Starting phenix.real_space_refine on Fri Aug 7 13:28:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gwk_34314/08_2026/8gwk_34314.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gwk_34314/08_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_34314/08_2026/8gwk_34314.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gwk_34314/08_2026/8gwk_34314.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gwk_34314/08_2026/8gwk_34314.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gwk_34314/08_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-2.2rc3-6140/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: 6.16, per 1000 atoms: 0.28 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: 1.80 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: 2.70 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: 4.67 Time building geometry restraints manager: 2.39 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: 8.040 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: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 27.590 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.070 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:8.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.210 ------------------------------------------------------------------------------- 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= 0.776 Angle : 1.207 73.793 30887 Z= 0.752 Chirality : 0.061 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 0.00859 / 0.51 (22516) covalent geometry : angle 1.18361 / 0.75 (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 : 0.910 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: 0.7691 (mtmt) REVERT: C 21 ARG cc_start: 0.8005 (mmp80) cc_final: 0.7753 (mmt180) REVERT: D 40 LYS cc_start: 0.5106 (OUTLIER) cc_final: 0.3553 (mmpt) REVERT: D 48 GLU cc_start: 0.7652 (tp30) cc_final: 0.7248 (mm-30) REVERT: D 69 GLN cc_start: 0.7326 (tt0) cc_final: 0.6785 (tm-30) REVERT: D 143 ASP cc_start: 0.7144 (t70) cc_final: 0.6935 (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: 0.3798 (p0) REVERT: E 185 TYR cc_start: 0.5132 (m-80) cc_final: 0.4708 (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: 0.2246 (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: 0.4388 (mmtp) outliers start: 141 outliers final: 109 residues processed: 348 average time/residue: 0.5352 time to fit residues: 218.0232 Evaluate side-chains 299 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 189 time to evaluate : 0.828 ------------------------------------------------------------------------------- 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 40 LYS 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 = 0.4679 r_free = 0.4679 target = 0.221568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.151965 restraints weight = 60067.455| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 3.66 r_work: 0.3578 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3247 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3247 r_free = 0.3247 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3247 r_free = 0.3247 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3247 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1098 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= 0.163 Angle : 0.769 14.943 30887 Z= 0.392 Chirality : 0.046 0.311 3575 Planarity : 0.006 0.075 3743 Dihedral : 14.156 123.121 3895 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.16 % Favored : 92.69 % Rotamer: Outliers : 6.97 % Allowed : 28.60 % Favored : 64.43 % 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: -2.55 (0.15), residues: 2647 helix: -0.65 (0.17), residues: 951 sheet: -1.69 (0.32), residues: 226 loop : -2.50 (0.15), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 443 TYR 0.021 0.002 TYR E 541 PHE 0.035 0.002 PHE A 504 TRP 0.021 0.002 TRP E 167 HIS 0.007 0.001 HIS E 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (22516) covalent geometry : angle 0.74908 / 0.39 (30860) hydrogen bonds : bond 0.06892 / 4.51 ( 785) hydrogen bonds : angle 5.48188 / 3.85 ( 2235) metal coordination : bond 0.01929 / 1.29 ( 32) metal coordination : angle 5.96975 / 3.78 ( 27) Misc. bond : bond 0.00570 / 0.30 ( 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 : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 TYR cc_start: 0.8668 (t80) cc_final: 0.8421 (t80) REVERT: A 267 LYS cc_start: 0.8785 (tmtt) cc_final: 0.8450 (mmmt) REVERT: A 380 MET cc_start: 0.9024 (OUTLIER) cc_final: 0.8815 (mmm) REVERT: A 553 ARG cc_start: 0.8373 (ptt180) cc_final: 0.7813 (ptm-80) REVERT: A 668 MET cc_start: 0.9346 (OUTLIER) cc_final: 0.9008 (ttm) REVERT: A 778 SER cc_start: 0.8789 (OUTLIER) cc_final: 0.8571 (m) REVERT: A 894 GLU cc_start: 0.8240 (tt0) cc_final: 0.7925 (tt0) REVERT: A 898 HIS cc_start: 0.7655 (OUTLIER) cc_final: 0.6984 (t-90) REVERT: B 72 LYS cc_start: 0.8382 (mttm) cc_final: 0.8042 (mtpt) REVERT: B 82 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.8075 (mmmt) REVERT: B 97 LYS cc_start: 0.8339 (mtpt) cc_final: 0.7846 (mtmt) REVERT: C 21 ARG cc_start: 0.8469 (mmp80) cc_final: 0.8201 (mmt180) REVERT: C 75 MET cc_start: 0.5290 (OUTLIER) cc_final: 0.4534 (mmm) REVERT: D 48 GLU cc_start: 0.7848 (tp30) cc_final: 0.7622 (mm-30) REVERT: D 49 PHE cc_start: 0.5917 (t80) cc_final: 0.5715 (t80) REVERT: D 69 GLN cc_start: 0.7919 (tm-30) cc_final: 0.7426 (tm-30) REVERT: D 143 ASP cc_start: 0.7172 (t70) cc_final: 0.6907 (t0) REVERT: D 174 MET cc_start: 0.6005 (OUTLIER) cc_final: 0.5076 (tmm) REVERT: D 176 ASN cc_start: 0.7089 (m-40) cc_final: 0.6681 (t0) REVERT: E 9 ASN cc_start: 0.4535 (t0) cc_final: 0.4180 (p0) REVERT: E 274 MET cc_start: 0.1266 (ppp) cc_final: 0.1045 (mtm) REVERT: E 276 LYS cc_start: 0.3516 (mmmt) cc_final: 0.3309 (mmpt) REVERT: E 299 TYR cc_start: 0.2076 (m-80) cc_final: 0.1599 (m-10) REVERT: E 373 PHE cc_start: 0.5334 (OUTLIER) cc_final: 0.4631 (t80) REVERT: E 436 MET cc_start: 0.2276 (mmm) cc_final: 0.1507 (mmm) REVERT: F 65 LEU cc_start: 0.5810 (OUTLIER) cc_final: 0.5384 (tp) REVERT: F 309 CYS cc_start: 0.3205 (OUTLIER) cc_final: 0.1621 (t) REVERT: F 373 PHE cc_start: 0.4951 (m-10) cc_final: 0.4667 (m-10) REVERT: F 399 ILE cc_start: 0.4843 (mp) cc_final: 0.4115 (mm) outliers start: 156 outliers final: 73 residues processed: 332 average time/residue: 0.5184 time to fit residues: 200.4636 Evaluate side-chains 258 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 175 time to evaluate : 0.837 ------------------------------------------------------------------------------- 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 380 MET 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 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 141 THR 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: 0.0870 chunk 80 optimal weight: 0.0050 chunk 149 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 264 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 150 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 255 optimal weight: 0.9980 chunk 136 optimal weight: 50.0000 chunk 56 optimal weight: 3.9990 overall best weight: 0.6174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 79 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** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 275 GLN F 516 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.223262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.146745 restraints weight = 59501.747| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 4.40 r_work: 0.3563 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3469 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3267 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3267 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1638 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= 0.134 Angle : 0.668 13.075 30887 Z= 0.341 Chirality : 0.043 0.288 3575 Planarity : 0.005 0.074 3743 Dihedral : 13.183 123.213 3818 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.06 % Favored : 93.79 % Rotamer: Outliers : 5.96 % Allowed : 29.12 % Favored : 64.91 % 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: -0.18 (0.17), residues: 932 sheet: -1.42 (0.32), residues: 235 loop : -2.34 (0.15), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 443 TYR 0.019 0.002 TYR E 541 PHE 0.023 0.002 PHE F 561 TRP 0.014 0.001 TRP A 916 HIS 0.005 0.001 HIS E 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (22516) covalent geometry : angle 0.65412 / 0.34 (30860) hydrogen bonds : bond 0.05595 / 3.64 ( 785) hydrogen bonds : angle 4.95674 / 3.47 ( 2235) metal coordination : bond 0.01726 / 1.18 ( 32) metal coordination : angle 4.66236 / 2.86 ( 27) Misc. bond : bond 0.00330 / 0.17 ( 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 321 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 188 time to evaluate : 0.736 Fit side-chains REVERT: A 32 TYR cc_start: 0.8578 (t80) cc_final: 0.8326 (t80) REVERT: A 136 GLU cc_start: 0.8934 (OUTLIER) cc_final: 0.7795 (pm20) REVERT: A 267 LYS cc_start: 0.8794 (tmtt) cc_final: 0.8458 (mmmt) REVERT: A 553 ARG cc_start: 0.8335 (ptt180) cc_final: 0.7733 (ptm160) REVERT: A 790 ASN cc_start: 0.9000 (OUTLIER) cc_final: 0.8711 (m-40) REVERT: A 894 GLU cc_start: 0.8129 (tt0) cc_final: 0.7789 (tt0) REVERT: B 72 LYS cc_start: 0.8443 (mttm) cc_final: 0.8102 (mtpt) REVERT: B 75 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.7418 (mtm180) REVERT: B 82 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.8104 (mmmt) REVERT: B 97 LYS cc_start: 0.8204 (mtpt) cc_final: 0.7710 (mtmt) REVERT: B 189 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8740 (mp) REVERT: C 21 ARG cc_start: 0.8352 (mmp80) cc_final: 0.8081 (mmt180) REVERT: D 49 PHE cc_start: 0.5908 (t80) cc_final: 0.5690 (t80) REVERT: D 60 GLU cc_start: 0.5544 (OUTLIER) cc_final: 0.5115 (mt-10) REVERT: D 174 MET cc_start: 0.5846 (mtt) cc_final: 0.4942 (tmm) REVERT: E 9 ASN cc_start: 0.4870 (t0) cc_final: 0.4632 (p0) REVERT: E 131 LYS cc_start: 0.4451 (mmtp) cc_final: 0.4135 (pttt) REVERT: E 274 MET cc_start: 0.1184 (ppp) cc_final: 0.0751 (mtt) REVERT: E 373 PHE cc_start: 0.5387 (OUTLIER) cc_final: 0.4750 (t80) REVERT: E 405 LEU cc_start: 0.5861 (mp) cc_final: 0.5410 (pt) REVERT: E 436 MET cc_start: 0.1866 (mmm) cc_final: 0.1358 (mmm) REVERT: F 65 LEU cc_start: 0.6234 (OUTLIER) cc_final: 0.5982 (tp) REVERT: F 175 PRO cc_start: 0.2258 (Cg_exo) cc_final: 0.1874 (Cg_endo) REVERT: F 280 LEU cc_start: 0.4517 (OUTLIER) cc_final: 0.4112 (tp) REVERT: F 309 CYS cc_start: 0.3460 (OUTLIER) cc_final: 0.2183 (t) REVERT: F 319 GLU cc_start: 0.3965 (OUTLIER) cc_final: 0.3740 (tt0) REVERT: F 399 ILE cc_start: 0.4953 (mp) cc_final: 0.4336 (mm) REVERT: F 414 LYS cc_start: 0.4017 (mmpt) cc_final: 0.2979 (ttpt) REVERT: F 428 LEU cc_start: 0.2580 (OUTLIER) cc_final: 0.1690 (mm) REVERT: F 429 MET cc_start: 0.2046 (mtt) cc_final: 0.1781 (mmp) REVERT: G 32 TYR cc_start: 0.6025 (OUTLIER) cc_final: 0.5266 (p90) outliers start: 133 outliers final: 57 residues processed: 298 average time/residue: 0.5436 time to fit residues: 188.3099 Evaluate side-chains 249 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 179 time to evaluate : 0.807 ------------------------------------------------------------------------------- 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 361 LEU Chi-restraints excluded: chain A residue 363 SER 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 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 27 LYS Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 72 CYS Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 123 THR 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 76 LYS Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 119 ASP Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 241 VAL 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 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 280 LEU 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 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 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: 20.0000 chunk 16 optimal weight: 3.9990 chunk 228 optimal weight: 20.0000 chunk 59 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 213 optimal weight: 9.9990 chunk 66 optimal weight: 0.0870 chunk 34 optimal weight: 2.9990 chunk 152 optimal weight: 7.9990 chunk 240 optimal weight: 8.9990 chunk 153 optimal weight: 6.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 88 ASN A 734 ASN 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 548 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4665 r_free = 0.4665 target = 0.220253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.149057 restraints weight = 52020.639| |-----------------------------------------------------------------------------| r_work (start): 0.3925 rms_B_bonded: 3.76 r_work: 0.3530 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3439 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3187 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3187 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 22550 Z= 0.227 Angle : 0.732 13.350 30887 Z= 0.377 Chirality : 0.048 0.301 3575 Planarity : 0.006 0.083 3743 Dihedral : 13.030 123.178 3795 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.08 % Favored : 92.81 % Rotamer: Outliers : 6.36 % Allowed : 29.12 % Favored : 64.52 % 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: -2.32 (0.15), residues: 2647 helix: -0.39 (0.17), residues: 944 sheet: -1.58 (0.30), residues: 264 loop : -2.41 (0.15), residues: 1439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 443 TYR 0.023 0.002 TYR F 31 PHE 0.038 0.002 PHE A 504 TRP 0.030 0.002 TRP G 53 HIS 0.010 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00540 / 0.23 (22516) covalent geometry : angle 0.71880 / 0.38 (30860) hydrogen bonds : bond 0.07633 / 4.91 ( 785) hydrogen bonds : angle 5.04029 / 3.51 ( 2235) metal coordination : bond 0.01936 / 1.28 ( 32) metal coordination : angle 4.69733 / 2.84 ( 27) Misc. bond : bond 0.00506 / 0.26 ( 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 332 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 190 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 GLU cc_start: 0.9035 (OUTLIER) cc_final: 0.7898 (pm20) REVERT: A 267 LYS cc_start: 0.8836 (tmtt) cc_final: 0.8498 (mmmt) REVERT: A 553 ARG cc_start: 0.8413 (ptt180) cc_final: 0.7809 (ptm-80) REVERT: A 790 ASN cc_start: 0.8943 (OUTLIER) cc_final: 0.8705 (t0) REVERT: A 811 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8367 (tp30) REVERT: A 885 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8835 (mp) REVERT: A 894 GLU cc_start: 0.8282 (tt0) cc_final: 0.7976 (tt0) REVERT: A 898 HIS cc_start: 0.7684 (OUTLIER) cc_final: 0.6932 (t-90) REVERT: B 72 LYS cc_start: 0.8397 (mttm) cc_final: 0.8060 (mtpt) REVERT: B 75 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7465 (mtm180) REVERT: B 82 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8213 (mmmt) REVERT: B 97 LYS cc_start: 0.8276 (mtpt) cc_final: 0.7810 (mtmt) REVERT: B 189 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8751 (mp) REVERT: C 21 ARG cc_start: 0.8490 (mmp80) cc_final: 0.8219 (mmt180) REVERT: C 73 GLU cc_start: 0.7254 (OUTLIER) cc_final: 0.6914 (mp0) REVERT: D 174 MET cc_start: 0.6018 (OUTLIER) cc_final: 0.5096 (tmm) REVERT: E 9 ASN cc_start: 0.4953 (t0) cc_final: 0.4633 (p0) REVERT: E 21 ARG cc_start: 0.3630 (OUTLIER) cc_final: 0.3202 (mmp-170) REVERT: E 250 THR cc_start: 0.0766 (OUTLIER) cc_final: 0.0170 (t) REVERT: E 274 MET cc_start: 0.1568 (ppp) cc_final: 0.1041 (mtt) REVERT: E 373 PHE cc_start: 0.5432 (OUTLIER) cc_final: 0.4833 (t80) REVERT: E 405 LEU cc_start: 0.5531 (mp) cc_final: 0.5305 (pt) REVERT: E 436 MET cc_start: 0.2129 (mmm) cc_final: 0.1622 (mmm) REVERT: F 309 CYS cc_start: 0.3424 (OUTLIER) cc_final: 0.2177 (t) REVERT: F 399 ILE cc_start: 0.4678 (mp) cc_final: 0.4158 (mm) REVERT: F 414 LYS cc_start: 0.3818 (mmtt) cc_final: 0.2759 (ttpt) REVERT: F 428 LEU cc_start: 0.2348 (OUTLIER) cc_final: 0.1388 (mm) REVERT: F 429 MET cc_start: 0.2000 (mtt) cc_final: 0.1783 (mmp) REVERT: F 516 ASN cc_start: 0.1954 (p0) cc_final: 0.1687 (m110) REVERT: G 32 TYR cc_start: 0.6121 (OUTLIER) cc_final: 0.5274 (p90) outliers start: 142 outliers final: 75 residues processed: 303 average time/residue: 0.5267 time to fit residues: 185.2752 Evaluate side-chains 265 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 174 time to evaluate : 0.806 ------------------------------------------------------------------------------- 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 208 ASP Chi-restraints excluded: chain A residue 235 ASP 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 404 ASN Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 615 MET 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 790 ASN Chi-restraints excluded: chain A residue 798 LYS Chi-restraints excluded: chain A residue 811 GLU Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 896 THR 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 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 27 LYS 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 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 2 VAL 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 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 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 548 GLN 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 261 GLU Chi-restraints excluded: chain F residue 272 VAL 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 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 27 ASN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 66 optimal weight: 2.9990 chunk 237 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 259 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 96 optimal weight: 7.9990 chunk 258 optimal weight: 9.9990 chunk 13 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 94 optimal weight: 9.9990 chunk 211 optimal weight: 9.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4674 r_free = 0.4674 target = 0.221244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.143786 restraints weight = 60013.455| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 4.49 r_work: 0.3522 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3429 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3218 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3218 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 22550 Z= 0.165 Angle : 0.679 16.307 30887 Z= 0.347 Chirality : 0.045 0.299 3575 Planarity : 0.005 0.080 3743 Dihedral : 12.835 123.743 3785 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.21 % Favored : 93.68 % Rotamer: Outliers : 6.05 % Allowed : 29.12 % Favored : 64.82 % 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: -2.15 (0.15), residues: 2647 helix: -0.22 (0.17), residues: 938 sheet: -1.40 (0.31), residues: 244 loop : -2.34 (0.15), residues: 1465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 443 TYR 0.021 0.002 TYR F 31 PHE 0.033 0.002 PHE A 504 TRP 0.017 0.002 TRP A 916 HIS 0.008 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (22516) covalent geometry : angle 0.66021 / 0.35 (30860) hydrogen bonds : bond 0.06506 / 4.19 ( 785) hydrogen bonds : angle 4.87827 / 3.40 ( 2235) metal coordination : bond 0.01876 / 1.29 ( 32) metal coordination : angle 5.41892 / 3.13 ( 27) Misc. bond : bond 0.00298 / 0.16 ( 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 320 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 185 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 GLU cc_start: 0.8971 (OUTLIER) cc_final: 0.7789 (pm20) REVERT: A 267 LYS cc_start: 0.8803 (tmtt) cc_final: 0.8453 (mmmt) REVERT: A 553 ARG cc_start: 0.8362 (ptt180) cc_final: 0.7740 (ptm-80) REVERT: A 811 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8307 (tp30) REVERT: A 885 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8741 (mp) REVERT: A 894 GLU cc_start: 0.8215 (tt0) cc_final: 0.7940 (tt0) REVERT: B 72 LYS cc_start: 0.8400 (mttm) cc_final: 0.8051 (mtpt) REVERT: B 75 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.7400 (mtm180) REVERT: B 82 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.8191 (mmmt) REVERT: B 97 LYS cc_start: 0.8212 (mtpt) cc_final: 0.7724 (mtmt) REVERT: B 189 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8722 (mp) REVERT: C 21 ARG cc_start: 0.8439 (mmp80) cc_final: 0.8153 (mmt180) REVERT: C 73 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.7025 (mp0) REVERT: D 174 MET cc_start: 0.5901 (OUTLIER) cc_final: 0.4973 (tmm) REVERT: E 9 ASN cc_start: 0.4928 (t0) cc_final: 0.4716 (p0) REVERT: E 21 ARG cc_start: 0.3785 (OUTLIER) cc_final: 0.3320 (mmp-170) REVERT: E 131 LYS cc_start: 0.4701 (mmtp) cc_final: 0.4328 (pttt) REVERT: E 185 TYR cc_start: 0.5632 (OUTLIER) cc_final: 0.5229 (m-80) REVERT: E 250 THR cc_start: 0.0799 (OUTLIER) cc_final: 0.0206 (t) REVERT: E 274 MET cc_start: 0.1590 (ppp) cc_final: 0.1069 (mtt) REVERT: E 373 PHE cc_start: 0.5283 (OUTLIER) cc_final: 0.4748 (t80) REVERT: E 405 LEU cc_start: 0.5585 (mp) cc_final: 0.5350 (pt) REVERT: E 436 MET cc_start: 0.2089 (mmm) cc_final: 0.1867 (mmm) REVERT: F 180 TYR cc_start: 0.4396 (m-80) cc_final: 0.3905 (m-80) REVERT: F 194 GLN cc_start: 0.4911 (tm130) cc_final: 0.4709 (tm130) REVERT: F 309 CYS cc_start: 0.3978 (OUTLIER) cc_final: 0.2841 (t) REVERT: F 373 PHE cc_start: 0.5153 (t80) cc_final: 0.4894 (t80) REVERT: F 399 ILE cc_start: 0.4320 (mp) cc_final: 0.3935 (mm) REVERT: F 460 LYS cc_start: 0.0250 (tmtt) cc_final: -0.0256 (ptmm) REVERT: F 516 ASN cc_start: 0.1885 (p0) cc_final: 0.1617 (m110) REVERT: G 32 TYR cc_start: 0.6117 (OUTLIER) cc_final: 0.5262 (p90) outliers start: 135 outliers final: 79 residues processed: 296 average time/residue: 0.5625 time to fit residues: 192.1626 Evaluate side-chains 273 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 180 time to evaluate : 0.772 ------------------------------------------------------------------------------- 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 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 493 VAL Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 615 MET 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 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 148 THR 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 33 VAL Chi-restraints excluded: chain D residue 65 GLN 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 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 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 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 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 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 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 378 MET 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 438 LEU Chi-restraints excluded: chain F residue 449 VAL Chi-restraints excluded: chain F residue 525 ILE Chi-restraints excluded: chain F residue 573 LEU 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 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: 7.9990 chunk 225 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 120 optimal weight: 7.9990 chunk 212 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 252 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 56 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 734 ASN D 56 GLN ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.222019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.147814 restraints weight = 54527.106| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 3.78 r_work: 0.3561 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3470 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3223 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 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: 0.3223 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 22550 Z= 0.139 Angle : 0.647 15.268 30887 Z= 0.328 Chirality : 0.044 0.296 3575 Planarity : 0.005 0.079 3743 Dihedral : 12.639 123.586 3781 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.29 % Favored : 93.56 % Rotamer: Outliers : 5.22 % Allowed : 30.13 % 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: -1.99 (0.16), residues: 2647 helix: -0.06 (0.17), residues: 945 sheet: -1.44 (0.29), residues: 270 loop : -2.25 (0.15), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 443 TYR 0.022 0.002 TYR F 31 PHE 0.028 0.002 PHE A 504 TRP 0.015 0.001 TRP A 916 HIS 0.007 0.001 HIS E 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (22516) covalent geometry : angle 0.62847 / 0.33 (30860) hydrogen bonds : bond 0.05700 / 3.66 ( 785) hydrogen bonds : angle 4.69913 / 3.27 ( 2235) metal coordination : bond 0.01831 / 1.27 ( 32) metal coordination : angle 5.20605 / 3.05 ( 27) Misc. bond : bond 0.00182 / 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 300 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 184 time to evaluate : 0.761 Fit side-chains REVERT: A 136 GLU cc_start: 0.8941 (OUTLIER) cc_final: 0.7766 (pm20) REVERT: A 553 ARG cc_start: 0.8343 (ptt180) cc_final: 0.7736 (ptm-80) REVERT: A 790 ASN cc_start: 0.9059 (OUTLIER) cc_final: 0.8855 (t0) REVERT: A 811 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8334 (tp30) REVERT: A 885 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8709 (mp) REVERT: A 894 GLU cc_start: 0.8208 (tt0) cc_final: 0.7881 (tt0) REVERT: B 72 LYS cc_start: 0.8445 (mttm) cc_final: 0.8104 (mtpt) REVERT: B 75 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7464 (mtm180) REVERT: B 82 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.8126 (mmmt) REVERT: B 97 LYS cc_start: 0.8215 (mtpt) cc_final: 0.7745 (mtmt) REVERT: B 189 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8728 (mp) REVERT: C 21 ARG cc_start: 0.8409 (mmp80) cc_final: 0.8121 (mmt180) REVERT: C 73 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.7012 (mp0) REVERT: D 174 MET cc_start: 0.5867 (OUTLIER) cc_final: 0.4921 (tmm) REVERT: E 185 TYR cc_start: 0.5700 (OUTLIER) cc_final: 0.5358 (m-80) REVERT: E 250 THR cc_start: 0.0715 (OUTLIER) cc_final: 0.0143 (t) REVERT: E 274 MET cc_start: 0.1561 (ppp) cc_final: 0.1107 (mtt) REVERT: E 279 THR cc_start: -0.0836 (OUTLIER) cc_final: -0.1045 (m) REVERT: E 373 PHE cc_start: 0.5374 (OUTLIER) cc_final: 0.4835 (t80) REVERT: E 405 LEU cc_start: 0.5655 (mp) cc_final: 0.5444 (pt) REVERT: E 436 MET cc_start: 0.2192 (mmm) cc_final: 0.1629 (mmm) REVERT: E 468 SER cc_start: -0.0845 (OUTLIER) cc_final: -0.1338 (m) REVERT: F 142 GLU cc_start: 0.5471 (OUTLIER) cc_final: 0.5064 (tm-30) REVERT: F 180 TYR cc_start: 0.4261 (m-80) cc_final: 0.3824 (m-80) REVERT: F 373 PHE cc_start: 0.5128 (t80) cc_final: 0.4884 (t80) REVERT: F 399 ILE cc_start: 0.4477 (mp) cc_final: 0.4138 (mm) REVERT: F 414 LYS cc_start: 0.3811 (mmtt) cc_final: 0.2675 (ttpt) REVERT: F 428 LEU cc_start: 0.2323 (OUTLIER) cc_final: 0.1450 (mm) REVERT: F 429 MET cc_start: 0.2328 (mtt) cc_final: 0.2075 (mmp) REVERT: F 460 LYS cc_start: 0.0358 (tmtt) cc_final: -0.0128 (ptmm) REVERT: G 32 TYR cc_start: 0.6079 (OUTLIER) cc_final: 0.5238 (p90) outliers start: 116 outliers final: 69 residues processed: 278 average time/residue: 0.5892 time to fit residues: 189.6904 Evaluate side-chains 265 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 179 time to evaluate : 0.818 ------------------------------------------------------------------------------- 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 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 361 LEU Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 615 MET 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 790 ASN 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 148 THR 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 72 CYS Chi-restraints excluded: chain C residue 73 GLU Chi-restraints excluded: chain D residue 19 GLN 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 174 MET Chi-restraints excluded: chain D residue 189 LEU 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 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 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 468 SER 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 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 286 THR Chi-restraints excluded: chain F residue 307 THR 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 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 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: 0.2980 chunk 184 optimal weight: 0.5980 chunk 226 optimal weight: 20.0000 chunk 185 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 251 optimal weight: 10.0000 chunk 6 optimal weight: 0.4980 chunk 83 optimal weight: 0.7980 chunk 162 optimal weight: 9.9990 chunk 7 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 56 GLN ** E 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 ASN ** E 265 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.212905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.165136 restraints weight = 56299.537| |-----------------------------------------------------------------------------| r_work (start): 0.4026 rms_B_bonded: 3.07 r_work: 0.3094 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3090 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3090 r_free = 0.3090 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3090 r_free = 0.3090 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3090 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 22550 Z= 0.134 Angle : 0.635 13.989 30887 Z= 0.323 Chirality : 0.043 0.293 3575 Planarity : 0.005 0.077 3743 Dihedral : 12.503 123.579 3774 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.87 % Favored : 93.98 % Rotamer: Outliers : 5.18 % Allowed : 30.31 % Favored : 64.52 % 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: -1.87 (0.16), residues: 2647 helix: 0.04 (0.17), residues: 946 sheet: -1.37 (0.30), residues: 270 loop : -2.19 (0.15), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 443 TYR 0.019 0.001 TYR F 306 PHE 0.028 0.002 PHE A 504 TRP 0.015 0.001 TRP A 916 HIS 0.006 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (22516) covalent geometry : angle 0.61900 / 0.32 (30860) hydrogen bonds : bond 0.05549 / 3.56 ( 785) hydrogen bonds : angle 4.65920 / 3.24 ( 2235) metal coordination : bond 0.01598 / 1.13 ( 32) metal coordination : angle 4.85549 / 2.87 ( 27) Misc. bond : bond 0.00236 / 0.12 ( 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 301 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 186 time to evaluate : 0.856 Fit side-chains revert: symmetry clash REVERT: A 29 ASP cc_start: 0.6578 (t0) cc_final: 0.6289 (t0) REVERT: A 136 GLU cc_start: 0.9007 (OUTLIER) cc_final: 0.8007 (pm20) REVERT: A 553 ARG cc_start: 0.8675 (ptt180) cc_final: 0.8315 (ptm-80) REVERT: A 811 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.8192 (tp30) REVERT: A 885 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.8871 (mp) REVERT: B 72 LYS cc_start: 0.8787 (mttm) cc_final: 0.8568 (mtpt) REVERT: B 75 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.7895 (mtm180) REVERT: B 82 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8522 (mmmt) REVERT: B 189 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.8898 (mp) REVERT: C 21 ARG cc_start: 0.8439 (mmp80) cc_final: 0.8184 (mmt180) REVERT: C 69 ASN cc_start: 0.7696 (m-40) cc_final: 0.7280 (t0) REVERT: C 73 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.7237 (mp0) REVERT: D 174 MET cc_start: 0.6002 (OUTLIER) cc_final: 0.5042 (tmm) REVERT: E 131 LYS cc_start: 0.4154 (mmtm) cc_final: 0.3806 (mmmt) REVERT: E 185 TYR cc_start: 0.4989 (OUTLIER) cc_final: 0.4365 (m-80) REVERT: E 250 THR cc_start: 0.1070 (OUTLIER) cc_final: 0.0358 (t) REVERT: E 274 MET cc_start: 0.2447 (ppp) cc_final: 0.1765 (mtt) REVERT: E 279 THR cc_start: -0.0665 (OUTLIER) cc_final: -0.0962 (m) REVERT: E 373 PHE cc_start: 0.4611 (OUTLIER) cc_final: 0.4338 (t80) REVERT: E 436 MET cc_start: 0.2377 (mmm) cc_final: 0.1977 (mmm) REVERT: E 468 SER cc_start: -0.1663 (OUTLIER) cc_final: -0.2348 (m) REVERT: E 472 PHE cc_start: 0.3230 (m-10) cc_final: 0.2626 (m-10) REVERT: F 142 GLU cc_start: 0.5557 (OUTLIER) cc_final: 0.4765 (tm-30) REVERT: F 180 TYR cc_start: 0.3586 (m-80) cc_final: 0.3256 (m-80) REVERT: F 373 PHE cc_start: 0.4704 (t80) cc_final: 0.4384 (t80) REVERT: F 399 ILE cc_start: 0.3810 (mp) cc_final: 0.3468 (mm) REVERT: F 414 LYS cc_start: 0.4327 (mmtt) cc_final: 0.3109 (ttpt) REVERT: F 428 LEU cc_start: 0.2905 (OUTLIER) cc_final: 0.1501 (mm) REVERT: F 429 MET cc_start: 0.2913 (mtt) cc_final: 0.2353 (mmp) REVERT: F 460 LYS cc_start: 0.0198 (tmtt) cc_final: -0.0174 (ptmm) REVERT: G 3 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8561 (mt-10) REVERT: G 32 TYR cc_start: 0.6372 (OUTLIER) cc_final: 0.5625 (p90) outliers start: 115 outliers final: 67 residues processed: 282 average time/residue: 0.5877 time to fit residues: 191.9209 Evaluate side-chains 263 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 180 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR 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 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 647 SER 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 885 LEU 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 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 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 72 CYS Chi-restraints excluded: chain C residue 73 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 174 MET Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain E residue 2 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 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 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 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 307 THR 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 438 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: 0.5980 chunk 36 optimal weight: 5.9990 chunk 67 optimal weight: 0.2980 chunk 257 optimal weight: 8.9990 chunk 189 optimal weight: 0.0980 chunk 149 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 157 optimal weight: 9.9990 chunk 10 optimal weight: 0.0670 chunk 221 optimal weight: 0.4980 overall best weight: 0.3118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 168 ASN A 790 ASN D 56 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 = 0.4558 r_free = 0.4558 target = 0.215641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.155446 restraints weight = 64830.344| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 12.43 r_work: 0.2988 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3022 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3022 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 22550 Z= 0.110 Angle : 0.598 13.215 30887 Z= 0.304 Chirality : 0.041 0.287 3575 Planarity : 0.005 0.072 3743 Dihedral : 12.296 123.412 3771 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.64 % Favored : 94.24 % Rotamer: Outliers : 4.08 % Allowed : 31.84 % Favored : 64.08 % 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: -1.62 (0.16), residues: 2647 helix: 0.30 (0.17), residues: 949 sheet: -1.32 (0.30), residues: 272 loop : -2.05 (0.15), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 490 TYR 0.019 0.001 TYR F 306 PHE 0.020 0.001 PHE F 422 TRP 0.017 0.001 TRP D 182 HIS 0.004 0.001 HIS E 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (22516) covalent geometry : angle 0.58405 / 0.30 (30860) hydrogen bonds : bond 0.04239 / 2.73 ( 785) hydrogen bonds : angle 4.45419 / 3.10 ( 2235) metal coordination : bond 0.01542 / 1.08 ( 32) metal coordination : angle 4.44896 / 2.65 ( 27) Misc. bond : bond 0.00065 / 0.03 ( 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 280 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 190 time to evaluate : 0.840 Fit side-chains REVERT: A 29 ASP cc_start: 0.6400 (t0) cc_final: 0.6147 (t0) REVERT: A 553 ARG cc_start: 0.8448 (ptt180) cc_final: 0.7918 (ptm-80) REVERT: A 883 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8766 (tp) REVERT: B 72 LYS cc_start: 0.8536 (mttm) cc_final: 0.8188 (mtpt) REVERT: B 75 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7582 (mtm180) REVERT: B 82 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8340 (mmmt) REVERT: B 189 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8804 (mp) REVERT: C 21 ARG cc_start: 0.8364 (mmp80) cc_final: 0.8122 (mmt180) REVERT: D 112 ASP cc_start: 0.5963 (p0) cc_final: 0.5694 (p0) REVERT: D 174 MET cc_start: 0.6015 (OUTLIER) cc_final: 0.5050 (tmm) REVERT: E 131 LYS cc_start: 0.4188 (mmtm) cc_final: 0.3906 (mmmt) REVERT: E 185 TYR cc_start: 0.5884 (OUTLIER) cc_final: 0.4904 (m-80) REVERT: E 250 THR cc_start: 0.0564 (OUTLIER) cc_final: 0.0030 (t) REVERT: E 274 MET cc_start: 0.1999 (ppp) cc_final: 0.1579 (mtt) REVERT: E 279 THR cc_start: -0.0695 (OUTLIER) cc_final: -0.0910 (m) REVERT: E 280 LEU cc_start: 0.0003 (mm) cc_final: -0.0271 (mp) REVERT: E 373 PHE cc_start: 0.5507 (OUTLIER) cc_final: 0.4960 (t80) REVERT: E 436 MET cc_start: 0.2063 (mmm) cc_final: 0.1457 (mmm) REVERT: F 142 GLU cc_start: 0.5582 (OUTLIER) cc_final: 0.5252 (mm-30) REVERT: F 358 CYS cc_start: 0.4252 (p) cc_final: 0.3503 (p) REVERT: F 373 PHE cc_start: 0.5086 (t80) cc_final: 0.4846 (t80) REVERT: F 399 ILE cc_start: 0.4511 (mp) cc_final: 0.4208 (mm) REVERT: F 460 LYS cc_start: 0.0349 (tmtt) cc_final: 0.0049 (ptmm) REVERT: G 3 GLU cc_start: 0.8883 (mt-10) cc_final: 0.8587 (mt-10) outliers start: 90 outliers final: 54 residues processed: 261 average time/residue: 0.5964 time to fit residues: 179.8606 Evaluate side-chains 242 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 178 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 499 ASP 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 790 ASN Chi-restraints excluded: chain A residue 798 LYS Chi-restraints excluded: chain A residue 855 MET Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 928 HIS Chi-restraints excluded: chain B residue 75 ARG 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 6 VAL Chi-restraints excluded: chain C residue 23 GLU Chi-restraints excluded: chain D residue 56 GLN Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain E residue 2 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 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 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 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 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 286 THR Chi-restraints excluded: chain F residue 307 THR 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 437 PHE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 86 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 240 optimal weight: 0.0770 chunk 39 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 chunk 195 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 250 optimal weight: 40.0000 chunk 79 optimal weight: 1.9990 chunk 135 optimal weight: 5.9990 overall best weight: 0.9142 ------------------------------------------------------------------------------- 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 = 0.4546 r_free = 0.4546 target = 0.214382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.155845 restraints weight = 59862.481| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 10.61 r_work: 0.2957 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2985 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2985 r_free = 0.2985 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2985 r_free = 0.2985 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2985 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2679 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= 0.128 Angle : 0.616 12.612 30887 Z= 0.313 Chirality : 0.042 0.288 3575 Planarity : 0.005 0.077 3743 Dihedral : 12.224 123.597 3763 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.30 % Favored : 94.55 % Rotamer: Outliers : 3.95 % Allowed : 32.06 % Favored : 63.99 % 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: -1.57 (0.16), residues: 2647 helix: 0.33 (0.17), residues: 949 sheet: -1.22 (0.29), residues: 289 loop : -2.03 (0.16), residues: 1409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 57 TYR 0.061 0.001 TYR F 180 PHE 0.047 0.002 PHE E 472 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 0.00287 / 0.13 (22516) covalent geometry : angle 0.60274 / 0.31 (30860) hydrogen bonds : bond 0.04830 / 3.10 ( 785) hydrogen bonds : angle 4.44398 / 3.09 ( 2235) metal coordination : bond 0.01494 / 1.03 ( 32) metal coordination : angle 4.36098 / 2.58 ( 27) Misc. bond : bond 0.00162 / 0.08 ( 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 266 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 179 time to evaluate : 0.999 Fit side-chains REVERT: A 553 ARG cc_start: 0.8472 (ptt180) cc_final: 0.7911 (ptm-80) REVERT: A 885 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8715 (mp) REVERT: B 72 LYS cc_start: 0.8501 (mttm) cc_final: 0.8155 (mtpt) REVERT: B 75 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7619 (mtm180) REVERT: B 82 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8333 (mmmt) REVERT: B 189 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8819 (mp) REVERT: C 21 ARG cc_start: 0.8380 (mmp80) cc_final: 0.8129 (mmt180) REVERT: C 75 MET cc_start: 0.4682 (tpt) cc_final: 0.4330 (mmm) REVERT: D 60 GLU cc_start: 0.5606 (OUTLIER) cc_final: 0.5189 (mt-10) REVERT: D 174 MET cc_start: 0.6047 (OUTLIER) cc_final: 0.5122 (tmm) REVERT: E 131 LYS cc_start: 0.4204 (mmtm) cc_final: 0.3930 (mmmt) REVERT: E 185 TYR cc_start: 0.5910 (OUTLIER) cc_final: 0.4962 (m-80) REVERT: E 233 MET cc_start: 0.4927 (mpp) cc_final: 0.4128 (ppp) REVERT: E 250 THR cc_start: 0.0542 (OUTLIER) cc_final: 0.0022 (t) REVERT: E 274 MET cc_start: 0.1951 (ppp) cc_final: 0.1551 (mtt) REVERT: E 279 THR cc_start: -0.0670 (OUTLIER) cc_final: -0.0877 (m) REVERT: E 280 LEU cc_start: -0.0076 (mm) cc_final: -0.0336 (mp) REVERT: E 373 PHE cc_start: 0.5567 (OUTLIER) cc_final: 0.5016 (t80) REVERT: E 436 MET cc_start: 0.2047 (mmm) cc_final: 0.1426 (mmm) REVERT: E 468 SER cc_start: -0.0985 (OUTLIER) cc_final: -0.1460 (m) REVERT: F 142 GLU cc_start: 0.5491 (OUTLIER) cc_final: 0.5256 (mm-30) REVERT: F 180 TYR cc_start: 0.2642 (OUTLIER) cc_final: 0.2028 (t80) REVERT: F 358 CYS cc_start: 0.4380 (p) cc_final: 0.3623 (p) REVERT: F 373 PHE cc_start: 0.5065 (t80) cc_final: 0.4816 (t80) REVERT: F 399 ILE cc_start: 0.4561 (mp) cc_final: 0.4269 (mm) REVERT: F 460 LYS cc_start: 0.0330 (tmtt) cc_final: 0.0059 (ptmm) REVERT: G 3 GLU cc_start: 0.8916 (mt-10) cc_final: 0.8618 (mt-10) outliers start: 87 outliers final: 61 residues processed: 247 average time/residue: 0.5903 time to fit residues: 168.6277 Evaluate side-chains 247 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 173 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 499 ASP 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 855 MET Chi-restraints excluded: chain A residue 885 LEU 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 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 69 ASN Chi-restraints excluded: chain D residue 60 GLU Chi-restraints excluded: chain D residue 115 VAL 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 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 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 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 558 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 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 307 THR 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 437 PHE 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: 10.0000 chunk 201 optimal weight: 0.0070 chunk 242 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 265 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 118 optimal weight: 0.0370 chunk 222 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 overall best weight: 0.7678 ------------------------------------------------------------------------------- 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** E 395 HIS ** 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 = 0.4548 r_free = 0.4548 target = 0.214517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.165031 restraints weight = 48531.608| |-----------------------------------------------------------------------------| r_work (start): 0.4017 rms_B_bonded: 3.08 r_work: 0.3116 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3099 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3099 r_free = 0.3099 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3099 r_free = 0.3099 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (12 function evaluations) r_final: 0.3099 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 22550 Z= 0.118 Angle : 0.600 12.428 30887 Z= 0.305 Chirality : 0.042 0.287 3575 Planarity : 0.005 0.076 3743 Dihedral : 12.175 124.211 3762 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.26 % Favored : 94.59 % Rotamer: Outliers : 3.68 % Allowed : 32.50 % Favored : 63.82 % 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: -1.49 (0.16), residues: 2647 helix: 0.38 (0.17), residues: 950 sheet: -1.15 (0.29), residues: 289 loop : -1.98 (0.16), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 111 TYR 0.034 0.001 TYR F 180 PHE 0.026 0.001 PHE F 475 TRP 0.015 0.001 TRP D 182 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 0.58614 / 0.30 (30860) hydrogen bonds : bond 0.04773 / 3.07 ( 785) hydrogen bonds : angle 4.42320 / 3.07 ( 2235) metal coordination : bond 0.01525 / 1.06 ( 32) metal coordination : angle 4.34287 / 2.57 ( 27) Misc. bond : bond 0.00141 / 0.07 ( 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 254 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 173 time to evaluate : 0.785 Fit side-chains REVERT: A 136 GLU cc_start: 0.8941 (OUTLIER) cc_final: 0.7886 (pm20) REVERT: A 553 ARG cc_start: 0.8495 (ptt180) cc_final: 0.8107 (ptm-80) REVERT: A 885 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.8870 (mp) REVERT: B 75 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.7693 (mtm180) REVERT: B 82 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8428 (mmmt) REVERT: B 189 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.8887 (mp) REVERT: C 21 ARG cc_start: 0.8393 (mmp80) cc_final: 0.8145 (mmt180) REVERT: C 75 MET cc_start: 0.4796 (tpt) cc_final: 0.4309 (mmt) REVERT: D 75 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.7582 (mmp-170) REVERT: D 174 MET cc_start: 0.6139 (OUTLIER) cc_final: 0.5160 (tmm) REVERT: E 131 LYS cc_start: 0.4235 (mmtm) cc_final: 0.3887 (mmmt) REVERT: E 185 TYR cc_start: 0.5297 (OUTLIER) cc_final: 0.4242 (m-80) REVERT: E 233 MET cc_start: 0.4973 (mpp) cc_final: 0.4006 (ppp) REVERT: E 250 THR cc_start: 0.0685 (OUTLIER) cc_final: 0.0061 (t) REVERT: E 274 MET cc_start: 0.2250 (ppp) cc_final: 0.1692 (mtt) REVERT: E 279 THR cc_start: -0.0627 (OUTLIER) cc_final: -0.0888 (m) REVERT: E 280 LEU cc_start: -0.0174 (mm) cc_final: -0.0403 (mp) REVERT: E 373 PHE cc_start: 0.4881 (OUTLIER) cc_final: 0.4540 (t80) REVERT: E 436 MET cc_start: 0.2148 (mmm) cc_final: 0.1655 (mmm) REVERT: E 468 SER cc_start: -0.2004 (OUTLIER) cc_final: -0.2629 (m) REVERT: F 149 TYR cc_start: 0.4105 (m-80) cc_final: 0.3555 (m-80) REVERT: F 358 CYS cc_start: 0.3542 (p) cc_final: 0.3163 (p) REVERT: F 373 PHE cc_start: 0.4708 (t80) cc_final: 0.4382 (t80) REVERT: F 399 ILE cc_start: 0.4010 (mp) cc_final: 0.3681 (mm) REVERT: G 3 GLU cc_start: 0.8773 (mt-10) cc_final: 0.8498 (mt-10) outliers start: 81 outliers final: 55 residues processed: 238 average time/residue: 0.6227 time to fit residues: 170.1552 Evaluate side-chains 237 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 170 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 30 VAL 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 239 SER Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 499 ASP 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 855 MET Chi-restraints excluded: chain A residue 885 LEU 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 100 ASN 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 D residue 75 ARG 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 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 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 372 VAL Chi-restraints excluded: chain E residue 373 PHE 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 558 VAL Chi-restraints excluded: chain E residue 589 SER Chi-restraints excluded: chain F residue 60 VAL 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 371 VAL Chi-restraints excluded: chain F residue 425 VAL Chi-restraints excluded: chain F residue 437 PHE 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: 4.9990 chunk 242 optimal weight: 10.0000 chunk 186 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 223 optimal weight: 6.9990 chunk 173 optimal weight: 5.9990 chunk 261 optimal weight: 1.9990 chunk 206 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 111 optimal weight: 0.9980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 168 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 = 0.4520 r_free = 0.4520 target = 0.211791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.161223 restraints weight = 54393.166| |-----------------------------------------------------------------------------| r_work (start): 0.3970 rms_B_bonded: 3.33 r_work: 0.3036 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3029 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3029 r_free = 0.3029 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3029 r_free = 0.3029 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3029 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22550 Z= 0.171 Angle : 0.661 12.812 30887 Z= 0.337 Chirality : 0.045 0.295 3575 Planarity : 0.005 0.082 3743 Dihedral : 12.129 125.633 3757 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.10 % Favored : 93.75 % Rotamer: Outliers : 3.73 % Allowed : 32.28 % Favored : 63.99 % 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: -1.62 (0.16), residues: 2647 helix: 0.26 (0.17), residues: 939 sheet: -1.26 (0.28), residues: 301 loop : -2.03 (0.16), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 111 TYR 0.030 0.002 TYR F 306 PHE 0.036 0.002 PHE A 504 TRP 0.015 0.002 TRP A 916 HIS 0.009 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 (22516) covalent geometry : angle 0.64554 / 0.34 (30860) hydrogen bonds : bond 0.06522 / 4.18 ( 785) hydrogen bonds : angle 4.60814 / 3.20 ( 2235) metal coordination : bond 0.01529 / 1.02 ( 32) metal coordination : angle 4.77474 / 2.78 ( 27) Misc. bond : bond 0.00231 / 0.12 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12605.43 seconds wall clock time: 214 minutes 20.57 seconds (12860.57 seconds total)