {'peptide': 585} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 30, 'TRANS': 554} 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: 4593 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: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 35 Unusual residues: {' MG': 1, ' ZN': 2, 'GNP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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} Chain: "G" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'F86': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2465 SG CYS A 301 72.233 54.465 124.579 1.00 67.84 S ATOM 2506 SG CYS A 306 72.212 56.341 127.800 1.00 79.19 S ATOM 2538 SG CYS A 310 73.640 52.762 127.678 1.00 79.47 S ATOM 3946 SG CYS A 487 75.098 68.759 108.774 1.00 70.80 S ATOM 5199 SG CYS A 645 74.118 70.775 111.852 1.00 72.59 S ATOM 5205 SG CYS A 646 73.084 67.093 111.555 1.00 76.98 S ATOM 12094 SG CYS E 16 104.516 64.617 53.364 1.00201.51 S ATOM 12109 SG CYS E 19 103.073 61.259 51.898 1.00201.84 S ATOM 12012 SG CYS E 5 113.475 64.593 53.812 1.00183.79 S ATOM 12033 SG CYS E 8 115.513 67.633 52.301 1.00199.76 S ATOM 12171 SG CYS E 26 114.438 67.766 55.438 1.00183.21 S ATOM 12188 SG CYS E 29 111.635 67.563 52.339 1.00162.89 S ATOM 12353 SG CYS E 50 90.841 72.158 63.523 1.00165.72 S ATOM 12383 SG CYS E 55 87.567 72.726 62.216 1.00168.43 S ATOM 12516 SG CYS E 72 90.540 75.199 61.502 1.00181.45 S ATOM 16606 SG CYS F 16 60.303 72.214 66.094 1.00170.84 S ATOM 16621 SG CYS F 19 57.233 69.823 66.266 1.00166.87 S ATOM 16524 SG CYS F 5 68.110 68.667 60.431 1.00169.03 S ATOM 16545 SG CYS F 8 68.167 70.451 57.134 1.00171.27 S ATOM 16683 SG CYS F 26 68.988 72.225 59.823 1.00182.64 S ATOM 16700 SG CYS F 29 65.266 71.602 59.587 1.00187.51 S ATOM 16865 SG CYS F 50 62.087 84.817 78.963 1.00183.62 S ATOM 16895 SG CYS F 55 58.996 85.619 81.015 1.00184.58 S ATOM 17028 SG CYS F 72 61.078 88.297 79.038 1.00189.62 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AMET E 474 " occ=0.22 ... (14 atoms not shown) pdb=" CE BMET E 474 " occ=0.78 residue: pdb=" N AMET F 474 " occ=0.80 ... (14 atoms not shown) pdb=" CE BMET F 474 " occ=0.20 Time building chain proxies: 6.64, per 1000 atoms: 0.30 Number of scatterers: 21949 At special positions: 0 Unit cell: (153.6, 136.32, 190.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 8 29.99 S 158 16.00 P 55 15.00 Mg 1 11.99 O 4301 8.00 N 3695 7.00 C 13731 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.84 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " pdb=" ZN E 701 " pdb="ZN ZN E 701 " - pdb=" ND1 HIS E 39 " pdb="ZN ZN E 701 " - pdb=" NE2 HIS E 33 " pdb="ZN ZN E 701 " - pdb=" SG CYS E 19 " 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 ZN E 702 " - pdb=" SG CYS E 5 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 26 " pdb="ZN ZN E 702 " - pdb=" SG CYS E 29 " pdb=" ZN E 703 " pdb="ZN ZN E 703 " - pdb=" ND1 HIS E 75 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 50 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 72 " pdb="ZN ZN E 703 " - pdb=" SG CYS E 55 " pdb=" ZN F 701 " pdb="ZN ZN F 701 " - pdb=" NE2 HIS F 33 " pdb="ZN ZN F 701 " - pdb=" ND1 HIS F 39 " pdb="ZN ZN F 701 " - pdb=" SG CYS F 19 " pdb="ZN ZN F 701 " - pdb=" SG CYS F 16 " pdb=" ZN F 702 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 26 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 8 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 5 " pdb="ZN ZN F 702 " - pdb=" SG CYS F 29 " pdb=" ZN F 703 " pdb="ZN ZN F 703 " - pdb=" ND1 HIS F 75 " pdb="ZN ZN F 703 " - pdb=" SG CYS F 50 " pdb="ZN ZN F 703 " - pdb=" SG CYS F 72 " pdb="ZN ZN F 703 " - pdb=" SG CYS F 55 " Number of angles added : 27 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5084 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 31 sheets defined 41.1% alpha, 13.5% beta 17 base pairs and 34 stacking pairs defined. Time for finding SS restraints: 2.45 Creating SS restraints... Processing helix chain 'A' and resid 4 through 13 removed outlier: 3.766A pdb=" N CYS A 12 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLY A 13 " --> pdb=" O ASN A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 63 No H-bonds generated for 'chain 'A' and resid 61 through 63' Processing helix chain 'A' and resid 77 through 91 Processing helix chain 'A' and resid 123 through 133 removed outlier: 3.778A pdb=" N LEU A 127 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 149 Processing helix chain 'A' and resid 153 through 159 removed outlier: 3.675A pdb=" N PHE A 157 " --> pdb=" O ASP A 154 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS A 159 " --> pdb=" O TYR A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 176 Processing helix chain 'A' and resid 178 through 200 removed outlier: 3.519A pdb=" N VAL A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 242 removed outlier: 3.564A pdb=" N TYR A 238 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER A 239 " --> pdb=" O ASP A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 248 removed outlier: 3.803A pdb=" N LEU A 247 " --> pdb=" O PRO A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 256 removed outlier: 3.723A pdb=" N THR A 252 " --> pdb=" O ARG A 249 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ALA A 253 " --> pdb=" O ALA A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 287 Processing helix chain 'A' and resid 297 through 301 removed outlier: 3.552A pdb=" N CYS A 301 " --> pdb=" O CYS A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.693A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 377 Processing helix chain 'A' and resid 378 through 383 Processing helix chain 'A' and resid 416 through 425 Processing helix chain 'A' and resid 447 through 454 removed outlier: 3.585A pdb=" N SER A 451 " --> pdb=" O ASN A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 459 removed outlier: 3.535A pdb=" N TYR A 458 " --> pdb=" O TYR A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 479 removed outlier: 3.880A pdb=" N PHE A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 509 removed outlier: 3.504A pdb=" N LYS A 508 " --> pdb=" O PRO A 505 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TRP A 509 " --> pdb=" O PHE A 506 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 505 through 509' Processing helix chain 'A' and resid 511 through 519 removed outlier: 3.761A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N MET A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 531 removed outlier: 3.584A pdb=" N ASP A 525 " --> pdb=" O TYR A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 580 removed outlier: 4.228A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLN A 570 " --> pdb=" O MET A 566 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 607 Processing helix chain 'A' and resid 621 through 626 removed outlier: 3.620A pdb=" N MET A 626 " --> pdb=" O CYS A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 640 removed outlier: 3.532A pdb=" N ARG A 631 " --> pdb=" O PRO A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 663 removed outlier: 3.581A pdb=" N ARG A 651 " --> pdb=" O SER A 647 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE A 652 " --> pdb=" O LEU A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 709 removed outlier: 3.632A pdb=" N SER A 692 " --> pdb=" O ALA A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 732 removed outlier: 3.650A pdb=" N ARG A 721 " --> pdb=" O ASP A 717 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN A 722 " --> pdb=" O LYS A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 768 through 773 Processing helix chain 'A' and resid 778 through 791 removed outlier: 3.862A pdb=" N PHE A 782 " --> pdb=" O SER A 778 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN A 791 " --> pdb=" O TYR A 787 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 842 removed outlier: 3.666A pdb=" N ILE A 837 " --> pdb=" O ASP A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 855 removed outlier: 5.022A pdb=" N GLY A 852 " --> pdb=" O LYS A 849 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N THR A 853 " --> pdb=" O THR A 850 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU A 854 " --> pdb=" O ASP A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 866 Processing helix chain 'A' and resid 867 through 872 removed outlier: 3.524A pdb=" N LYS A 871 " --> pdb=" O PRO A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 897 removed outlier: 3.939A pdb=" N ALA A 878 " --> pdb=" O ASN A 874 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP A 879 " --> pdb=" O GLN A 875 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N VAL A 880 " --> pdb=" O GLU A 876 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 917 removed outlier: 3.768A pdb=" N ARG A 914 " --> pdb=" O ASN A 911 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR A 915 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N TRP A 916 " --> pdb=" O SER A 913 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU A 917 " --> pdb=" O ARG A 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 911 through 917' Processing helix chain 'A' and resid 918 through 923 Processing helix chain 'A' and resid 924 through 926 No H-bonds generated for 'chain 'A' and resid 924 through 926' Processing helix chain 'B' and resid 9 through 29 removed outlier: 4.385A pdb=" N ALA B 13 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ALA B 14 " --> pdb=" O PRO B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 41 removed outlier: 3.709A pdb=" N LEU B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 52 Processing helix chain 'B' and resid 58 through 95 removed outlier: 3.539A pdb=" N ARG B 80 " --> pdb=" O SER B 76 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA B 81 " --> pdb=" O GLU B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 98 No H-bonds generated for 'chain 'B' and resid 96 through 98' Processing helix chain 'B' and resid 100 through 109 removed outlier: 3.966A pdb=" N ASN B 104 " --> pdb=" O ASN B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 125 Processing helix chain 'B' and resid 134 through 142 removed outlier: 3.564A 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 3 through 20 Processing helix chain 'C' and resid 21 through 24 removed outlier: 3.800A pdb=" N SER C 24 " --> pdb=" O ARG C 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 21 through 24' Processing helix chain 'C' and resid 25 through 40 Processing helix chain 'C' and resid 46 through 62 removed outlier: 3.940A pdb=" N GLU C 50 " --> pdb=" O THR C 46 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N MET C 62 " --> pdb=" O VAL C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 75 removed outlier: 3.685A pdb=" N LEU C 71 " --> pdb=" O ASP C 67 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N MET C 75 " --> pdb=" O LEU C 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 29 removed outlier: 4.284A pdb=" N ALA D 14 " --> pdb=" O PRO D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 44 removed outlier: 3.767A pdb=" N LYS D 39 " --> pdb=" O LEU D 35 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 80 removed outlier: 3.758A pdb=" N LYS D 61 " --> pdb=" O ARG D 57 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG D 80 " --> pdb=" O SER D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 99 removed outlier: 5.496A pdb=" N GLN D 88 " --> pdb=" O THR D 84 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASP D 99 " --> pdb=" O LEU D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 134 through 142 removed outlier: 3.634A pdb=" N ASN D 140 " --> pdb=" O ASN D 136 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N THR D 141 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 172 Processing helix chain 'D' and resid 176 through 180 removed outlier: 3.675A pdb=" N LEU D 180 " --> pdb=" O SER D 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 26 through 36 Processing helix chain 'E' and resid 103 through 112 Processing helix chain 'E' and resid 116 through 124 removed outlier: 4.034A pdb=" N TYR E 120 " --> pdb=" O ASN E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 148 removed outlier: 3.878A pdb=" N SER E 148 " --> pdb=" O THR E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 261 No H-bonds generated for 'chain 'E' and resid 259 through 261' Processing helix chain 'E' and resid 262 through 275 removed outlier: 4.112A pdb=" N ALA E 267 " --> pdb=" O SER E 263 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ASN E 268 " --> pdb=" O SER E 264 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LYS E 271 " --> pdb=" O ALA E 267 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN E 275 " --> pdb=" O LYS E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 299 removed outlier: 4.952A pdb=" N ALA E 296 " --> pdb=" O ALA E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 320 removed outlier: 3.787A pdb=" N VAL E 314 " --> pdb=" O SER E 310 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA E 316 " --> pdb=" O ALA E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 320 through 325 Processing helix chain 'E' and resid 326 through 330 removed outlier: 3.892A pdb=" N LYS E 329 " --> pdb=" O PRO E 326 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N CYS E 330 " --> pdb=" O ILE E 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 326 through 330' Processing helix chain 'E' and resid 380 through 391 removed outlier: 4.471A pdb=" N VAL E 387 " --> pdb=" O ASP E 383 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ASN E 388 " --> pdb=" O LEU E 384 " (cutoff:3.500A) Processing helix chain 'E' and resid 418 through 422 removed outlier: 3.666A pdb=" N PHE E 422 " --> pdb=" O PRO E 419 " (cutoff:3.500A) Processing helix chain 'E' and resid 423 through 432 removed outlier: 4.235A pdb=" N ARG E 427 " --> pdb=" O ASN E 423 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET E 429 " --> pdb=" O VAL E 425 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LYS E 430 " --> pdb=" O CYS E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 447 through 456 removed outlier: 3.592A pdb=" N SER E 453 " --> pdb=" O VAL E 449 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ALA E 454 " --> pdb=" O ASP E 450 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU E 455 " --> pdb=" O THR E 451 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL E 456 " --> pdb=" O VAL E 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 489 through 501 removed outlier: 3.651A pdb=" N ILE E 493 " --> pdb=" O ASN E 489 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL E 495 " --> pdb=" O PRO E 491 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N VAL E 496 " --> pdb=" O GLN E 492 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG E 497 " --> pdb=" O ILE E 493 " (cutoff:3.500A) Processing helix chain 'E' and resid 502 through 507 removed outlier: 6.487A pdb=" N ALA E 505 " --> pdb=" O ARG E 502 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ARG E 507 " --> pdb=" O PRO E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 515 through 527 removed outlier: 4.056A pdb=" N ASN E 519 " --> pdb=" O TYR E 515 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA E 520 " --> pdb=" O ASN E 516 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LYS E 524 " --> pdb=" O ALA E 520 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE E 525 " --> pdb=" O VAL E 521 " (cutoff:3.500A) Processing helix chain 'E' and resid 532 through 536 Processing helix chain 'E' and resid 561 through 566 removed outlier: 3.610A pdb=" N ILE E 565 " --> pdb=" O PHE E 561 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N THR E 566 " --> pdb=" O ASN E 562 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 561 through 566' Processing helix chain 'F' and resid 26 through 37 Processing helix chain 'F' and resid 72 through 76 removed outlier: 4.013A pdb=" N LYS F 76 " --> pdb=" O LYS F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 112 Processing helix chain 'F' and resid 116 through 124 removed outlier: 4.041A pdb=" N TYR F 120 " --> pdb=" O ASN F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 148 removed outlier: 4.012A pdb=" N SER F 148 " --> pdb=" O THR F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 261 No H-bonds generated for 'chain 'F' and resid 259 through 261' Processing helix chain 'F' and resid 262 through 275 removed outlier: 4.217A pdb=" N ALA F 267 " --> pdb=" O SER F 263 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ASN F 268 " --> pdb=" O SER F 264 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN F 270 " --> pdb=" O VAL F 266 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LYS F 271 " --> pdb=" O ALA F 267 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL F 272 " --> pdb=" O ASN F 268 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY F 273 " --> pdb=" O TYR F 269 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN F 275 " --> pdb=" O LYS F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 299 removed outlier: 4.779A pdb=" N ALA F 296 " --> pdb=" O ALA F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 320 removed outlier: 4.042A pdb=" N VAL F 314 " --> pdb=" O SER F 310 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA F 316 " --> pdb=" O ALA F 312 " (cutoff:3.500A) Processing helix chain 'F' and resid 320 through 325 removed outlier: 3.510A pdb=" N TYR F 324 " --> pdb=" O LYS F 320 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 328 No H-bonds generated for 'chain 'F' and resid 326 through 328' Processing helix chain 'F' and resid 375 through 379 Processing helix chain 'F' and resid 380 through 391 removed outlier: 4.654A pdb=" N VAL F 387 " --> pdb=" O ASP F 383 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ASN F 388 " --> pdb=" O LEU F 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 423 through 429 removed outlier: 3.688A pdb=" N ARG F 427 " --> pdb=" O ASN F 423 " (cutoff:3.500A) Processing helix chain 'F' and resid 447 through 456 removed outlier: 3.590A pdb=" N SER F 453 " --> pdb=" O VAL F 449 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ALA F 454 " --> pdb=" O ASP F 450 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU F 455 " --> pdb=" O THR F 451 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL F 456 " --> pdb=" O VAL F 452 " (cutoff:3.500A) Processing helix chain 'F' and resid 489 through 501 removed outlier: 4.043A pdb=" N VAL F 495 " --> pdb=" O PRO F 491 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N VAL F 496 " --> pdb=" O GLN F 492 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG F 497 " --> pdb=" O ILE F 493 " (cutoff:3.500A) Processing helix chain 'F' and resid 515 through 526 removed outlier: 4.182A pdb=" N ASN F 519 " --> pdb=" O TYR F 515 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA F 520 " --> pdb=" O ASN F 516 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N LYS F 524 " --> pdb=" O ALA F 520 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE F 525 " --> pdb=" O VAL F 521 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 110 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 21 removed outlier: 5.507A pdb=" N SER A 68 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N VAL A 71 " --> pdb=" O GLN A 117 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N GLN A 117 " --> pdb=" O VAL A 71 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 38 Processing sheet with id=AA3, first strand: chain 'A' and resid 223 through 224 removed outlier: 6.625A pdb=" N ILE A 201 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N VAL A 233 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 7.008A 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: 3.552A pdb=" N GLY A 352 " --> pdb=" O PHE A 348 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 334 through 335 Processing sheet with id=AA6, first strand: chain 'A' and resid 556 through 559 removed outlier: 6.770A pdb=" N THR A 540 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER A 672 " --> pdb=" O CYS A 669 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU A 673 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N VAL A 398 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LEU A 388 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE B 185 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N VAL B 159 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N THR B 187 " --> pdb=" O GLN B 157 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 556 through 559 removed outlier: 6.770A pdb=" N THR A 540 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER A 672 " --> pdb=" O CYS A 669 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU A 673 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N VAL A 398 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LEU A 388 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE B 185 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N VAL B 159 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N THR B 187 " --> pdb=" O GLN B 157 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N VAL B 159 " --> pdb=" O VAL B 167 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 414 through 415 Processing sheet with id=AA9, first strand: chain 'A' and resid 753 through 758 Processing sheet with id=AB1, first strand: chain 'A' and resid 816 through 822 removed outlier: 3.559A pdb=" N ASP A 825 " --> pdb=" O GLN A 822 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 115 through 116 removed outlier: 3.716A pdb=" N VAL D 115 " --> pdb=" O VAL D 131 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ILE D 185 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N VAL D 159 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N THR D 187 " --> pdb=" O GLN D 157 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 115 through 116 removed outlier: 3.716A pdb=" N VAL D 115 " --> pdb=" O VAL D 131 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ILE D 185 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N VAL D 159 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N THR D 187 " --> pdb=" O GLN D 157 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N VAL D 159 " --> pdb=" O VAL D 167 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 3 through 4 removed outlier: 3.512A pdb=" N GLY E 3 " --> pdb=" O THR E 12 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 24 through 25 removed outlier: 3.539A pdb=" N LEU E 25 " --> pdb=" O LEU E 14 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU E 14 " --> pdb=" O LEU E 25 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 70 through 71 Processing sheet with id=AB7, first strand: chain 'E' and resid 84 through 85 removed outlier: 3.595A pdb=" N ALA E 85 " --> pdb=" O GLN E 88 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 156 through 157 removed outlier: 3.983A pdb=" N GLU E 156 " --> pdb=" O HIS E 164 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 192 through 196 removed outlier: 5.716A pdb=" N GLN E 194 " --> pdb=" O ARG E 186 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ARG E 186 " --> pdb=" O GLN E 194 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY E 196 " --> pdb=" O GLY E 184 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N TYR E 185 " --> pdb=" O TYR E 224 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N TYR E 224 " --> pdb=" O TYR E 185 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 200 through 201 Processing sheet with id=AC2, first strand: chain 'E' and resid 277 through 278 removed outlier: 3.616A pdb=" N SER E 278 " --> pdb=" O TYR E 396 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N TYR E 398 " --> pdb=" O SER E 278 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL E 371 " --> pdb=" O HIS E 395 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 511 through 512 removed outlier: 3.803A pdb=" N THR E 547 " --> pdb=" O ILE E 512 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL E 544 " --> pdb=" O LEU E 573 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N ILE E 575 " --> pdb=" O VAL E 544 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N PHE E 546 " --> pdb=" O ILE E 575 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N PHE E 472 " --> pdb=" O CYS E 574 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N MET E 576 " --> pdb=" O PHE E 472 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N AMET E 474 " --> pdb=" O MET E 576 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 15 through 16 Processing sheet with id=AC5, first strand: chain 'F' and resid 70 through 71 Processing sheet with id=AC6, first strand: chain 'F' and resid 84 through 85 removed outlier: 3.688A pdb=" N ALA F 85 " --> pdb=" O GLN F 88 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 153 through 159 removed outlier: 5.939A pdb=" N ARG F 155 " --> pdb=" O SER F 166 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N SER F 166 " --> pdb=" O ARG F 155 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N VAL F 157 " --> pdb=" O HIS F 164 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N HIS F 164 " --> pdb=" O VAL F 157 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 192 through 196 removed outlier: 5.652A pdb=" N GLN F 194 " --> pdb=" O ARG F 186 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N ARG F 186 " --> pdb=" O GLN F 194 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY F 196 " --> pdb=" O GLY F 184 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N TYR F 185 " --> pdb=" O TYR F 224 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N TYR F 224 " --> pdb=" O TYR F 185 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 199 through 201 removed outlier: 3.704A pdb=" N THR F 199 " --> pdb=" O ARG F 212 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL F 210 " --> pdb=" O GLU F 201 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 330 through 332 removed outlier: 6.169A pdb=" N SER F 331 " --> pdb=" O PHE F 357 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N VAL F 305 " --> pdb=" O VAL F 372 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL F 371 " --> pdb=" O HIS F 395 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 470 through 475 removed outlier: 6.547A pdb=" N GLN F 470 " --> pdb=" O ILE F 572 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N CYS F 574 " --> pdb=" O GLN F 470 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N PHE F 472 " --> pdb=" O CYS F 574 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N MET F 576 " --> pdb=" O PHE F 472 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N AMET F 474 " --> pdb=" O MET F 576 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N PHE F 546 " --> pdb=" O ILE F 575 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N THR F 547 " --> pdb=" O ILE F 512 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 40 through 41 removed outlier: 6.570A pdb=" N ASP G 26 " --> pdb=" O ALA G 16 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ALA G 16 " --> pdb=" O ASP G 26 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N CYS G 14 " --> pdb=" O ALA G 28 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA G 30 " --> pdb=" O MET G 12 " (cutoff:3.500A) removed outlier: 12.565A pdb=" N SER G 13 " --> pdb=" O PRO G 57 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA G 15 " --> pdb=" O ARG G 55 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N PHE G 56 " --> pdb=" O ILE G 65 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 43 through 46 removed outlier: 3.514A pdb=" N SER G 46 " --> pdb=" O TYR G 87 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THR G 77 " --> pdb=" O LYS G 84 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS G 86 " --> pdb=" O PHE G 75 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N PHE G 75 " --> pdb=" O LYS G 86 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU G 88 " --> pdb=" O CYS G 73 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N CYS G 73 " --> pdb=" O LEU G 88 " (cutoff:3.500A) 773 hydrogen bonds defined for protein. 2145 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 45 hydrogen bonds 90 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 34 stacking parallelities Total time for adding SS restraints: 4.93 Time building geometry restraints manager: 2.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.12: 2 1.12 - 1.29: 3466 1.29 - 1.47: 9210 1.47 - 1.65: 9609 1.65 - 1.82: 229 Bond restraints: 22516 Sorted by residual: bond pdb=" N PRO F 300 " pdb=" CD PRO F 300 " ideal model delta sigma weight residual 1.473 0.939 0.534 1.40e-02 5.10e+03 1.45e+03 bond pdb=" N PRO F 434 " pdb=" CD PRO F 434 " ideal model delta sigma weight residual 1.473 1.816 -0.343 1.40e-02 5.10e+03 6.00e+02 bond pdb=" C1 F86 G 201 " pdb=" C2 F86 G 201 " ideal model delta sigma weight residual 1.544 1.309 0.235 1.00e-02 1.00e+04 5.51e+02 bond pdb=" C8 F86 G 201 " pdb=" N3 F86 G 201 " ideal model delta sigma weight residual 1.138 1.438 -0.300 1.30e-02 5.92e+03 5.33e+02 bond pdb=" C11 F86 G 201 " pdb=" N5 F86 G 201 " ideal model delta sigma weight residual 1.337 1.484 -0.147 1.00e-02 1.00e+04 2.16e+02 ... (remaining 22511 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.76: 30846 14.76 - 29.52: 11 29.52 - 44.28: 1 44.28 - 59.03: 0 59.03 - 73.79: 2 Bond angle restraints: 30860 Sorted by residual: angle pdb=" C1 F86 G 201 " pdb=" C8 F86 G 201 " pdb=" N3 F86 G 201 " ideal model delta sigma weight residual 177.87 110.37 67.50 1.00e+00 1.00e+00 4.56e+03 angle pdb=" CB PRO F 434 " pdb=" CG PRO F 434 " pdb=" CD PRO F 434 " ideal model delta sigma weight residual 106.10 179.89 -73.79 3.20e+00 9.77e-02 5.32e+02 angle pdb=" N PRO F 434 " pdb=" CD PRO F 434 " pdb=" CG PRO F 434 " ideal model delta sigma weight residual 103.20 70.86 32.34 1.50e+00 4.44e-01 4.65e+02 angle pdb=" CA PRO F 434 " pdb=" N PRO F 434 " pdb=" CD PRO F 434 " ideal model delta sigma weight residual 112.00 89.40 22.60 1.40e+00 5.10e-01 2.60e+02 angle pdb=" CA PRO F 434 " pdb=" CB PRO F 434 " pdb=" CG PRO F 434 " ideal model delta sigma weight residual 104.50 75.41 29.09 1.90e+00 2.77e-01 2.34e+02 ... (remaining 30855 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.88: 12104 24.88 - 49.75: 1182 49.75 - 74.63: 255 74.63 - 99.50: 22 99.50 - 124.38: 2 Dihedral angle restraints: 13565 sinusoidal: 5685 harmonic: 7880 Sorted by residual: dihedral pdb=" C SER D 41 " pdb=" N SER D 41 " pdb=" CA SER D 41 " pdb=" CB SER D 41 " ideal model delta harmonic sigma weight residual -122.60 -152.76 30.16 0 2.50e+00 1.60e-01 1.46e+02 dihedral pdb=" CA TRP B 182 " pdb=" C TRP B 182 " pdb=" N PRO B 183 " pdb=" CA PRO B 183 " ideal model delta harmonic sigma weight residual 180.00 126.67 53.33 0 5.00e+00 4.00e-02 1.14e+02 dihedral pdb=" N SER D 41 " pdb=" C SER D 41 " pdb=" CA SER D 41 " pdb=" CB SER D 41 " ideal model delta harmonic sigma weight residual 122.80 145.74 -22.94 0 2.50e+00 1.60e-01 8.42e+01 ... (remaining 13562 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.245: 3567 0.245 - 0.489: 3 0.489 - 0.734: 2 0.734 - 0.979: 2 0.979 - 1.223: 1 Chirality restraints: 3575 Sorted by residual: chirality pdb=" CA SER D 41 " pdb=" N SER D 41 " pdb=" C SER D 41 " pdb=" CB SER D 41 " both_signs ideal model delta sigma weight residual False 2.51 1.29 1.22 2.00e-01 2.50e+01 3.74e+01 chirality pdb=" CA LEU D 38 " pdb=" N LEU D 38 " pdb=" C LEU D 38 " pdb=" CB LEU D 38 " both_signs ideal model delta sigma weight residual False 2.51 1.63 0.88 2.00e-01 2.50e+01 1.93e+01 chirality pdb=" CA PHE B 49 " pdb=" N PHE B 49 " pdb=" C PHE B 49 " pdb=" CB PHE B 49 " both_signs ideal model delta sigma weight residual False 2.51 1.76 0.75 2.00e-01 2.50e+01 1.39e+01 ... (remaining 3572 not shown) Planarity restraints: 3743 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY F 433 " 0.172 5.00e-02 4.00e+02 2.14e-01 7.29e+01 pdb=" N PRO F 434 " -0.365 5.00e-02 4.00e+02 pdb=" CA PRO F 434 " 0.116 5.00e-02 4.00e+02 pdb=" CD PRO F 434 " 0.078 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS D 37 " -0.038 2.00e-02 2.50e+03 7.40e-02 5.48e+01 pdb=" C LYS D 37 " 0.128 2.00e-02 2.50e+03 pdb=" O LYS D 37 " -0.046 2.00e-02 2.50e+03 pdb=" N LEU D 38 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 167 " -0.075 2.00e-02 2.50e+03 4.17e-02 4.34e+01 pdb=" CG TRP E 167 " 0.103 2.00e-02 2.50e+03 pdb=" CD1 TRP E 167 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP E 167 " 0.013 2.00e-02 2.50e+03 pdb=" NE1 TRP E 167 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP E 167 " -0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP E 167 " 0.018 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 167 " -0.015 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 167 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP E 167 " -0.015 2.00e-02 2.50e+03 ... (remaining 3740 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.24: 20 2.24 - 2.91: 9165 2.91 - 3.57: 30220 3.57 - 4.24: 52045 4.24 - 4.90: 84849 Nonbonded interactions: 176299 Sorted by model distance: nonbonded pdb=" OD1 ASP A 218 " pdb=" O3G GNP A1003 " model vdw 1.578 3.040 nonbonded pdb=" N GLU E 447 " pdb=" OE1 GLU E 447 " model vdw 1.994 3.120 nonbonded pdb=" O THR F 115 " pdb=" OG1 THR F 413 " model vdw 2.039 3.040 nonbonded pdb=" N TYR F 476 " pdb=" O MET F 576 " model vdw 2.106 3.120 nonbonded pdb=" O GLU E 447 " pdb=" OG1 THR E 451 " model vdw 2.107 3.040 ... (remaining 176294 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 191)) 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 191)) } ncs_group { reference = (chain 'E' and (resid 2 through 93 or (resid 94 and (name N or name CA or name C \ or name O or name CB )) or resid 95 through 473 or resid 475 through 703)) selection = (chain 'F' and (resid 2 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=0.20 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: 5.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 27.770 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.882 22550 Z= 0.775 Angle : 1.195 73.793 30887 Z= 0.738 Chirality : 0.059 1.223 3575 Planarity : 0.007 0.214 3743 Dihedral : 19.628 124.377 8481 Min Nonbonded Distance : 1.578 Molprobity Statistics. All-atom Clashscore : 19.11 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.47 % Favored : 90.31 % Rotamer: Outliers : 6.32 % Allowed : 31.36 % Favored : 62.32 % Cbeta Deviations : 0.39 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % 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: -2.97 (0.15), residues: 2647 helix: -1.10 (0.16), residues: 916 sheet: -1.71 (0.31), residues: 222 loop : -2.68 (0.14), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 567 TYR 0.036 0.002 TYR E 382 PHE 0.032 0.002 PHE A 504 TRP 0.103 0.003 TRP E 167 HIS 0.015 0.002 HIS E 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00858 / 0.51 (22516) covalent geometry : angle 1.17093 / 0.74 (30860) hydrogen bonds : bond 0.22891 / 15.35 ( 785) hydrogen bonds : angle 7.39837 / 5.20 ( 2235) metal coordination : bond 0.02058 / 1.37 ( 32) metal coordination : angle 8.15298 / 4.84 ( 27) Misc. bond : bond 0.62371 / 32.83 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 212 time to evaluate : 0.841 Fit side-chains revert: symmetry clash REVERT: A 32 TYR cc_start: 0.8558 (t80) cc_final: 0.8306 (t80) REVERT: A 41 LYS cc_start: 0.7847 (mtmm) cc_final: 0.7570 (mtmt) REVERT: A 197 ARG cc_start: 0.7970 (ttp-170) cc_final: 0.7624 (ttp80) REVERT: A 267 LYS cc_start: 0.8552 (tmtt) cc_final: 0.8097 (mmmt) REVERT: A 270 LEU cc_start: 0.8499 (tp) cc_final: 0.8230 (tp) REVERT: A 380 MET cc_start: 0.8664 (mtp) cc_final: 0.8378 (mtm) REVERT: A 553 ARG cc_start: 0.7976 (ptt180) cc_final: 0.7195 (ptm-80) REVERT: A 718 LYS cc_start: 0.8336 (mptt) cc_final: 0.7919 (mmtt) REVERT: A 734 ASN cc_start: 0.8112 (t0) cc_final: 0.7901 (t160) REVERT: A 894 GLU cc_start: 0.7736 (tt0) cc_final: 0.7237 (mt-10) REVERT: B 72 LYS cc_start: 0.7718 (mttm) cc_final: 0.7319 (mtpt) REVERT: B 96 ARG cc_start: 0.7385 (ptp-110) cc_final: 0.7163 (ptp90) REVERT: B 97 LYS cc_start: 0.8121 (mtpt) cc_final: 0.7692 (mtmt) REVERT: C 21 ARG cc_start: 0.8005 (mmp80) cc_final: 0.7753 (mmt180) REVERT: D 48 GLU cc_start: 0.7652 (tp30) cc_final: 0.7249 (mm-30) REVERT: D 69 GLN cc_start: 0.7326 (tt0) cc_final: 0.6784 (tm-30) REVERT: D 143 ASP cc_start: 0.7144 (t70) cc_final: 0.6936 (t0) REVERT: D 174 MET cc_start: 0.5876 (mtt) cc_final: 0.4950 (tmm) REVERT: E 9 ASN cc_start: 0.4572 (t0) cc_final: 0.3799 (p0) REVERT: E 185 TYR cc_start: 0.5132 (m-80) cc_final: 0.4706 (m-80) REVERT: E 299 TYR cc_start: 0.1929 (m-80) cc_final: 0.1410 (m-10) REVERT: E 378 MET cc_start: 0.2454 (mtp) cc_final: 0.2245 (mtm) REVERT: E 477 LYS cc_start: 0.1886 (mtpp) cc_final: 0.1478 (tppt) REVERT: F 396 TYR cc_start: 0.3308 (m-10) cc_final: 0.2984 (m-80) REVERT: G 86 LYS cc_start: 0.4654 (mmtp) cc_final: 0.4387 (mmtp) outliers start: 141 outliers final: 109 residues processed: 348 average time/residue: 0.5144 time to fit residues: 209.0756 Evaluate side-chains 298 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 189 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 551 LYS Chi-restraints excluded: chain A residue 577 LYS Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 182 TRP Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 56 GLN Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 11 GLN Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 13 SER Chi-restraints excluded: chain E residue 29 CYS Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain E residue 50 CYS Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 63 LEU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 119 ASP Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 330 CYS Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 367 THR Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 534 ASP Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 548 GLN Chi-restraints excluded: chain E residue 550 THR Chi-restraints excluded: chain E residue 558 VAL Chi-restraints excluded: chain E residue 589 SER Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 22 ARG Chi-restraints excluded: chain F residue 25 LEU Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 69 SER Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 141 THR Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 169 VAL Chi-restraints excluded: chain F residue 211 TYR Chi-restraints excluded: chain F residue 221 VAL Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 236 SER Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain F residue 309 CYS Chi-restraints excluded: chain F residue 310 SER Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 358 CYS Chi-restraints excluded: chain F residue 425 VAL Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain F residue 440 THR Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain F residue 513 SER Chi-restraints excluded: chain F residue 557 ASN Chi-restraints excluded: chain F residue 566 THR Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 88 LEU Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 112 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.3980 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 8.9990 chunk 111 optimal weight: 0.0670 overall best weight: 0.8922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 138 ASN A 790 ASN B 73 GLN D 73 GLN D 157 GLN ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 354 GLN E 381 ASN E 404 GLN E 459 ASN E 519 ASN ** E 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 586 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 354 GLN F 381 ASN F 388 ASN F 516 ASN F 519 ASN G 49 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4681 r_free = 0.4681 target = 0.221648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.144268 restraints weight = 60048.481| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 4.70 r_work: 0.3531 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3438 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3232 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3232 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 22550 Z= 0.162 Angle : 0.767 14.628 30887 Z= 0.391 Chirality : 0.046 0.249 3575 Planarity : 0.006 0.075 3743 Dihedral : 14.135 120.393 3891 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.04 % Favored : 92.81 % Rotamer: Outliers : 6.97 % Allowed : 28.33 % Favored : 64.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % 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: -2.54 (0.15), residues: 2647 helix: -0.63 (0.17), residues: 951 sheet: -1.72 (0.31), residues: 238 loop : -2.50 (0.15), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 443 TYR 0.020 0.002 TYR E 541 PHE 0.031 0.002 PHE A 504 TRP 0.017 0.002 TRP E 167 HIS 0.007 0.001 HIS E 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.16 (22516) covalent geometry : angle 0.74662 / 0.39 (30860) hydrogen bonds : bond 0.06799 / 4.44 ( 785) hydrogen bonds : angle 5.42872 / 3.81 ( 2235) metal coordination : bond 0.01920 / 1.28 ( 32) metal coordination : angle 5.91953 / 3.75 ( 27) Misc. bond : bond 0.00046 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 200 time to evaluate : 0.847 Fit side-chains revert: symmetry clash REVERT: A 32 TYR cc_start: 0.8667 (t80) cc_final: 0.8423 (t80) REVERT: A 267 LYS cc_start: 0.8783 (tmtt) cc_final: 0.8450 (mmmt) REVERT: A 553 ARG cc_start: 0.8385 (ptt180) cc_final: 0.7793 (ptm-80) REVERT: A 668 MET cc_start: 0.9338 (OUTLIER) cc_final: 0.8997 (ttm) REVERT: A 778 SER cc_start: 0.8765 (OUTLIER) cc_final: 0.8550 (m) REVERT: A 894 GLU cc_start: 0.8190 (tt0) cc_final: 0.7876 (tt0) REVERT: A 898 HIS cc_start: 0.7596 (OUTLIER) cc_final: 0.6920 (t-90) REVERT: A 900 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7757 (mm) REVERT: B 72 LYS cc_start: 0.8345 (mttm) cc_final: 0.7996 (mtpt) REVERT: B 82 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.8049 (mmmt) REVERT: B 97 LYS cc_start: 0.8349 (mtpt) cc_final: 0.7848 (mtmt) REVERT: C 21 ARG cc_start: 0.8449 (mmp80) cc_final: 0.8182 (mmt180) REVERT: C 75 MET cc_start: 0.5267 (OUTLIER) cc_final: 0.4532 (mmm) REVERT: D 48 GLU cc_start: 0.7845 (tp30) cc_final: 0.7587 (mm-30) REVERT: D 49 PHE cc_start: 0.5931 (t80) cc_final: 0.5721 (t80) REVERT: D 69 GLN cc_start: 0.7887 (tm-30) cc_final: 0.7386 (tm-30) REVERT: D 143 ASP cc_start: 0.7210 (t70) cc_final: 0.6956 (t0) REVERT: D 174 MET cc_start: 0.5998 (OUTLIER) cc_final: 0.5076 (tmm) REVERT: D 176 ASN cc_start: 0.7044 (m-40) cc_final: 0.6605 (t0) REVERT: E 9 ASN cc_start: 0.4580 (t0) cc_final: 0.4223 (p0) REVERT: E 299 TYR cc_start: 0.2189 (m-80) cc_final: 0.1704 (m-10) REVERT: E 373 PHE cc_start: 0.5482 (OUTLIER) cc_final: 0.4793 (t80) REVERT: E 436 MET cc_start: 0.2326 (mmm) cc_final: 0.1528 (mmm) REVERT: F 65 LEU cc_start: 0.5782 (OUTLIER) cc_final: 0.5368 (tp) REVERT: F 280 LEU cc_start: 0.4438 (OUTLIER) cc_final: 0.4064 (tp) REVERT: F 309 CYS cc_start: 0.2963 (OUTLIER) cc_final: 0.1572 (t) REVERT: F 373 PHE cc_start: 0.5011 (m-10) cc_final: 0.4733 (m-10) REVERT: F 399 ILE cc_start: 0.4968 (mp) cc_final: 0.4382 (mm) outliers start: 156 outliers final: 71 residues processed: 331 average time/residue: 0.5141 time to fit residues: 198.0895 Evaluate side-chains 255 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 173 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 577 LYS Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 668 MET Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 778 SER Chi-restraints excluded: chain A residue 855 MET Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 898 HIS Chi-restraints excluded: chain A residue 900 LEU Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 182 TRP Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain E residue 11 GLN Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 29 CYS Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 50 CYS Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 94 LYS Chi-restraints excluded: chain E residue 119 ASP Chi-restraints excluded: chain E residue 185 TYR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 330 CYS Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 373 PHE Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 523 SER Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 548 GLN Chi-restraints excluded: chain E residue 550 THR Chi-restraints excluded: chain E residue 558 VAL Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 211 TYR Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 236 SER Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain F residue 309 CYS Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 425 VAL Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 112 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 140 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 chunk 149 optimal weight: 0.9990 chunk 141 optimal weight: 0.8980 chunk 264 optimal weight: 0.6980 chunk 108 optimal weight: 1.9990 chunk 150 optimal weight: 0.3980 chunk 103 optimal weight: 0.5980 chunk 255 optimal weight: 0.0670 chunk 136 optimal weight: 30.0000 chunk 56 optimal weight: 0.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 79 ASN A 138 ASN A 734 ASN A 790 ASN B 73 GLN D 56 GLN ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 548 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 275 GLN F 516 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4699 r_free = 0.4699 target = 0.223503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.148037 restraints weight = 59586.531| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 4.51 r_work: 0.3571 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3478 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3278 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3278 r_free = 0.3278 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3278 r_free = 0.3278 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3278 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 22550 Z= 0.130 Angle : 0.665 12.886 30887 Z= 0.340 Chirality : 0.043 0.218 3575 Planarity : 0.005 0.074 3743 Dihedral : 13.180 119.936 3817 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.02 % Favored : 93.83 % Rotamer: Outliers : 5.92 % Allowed : 29.21 % Favored : 64.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % 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: -2.12 (0.16), residues: 2647 helix: -0.16 (0.17), residues: 932 sheet: -1.38 (0.32), residues: 225 loop : -2.33 (0.15), residues: 1490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 443 TYR 0.028 0.002 TYR F 31 PHE 0.029 0.002 PHE F 422 TRP 0.014 0.001 TRP D 182 HIS 0.006 0.001 HIS E 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (22516) covalent geometry : angle 0.65104 / 0.34 (30860) hydrogen bonds : bond 0.05500 / 3.57 ( 785) hydrogen bonds : angle 4.94378 / 3.46 ( 2235) metal coordination : bond 0.01720 / 1.17 ( 32) metal coordination : angle 4.61354 / 2.85 ( 27) Misc. bond : bond 0.00388 / 0.20 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 192 time to evaluate : 0.858 Fit side-chains REVERT: A 32 TYR cc_start: 0.8569 (t80) cc_final: 0.8302 (t80) REVERT: A 136 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.7764 (pm20) REVERT: A 267 LYS cc_start: 0.8785 (tmtt) cc_final: 0.8444 (mmmt) REVERT: A 553 ARG cc_start: 0.8326 (ptt180) cc_final: 0.7737 (ptm160) REVERT: A 790 ASN cc_start: 0.8995 (OUTLIER) cc_final: 0.8710 (m-40) REVERT: A 894 GLU cc_start: 0.8115 (tt0) cc_final: 0.7782 (tt0) REVERT: B 72 LYS cc_start: 0.8447 (mttm) cc_final: 0.8114 (mtpt) REVERT: B 75 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.7409 (mtm180) REVERT: B 82 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.8096 (mmmt) REVERT: B 97 LYS cc_start: 0.8198 (mtpt) cc_final: 0.7700 (mtmt) REVERT: B 189 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8743 (mp) REVERT: C 21 ARG cc_start: 0.8337 (mmp80) cc_final: 0.8065 (mmt180) REVERT: D 48 GLU cc_start: 0.7839 (tp30) cc_final: 0.7623 (mm-30) REVERT: D 49 PHE cc_start: 0.5897 (t80) cc_final: 0.5689 (t80) REVERT: D 60 GLU cc_start: 0.5470 (OUTLIER) cc_final: 0.5040 (mt-10) REVERT: D 174 MET cc_start: 0.5921 (OUTLIER) cc_final: 0.5018 (tmm) REVERT: D 176 ASN cc_start: 0.7054 (m-40) cc_final: 0.6791 (t0) REVERT: E 9 ASN cc_start: 0.4851 (t0) cc_final: 0.4624 (p0) REVERT: E 131 LYS cc_start: 0.4445 (mmtp) cc_final: 0.4121 (pttt) REVERT: E 373 PHE cc_start: 0.5405 (OUTLIER) cc_final: 0.4765 (t80) REVERT: E 405 LEU cc_start: 0.5859 (mp) cc_final: 0.5415 (pt) REVERT: E 436 MET cc_start: 0.1995 (mmm) cc_final: 0.1465 (mmm) REVERT: F 65 LEU cc_start: 0.6220 (OUTLIER) cc_final: 0.5985 (tp) REVERT: F 175 PRO cc_start: 0.2220 (Cg_exo) cc_final: 0.1849 (Cg_endo) REVERT: F 309 CYS cc_start: 0.3477 (OUTLIER) cc_final: 0.2189 (t) REVERT: F 319 GLU cc_start: 0.3963 (OUTLIER) cc_final: 0.3733 (tt0) REVERT: F 399 ILE cc_start: 0.4746 (mp) cc_final: 0.4214 (mm) REVERT: F 414 LYS cc_start: 0.4043 (mmpt) cc_final: 0.2988 (ttpt) REVERT: F 428 LEU cc_start: 0.2592 (OUTLIER) cc_final: 0.1694 (mm) REVERT: F 429 MET cc_start: 0.2192 (mtt) cc_final: 0.1764 (mmp) outliers start: 132 outliers final: 54 residues processed: 299 average time/residue: 0.5481 time to fit residues: 190.4336 Evaluate side-chains 249 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 183 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 798 LYS Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain B residue 75 ARG Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 182 TRP Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain E residue 11 GLN Chi-restraints excluded: chain E residue 50 CYS Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 119 ASP Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 259 SER Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 330 CYS Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 373 PHE Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 550 THR Chi-restraints excluded: chain E residue 589 SER Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 211 TYR Chi-restraints excluded: chain F residue 230 HIS Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 309 CYS Chi-restraints excluded: chain F residue 319 GLU Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 425 VAL Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain F residue 437 PHE Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 112 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 160 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 228 optimal weight: 20.0000 chunk 59 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 213 optimal weight: 9.9990 chunk 66 optimal weight: 0.0470 chunk 34 optimal weight: 2.9990 chunk 152 optimal weight: 9.9990 chunk 240 optimal weight: 0.0370 chunk 153 optimal weight: 5.9990 overall best weight: 1.6162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 88 ASN A 734 ASN D 56 GLN D 157 GLN ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 548 GLN ** F 75 HIS ** 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 = 0.4679 r_free = 0.4679 target = 0.221548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.144266 restraints weight = 52111.116| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 3.35 r_work: 0.3546 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3246 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3246 r_free = 0.3246 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3246 r_free = 0.3246 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3246 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 22550 Z= 0.168 Angle : 0.679 12.524 30887 Z= 0.350 Chirality : 0.045 0.234 3575 Planarity : 0.005 0.079 3743 Dihedral : 12.889 118.807 3795 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.78 % Favored : 93.07 % Rotamer: Outliers : 5.44 % Allowed : 29.91 % Favored : 64.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % 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: -2.14 (0.16), residues: 2647 helix: -0.21 (0.17), residues: 945 sheet: -1.48 (0.31), residues: 252 loop : -2.33 (0.15), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 443 TYR 0.048 0.002 TYR F 31 PHE 0.034 0.002 PHE A 504 TRP 0.029 0.002 TRP G 53 HIS 0.009 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (22516) covalent geometry : angle 0.66612 / 0.35 (30860) hydrogen bonds : bond 0.06404 / 4.12 ( 785) hydrogen bonds : angle 4.87583 / 3.40 ( 2235) metal coordination : bond 0.01712 / 1.15 ( 32) metal coordination : angle 4.44820 / 2.73 ( 27) Misc. bond : bond 0.00357 / 0.19 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 188 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 GLU cc_start: 0.8942 (OUTLIER) cc_final: 0.7784 (pm20) REVERT: A 553 ARG cc_start: 0.8348 (ptt180) cc_final: 0.7740 (ptm160) REVERT: A 811 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8209 (tp30) REVERT: A 885 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8714 (mp) REVERT: A 894 GLU cc_start: 0.8140 (tt0) cc_final: 0.7847 (tt0) REVERT: A 898 HIS cc_start: 0.7590 (OUTLIER) cc_final: 0.6887 (t-90) REVERT: B 72 LYS cc_start: 0.8370 (mttm) cc_final: 0.8032 (mtpt) REVERT: B 75 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7347 (mtm180) REVERT: B 82 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.8130 (mmmt) REVERT: B 97 LYS cc_start: 0.8241 (mtpt) cc_final: 0.7763 (mtmt) REVERT: B 189 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8740 (mp) REVERT: C 21 ARG cc_start: 0.8390 (mmp80) cc_final: 0.8122 (mmt180) REVERT: C 73 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.6976 (mp0) REVERT: D 56 GLN cc_start: 0.3797 (OUTLIER) cc_final: 0.3406 (pp30) REVERT: D 60 GLU cc_start: 0.5467 (OUTLIER) cc_final: 0.5057 (mt-10) REVERT: D 174 MET cc_start: 0.5872 (OUTLIER) cc_final: 0.4939 (tmm) REVERT: E 9 ASN cc_start: 0.4849 (t0) cc_final: 0.4634 (p0) REVERT: E 21 ARG cc_start: 0.3650 (OUTLIER) cc_final: 0.3268 (mmp-170) REVERT: E 185 TYR cc_start: 0.5703 (OUTLIER) cc_final: 0.5365 (m-80) REVERT: E 250 THR cc_start: 0.0649 (OUTLIER) cc_final: 0.0019 (t) REVERT: E 373 PHE cc_start: 0.5411 (OUTLIER) cc_final: 0.4831 (t80) REVERT: E 405 LEU cc_start: 0.5591 (mp) cc_final: 0.5356 (pt) REVERT: E 436 MET cc_start: 0.1961 (mmm) cc_final: 0.1513 (mmm) REVERT: F 309 CYS cc_start: 0.3661 (OUTLIER) cc_final: 0.2594 (t) REVERT: F 399 ILE cc_start: 0.4695 (mp) cc_final: 0.4229 (mm) REVERT: F 414 LYS cc_start: 0.3887 (mmtt) cc_final: 0.2837 (ttpt) REVERT: F 428 LEU cc_start: 0.2347 (OUTLIER) cc_final: 0.1435 (mm) REVERT: F 429 MET cc_start: 0.2150 (mtt) cc_final: 0.1742 (mmp) REVERT: F 516 ASN cc_start: 0.1921 (p0) cc_final: 0.1660 (m110) REVERT: G 3 GLU cc_start: 0.8819 (mt-10) cc_final: 0.8499 (mt-10) REVERT: G 81 LYS cc_start: 0.2131 (OUTLIER) cc_final: 0.1694 (ptpt) outliers start: 121 outliers final: 67 residues processed: 284 average time/residue: 0.5867 time to fit residues: 192.7436 Evaluate side-chains 260 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 175 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 404 ASN Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 798 LYS Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 855 MET Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 898 HIS Chi-restraints excluded: chain B residue 75 ARG Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 182 TRP Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain C residue 3 MET Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain C residue 72 CYS Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain D residue 56 GLN Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain E residue 11 GLN Chi-restraints excluded: chain E residue 21 ARG Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 50 CYS Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 185 TYR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 330 CYS Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 373 PHE Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 488 ILE Chi-restraints excluded: chain E residue 512 ILE Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 548 GLN Chi-restraints excluded: chain E residue 589 SER Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 211 TYR Chi-restraints excluded: chain F residue 230 HIS Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 274 MET Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 307 THR Chi-restraints excluded: chain F residue 309 CYS Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 374 ASP Chi-restraints excluded: chain F residue 425 VAL Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain F residue 525 ILE Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 27 ASN Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 81 LYS Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 112 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 66 optimal weight: 0.7980 chunk 237 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 259 optimal weight: 8.9990 chunk 54 optimal weight: 0.9990 chunk 96 optimal weight: 5.9990 chunk 258 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 211 optimal weight: 10.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 790 ASN D 56 GLN D 157 GLN ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 270 GLN ** F 75 HIS ** 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 = 0.4691 r_free = 0.4691 target = 0.223109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.150863 restraints weight = 61087.510| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 3.55 r_work: 0.3579 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3242 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3242 r_free = 0.3242 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3242 r_free = 0.3242 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3242 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 22550 Z= 0.131 Angle : 0.639 16.063 30887 Z= 0.326 Chirality : 0.043 0.217 3575 Planarity : 0.005 0.076 3743 Dihedral : 12.691 118.846 3783 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.21 % Favored : 93.64 % Rotamer: Outliers : 5.48 % Allowed : 29.74 % Favored : 64.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % 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: -1.97 (0.16), residues: 2647 helix: -0.05 (0.17), residues: 945 sheet: -1.31 (0.31), residues: 244 loop : -2.26 (0.15), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 443 TYR 0.055 0.002 TYR F 31 PHE 0.036 0.002 PHE E 561 TRP 0.014 0.001 TRP A 916 HIS 0.006 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (22516) covalent geometry : angle 0.62056 / 0.32 (30860) hydrogen bonds : bond 0.05510 / 3.55 ( 785) hydrogen bonds : angle 4.71174 / 3.29 ( 2235) metal coordination : bond 0.01815 / 1.27 ( 32) metal coordination : angle 5.23274 / 3.04 ( 27) Misc. bond : bond 0.00199 / 0.10 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 189 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 GLU cc_start: 0.8927 (OUTLIER) cc_final: 0.7750 (pm20) REVERT: A 553 ARG cc_start: 0.8361 (ptt180) cc_final: 0.7740 (ptm160) REVERT: A 790 ASN cc_start: 0.8957 (OUTLIER) cc_final: 0.8667 (t0) REVERT: A 885 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8737 (mp) REVERT: A 894 GLU cc_start: 0.8203 (tt0) cc_final: 0.7875 (tt0) REVERT: B 72 LYS cc_start: 0.8435 (mttm) cc_final: 0.8104 (mtpt) REVERT: B 75 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.7427 (mtm180) REVERT: B 82 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.8146 (mmmt) REVERT: B 97 LYS cc_start: 0.8198 (mtpt) cc_final: 0.7752 (mtmt) REVERT: B 189 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8759 (mp) REVERT: C 21 ARG cc_start: 0.8399 (mmp80) cc_final: 0.8130 (mmt180) REVERT: C 73 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.7009 (mp0) REVERT: D 56 GLN cc_start: 0.3971 (OUTLIER) cc_final: 0.3714 (pp30) REVERT: D 60 GLU cc_start: 0.5575 (OUTLIER) cc_final: 0.5164 (mt-10) REVERT: D 174 MET cc_start: 0.5885 (OUTLIER) cc_final: 0.4961 (tmm) REVERT: E 131 LYS cc_start: 0.4680 (mmtp) cc_final: 0.4342 (pttt) REVERT: E 185 TYR cc_start: 0.5748 (OUTLIER) cc_final: 0.5425 (m-80) REVERT: E 250 THR cc_start: 0.0797 (OUTLIER) cc_final: 0.0195 (t) REVERT: E 373 PHE cc_start: 0.5391 (OUTLIER) cc_final: 0.4828 (t80) REVERT: E 405 LEU cc_start: 0.5634 (mp) cc_final: 0.5392 (pt) REVERT: E 436 MET cc_start: 0.1989 (mmm) cc_final: 0.1494 (mmm) REVERT: F 309 CYS cc_start: 0.3779 (OUTLIER) cc_final: 0.2722 (t) REVERT: F 373 PHE cc_start: 0.5182 (t80) cc_final: 0.4952 (t80) REVERT: F 399 ILE cc_start: 0.4522 (mp) cc_final: 0.4088 (mm) REVERT: F 428 LEU cc_start: 0.2543 (OUTLIER) cc_final: 0.1809 (mm) REVERT: F 429 MET cc_start: 0.2163 (mtt) cc_final: 0.1821 (mmp) REVERT: F 516 ASN cc_start: 0.1924 (p0) cc_final: 0.1656 (m110) REVERT: G 46 SER cc_start: 0.3649 (OUTLIER) cc_final: 0.3429 (m) REVERT: G 81 LYS cc_start: 0.2142 (OUTLIER) cc_final: 0.1713 (ptpt) outliers start: 122 outliers final: 64 residues processed: 289 average time/residue: 0.5848 time to fit residues: 195.2584 Evaluate side-chains 262 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 181 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 798 LYS Chi-restraints excluded: chain A residue 855 MET Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 75 ARG Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 182 TRP Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 72 CYS Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain D residue 56 GLN Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 11 GLN Chi-restraints excluded: chain E residue 50 CYS Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 185 TYR Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 330 CYS Chi-restraints excluded: chain E residue 373 PHE Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 488 ILE Chi-restraints excluded: chain E residue 512 ILE Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 589 SER Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 211 TYR Chi-restraints excluded: chain F residue 220 ASN Chi-restraints excluded: chain F residue 230 HIS Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 309 CYS Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 425 VAL Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain F residue 437 PHE Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain F residue 525 ILE Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 81 LYS Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 112 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 245 optimal weight: 20.0000 chunk 166 optimal weight: 0.9980 chunk 225 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 120 optimal weight: 0.3980 chunk 212 optimal weight: 6.9990 chunk 60 optimal weight: 0.9980 chunk 252 optimal weight: 0.0770 chunk 0 optimal weight: 7.9990 chunk 56 optimal weight: 0.9980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 157 GLN ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4694 r_free = 0.4694 target = 0.223517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.151115 restraints weight = 55369.038| |-----------------------------------------------------------------------------| r_work (start): 0.3962 rms_B_bonded: 3.03 r_work: 0.3607 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3518 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3269 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3269 r_free = 0.3269 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3269 r_free = 0.3269 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3269 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 22550 Z= 0.124 Angle : 0.629 14.728 30887 Z= 0.320 Chirality : 0.042 0.218 3575 Planarity : 0.005 0.076 3743 Dihedral : 12.532 118.304 3778 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.17 % Favored : 93.68 % Rotamer: Outliers : 5.22 % Allowed : 30.31 % Favored : 64.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % 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: -1.88 (0.16), residues: 2647 helix: 0.05 (0.17), residues: 955 sheet: -1.36 (0.30), residues: 271 loop : -2.22 (0.15), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 443 TYR 0.017 0.001 TYR F 306 PHE 0.025 0.001 PHE A 504 TRP 0.025 0.001 TRP G 53 HIS 0.005 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (22516) covalent geometry : angle 0.61281 / 0.32 (30860) hydrogen bonds : bond 0.05098 / 3.27 ( 785) hydrogen bonds : angle 4.58268 / 3.20 ( 2235) metal coordination : bond 0.01651 / 1.16 ( 32) metal coordination : angle 4.87128 / 2.83 ( 27) Misc. bond : bond 0.00170 / 0.09 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 186 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 GLU cc_start: 0.8917 (OUTLIER) cc_final: 0.7763 (pm20) REVERT: A 553 ARG cc_start: 0.8330 (ptt180) cc_final: 0.7719 (ptm160) REVERT: A 811 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8282 (tp30) REVERT: A 894 GLU cc_start: 0.8164 (tt0) cc_final: 0.7860 (tt0) REVERT: B 72 LYS cc_start: 0.8379 (mttm) cc_final: 0.8047 (mtpt) REVERT: B 75 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7435 (mtm180) REVERT: B 82 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.8135 (mmmt) REVERT: B 189 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8745 (mp) REVERT: C 21 ARG cc_start: 0.8358 (mmp80) cc_final: 0.8089 (mmt180) REVERT: C 73 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.7004 (mp0) REVERT: D 60 GLU cc_start: 0.5548 (OUTLIER) cc_final: 0.5159 (mt-10) REVERT: D 174 MET cc_start: 0.5952 (mtt) cc_final: 0.4978 (tmm) REVERT: D 176 ASN cc_start: 0.7084 (m-40) cc_final: 0.6703 (t0) REVERT: E 185 TYR cc_start: 0.5800 (OUTLIER) cc_final: 0.5456 (m-80) REVERT: E 250 THR cc_start: 0.0791 (OUTLIER) cc_final: 0.0214 (t) REVERT: E 279 THR cc_start: -0.0943 (OUTLIER) cc_final: -0.1167 (m) REVERT: E 373 PHE cc_start: 0.5346 (OUTLIER) cc_final: 0.4811 (t80) REVERT: E 405 LEU cc_start: 0.5643 (mp) cc_final: 0.5439 (pt) REVERT: E 436 MET cc_start: 0.2049 (mmm) cc_final: 0.1592 (mmm) REVERT: F 142 GLU cc_start: 0.5500 (OUTLIER) cc_final: 0.5114 (tm-30) REVERT: F 373 PHE cc_start: 0.5127 (t80) cc_final: 0.4921 (t80) REVERT: F 399 ILE cc_start: 0.4431 (mp) cc_final: 0.4051 (mm) REVERT: F 414 LYS cc_start: 0.3901 (mmtt) cc_final: 0.2714 (ttpt) REVERT: F 428 LEU cc_start: 0.2566 (OUTLIER) cc_final: 0.1811 (mm) REVERT: F 429 MET cc_start: 0.2140 (mtt) cc_final: 0.1827 (mmp) REVERT: F 460 LYS cc_start: 0.0376 (tmtt) cc_final: -0.0159 (ptmm) REVERT: G 3 GLU cc_start: 0.8784 (mt-10) cc_final: 0.8505 (mt-10) REVERT: G 46 SER cc_start: 0.3629 (OUTLIER) cc_final: 0.3404 (m) REVERT: G 81 LYS cc_start: 0.1989 (OUTLIER) cc_final: 0.1576 (ptpt) outliers start: 116 outliers final: 67 residues processed: 282 average time/residue: 0.5666 time to fit residues: 185.0969 Evaluate side-chains 264 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 182 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASP Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 798 LYS Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 855 MET Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 75 ARG Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 182 TRP Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 72 CYS Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain D residue 19 GLN Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 65 GLN Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 50 CYS Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 149 TYR Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 185 TYR Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 330 CYS Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 373 PHE Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 512 ILE Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 589 SER Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 211 TYR Chi-restraints excluded: chain F residue 230 HIS Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 397 VAL Chi-restraints excluded: chain F residue 425 VAL Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain F residue 525 ILE Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 27 ASN Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 81 LYS Chi-restraints excluded: chain G residue 97 LEU 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 216 optimal weight: 20.0000 chunk 91 optimal weight: 0.6980 chunk 184 optimal weight: 9.9990 chunk 226 optimal weight: 20.0000 chunk 185 optimal weight: 7.9990 chunk 73 optimal weight: 2.9990 chunk 251 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 162 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 790 ASN C 18 GLN D 56 GLN D 157 GLN ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 ASN ** F 75 HIS ** 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 = 0.4538 r_free = 0.4538 target = 0.213698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.165943 restraints weight = 56382.267| |-----------------------------------------------------------------------------| r_work (start): 0.4036 rms_B_bonded: 3.07 r_work: 0.3095 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3081 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3081 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 22550 Z= 0.127 Angle : 0.620 14.038 30887 Z= 0.315 Chirality : 0.042 0.215 3575 Planarity : 0.005 0.077 3743 Dihedral : 12.400 117.908 3773 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.02 % Favored : 93.83 % Rotamer: Outliers : 5.18 % Allowed : 30.18 % Favored : 64.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % 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: -1.76 (0.16), residues: 2647 helix: 0.17 (0.17), residues: 951 sheet: -1.34 (0.29), residues: 275 loop : -2.16 (0.15), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 111 TYR 0.019 0.001 TYR F 306 PHE 0.027 0.001 PHE A 504 TRP 0.014 0.001 TRP A 916 HIS 0.006 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (22516) covalent geometry : angle 0.60441 / 0.31 (30860) hydrogen bonds : bond 0.05227 / 3.36 ( 785) hydrogen bonds : angle 4.56192 / 3.18 ( 2235) metal coordination : bond 0.01641 / 1.14 ( 32) metal coordination : angle 4.75044 / 2.76 ( 27) Misc. bond : bond 0.00203 / 0.11 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 190 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.6482 (t0) cc_final: 0.6278 (t0) REVERT: A 136 GLU cc_start: 0.8984 (OUTLIER) cc_final: 0.7940 (pm20) REVERT: A 553 ARG cc_start: 0.8560 (ptt180) cc_final: 0.8152 (ptm160) REVERT: A 811 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8165 (tp30) REVERT: A 885 LEU cc_start: 0.9310 (OUTLIER) cc_final: 0.8894 (mp) REVERT: B 72 LYS cc_start: 0.8731 (mttm) cc_final: 0.8468 (mtpt) REVERT: B 75 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.7749 (mtm180) REVERT: B 82 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.8488 (mmmt) REVERT: B 189 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.8903 (mp) REVERT: C 21 ARG cc_start: 0.8449 (mmp80) cc_final: 0.8205 (mmt180) REVERT: C 69 ASN cc_start: 0.7629 (m-40) cc_final: 0.7242 (t0) REVERT: C 73 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.7199 (mp0) REVERT: D 60 GLU cc_start: 0.6090 (OUTLIER) cc_final: 0.5730 (mt-10) REVERT: D 174 MET cc_start: 0.6056 (mtt) cc_final: 0.5139 (tmm) REVERT: D 176 ASN cc_start: 0.7037 (m-40) cc_final: 0.6818 (t0) REVERT: E 131 LYS cc_start: 0.4199 (mmtm) cc_final: 0.3873 (mmmt) REVERT: E 185 TYR cc_start: 0.5161 (OUTLIER) cc_final: 0.4597 (m-80) REVERT: E 250 THR cc_start: 0.0843 (OUTLIER) cc_final: 0.0210 (t) REVERT: E 279 THR cc_start: -0.0935 (OUTLIER) cc_final: -0.1160 (m) REVERT: E 319 GLU cc_start: 0.1212 (OUTLIER) cc_final: 0.0565 (mt-10) REVERT: E 373 PHE cc_start: 0.4827 (OUTLIER) cc_final: 0.4441 (t80) REVERT: E 436 MET cc_start: 0.2225 (mmm) cc_final: 0.1971 (mmm) REVERT: F 142 GLU cc_start: 0.5573 (OUTLIER) cc_final: 0.4922 (tm-30) REVERT: F 373 PHE cc_start: 0.4927 (t80) cc_final: 0.4641 (t80) REVERT: F 399 ILE cc_start: 0.3873 (mp) cc_final: 0.3524 (mm) REVERT: F 428 LEU cc_start: 0.2923 (OUTLIER) cc_final: 0.1482 (mm) REVERT: F 460 LYS cc_start: 0.0139 (tmtt) cc_final: -0.0314 (ptmm) REVERT: G 3 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8466 (mt-10) REVERT: G 46 SER cc_start: 0.3647 (OUTLIER) cc_final: 0.3431 (m) outliers start: 115 outliers final: 69 residues processed: 286 average time/residue: 0.5518 time to fit residues: 182.4007 Evaluate side-chains 269 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 184 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ASP Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 798 LYS Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 855 MET Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 75 ARG Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 182 TRP Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 72 CYS Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 65 GLN Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 50 CYS Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 149 TYR Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 185 TYR Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 319 GLU Chi-restraints excluded: chain E residue 330 CYS Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 373 PHE Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 512 ILE Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 589 SER Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 185 TYR Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 211 TYR Chi-restraints excluded: chain F residue 230 HIS Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 397 VAL Chi-restraints excluded: chain F residue 425 VAL Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 97 LEU 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 184 optimal weight: 5.9990 chunk 36 optimal weight: 0.0980 chunk 67 optimal weight: 1.9990 chunk 257 optimal weight: 0.9990 chunk 189 optimal weight: 6.9990 chunk 149 optimal weight: 7.9990 chunk 16 optimal weight: 0.6980 chunk 89 optimal weight: 0.6980 chunk 157 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 221 optimal weight: 10.0000 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 168 ASN A 790 ASN D 56 GLN D 157 GLN ** E 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 27 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.214484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.159593 restraints weight = 64214.263| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 8.53 r_work: 0.2960 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2977 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2977 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 22550 Z= 0.118 Angle : 0.607 13.302 30887 Z= 0.308 Chirality : 0.042 0.213 3575 Planarity : 0.005 0.076 3743 Dihedral : 12.277 117.717 3771 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.64 % Favored : 94.21 % Rotamer: Outliers : 4.87 % Allowed : 30.70 % Favored : 64.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % 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: -1.64 (0.16), residues: 2647 helix: 0.27 (0.17), residues: 948 sheet: -1.30 (0.29), residues: 289 loop : -2.07 (0.16), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 111 TYR 0.028 0.001 TYR F 306 PHE 0.024 0.001 PHE A 504 TRP 0.013 0.001 TRP A 916 HIS 0.006 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (22516) covalent geometry : angle 0.59273 / 0.31 (30860) hydrogen bonds : bond 0.04794 / 3.08 ( 785) hydrogen bonds : angle 4.47963 / 3.12 ( 2235) metal coordination : bond 0.01584 / 1.11 ( 32) metal coordination : angle 4.43559 / 2.63 ( 27) Misc. bond : bond 0.00152 / 0.08 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 191 time to evaluate : 0.778 Fit side-chains revert: symmetry clash REVERT: A 29 ASP cc_start: 0.6295 (t0) cc_final: 0.6049 (t0) REVERT: A 553 ARG cc_start: 0.8496 (ptt180) cc_final: 0.7933 (ptm160) REVERT: A 811 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8299 (tp30) REVERT: A 883 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8851 (tp) REVERT: A 885 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8783 (mp) REVERT: B 72 LYS cc_start: 0.8573 (mttm) cc_final: 0.8223 (mtpt) REVERT: B 75 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7635 (mtm180) REVERT: B 82 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8389 (mmmt) REVERT: B 189 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.8825 (mp) REVERT: C 21 ARG cc_start: 0.8412 (mmp80) cc_final: 0.8168 (mmt180) REVERT: C 75 MET cc_start: 0.4401 (tpt) cc_final: 0.4032 (mmm) REVERT: D 60 GLU cc_start: 0.5721 (OUTLIER) cc_final: 0.5316 (mt-10) REVERT: D 174 MET cc_start: 0.6072 (mtt) cc_final: 0.5007 (tmm) REVERT: E 131 LYS cc_start: 0.4264 (mmtm) cc_final: 0.3987 (mmmt) REVERT: E 185 TYR cc_start: 0.5892 (OUTLIER) cc_final: 0.4950 (m-80) REVERT: E 250 THR cc_start: 0.0470 (OUTLIER) cc_final: -0.0043 (t) REVERT: E 279 THR cc_start: -0.0674 (OUTLIER) cc_final: -0.0988 (m) REVERT: E 319 GLU cc_start: 0.0539 (OUTLIER) cc_final: 0.0204 (mt-10) REVERT: E 373 PHE cc_start: 0.5537 (OUTLIER) cc_final: 0.4963 (t80) REVERT: E 436 MET cc_start: 0.2030 (mmm) cc_final: 0.1391 (mmm) REVERT: E 468 SER cc_start: -0.0816 (OUTLIER) cc_final: -0.1285 (m) REVERT: F 142 GLU cc_start: 0.5501 (OUTLIER) cc_final: 0.5218 (mm-30) REVERT: F 358 CYS cc_start: 0.4038 (p) cc_final: 0.3219 (p) REVERT: F 373 PHE cc_start: 0.5048 (t80) cc_final: 0.4737 (t80) REVERT: F 399 ILE cc_start: 0.4546 (mp) cc_final: 0.4231 (mm) REVERT: F 428 LEU cc_start: 0.2112 (OUTLIER) cc_final: 0.1212 (mm) REVERT: F 460 LYS cc_start: 0.0352 (tmtt) cc_final: -0.0103 (ptmm) REVERT: G 3 GLU cc_start: 0.8900 (mt-10) cc_final: 0.8601 (mt-10) outliers start: 108 outliers final: 69 residues processed: 281 average time/residue: 0.5540 time to fit residues: 180.0560 Evaluate side-chains 269 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 185 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 798 LYS Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 818 MET Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 75 ARG Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 182 TRP Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 72 CYS Chi-restraints excluded: chain D residue 19 GLN Chi-restraints excluded: chain D residue 56 GLN Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 65 GLN Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 149 TYR Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 185 TYR Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 319 GLU Chi-restraints excluded: chain E residue 330 CYS Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 373 PHE Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 468 SER Chi-restraints excluded: chain E residue 472 PHE Chi-restraints excluded: chain E residue 512 ILE Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 589 SER Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 185 TYR Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 211 TYR Chi-restraints excluded: chain F residue 230 HIS Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 397 VAL Chi-restraints excluded: chain F residue 425 VAL Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 112 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 86 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 240 optimal weight: 0.4980 chunk 39 optimal weight: 1.9990 chunk 123 optimal weight: 0.7980 chunk 195 optimal weight: 8.9990 chunk 91 optimal weight: 0.9990 chunk 250 optimal weight: 5.9990 chunk 79 optimal weight: 0.0040 chunk 135 optimal weight: 0.7980 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 790 ASN D 56 GLN D 157 GLN ** E 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.214738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.163639 restraints weight = 58433.730| |-----------------------------------------------------------------------------| r_work (start): 0.3998 rms_B_bonded: 3.52 r_work: 0.3086 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3071 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3071 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 22550 Z= 0.119 Angle : 0.602 12.950 30887 Z= 0.307 Chirality : 0.042 0.213 3575 Planarity : 0.005 0.075 3743 Dihedral : 12.217 117.527 3766 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.53 % Favored : 94.32 % Rotamer: Outliers : 4.30 % Allowed : 31.27 % Favored : 64.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % 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: -1.56 (0.16), residues: 2647 helix: 0.33 (0.17), residues: 949 sheet: -1.31 (0.29), residues: 291 loop : -1.99 (0.16), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 427 TYR 0.062 0.001 TYR F 180 PHE 0.023 0.001 PHE A 504 TRP 0.013 0.001 TRP A 916 HIS 0.005 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (22516) covalent geometry : angle 0.58741 / 0.31 (30860) hydrogen bonds : bond 0.04704 / 3.01 ( 785) hydrogen bonds : angle 4.44054 / 3.09 ( 2235) metal coordination : bond 0.01716 / 1.19 ( 32) metal coordination : angle 4.45923 / 2.64 ( 27) Misc. bond : bond 0.00138 / 0.07 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 191 time to evaluate : 0.882 Fit side-chains revert: symmetry clash REVERT: A 29 ASP cc_start: 0.6402 (t0) cc_final: 0.6201 (t0) REVERT: A 553 ARG cc_start: 0.8455 (ptt180) cc_final: 0.8081 (ptp-110) REVERT: A 883 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8838 (tp) REVERT: A 885 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.8840 (mp) REVERT: B 75 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.7672 (mtm180) REVERT: B 82 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8374 (mmmt) REVERT: B 189 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.8884 (mp) REVERT: C 21 ARG cc_start: 0.8377 (mmp80) cc_final: 0.8128 (mmt180) REVERT: D 56 GLN cc_start: 0.4377 (OUTLIER) cc_final: 0.3998 (pp30) REVERT: D 60 GLU cc_start: 0.5843 (OUTLIER) cc_final: 0.5489 (mt-10) REVERT: D 174 MET cc_start: 0.6023 (mtt) cc_final: 0.5044 (tmm) REVERT: E 131 LYS cc_start: 0.4314 (mmtm) cc_final: 0.3989 (mmmt) REVERT: E 185 TYR cc_start: 0.5573 (OUTLIER) cc_final: 0.4438 (m-80) REVERT: E 250 THR cc_start: 0.0660 (OUTLIER) cc_final: 0.0039 (t) REVERT: E 279 THR cc_start: -0.0731 (OUTLIER) cc_final: -0.1086 (m) REVERT: E 319 GLU cc_start: 0.0992 (OUTLIER) cc_final: 0.0488 (mt-10) REVERT: E 373 PHE cc_start: 0.5142 (OUTLIER) cc_final: 0.4683 (t80) REVERT: E 436 MET cc_start: 0.2067 (mmm) cc_final: 0.1529 (mmm) REVERT: E 468 SER cc_start: -0.1580 (OUTLIER) cc_final: -0.2466 (m) REVERT: F 180 TYR cc_start: 0.2353 (OUTLIER) cc_final: 0.1615 (t80) REVERT: F 358 CYS cc_start: 0.3470 (p) cc_final: 0.2908 (p) REVERT: F 373 PHE cc_start: 0.4870 (t80) cc_final: 0.4585 (t80) REVERT: F 399 ILE cc_start: 0.4232 (mp) cc_final: 0.3927 (mm) REVERT: F 428 LEU cc_start: 0.2159 (OUTLIER) cc_final: 0.1056 (mm) REVERT: F 460 LYS cc_start: 0.0192 (tmtt) cc_final: -0.0039 (ptmm) REVERT: G 3 GLU cc_start: 0.8783 (mt-10) cc_final: 0.8514 (mt-10) outliers start: 95 outliers final: 67 residues processed: 267 average time/residue: 0.5452 time to fit residues: 168.2183 Evaluate side-chains 259 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 177 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 790 ASN Chi-restraints excluded: chain A residue 798 LYS Chi-restraints excluded: chain A residue 818 MET Chi-restraints excluded: chain A residue 855 MET Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 75 ARG Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 182 TRP Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 72 CYS Chi-restraints excluded: chain D residue 56 GLN Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 65 GLN Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 149 TYR Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 185 TYR Chi-restraints excluded: chain E residue 188 THR Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 307 THR Chi-restraints excluded: chain E residue 319 GLU Chi-restraints excluded: chain E residue 330 CYS Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 373 PHE Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 468 SER Chi-restraints excluded: chain E residue 512 ILE Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 589 SER Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 180 TYR Chi-restraints excluded: chain F residue 185 TYR Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 211 TYR Chi-restraints excluded: chain F residue 230 HIS Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 397 VAL Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 112 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 227 optimal weight: 7.9990 chunk 201 optimal weight: 0.0170 chunk 242 optimal weight: 0.0870 chunk 69 optimal weight: 1.9990 chunk 74 optimal weight: 0.0980 chunk 265 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 118 optimal weight: 9.9990 chunk 222 optimal weight: 0.0670 chunk 8 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 overall best weight: 0.2536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 790 ASN D 157 GLN ** E 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.215878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.166776 restraints weight = 48391.497| |-----------------------------------------------------------------------------| r_work (start): 0.4041 rms_B_bonded: 3.11 r_work: 0.3137 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3131 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3131 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 22550 Z= 0.110 Angle : 0.588 12.439 30887 Z= 0.299 Chirality : 0.041 0.210 3575 Planarity : 0.005 0.074 3743 Dihedral : 12.106 117.220 3762 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.45 % Favored : 94.40 % Rotamer: Outliers : 3.55 % Allowed : 32.32 % Favored : 64.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % 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: -1.43 (0.16), residues: 2647 helix: 0.44 (0.17), residues: 950 sheet: -1.25 (0.28), residues: 297 loop : -1.93 (0.16), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 57 TYR 0.042 0.001 TYR F 306 PHE 0.019 0.001 PHE F 422 TRP 0.015 0.001 TRP D 182 HIS 0.003 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 (22516) covalent geometry : angle 0.57403 / 0.30 (30860) hydrogen bonds : bond 0.04205 / 2.69 ( 785) hydrogen bonds : angle 4.37189 / 3.04 ( 2235) metal coordination : bond 0.01640 / 1.15 ( 32) metal coordination : angle 4.28393 / 2.56 ( 27) Misc. bond : bond 0.00093 / 0.05 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5294 Ramachandran restraints generated. 2647 Oldfield, 0 Emsley, 2647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 182 time to evaluate : 0.957 Fit side-chains revert: symmetry clash REVERT: A 136 GLU cc_start: 0.8917 (OUTLIER) cc_final: 0.7893 (pm20) REVERT: A 553 ARG cc_start: 0.8490 (ptt180) cc_final: 0.8179 (ptp-110) REVERT: A 811 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.8055 (tp30) REVERT: A 883 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8792 (tp) REVERT: B 75 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.7761 (mtm180) REVERT: B 82 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8420 (mmmt) REVERT: B 189 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.8909 (mp) REVERT: C 21 ARG cc_start: 0.8380 (mmp80) cc_final: 0.8136 (mmt180) REVERT: C 75 MET cc_start: 0.4664 (tpt) cc_final: 0.4202 (mmt) REVERT: D 60 GLU cc_start: 0.5931 (OUTLIER) cc_final: 0.5609 (mt-10) REVERT: D 174 MET cc_start: 0.6032 (mtt) cc_final: 0.5295 (tmm) REVERT: E 104 THR cc_start: 0.3272 (m) cc_final: 0.3070 (p) REVERT: E 131 LYS cc_start: 0.4339 (mmtm) cc_final: 0.4019 (mmmt) REVERT: E 185 TYR cc_start: 0.5261 (OUTLIER) cc_final: 0.4206 (m-80) REVERT: E 233 MET cc_start: 0.4900 (mpp) cc_final: 0.3944 (ppp) REVERT: E 250 THR cc_start: 0.0609 (OUTLIER) cc_final: 0.0054 (t) REVERT: E 279 THR cc_start: -0.0868 (OUTLIER) cc_final: -0.1211 (m) REVERT: E 319 GLU cc_start: 0.1272 (OUTLIER) cc_final: 0.0683 (mt-10) REVERT: E 373 PHE cc_start: 0.4850 (OUTLIER) cc_final: 0.4520 (t80) REVERT: E 436 MET cc_start: 0.2108 (mmm) cc_final: 0.1625 (mmm) REVERT: E 468 SER cc_start: -0.2328 (OUTLIER) cc_final: -0.2917 (m) REVERT: F 180 TYR cc_start: 0.2501 (OUTLIER) cc_final: 0.2045 (t80) REVERT: F 343 PHE cc_start: -0.0366 (t80) cc_final: -0.0579 (t80) REVERT: F 358 CYS cc_start: 0.3072 (p) cc_final: 0.2782 (p) REVERT: F 373 PHE cc_start: 0.4801 (t80) cc_final: 0.4517 (t80) REVERT: F 399 ILE cc_start: 0.3982 (mp) cc_final: 0.3699 (mm) REVERT: F 428 LEU cc_start: 0.2172 (OUTLIER) cc_final: 0.1043 (mm) REVERT: F 460 LYS cc_start: 0.0146 (tmtt) cc_final: -0.0056 (ptmm) REVERT: G 3 GLU cc_start: 0.8682 (mt-10) cc_final: 0.8430 (mt-10) outliers start: 78 outliers final: 51 residues processed: 245 average time/residue: 0.5959 time to fit residues: 167.4910 Evaluate side-chains 243 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 177 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 75 HIS Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 649 SER Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 760 ASP Chi-restraints excluded: chain A residue 798 LYS Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 855 MET Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain B residue 75 ARG Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 182 TRP Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 72 CYS Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 69 SER Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 149 TYR Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 185 TYR Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 250 THR Chi-restraints excluded: chain E residue 279 THR Chi-restraints excluded: chain E residue 319 GLU Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 373 PHE Chi-restraints excluded: chain E residue 456 VAL Chi-restraints excluded: chain E residue 468 SER Chi-restraints excluded: chain E residue 512 ILE Chi-restraints excluded: chain E residue 544 VAL Chi-restraints excluded: chain E residue 589 SER Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 180 TYR Chi-restraints excluded: chain F residue 185 TYR Chi-restraints excluded: chain F residue 193 VAL Chi-restraints excluded: chain F residue 211 TYR Chi-restraints excluded: chain F residue 230 HIS Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 366 THR Chi-restraints excluded: chain F residue 397 VAL Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain G residue 23 CYS Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 97 LEU Chi-restraints excluded: chain G residue 112 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 155 optimal weight: 0.9990 chunk 242 optimal weight: 2.9990 chunk 186 optimal weight: 6.9990 chunk 10 optimal weight: 0.5980 chunk 223 optimal weight: 0.9980 chunk 173 optimal weight: 6.9990 chunk 261 optimal weight: 0.9980 chunk 206 optimal weight: 8.9990 chunk 54 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 56 GLN D 157 GLN ** E 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 548 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.214397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.164150 restraints weight = 53918.441| |-----------------------------------------------------------------------------| r_work (start): 0.4008 rms_B_bonded: 3.34 r_work: 0.3085 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3077 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3077 r_free = 0.3077 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3077 r_free = 0.3077 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3077 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 22550 Z= 0.123 Angle : 0.601 12.273 30887 Z= 0.306 Chirality : 0.042 0.213 3575 Planarity : 0.005 0.078 3743 Dihedral : 12.031 117.298 3760 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.57 % Favored : 94.28 % Rotamer: Outliers : 3.51 % Allowed : 32.37 % Favored : 64.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % 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: -1.43 (0.16), residues: 2647 helix: 0.44 (0.17), residues: 950 sheet: -1.18 (0.29), residues: 302 loop : -1.95 (0.16), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 111 TYR 0.040 0.001 TYR F 306 PHE 0.028 0.002 PHE A 504 TRP 0.013 0.001 TRP A 916 HIS 0.007 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (22516) covalent geometry : angle 0.58774 / 0.31 (30860) hydrogen bonds : bond 0.04998 / 3.21 ( 785) hydrogen bonds : angle 4.39422 / 3.05 ( 2235) metal coordination : bond 0.01523 / 1.05 ( 32) metal coordination : angle 4.31307 / 2.53 ( 27) Misc. bond : bond 0.00180 / 0.09 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12545.81 seconds wall clock time: 213 minutes 29.40 seconds (12809.40 seconds total)