Starting phenix.real_space_refine on Tue Aug 26 05:50:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5m3f_4147/08_2025/5m3f_4147.cif Found real_map, /net/cci-nas-00/data/ceres_data/5m3f_4147/08_2025/5m3f_4147.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5m3f_4147/08_2025/5m3f_4147.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5m3f_4147/08_2025/5m3f_4147.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5m3f_4147/08_2025/5m3f_4147.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5m3f_4147/08_2025/5m3f_4147.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.010 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 6 6.06 5 P 45 5.49 5 Mg 1 5.21 5 S 167 5.16 5 C 21380 2.51 5 N 5908 2.21 5 O 6525 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34032 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 11526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1459, 11526 Classifications: {'peptide': 1459} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 5, 'PTRANS': 54, 'TRANS': 1398} Chain breaks: 5 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 9350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1177, 9350 Classifications: {'peptide': 1177} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 58, 'TRANS': 1117} Chain breaks: 2 Chain: "C" Number of atoms: 2423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2423 Classifications: {'peptide': 305} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 285} Chain: "E" Number of atoms: 1735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1735 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 199} Chain: "F" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 823 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 6, 'TRANS': 93} Chain: "H" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1052 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain breaks: 1 Chain: "I" Number of atoms: 466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 466 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "J" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "K" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 793 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "L" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 352 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'TRANS': 43} Chain: "T" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 509 Classifications: {'DNA': 25} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 24} Chain: "U" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 285 Classifications: {'DNA': 14} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 13} Chain: "R" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 173 Classifications: {'RNA': 8} Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 3} Link IDs: {'rna3p': 7} Chain: "M" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 856 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "N" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1151 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 9, 'TRANS': 135} Chain breaks: 2 Chain: "D" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 431 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain breaks: 1 Chain: "G" Number of atoms: 1526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1526 Classifications: {'peptide': 193} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 180} Chain breaks: 1 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Unusual residues: {' ZN': 1, 'SO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 461 SG CYS A 62 72.642 62.910 53.873 1.00 59.17 S ATOM 480 SG CYS A 65 70.543 63.350 53.569 1.00 55.24 S ATOM 535 SG CYS A 72 70.879 63.597 55.699 1.00 61.70 S ATOM 781 SG CYS A 102 74.680 19.880 85.337 1.00 75.20 S ATOM 806 SG CYS A 105 72.543 19.285 84.629 1.00 72.59 S ATOM 1589 SG CYS A 233 73.234 18.888 87.862 1.00 73.01 S ATOM 1611 SG CYS A 236 75.151 16.114 86.831 1.00 79.29 S ATOM 20169 SG CYS B1104 58.484 51.529 60.019 1.00 49.88 S ATOM 20195 SG CYS B1107 59.954 50.715 61.020 1.00 53.44 S ATOM 20342 SG CYS B1128 61.633 51.666 58.582 1.00 43.19 S ATOM 20370 SG CYS B1131 59.848 47.863 59.290 1.00 75.37 S ATOM 26972 SG CYS I 10 123.556 43.290 133.412 1.00 78.72 S ATOM 26994 SG CYS I 13 123.549 44.022 129.796 1.00 73.48 S ATOM 27114 SG CYS I 30 122.283 42.161 129.097 1.00 66.99 S ATOM 27135 SG CYS I 33 125.138 43.008 131.039 1.00 70.99 S ATOM 27429 SG CYS J 7 74.068 122.759 96.635 1.00 59.10 S ATOM 27452 SG CYS J 10 70.490 124.973 98.396 1.00 55.25 S ATOM 27732 SG CYS J 45 71.391 122.774 98.755 1.00 99.91 S ATOM 27738 SG CYS J 46 73.181 126.271 97.767 1.00 61.84 S ATOM 28800 SG CYS L 34 110.915 109.289 72.203 1.00 85.12 S ATOM 28927 SG CYS L 51 113.727 107.525 74.226 1.00147.14 S Time building chain proxies: 6.82, per 1000 atoms: 0.20 Number of scatterers: 34032 At special positions: 0 Unit cell: (158.55, 160.65, 175.35, 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 6 29.99 S 167 16.00 P 45 15.00 Mg 1 11.99 O 6525 8.00 N 5908 7.00 C 21380 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.59 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 953.7 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A3001 " pdb="ZN ZN A3001 " - pdb=" NE2 HIS A 75 " pdb="ZN ZN A3001 " - pdb=" SG CYS A 65 " pdb="ZN ZN A3001 " - pdb=" SG CYS A 72 " pdb="ZN ZN A3001 " - pdb=" SG CYS A 62 " pdb=" ZN A3002 " pdb="ZN ZN A3002 " - pdb=" SG CYS A 105 " pdb="ZN ZN A3002 " - pdb=" SG CYS A 236 " pdb="ZN ZN A3002 " - pdb=" SG CYS A 233 " pdb="ZN ZN A3002 " - pdb=" SG CYS A 102 " pdb=" ZN B1302 " pdb="ZN ZN B1302 " - pdb=" SG CYS B1131 " pdb="ZN ZN B1302 " - pdb=" SG CYS B1128 " pdb="ZN ZN B1302 " - pdb=" SG CYS B1107 " pdb="ZN ZN B1302 " - pdb=" SG CYS B1104 " pdb=" ZN I3001 " pdb="ZN ZN I3001 " - pdb=" SG CYS I 13 " pdb="ZN ZN I3001 " - pdb=" SG CYS I 33 " pdb="ZN ZN I3001 " - pdb=" SG CYS I 30 " pdb="ZN ZN I3001 " - pdb=" SG CYS I 10 " pdb=" ZN J3001 " pdb="ZN ZN J3001 " - pdb=" SG CYS J 10 " pdb="ZN ZN J3001 " - pdb=" SG CYS J 46 " pdb="ZN ZN J3001 " - pdb=" SG CYS J 45 " pdb="ZN ZN J3001 " - pdb=" SG CYS J 7 " pdb=" ZN L3001 " pdb="ZN ZN L3001 " - pdb=" SG CYS L 34 " pdb="ZN ZN L3001 " - pdb=" SG CYS L 51 " Number of angles added : 27 8218 Ramachandran restraints generated. 4109 Oldfield, 0 Emsley, 4109 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7828 Finding SS restraints... Secondary structure from input PDB file: 151 helices and 47 sheets defined 36.2% alpha, 19.1% beta 11 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 4.29 Creating SS restraints... Processing helix chain 'A' and resid 20 through 28 removed outlier: 3.687A pdb=" N ILE A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ARG A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN A 26 " --> pdb=" O LYS A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 99 Processing helix chain 'A' and resid 111 through 125 removed outlier: 4.244A pdb=" N TYR A 118 " --> pdb=" O GLU A 114 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ARG A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 136 removed outlier: 3.528A pdb=" N TYR A 134 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 139 No H-bonds generated for 'chain 'A' and resid 137 through 139' Processing helix chain 'A' and resid 175 through 199 removed outlier: 3.691A pdb=" N ASN A 179 " --> pdb=" O SER A 175 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU A 180 " --> pdb=" O THR A 176 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ALA A 194 " --> pdb=" O ASP A 190 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ASP A 199 " --> pdb=" O LYS A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 226 removed outlier: 3.709A pdb=" N LYS A 225 " --> pdb=" O HIS A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 268 removed outlier: 3.653A pdb=" N THR A 262 " --> pdb=" O GLU A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 331 removed outlier: 4.313A pdb=" N THR A 326 " --> pdb=" O ASN A 322 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL A 327 " --> pdb=" O ILE A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 339 removed outlier: 3.636A pdb=" N TYR A 337 " --> pdb=" O CYS A 333 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE A 339 " --> pdb=" O LEU A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 354 Processing helix chain 'A' and resid 364 through 368 Processing helix chain 'A' and resid 380 through 406 removed outlier: 3.639A pdb=" N GLN A 384 " --> pdb=" O ASN A 380 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU A 385 " --> pdb=" O SER A 381 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER A 404 " --> pdb=" O ASN A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 439 removed outlier: 3.916A pdb=" N ARG A 417 " --> pdb=" O LEU A 413 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER A 421 " --> pdb=" O ARG A 417 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ARG A 422 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N VAL A 428 " --> pdb=" O MET A 424 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR A 429 " --> pdb=" O ASN A 425 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N VAL A 434 " --> pdb=" O ILE A 430 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASN A 435 " --> pdb=" O GLN A 431 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA A 436 " --> pdb=" O ASN A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 443 Processing helix chain 'A' and resid 455 through 460 removed outlier: 3.670A pdb=" N LEU A 460 " --> pdb=" O VAL A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 505 removed outlier: 3.670A pdb=" N LYS A 504 " --> pdb=" O VAL A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 526 removed outlier: 3.561A pdb=" N LEU A 519 " --> pdb=" O ASN A 515 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N GLN A 521 " --> pdb=" O ALA A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 561 removed outlier: 4.220A pdb=" N LEU A 557 " --> pdb=" O GLN A 553 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASN A 559 " --> pdb=" O LYS A 555 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLN A 560 " --> pdb=" O ALA A 556 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU A 561 " --> pdb=" O LEU A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 598 No H-bonds generated for 'chain 'A' and resid 596 through 598' Processing helix chain 'A' and resid 620 through 625 removed outlier: 3.872A pdb=" N TYR A 624 " --> pdb=" O ASN A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 650 removed outlier: 3.788A pdb=" N ASN A 649 " --> pdb=" O ALA A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 656 Processing helix chain 'A' and resid 671 through 676 Processing helix chain 'A' and resid 676 through 681 Processing helix chain 'A' and resid 688 through 699 removed outlier: 3.629A pdb=" N TYR A 697 " --> pdb=" O GLN A 693 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N CYS A 699 " --> pdb=" O TYR A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 740 removed outlier: 4.087A pdb=" N ILE A 732 " --> pdb=" O GLY A 728 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR A 733 " --> pdb=" O LYS A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 760 removed outlier: 3.553A pdb=" N TYR A 759 " --> pdb=" O LYS A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 787 removed outlier: 3.869A pdb=" N TYR A 786 " --> pdb=" O ASP A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 801 Processing helix chain 'A' and resid 802 through 825 removed outlier: 3.647A pdb=" N ALA A 806 " --> pdb=" O GLY A 802 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA A 807 " --> pdb=" O PRO A 803 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 848 Processing helix chain 'A' and resid 849 through 851 No H-bonds generated for 'chain 'A' and resid 849 through 851' Processing helix chain 'A' and resid 852 through 863 removed outlier: 4.067A pdb=" N GLU A 856 " --> pdb=" O ASP A 852 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA A 857 " --> pdb=" O THR A 853 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU A 860 " --> pdb=" O GLU A 856 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL A 861 " --> pdb=" O ALA A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 885 removed outlier: 4.102A pdb=" N LEU A 883 " --> pdb=" O LEU A 879 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ARG A 884 " --> pdb=" O GLN A 880 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ASP A 885 " --> pdb=" O GLU A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 912 removed outlier: 4.002A pdb=" N SER A 889 " --> pdb=" O ASP A 885 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA A 894 " --> pdb=" O GLY A 890 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER A 898 " --> pdb=" O ALA A 894 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LYS A 899 " --> pdb=" O VAL A 895 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR A 904 " --> pdb=" O VAL A 900 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER A 905 " --> pdb=" O ASN A 901 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER A 909 " --> pdb=" O SER A 905 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS A 910 " --> pdb=" O GLN A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 931 Processing helix chain 'A' and resid 936 through 945 removed outlier: 3.645A pdb=" N ILE A 943 " --> pdb=" O ASN A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 980 Processing helix chain 'A' and resid 991 through 1027 removed outlier: 3.934A pdb=" N MET A1000 " --> pdb=" O TYR A 996 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA A1001 " --> pdb=" O PHE A 997 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY A1005 " --> pdb=" O ALA A1001 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N THR A1013 " --> pdb=" O THR A1009 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N SER A1014 " --> pdb=" O ALA A1010 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG A1015 " --> pdb=" O VAL A1011 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N SER A1016 " --> pdb=" O LYS A1012 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ARG A1021 " --> pdb=" O GLY A1017 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N CYS A1022 " --> pdb=" O TYR A1018 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A1023 " --> pdb=" O LEU A1019 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS A1025 " --> pdb=" O ARG A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1071 removed outlier: 3.860A pdb=" N CYS A1069 " --> pdb=" O GLN A1065 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ASP A1071 " --> pdb=" O GLU A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1072 through 1081 removed outlier: 4.312A pdb=" N LYS A1078 " --> pdb=" O TYR A1074 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR A1080 " --> pdb=" O LEU A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1082 through 1085 Processing helix chain 'A' and resid 1092 through 1108 removed outlier: 4.080A pdb=" N LYS A1103 " --> pdb=" O LYS A1099 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TYR A1104 " --> pdb=" O LYS A1100 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1127 removed outlier: 4.179A pdb=" N LYS A1126 " --> pdb=" O PRO A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1151 removed outlier: 3.541A pdb=" N ASP A1142 " --> pdb=" O GLU A1138 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU A1144 " --> pdb=" O PHE A1140 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU A1145 " --> pdb=" O GLN A1141 " (cutoff:3.500A) Processing helix chain 'A' and resid 1152 through 1156 removed outlier: 3.662A pdb=" N LYS A1156 " --> pdb=" O LYS A1153 " (cutoff:3.500A) Processing helix chain 'A' and resid 1162 through 1177 removed outlier: 4.261A pdb=" N LEU A1172 " --> pdb=" O ALA A1168 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N TYR A1174 " --> pdb=" O MET A1170 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N MET A1175 " --> pdb=" O GLN A1171 " (cutoff:3.500A) Processing helix chain 'A' and resid 1184 through 1191 removed outlier: 3.816A pdb=" N ILE A1188 " --> pdb=" O ALA A1184 " (cutoff:3.500A) Processing helix chain 'A' and resid 1195 through 1200 Processing helix chain 'A' and resid 1218 through 1227 removed outlier: 3.946A pdb=" N GLU A1224 " --> pdb=" O PRO A1220 " (cutoff:3.500A) Processing helix chain 'A' and resid 1247 through 1255 removed outlier: 3.627A pdb=" N ASP A1252 " --> pdb=" O ASP A1248 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N CYS A1255 " --> pdb=" O ALA A1251 " (cutoff:3.500A) Processing helix chain 'A' and resid 1298 through 1305 removed outlier: 3.594A pdb=" N GLU A1304 " --> pdb=" O ASN A1300 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU A1305 " --> pdb=" O GLU A1301 " (cutoff:3.500A) Processing helix chain 'A' and resid 1309 through 1319 removed outlier: 3.681A pdb=" N ILE A1317 " --> pdb=" O LEU A1313 " (cutoff:3.500A) Processing helix chain 'A' and resid 1319 through 1337 removed outlier: 3.595A pdb=" N HIS A1323 " --> pdb=" O ASN A1319 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN A1336 " --> pdb=" O GLU A1332 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS A1337 " --> pdb=" O ILE A1333 " (cutoff:3.500A) Processing helix chain 'A' and resid 1442 through 1454 removed outlier: 4.230A pdb=" N ARG A1446 " --> pdb=" O VAL A1442 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N HIS A1454 " --> pdb=" O ILE A1450 " (cutoff:3.500A) Processing helix chain 'A' and resid 1485 through 1494 removed outlier: 3.810A pdb=" N ARG A1494 " --> pdb=" O GLU A1490 " (cutoff:3.500A) Processing helix chain 'A' and resid 1512 through 1516 removed outlier: 4.054A pdb=" N GLY A1515 " --> pdb=" O PRO A1512 " (cutoff:3.500A) Processing helix chain 'A' and resid 1525 through 1530 removed outlier: 3.685A pdb=" N MET A1529 " --> pdb=" O ASN A1525 " (cutoff:3.500A) Processing helix chain 'A' and resid 1546 through 1553 Processing helix chain 'A' and resid 1554 through 1573 removed outlier: 3.890A pdb=" N VAL A1563 " --> pdb=" O ARG A1559 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN A1564 " --> pdb=" O ASN A1560 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN A1568 " --> pdb=" O ASN A1564 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE A1570 " --> pdb=" O ILE A1566 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG A1572 " --> pdb=" O ASN A1568 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N TYR A1573 " --> pdb=" O VAL A1569 " (cutoff:3.500A) Processing helix chain 'A' and resid 1578 through 1590 removed outlier: 3.900A pdb=" N LEU A1582 " --> pdb=" O SER A1578 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A1584 " --> pdb=" O ARG A1580 " (cutoff:3.500A) Processing helix chain 'A' and resid 1591 through 1593 No H-bonds generated for 'chain 'A' and resid 1591 through 1593' Processing helix chain 'A' and resid 1599 through 1604 Processing helix chain 'A' and resid 1608 through 1614 removed outlier: 4.053A pdb=" N LYS A1612 " --> pdb=" O SER A1608 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER A1614 " --> pdb=" O PHE A1610 " (cutoff:3.500A) Processing helix chain 'A' and resid 1617 through 1627 removed outlier: 3.806A pdb=" N PHE A1621 " --> pdb=" O THR A1617 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS A1624 " --> pdb=" O GLN A1620 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 27 removed outlier: 3.522A pdb=" N ARG B 21 " --> pdb=" O ARG B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 41 removed outlier: 3.673A pdb=" N GLN B 39 " --> pdb=" O PHE B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 51 removed outlier: 3.639A pdb=" N ILE B 46 " --> pdb=" O VAL B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 68 removed outlier: 3.511A pdb=" N LEU B 63 " --> pdb=" O GLY B 59 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS B 66 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE B 68 " --> pdb=" O GLY B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 129 removed outlier: 3.767A pdb=" N GLN B 128 " --> pdb=" O SER B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 183 removed outlier: 3.505A pdb=" N VAL B 181 " --> pdb=" O PRO B 177 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN B 182 " --> pdb=" O TYR B 178 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N HIS B 183 " --> pdb=" O GLU B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 223 Processing helix chain 'B' and resid 273 through 281 removed outlier: 3.836A pdb=" N CYS B 281 " --> pdb=" O LEU B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 293 removed outlier: 3.796A pdb=" N ILE B 288 " --> pdb=" O SER B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 314 removed outlier: 4.050A pdb=" N THR B 303 " --> pdb=" O ASP B 299 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP B 304 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ARG B 305 " --> pdb=" O PHE B 301 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY B 312 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE B 313 " --> pdb=" O LEU B 309 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS B 314 " --> pdb=" O LEU B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 335 removed outlier: 3.748A pdb=" N LYS B 333 " --> pdb=" O TYR B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 357 removed outlier: 3.639A pdb=" N GLN B 351 " --> pdb=" O LEU B 347 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU B 354 " --> pdb=" O GLY B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 363 Processing helix chain 'B' and resid 366 through 386 removed outlier: 3.770A pdb=" N ARG B 372 " --> pdb=" O GLN B 368 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU B 375 " --> pdb=" O PHE B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 434 removed outlier: 3.867A pdb=" N MET B 411 " --> pdb=" O PHE B 407 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE B 412 " --> pdb=" O LEU B 408 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU B 413 " --> pdb=" O TYR B 409 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS B 414 " --> pdb=" O GLY B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 453 removed outlier: 4.284A pdb=" N MET B 451 " --> pdb=" O SER B 447 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ARG B 452 " --> pdb=" O ARG B 448 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL B 453 " --> pdb=" O VAL B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 468 Processing helix chain 'B' and resid 492 through 499 removed outlier: 3.581A pdb=" N PHE B 496 " --> pdb=" O ASN B 492 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N HIS B 499 " --> pdb=" O ARG B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 525 Processing helix chain 'B' and resid 560 through 568 removed outlier: 3.572A pdb=" N ILE B 564 " --> pdb=" O ARG B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 615 removed outlier: 3.549A pdb=" N ILE B 603 " --> pdb=" O GLU B 599 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG B 609 " --> pdb=" O ALA B 605 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY B 615 " --> pdb=" O TRP B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 697 removed outlier: 3.599A pdb=" N ILE B 696 " --> pdb=" O PRO B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 698 through 703 Processing helix chain 'B' and resid 711 through 722 Processing helix chain 'B' and resid 755 through 760 removed outlier: 3.709A pdb=" N ASP B 759 " --> pdb=" O ASN B 755 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR B 760 " --> pdb=" O LEU B 756 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 755 through 760' Processing helix chain 'B' and resid 761 through 765 removed outlier: 3.511A pdb=" N ASN B 764 " --> pdb=" O GLY B 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 791 through 795 removed outlier: 3.622A pdb=" N GLU B 795 " --> pdb=" O LYS B 791 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 791 through 795' Processing helix chain 'B' and resid 950 through 952 No H-bonds generated for 'chain 'B' and resid 950 through 952' Processing helix chain 'B' and resid 953 through 958 removed outlier: 3.515A pdb=" N ARG B 957 " --> pdb=" O ALA B 953 " (cutoff:3.500A) Processing helix chain 'B' and resid 960 through 976 removed outlier: 3.682A pdb=" N LEU B 967 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N HIS B 975 " --> pdb=" O ALA B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 1002 removed outlier: 3.655A pdb=" N GLN B 999 " --> pdb=" O TYR B 995 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS B1002 " --> pdb=" O GLU B 998 " (cutoff:3.500A) Processing helix chain 'B' and resid 1074 through 1082 removed outlier: 3.641A pdb=" N LEU B1079 " --> pdb=" O GLU B1075 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE B1080 " --> pdb=" O ARG B1076 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N HIS B1082 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing helix chain 'B' and resid 1085 through 1093 removed outlier: 3.559A pdb=" N ARG B1091 " --> pdb=" O LEU B1087 " (cutoff:3.500A) Processing helix chain 'B' and resid 1135 through 1139 removed outlier: 4.158A pdb=" N LYS B1139 " --> pdb=" O PHE B1135 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1135 through 1139' Processing helix chain 'B' and resid 1180 through 1188 removed outlier: 3.637A pdb=" N TYR B1184 " --> pdb=" O PHE B1180 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 40 removed outlier: 3.995A pdb=" N ASP C 39 " --> pdb=" O LYS C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 73 removed outlier: 3.606A pdb=" N ALA C 64 " --> pdb=" O ASP C 60 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG C 68 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG C 69 " --> pdb=" O ASN C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 102 removed outlier: 3.760A pdb=" N HIS C 99 " --> pdb=" O GLU C 95 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY C 102 " --> pdb=" O ALA C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 113 Processing helix chain 'C' and resid 121 through 126 removed outlier: 3.548A pdb=" N LYS C 125 " --> pdb=" O PRO C 121 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N PHE C 126 " --> pdb=" O ASP C 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 121 through 126' Processing helix chain 'C' and resid 152 through 156 Processing helix chain 'C' and resid 165 through 167 No H-bonds generated for 'chain 'C' and resid 165 through 167' Processing helix chain 'C' and resid 174 through 179 Processing helix chain 'C' and resid 180 through 182 No H-bonds generated for 'chain 'C' and resid 180 through 182' Processing helix chain 'C' and resid 216 through 220 removed outlier: 3.523A pdb=" N SER C 220 " --> pdb=" O ALA C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 249 removed outlier: 4.171A pdb=" N ARG C 245 " --> pdb=" O GLY C 241 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS C 249 " --> pdb=" O ARG C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 273 removed outlier: 3.636A pdb=" N LYS C 272 " --> pdb=" O ASP C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 286 removed outlier: 5.147A pdb=" N GLU C 283 " --> pdb=" O LEU C 280 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N GLU C 284 " --> pdb=" O ARG C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 331 removed outlier: 3.573A pdb=" N LYS C 316 " --> pdb=" O GLU C 312 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU C 321 " --> pdb=" O SER C 317 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS C 322 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N CYS C 331 " --> pdb=" O TYR C 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 26 removed outlier: 3.640A pdb=" N LEU E 12 " --> pdb=" O ASN E 8 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LYS E 20 " --> pdb=" O PHE E 16 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU E 21 " --> pdb=" O ARG E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 removed outlier: 3.524A pdb=" N VAL E 35 " --> pdb=" O THR E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 46 Processing helix chain 'E' and resid 55 through 59 removed outlier: 3.940A pdb=" N SER E 59 " --> pdb=" O LYS E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 89 through 104 removed outlier: 3.677A pdb=" N MET E 93 " --> pdb=" O GLY E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 124 Processing helix chain 'E' and resid 143 through 147 Processing helix chain 'E' and resid 157 through 169 Processing helix chain 'E' and resid 171 through 175 removed outlier: 4.080A pdb=" N LEU E 175 " --> pdb=" O GLU E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 189 removed outlier: 3.684A pdb=" N LEU E 188 " --> pdb=" O VAL E 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 73 Processing helix chain 'F' and resid 75 through 79 removed outlier: 3.761A pdb=" N ARG F 79 " --> pdb=" O LYS F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 101 removed outlier: 3.524A pdb=" N GLN F 100 " --> pdb=" O THR F 96 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE F 101 " --> pdb=" O ARG F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 104 No H-bonds generated for 'chain 'F' and resid 102 through 104' Processing helix chain 'F' and resid 116 through 125 removed outlier: 3.628A pdb=" N ALA F 121 " --> pdb=" O PRO F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 149 through 151 No H-bonds generated for 'chain 'F' and resid 149 through 151' Processing helix chain 'H' and resid 88 through 93 Processing helix chain 'H' and resid 129 through 133 Processing helix chain 'J' and resid 16 through 27 removed outlier: 4.790A pdb=" N SER J 20 " --> pdb=" O ASP J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 39 removed outlier: 3.553A pdb=" N LEU J 39 " --> pdb=" O ALA J 35 " (cutoff:3.500A) Processing helix chain 'J' and resid 43 through 52 removed outlier: 3.738A pdb=" N ARG J 48 " --> pdb=" O TYR J 44 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR J 52 " --> pdb=" O ARG J 48 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 61 Processing helix chain 'K' and resid 69 through 82 removed outlier: 3.744A pdb=" N ALA K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TYR K 78 " --> pdb=" O ASN K 74 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL K 79 " --> pdb=" O ALA K 75 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS K 82 " --> pdb=" O TYR K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 121 Processing helix chain 'K' and resid 121 through 142 removed outlier: 3.941A pdb=" N MET K 125 " --> pdb=" O LEU K 121 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL K 130 " --> pdb=" O ASP K 126 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL K 131 " --> pdb=" O LEU K 127 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR K 136 " --> pdb=" O GLU K 132 " (cutoff:3.500A) Processing helix chain 'M' and resid 69 through 72 removed outlier: 3.503A pdb=" N ALA M 72 " --> pdb=" O SER M 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 69 through 72' Processing helix chain 'M' and resid 103 through 107 removed outlier: 4.799A pdb=" N ASN M 107 " --> pdb=" O LYS M 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 103 through 107' Processing helix chain 'N' and resid 92 through 97 Processing helix chain 'N' and resid 149 through 154 Processing helix chain 'N' and resid 176 through 180 Processing helix chain 'D' and resid 32 through 47 Processing helix chain 'D' and resid 81 through 96 Processing helix chain 'G' and resid 50 through 54 Processing helix chain 'G' and resid 56 through 65 Processing helix chain 'G' and resid 66 through 70 Processing sheet with id=AA1, first strand: chain 'A' and resid 1631 through 1632 removed outlier: 6.123A pdb=" N ILE A 11 " --> pdb=" O GLU B1201 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N GLU B1201 " --> pdb=" O ILE A 11 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER A 13 " --> pdb=" O ASN B1199 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 86 removed outlier: 6.696A pdb=" N ASP A 358 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 10.637A pdb=" N VAL A 83 " --> pdb=" O PHE A 356 " (cutoff:3.500A) removed outlier: 9.262A pdb=" N PHE A 356 " --> pdb=" O VAL A 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 243 through 244 Processing sheet with id=AA4, first strand: chain 'A' and resid 371 through 373 Processing sheet with id=AA5, first strand: chain 'A' and resid 475 through 476 removed outlier: 3.980A pdb=" N ILE B1069 " --> pdb=" O VAL A 476 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1045 through 1046 removed outlier: 3.577A pdb=" N SER A 482 " --> pdb=" O MET A 633 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG A 615 " --> pdb=" O GLY A 496 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 506 through 510 removed outlier: 3.616A pdb=" N TYR A 578 " --> pdb=" O GLN A 535 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLN A 535 " --> pdb=" O TYR A 578 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N HIS A 580 " --> pdb=" O ALA A 533 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ALA A 533 " --> pdb=" O HIS A 580 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 686 through 687 Processing sheet with id=AA9, first strand: chain 'A' and resid 719 through 721 removed outlier: 6.720A pdb=" N VAL H 96 " --> pdb=" O PHE A 720 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ALA H 113 " --> pdb=" O PHE H 104 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N PHE H 104 " --> pdb=" O ALA H 113 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N TYR H 115 " --> pdb=" O TYR H 102 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 749 through 752 removed outlier: 6.654A pdb=" N LEU A 770 " --> pdb=" O LEU A 777 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA A 775 " --> pdb=" O LYS A 772 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1031 through 1032 removed outlier: 3.560A pdb=" N GLN A1047 " --> pdb=" O ILE A1038 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1507 through 1508 removed outlier: 3.556A pdb=" N VAL A1520 " --> pdb=" O VAL A1508 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR A1521 " --> pdb=" O MET A1238 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1261 through 1262 removed outlier: 7.058A pdb=" N VAL A1261 " --> pdb=" O ILE A1498 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1267 through 1273 removed outlier: 4.012A pdb=" N LYS A1269 " --> pdb=" O ARG A1295 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG A1295 " --> pdb=" O LYS A1269 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR A1290 " --> pdb=" O LEU A1474 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS A1459 " --> pdb=" O LYS A1473 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N GLU A1475 " --> pdb=" O ILE A1457 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N ILE A1457 " --> pdb=" O GLU A1475 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1655 through 1658 Processing sheet with id=AB7, first strand: chain 'B' and resid 71 through 74 removed outlier: 3.501A pdb=" N LEU B 95 " --> pdb=" O ILE B 73 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N VAL B 97 " --> pdb=" O SER B 144 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N SER B 144 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N VAL B 99 " --> pdb=" O LYS B 142 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N LYS B 142 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLN B 101 " --> pdb=" O LYS B 140 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLY B 159 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N LEU B 139 " --> pdb=" O ASP B 157 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N ASP B 157 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LEU B 141 " --> pdb=" O VAL B 155 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N VAL B 155 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N TRP B 143 " --> pdb=" O PHE B 153 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N PHE B 153 " --> pdb=" O TRP B 143 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL B 145 " --> pdb=" O ASN B 151 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ASN B 151 " --> pdb=" O VAL B 145 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 194 through 196 Processing sheet with id=AB9, first strand: chain 'B' and resid 400 through 403 removed outlier: 4.033A pdb=" N MET B 205 " --> pdb=" O MET B 502 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 214 through 218 removed outlier: 5.619A pdb=" N TYR B 232 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N TYR B 252 " --> pdb=" O TYR B 232 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N THR B 247 " --> pdb=" O SER B 263 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N SER B 263 " --> pdb=" O THR B 247 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE B 262 " --> pdb=" O TYR B 269 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 550 through 552 removed outlier: 3.980A pdb=" N ARG B 648 " --> pdb=" O SER B 552 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS B 660 " --> pdb=" O TYR B 655 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 550 through 552 removed outlier: 3.980A pdb=" N ARG B 648 " --> pdb=" O SER B 552 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 571 through 572 removed outlier: 3.887A pdb=" N ALA B 571 " --> pdb=" O TRP B 595 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N TRP B 595 " --> pdb=" O ALA B 571 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N VAL B 586 " --> pdb=" O ILE B 593 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 625 through 626 removed outlier: 3.768A pdb=" N GLU B 625 " --> pdb=" O PHE B 643 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N PHE B 643 " --> pdb=" O GLU B 625 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 740 through 744 removed outlier: 7.724A pdb=" N THR B 900 " --> pdb=" O LEU B 887 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N LEU B 887 " --> pdb=" O THR B 900 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N SER B 902 " --> pdb=" O VAL B 885 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VAL B 885 " --> pdb=" O SER B 902 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LYS B 904 " --> pdb=" O GLU B 883 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 740 through 744 removed outlier: 7.724A pdb=" N THR B 900 " --> pdb=" O LEU B 887 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N LEU B 887 " --> pdb=" O THR B 900 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N SER B 902 " --> pdb=" O VAL B 885 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VAL B 885 " --> pdb=" O SER B 902 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LYS B 904 " --> pdb=" O GLU B 883 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N VAL B 885 " --> pdb=" O LYS L 58 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 1010 through 1011 removed outlier: 7.486A pdb=" N MET B 787 " --> pdb=" O SER B 928 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LYS B 930 " --> pdb=" O MET B 787 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE B 789 " --> pdb=" O LYS B 930 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N ILE B 947 " --> pdb=" O ASN B 770 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL B 772 " --> pdb=" O ILE B 947 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N ILE B 949 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ALA B 774 " --> pdb=" O ILE B 949 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N TYR B1027 " --> pdb=" O VAL B 775 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 823 through 825 Processing sheet with id=AD1, first strand: chain 'B' and resid 938 through 939 Processing sheet with id=AD2, first strand: chain 'B' and resid 1098 through 1104 Processing sheet with id=AD3, first strand: chain 'B' and resid 1114 through 1115 Processing sheet with id=AD4, first strand: chain 'B' and resid 1133 through 1134 removed outlier: 3.597A pdb=" N MET B1133 " --> pdb=" O VAL B1168 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 41 through 46 removed outlier: 6.476A pdb=" N VAL C 42 " --> pdb=" O ILE C 57 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N ILE C 57 " --> pdb=" O VAL C 42 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N ILE C 44 " --> pdb=" O ASP C 55 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ASP C 55 " --> pdb=" O ILE C 44 " (cutoff:3.500A) removed outlier: 10.467A pdb=" N ARG C 293 " --> pdb=" O ASN C 234 " (cutoff:3.500A) removed outlier: 9.429A pdb=" N ASN C 234 " --> pdb=" O ARG C 293 " (cutoff:3.500A) removed outlier: 9.479A pdb=" N ARG C 295 " --> pdb=" O GLN C 232 " (cutoff:3.500A) removed outlier: 10.677A pdb=" N GLN C 232 " --> pdb=" O ARG C 295 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N HIS C 297 " --> pdb=" O LEU C 230 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N THR C 224 " --> pdb=" O GLU C 303 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 168 through 170 removed outlier: 4.689A pdb=" N VAL C 133 " --> pdb=" O GLU C 170 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N GLU C 201 " --> pdb=" O ASN C 87 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ASN C 87 " --> pdb=" O GLU C 201 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N SER C 203 " --> pdb=" O PHE C 85 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N PHE C 85 " --> pdb=" O SER C 203 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LYS C 205 " --> pdb=" O VAL C 83 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N VAL C 83 " --> pdb=" O LYS C 205 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N HIS C 207 " --> pdb=" O GLU C 81 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE C 209 " --> pdb=" O ALA C 79 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA C 79 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL C 83 " --> pdb=" O PHE L 67 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 141 through 142 Processing sheet with id=AD8, first strand: chain 'C' and resid 161 through 163 removed outlier: 3.520A pdb=" N ALA C 194 " --> pdb=" O VAL C 162 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 256 through 258 Processing sheet with id=AE1, first strand: chain 'E' and resid 60 through 62 removed outlier: 3.905A pdb=" N PHE E 60 " --> pdb=" O VAL E 80 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL E 80 " --> pdb=" O PHE E 60 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU E 133 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE E 135 " --> pdb=" O PHE E 110 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TYR E 112 " --> pdb=" O PHE E 135 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 153 through 155 Processing sheet with id=AE3, first strand: chain 'I' and resid 3 through 4 Processing sheet with id=AE4, first strand: chain 'I' and resid 27 through 29 Processing sheet with id=AE5, first strand: chain 'K' and resid 60 through 66 Processing sheet with id=AE6, first strand: chain 'M' and resid 11 through 16 removed outlier: 6.278A pdb=" N ILE M 88 " --> pdb=" O ILE M 12 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER M 14 " --> pdb=" O ILE M 88 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER M 87 " --> pdb=" O ASN M 82 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL N 53 " --> pdb=" O LYS N 135 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N PHE N 137 " --> pdb=" O VAL N 53 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LEU N 55 " --> pdb=" O PHE N 137 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N VAL N 139 " --> pdb=" O LEU N 55 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LYS N 57 " --> pdb=" O VAL N 139 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N GLU N 141 " --> pdb=" O LYS N 57 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'N' and resid 30 through 31 removed outlier: 6.626A pdb=" N VAL M 23 " --> pdb=" O LEU M 96 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N SER M 98 " --> pdb=" O VAL M 23 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N SER M 25 " --> pdb=" O SER M 98 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N VAL M 100 " --> pdb=" O SER M 25 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N THR M 37 " --> pdb=" O GLU M 56 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 21 through 24 removed outlier: 3.863A pdb=" N VAL D 21 " --> pdb=" O TYR G 46 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 21 through 24 removed outlier: 3.863A pdb=" N VAL D 21 " --> pdb=" O TYR G 46 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N TRP G 117 " --> pdb=" O LYS G 88 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N LYS G 88 " --> pdb=" O TRP G 117 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N HIS G 119 " --> pdb=" O GLY G 86 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLY G 86 " --> pdb=" O HIS G 119 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ASN G 121 " --> pdb=" O TYR G 84 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N TYR G 84 " --> pdb=" O ASN G 121 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N TYR G 123 " --> pdb=" O LEU G 82 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY G 79 " --> pdb=" O ASN G 74 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 132 through 140 removed outlier: 6.715A pdb=" N GLY G 146 " --> pdb=" O PHE G 138 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N GLN G 140 " --> pdb=" O HIS G 144 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N HIS G 144 " --> pdb=" O GLN G 140 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ASN G 154 " --> pdb=" O VAL G 245 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N GLY G 247 " --> pdb=" O ASN G 154 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N SER G 156 " --> pdb=" O GLY G 247 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N THR G 248 " --> pdb=" O VAL G 233 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N VAL G 233 " --> pdb=" O THR G 248 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 167 through 169 1159 hydrogen bonds defined for protein. 3174 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 26 hydrogen bonds 52 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 33 stacking parallelities Total time for adding SS restraints: 10.70 Time building geometry restraints manager: 3.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10026 1.33 - 1.45: 5750 1.45 - 1.57: 18660 1.57 - 1.70: 89 1.70 - 1.82: 263 Bond restraints: 34788 Sorted by residual: bond pdb=" N PRO N 146 " pdb=" CD PRO N 146 " ideal model delta sigma weight residual 1.473 1.529 -0.056 1.40e-02 5.10e+03 1.59e+01 bond pdb=" C HIS B 213 " pdb=" N PRO B 214 " ideal model delta sigma weight residual 1.334 1.245 0.089 2.34e-02 1.83e+03 1.46e+01 bond pdb=" C VAL B 121 " pdb=" N TYR B 122 " ideal model delta sigma weight residual 1.329 1.234 0.095 3.03e-02 1.09e+03 9.87e+00 bond pdb=" CA MET A 424 " pdb=" C MET A 424 " ideal model delta sigma weight residual 1.522 1.482 0.040 1.43e-02 4.89e+03 7.76e+00 bond pdb=" N THR G 111 " pdb=" CA THR G 111 " ideal model delta sigma weight residual 1.455 1.473 -0.018 7.00e-03 2.04e+04 6.72e+00 ... (remaining 34783 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.80: 46441 2.80 - 5.60: 703 5.60 - 8.40: 53 8.40 - 11.19: 6 11.19 - 13.99: 1 Bond angle restraints: 47204 Sorted by residual: angle pdb=" C PHE A1254 " pdb=" N CYS A1255 " pdb=" CA CYS A1255 " ideal model delta sigma weight residual 122.85 114.97 7.88 1.39e+00 5.18e-01 3.21e+01 angle pdb=" CD ARG G 241 " pdb=" NE ARG G 241 " pdb=" CZ ARG G 241 " ideal model delta sigma weight residual 124.40 132.05 -7.65 1.40e+00 5.10e-01 2.99e+01 angle pdb=" N ASP N 127 " pdb=" CA ASP N 127 " pdb=" C ASP N 127 " ideal model delta sigma weight residual 114.16 106.18 7.98 1.48e+00 4.57e-01 2.90e+01 angle pdb=" NE ARG G 241 " pdb=" CZ ARG G 241 " pdb=" NH2 ARG G 241 " ideal model delta sigma weight residual 119.20 114.45 4.75 9.00e-01 1.23e+00 2.78e+01 angle pdb=" N ASP G 219 " pdb=" CA ASP G 219 " pdb=" C ASP G 219 " ideal model delta sigma weight residual 109.31 116.73 -7.42 1.42e+00 4.96e-01 2.73e+01 ... (remaining 47199 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 20138 17.78 - 35.57: 638 35.57 - 53.35: 251 53.35 - 71.14: 79 71.14 - 88.92: 34 Dihedral angle restraints: 21140 sinusoidal: 9027 harmonic: 12113 Sorted by residual: dihedral pdb=" CA LYS B1061 " pdb=" C LYS B1061 " pdb=" N GLY B1062 " pdb=" CA GLY B1062 " ideal model delta harmonic sigma weight residual -180.00 -138.68 -41.32 0 5.00e+00 4.00e-02 6.83e+01 dihedral pdb=" CA SER B1048 " pdb=" C SER B1048 " pdb=" N THR B1049 " pdb=" CA THR B1049 " ideal model delta harmonic sigma weight residual -180.00 -149.36 -30.64 0 5.00e+00 4.00e-02 3.76e+01 dihedral pdb=" CA HIS B 319 " pdb=" C HIS B 319 " pdb=" N LEU B 320 " pdb=" CA LEU B 320 " ideal model delta harmonic sigma weight residual 180.00 149.79 30.21 0 5.00e+00 4.00e-02 3.65e+01 ... (remaining 21137 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 4208 0.066 - 0.131: 946 0.131 - 0.197: 105 0.197 - 0.262: 11 0.262 - 0.328: 4 Chirality restraints: 5274 Sorted by residual: chirality pdb=" CA ASP N 86 " pdb=" N ASP N 86 " pdb=" C ASP N 86 " pdb=" CB ASP N 86 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" CA ASN M 57 " pdb=" N ASN M 57 " pdb=" C ASN M 57 " pdb=" CB ASN M 57 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.51e+00 chirality pdb=" CA ILE G 162 " pdb=" N ILE G 162 " pdb=" C ILE G 162 " pdb=" CB ILE G 162 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.28 2.00e-01 2.50e+01 1.91e+00 ... (remaining 5271 not shown) Planarity restraints: 5937 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL E 124 " 0.044 5.00e-02 4.00e+02 6.69e-02 7.16e+00 pdb=" N PRO E 125 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO E 125 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO E 125 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU N 70 " 0.043 5.00e-02 4.00e+02 6.58e-02 6.93e+00 pdb=" N PRO N 71 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO N 71 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO N 71 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 608 " -0.041 5.00e-02 4.00e+02 6.23e-02 6.21e+00 pdb=" N PRO A 609 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 609 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 609 " -0.034 5.00e-02 4.00e+02 ... (remaining 5934 not shown) Histogram of nonbonded interaction distances: 0.48 - 1.36: 8 1.36 - 2.25: 70 2.25 - 3.13: 27635 3.13 - 4.02: 81236 4.02 - 4.90: 153054 Warning: very small nonbonded interaction distances. Nonbonded interactions: 262003 Sorted by model distance: nonbonded pdb=" OE1 GLN I 32 " pdb=" CB SER M 105 " model vdw 0.477 3.440 nonbonded pdb=" O ASN A1662 " pdb=" O SER G 101 " model vdw 0.588 3.040 nonbonded pdb=" CD GLN I 32 " pdb=" CB SER M 105 " model vdw 0.843 3.670 nonbonded pdb=" OE1 GLN I 32 " pdb=" CA SER M 105 " model vdw 1.119 3.470 nonbonded pdb=" CD GLN I 32 " pdb=" OG SER M 105 " model vdw 1.228 3.270 ... (remaining 261998 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.900 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: 0.500 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 39.020 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 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 : 0.007 0.421 34814 Z= 0.426 Angle : 1.250 61.765 47231 Z= 0.567 Chirality : 0.055 0.328 5274 Planarity : 0.005 0.067 5937 Dihedral : 11.855 88.924 13312 Min Nonbonded Distance : 0.477 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.60 % Favored : 93.11 % Rotamer: Outliers : 1.14 % Allowed : 2.03 % Favored : 96.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.05 % Twisted Proline : 0.00 % 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 aren not related in a simple way. whole: -3.19 (0.11), residues: 4109 helix: -3.61 (0.10), residues: 1162 sheet: -1.36 (0.18), residues: 646 loop : -1.45 (0.11), residues: 2301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 26 TYR 0.030 0.002 TYR B 671 PHE 0.028 0.003 PHE B 895 TRP 0.034 0.003 TRP B 143 HIS 0.014 0.002 HIS B1082 Details of bonding type rmsd covalent geometry : bond 0.00646 (34788) covalent geometry : angle 0.89312 (47204) hydrogen bonds : bond 0.23190 ( 1162) hydrogen bonds : angle 10.33858 ( 3226) metal coordination : bond 0.04570 ( 22) metal coordination : angle 36.56550 ( 27) Misc. bond : bond 0.27429 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8218 Ramachandran restraints generated. 4109 Oldfield, 0 Emsley, 4109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8218 Ramachandran restraints generated. 4109 Oldfield, 0 Emsley, 4109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 960 residues out of total 3693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 918 time to evaluate : 1.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 ASP cc_start: 0.7968 (t0) cc_final: 0.7627 (p0) REVERT: A 33 THR cc_start: 0.6988 (p) cc_final: 0.6538 (t) REVERT: A 110 LEU cc_start: 0.8899 (tp) cc_final: 0.8585 (mt) REVERT: A 111 LYS cc_start: 0.8700 (ptpt) cc_final: 0.7893 (tttt) REVERT: A 234 ASP cc_start: 0.6732 (m-30) cc_final: 0.5952 (m-30) REVERT: A 348 LYS cc_start: 0.8766 (mttt) cc_final: 0.8452 (tttt) REVERT: A 388 LYS cc_start: 0.7895 (mtpp) cc_final: 0.7673 (mptt) REVERT: A 601 MET cc_start: 0.8744 (mtt) cc_final: 0.8466 (mtt) REVERT: A 606 ARG cc_start: 0.8118 (ttt180) cc_final: 0.7839 (ttt90) REVERT: A 634 ASN cc_start: 0.8713 (m-40) cc_final: 0.8412 (m-40) REVERT: A 660 PRO cc_start: 0.9140 (Cg_exo) cc_final: 0.8882 (Cg_endo) REVERT: A 804 GLU cc_start: 0.7610 (mp0) cc_final: 0.7369 (tt0) REVERT: A 887 ASN cc_start: 0.7381 (t0) cc_final: 0.6905 (m110) REVERT: A 949 GLN cc_start: 0.8751 (tp40) cc_final: 0.8317 (tt0) REVERT: A 987 TYR cc_start: 0.8587 (t80) cc_final: 0.8370 (t80) REVERT: A 1026 GLN cc_start: 0.8266 (tt0) cc_final: 0.7504 (tp-100) REVERT: A 1035 ASP cc_start: 0.7790 (p0) cc_final: 0.7566 (p0) REVERT: A 1040 ASP cc_start: 0.9012 (t0) cc_final: 0.8780 (t0) REVERT: A 1092 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7811 (pt0) REVERT: A 1100 LYS cc_start: 0.8284 (tptm) cc_final: 0.7937 (ttmt) REVERT: A 1101 THR cc_start: 0.6997 (p) cc_final: 0.6503 (m) REVERT: A 1120 TYR cc_start: 0.5821 (p90) cc_final: 0.4976 (p90) REVERT: A 1572 ARG cc_start: 0.8241 (ttm-80) cc_final: 0.7393 (tpm170) REVERT: A 1624 LYS cc_start: 0.8656 (mttt) cc_final: 0.8014 (mmmt) REVERT: B 35 PHE cc_start: 0.8828 (m-80) cc_final: 0.8582 (m-10) REVERT: B 54 GLU cc_start: 0.7410 (mt-10) cc_final: 0.7163 (mm-30) REVERT: B 108 MET cc_start: 0.8040 (mmm) cc_final: 0.7756 (mmt) REVERT: B 140 LYS cc_start: 0.8118 (tttt) cc_final: 0.7885 (ttmt) REVERT: B 187 SER cc_start: 0.8966 (t) cc_final: 0.8665 (m) REVERT: B 255 ASP cc_start: 0.8099 (p0) cc_final: 0.7134 (t70) REVERT: B 314 LYS cc_start: 0.5689 (mttt) cc_final: 0.5382 (mtpp) REVERT: B 332 ASP cc_start: 0.7946 (t70) cc_final: 0.7624 (t70) REVERT: B 448 ARG cc_start: 0.7554 (ttm110) cc_final: 0.6994 (mtt180) REVERT: B 493 PHE cc_start: 0.7557 (t80) cc_final: 0.7299 (t80) REVERT: B 517 VAL cc_start: 0.9236 (m) cc_final: 0.8954 (t) REVERT: B 588 ILE cc_start: 0.8621 (mt) cc_final: 0.8400 (pt) REVERT: B 602 LYS cc_start: 0.8595 (tttt) cc_final: 0.8305 (tptt) REVERT: B 623 ASP cc_start: 0.8300 (p0) cc_final: 0.7745 (m-30) REVERT: B 661 GLU cc_start: 0.7207 (tt0) cc_final: 0.6537 (mp0) REVERT: B 737 SER cc_start: 0.8000 (m) cc_final: 0.7711 (p) REVERT: B 789 ILE cc_start: 0.9045 (mt) cc_final: 0.8815 (pt) REVERT: B 803 MET cc_start: 0.8162 (ttp) cc_final: 0.7678 (ttt) REVERT: B 807 GLU cc_start: 0.7989 (tt0) cc_final: 0.7653 (pt0) REVERT: B 808 LYS cc_start: 0.8004 (tttt) cc_final: 0.7669 (tttt) REVERT: B 883 GLU cc_start: 0.8462 (tp30) cc_final: 0.8199 (tt0) REVERT: B 998 GLU cc_start: 0.8695 (tt0) cc_final: 0.8479 (tm-30) REVERT: B 1075 GLU cc_start: 0.7653 (mp0) cc_final: 0.7343 (mp0) REVERT: B 1115 GLN cc_start: 0.8297 (mm-40) cc_final: 0.8030 (tm-30) REVERT: C 47 LEU cc_start: 0.8282 (tt) cc_final: 0.7844 (pp) REVERT: C 152 ASP cc_start: 0.6561 (t70) cc_final: 0.6250 (t0) REVERT: C 168 LYS cc_start: 0.8086 (mmtt) cc_final: 0.7531 (mtpt) REVERT: C 174 ARG cc_start: 0.8034 (mtt180) cc_final: 0.7574 (ptt-90) REVERT: C 201 GLU cc_start: 0.8456 (pt0) cc_final: 0.7812 (tt0) REVERT: C 295 ARG cc_start: 0.7934 (mmt180) cc_final: 0.7381 (mmm160) REVERT: C 312 GLU cc_start: 0.8185 (tt0) cc_final: 0.7958 (mm-30) REVERT: E 31 THR cc_start: 0.8362 (p) cc_final: 0.8083 (t) REVERT: E 32 GLN cc_start: 0.7564 (tp-100) cc_final: 0.7355 (tp40) REVERT: E 36 GLU cc_start: 0.6360 (mt-10) cc_final: 0.5968 (mt-10) REVERT: E 57 MET cc_start: 0.6694 (mtm) cc_final: 0.6266 (tmm) REVERT: E 81 GLU cc_start: 0.6939 (tp30) cc_final: 0.6503 (mt-10) REVERT: E 127 ILE cc_start: 0.7372 (pt) cc_final: 0.7048 (tp) REVERT: E 143 ASN cc_start: 0.7995 (t0) cc_final: 0.7701 (t0) REVERT: E 146 HIS cc_start: 0.7382 (m170) cc_final: 0.6993 (m-70) REVERT: E 170 LEU cc_start: 0.8865 (mt) cc_final: 0.8615 (mt) REVERT: F 61 HIS cc_start: 0.7066 (t-90) cc_final: 0.6393 (t-90) REVERT: F 109 VAL cc_start: 0.8391 (p) cc_final: 0.8005 (m) REVERT: F 119 ARG cc_start: 0.7504 (mmt180) cc_final: 0.7165 (mmm160) REVERT: F 128 LYS cc_start: 0.7717 (mttp) cc_final: 0.7482 (mtmt) REVERT: J 39 LEU cc_start: 0.9089 (mt) cc_final: 0.8848 (mp) REVERT: J 68 LYS cc_start: 0.7852 (mmtp) cc_final: 0.7197 (ttpt) REVERT: K 45 GLU cc_start: 0.6828 (mt-10) cc_final: 0.6478 (pt0) REVERT: K 112 THR cc_start: 0.9149 (p) cc_final: 0.8852 (t) REVERT: K 132 GLU cc_start: 0.8482 (tp30) cc_final: 0.8088 (tm-30) REVERT: K 142 MET cc_start: 0.8026 (ttt) cc_final: 0.7780 (ttp) REVERT: L 28 LYS cc_start: 0.8224 (mttp) cc_final: 0.7516 (mmtm) REVERT: N 90 MET cc_start: 0.4192 (mtm) cc_final: 0.3028 (tpt) REVERT: N 167 LYS cc_start: 0.2340 (OUTLIER) cc_final: 0.1851 (mttp) REVERT: G 223 GLU cc_start: -0.0408 (OUTLIER) cc_final: -0.0633 (mt-10) outliers start: 42 outliers final: 8 residues processed: 956 average time/residue: 0.2251 time to fit residues: 331.6847 Evaluate side-chains 532 residues out of total 3693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 522 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 18 GLN Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain N residue 89 ILE Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain N residue 167 LYS Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 223 GLU Chi-restraints excluded: chain G residue 243 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 9.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 30.0000 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 30.0000 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 264 ASN A 332 GLN A 580 HIS A 592 GLN A 610 ASN A 706 HIS A1108 HIS ** A1141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1180 ASN A1314 GLN A1544 ASN B 27 ASN B 39 GLN B 45 HIS B 321 GLN B 399 HIS B 504 HIS B 598 HIS ** B 646 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 ASN ** B 975 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1066 HIS B1157 GLN B1199 ASN C 58 ASN ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 ASN F 59 GLN H 83 GLN I 44 ASN J 23 ASN K 64 GLN K 106 GLN L 53 HIS ** D 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 126 GLN G 150 HIS G 237 HIS Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.186158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.157714 restraints weight = 45800.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.155915 restraints weight = 76685.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.156924 restraints weight = 74722.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.157114 restraints weight = 46889.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.157817 restraints weight = 41434.197| |-----------------------------------------------------------------------------| r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 34814 Z= 0.175 Angle : 0.800 47.561 47231 Z= 0.374 Chirality : 0.047 0.208 5274 Planarity : 0.005 0.066 5937 Dihedral : 11.554 73.189 5081 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.07 % Favored : 96.79 % Rotamer: Outliers : 2.30 % Allowed : 8.48 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.83 (0.12), residues: 4109 helix: -1.65 (0.13), residues: 1228 sheet: -0.99 (0.18), residues: 667 loop : -0.92 (0.12), residues: 2214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 80 TYR 0.027 0.002 TYR H 95 PHE 0.025 0.002 PHE B 895 TRP 0.022 0.002 TRP B 143 HIS 0.011 0.001 HIS A1453 Details of bonding type rmsd covalent geometry : bond 0.00399 (34788) covalent geometry : angle 0.69391 (47204) hydrogen bonds : bond 0.05041 ( 1162) hydrogen bonds : angle 6.03650 ( 3226) metal coordination : bond 0.01682 ( 22) metal coordination : angle 16.66296 ( 27) Misc. bond : bond 0.00404 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8218 Ramachandran restraints generated. 4109 Oldfield, 0 Emsley, 4109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8218 Ramachandran restraints generated. 4109 Oldfield, 0 Emsley, 4109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 3693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 600 time to evaluate : 1.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 THR cc_start: 0.6429 (p) cc_final: 0.5972 (t) REVERT: A 319 GLU cc_start: 0.4354 (mm-30) cc_final: 0.4099 (mm-30) REVERT: A 460 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7746 (mt) REVERT: A 592 GLN cc_start: 0.7505 (OUTLIER) cc_final: 0.7273 (mp10) REVERT: A 660 PRO cc_start: 0.9000 (Cg_exo) cc_final: 0.8661 (Cg_endo) REVERT: A 830 MET cc_start: 0.9183 (mmm) cc_final: 0.8886 (tpp) REVERT: A 987 TYR cc_start: 0.8452 (t80) cc_final: 0.8045 (t80) REVERT: A 1026 GLN cc_start: 0.7544 (tt0) cc_final: 0.7221 (tp-100) REVERT: A 1118 VAL cc_start: 0.7343 (OUTLIER) cc_final: 0.6982 (t) REVERT: A 1238 MET cc_start: 0.7911 (mtp) cc_final: 0.7192 (ttm) REVERT: A 1297 PHE cc_start: 0.7377 (m-80) cc_final: 0.7078 (m-80) REVERT: B 164 MET cc_start: 0.7722 (ttt) cc_final: 0.7492 (ttt) REVERT: B 255 ASP cc_start: 0.7581 (p0) cc_final: 0.6888 (t0) REVERT: B 271 VAL cc_start: 0.8980 (t) cc_final: 0.8779 (m) REVERT: B 314 LYS cc_start: 0.5529 (mttt) cc_final: 0.5295 (mtpp) REVERT: B 316 ARG cc_start: 0.6883 (mmm160) cc_final: 0.6496 (mtt90) REVERT: B 493 PHE cc_start: 0.7572 (t80) cc_final: 0.7251 (t80) REVERT: B 517 VAL cc_start: 0.8778 (m) cc_final: 0.8459 (t) REVERT: B 808 LYS cc_start: 0.7430 (tttt) cc_final: 0.7139 (tttp) REVERT: B 977 ILE cc_start: 0.7842 (tt) cc_final: 0.7603 (pt) REVERT: B 1075 GLU cc_start: 0.7572 (mp0) cc_final: 0.7331 (mp0) REVERT: B 1126 VAL cc_start: 0.8945 (t) cc_final: 0.8722 (p) REVERT: F 61 HIS cc_start: 0.6526 (t-90) cc_final: 0.5786 (t-90) REVERT: F 67 LYS cc_start: 0.7729 (tmmt) cc_final: 0.7453 (ttpt) REVERT: K 132 GLU cc_start: 0.7521 (tp30) cc_final: 0.7195 (tm-30) REVERT: N 90 MET cc_start: 0.3799 (mtm) cc_final: 0.3060 (tpt) REVERT: N 124 THR cc_start: -0.2008 (OUTLIER) cc_final: -0.2314 (t) REVERT: N 167 LYS cc_start: 0.4483 (OUTLIER) cc_final: 0.3995 (mttt) REVERT: D 29 GLN cc_start: 0.4230 (OUTLIER) cc_final: 0.3950 (pm20) outliers start: 85 outliers final: 40 residues processed: 649 average time/residue: 0.2022 time to fit residues: 212.1469 Evaluate side-chains 519 residues out of total 3693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 473 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 592 GLN Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1136 VAL Chi-restraints excluded: chain A residue 1163 GLU Chi-restraints excluded: chain A residue 1498 ILE Chi-restraints excluded: chain A residue 1521 THR Chi-restraints excluded: chain A residue 1543 SER Chi-restraints excluded: chain A residue 1617 THR Chi-restraints excluded: chain A residue 1629 ASN Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 672 MET Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 900 THR Chi-restraints excluded: chain B residue 1089 GLN Chi-restraints excluded: chain B residue 1113 THR Chi-restraints excluded: chain B residue 1196 LEU Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain J residue 45 CYS Chi-restraints excluded: chain J residue 50 ILE Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain L residue 35 SER Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain N residue 124 THR Chi-restraints excluded: chain N residue 153 VAL Chi-restraints excluded: chain N residue 167 LYS Chi-restraints excluded: chain D residue 29 GLN Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain G residue 169 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 77 optimal weight: 10.0000 chunk 85 optimal weight: 6.9990 chunk 196 optimal weight: 4.9990 chunk 7 optimal weight: 20.0000 chunk 279 optimal weight: 8.9990 chunk 233 optimal weight: 4.9990 chunk 135 optimal weight: 10.0000 chunk 56 optimal weight: 5.9990 chunk 264 optimal weight: 10.0000 chunk 191 optimal weight: 6.9990 chunk 26 optimal weight: 0.0070 overall best weight: 4.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN A 537 GLN A 580 HIS ** A 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 646 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 899 GLN ** B 975 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 979 GLN B 999 GLN ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 323 ASN I 44 ASN ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 HIS N 51 GLN ** D 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.181655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.153118 restraints weight = 45769.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.151460 restraints weight = 82101.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.152539 restraints weight = 73790.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.152471 restraints weight = 50290.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.153229 restraints weight = 44306.259| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 34814 Z= 0.232 Angle : 0.765 37.439 47231 Z= 0.365 Chirality : 0.047 0.216 5274 Planarity : 0.005 0.071 5937 Dihedral : 11.228 73.239 5071 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.21 % Favored : 95.62 % Rotamer: Outliers : 2.60 % Allowed : 10.86 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.47 (0.12), residues: 4109 helix: -1.04 (0.14), residues: 1252 sheet: -0.73 (0.19), residues: 691 loop : -0.92 (0.13), residues: 2166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 606 TYR 0.020 0.002 TYR H 95 PHE 0.023 0.002 PHE B 895 TRP 0.030 0.002 TRP E 79 HIS 0.010 0.001 HIS A 603 Details of bonding type rmsd covalent geometry : bond 0.00532 (34788) covalent geometry : angle 0.68626 (47204) hydrogen bonds : bond 0.04853 ( 1162) hydrogen bonds : angle 5.59776 ( 3226) metal coordination : bond 0.01907 ( 22) metal coordination : angle 14.16595 ( 27) Misc. bond : bond 0.00142 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8218 Ramachandran restraints generated. 4109 Oldfield, 0 Emsley, 4109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8218 Ramachandran restraints generated. 4109 Oldfield, 0 Emsley, 4109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 3693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 512 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 660 PRO cc_start: 0.8868 (Cg_exo) cc_final: 0.8561 (Cg_endo) REVERT: A 703 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8164 (mt-10) REVERT: A 786 TYR cc_start: 0.8181 (p90) cc_final: 0.7805 (p90) REVERT: A 925 MET cc_start: 0.8075 (tpp) cc_final: 0.7841 (tpp) REVERT: A 1026 GLN cc_start: 0.7845 (tt0) cc_final: 0.7213 (tp-100) REVERT: A 1120 TYR cc_start: 0.5795 (p90) cc_final: 0.5104 (p90) REVERT: A 1238 MET cc_start: 0.7949 (mtp) cc_final: 0.7277 (ttm) REVERT: A 1572 ARG cc_start: 0.7572 (tpm170) cc_final: 0.7334 (tpm170) REVERT: B 255 ASP cc_start: 0.7614 (p0) cc_final: 0.6825 (t0) REVERT: B 314 LYS cc_start: 0.5539 (mttt) cc_final: 0.5291 (mtpp) REVERT: B 316 ARG cc_start: 0.6981 (mmm160) cc_final: 0.6396 (mtt90) REVERT: B 493 PHE cc_start: 0.7700 (t80) cc_final: 0.7331 (t80) REVERT: B 517 VAL cc_start: 0.8701 (m) cc_final: 0.8483 (t) REVERT: B 913 ILE cc_start: 0.9265 (mm) cc_final: 0.8767 (mt) REVERT: B 1013 MET cc_start: 0.8534 (mtp) cc_final: 0.8321 (mtp) REVERT: E 12 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.8024 (mp) REVERT: E 146 HIS cc_start: 0.7318 (m-70) cc_final: 0.7111 (m-70) REVERT: E 187 TYR cc_start: 0.8151 (t80) cc_final: 0.7762 (t80) REVERT: F 61 HIS cc_start: 0.6452 (t-90) cc_final: 0.5710 (t-90) REVERT: J 68 LYS cc_start: 0.7454 (OUTLIER) cc_final: 0.6754 (tttt) REVERT: K 82 LYS cc_start: 0.8713 (mmtp) cc_final: 0.8349 (mmtp) REVERT: N 90 MET cc_start: 0.4058 (mtm) cc_final: 0.3280 (tpt) REVERT: D 29 GLN cc_start: 0.4696 (OUTLIER) cc_final: 0.4421 (pm20) REVERT: G 71 MET cc_start: 0.6286 (ppp) cc_final: 0.4319 (mmt) outliers start: 96 outliers final: 63 residues processed: 572 average time/residue: 0.1959 time to fit residues: 182.3847 Evaluate side-chains 504 residues out of total 3693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 437 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 953 GLU Chi-restraints excluded: chain A residue 1020 GLN Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain A residue 1136 VAL Chi-restraints excluded: chain A residue 1498 ILE Chi-restraints excluded: chain A residue 1520 VAL Chi-restraints excluded: chain A residue 1521 THR Chi-restraints excluded: chain A residue 1543 SER Chi-restraints excluded: chain A residue 1559 ARG Chi-restraints excluded: chain A residue 1607 THR Chi-restraints excluded: chain A residue 1617 THR Chi-restraints excluded: chain A residue 1629 ASN Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 672 MET Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 899 GLN Chi-restraints excluded: chain B residue 900 THR Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 946 ASP Chi-restraints excluded: chain B residue 1125 THR Chi-restraints excluded: chain B residue 1173 THR Chi-restraints excluded: chain B residue 1196 LEU Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain I residue 33 CYS Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain J residue 45 CYS Chi-restraints excluded: chain J residue 68 LYS Chi-restraints excluded: chain L residue 35 SER Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain N residue 153 VAL Chi-restraints excluded: chain N residue 176 ASP Chi-restraints excluded: chain D residue 29 GLN Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain G residue 169 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 229 optimal weight: 8.9990 chunk 311 optimal weight: 10.0000 chunk 380 optimal weight: 10.0000 chunk 344 optimal weight: 6.9990 chunk 167 optimal weight: 5.9990 chunk 142 optimal weight: 10.0000 chunk 114 optimal weight: 1.9990 chunk 293 optimal weight: 10.0000 chunk 411 optimal weight: 9.9990 chunk 365 optimal weight: 20.0000 chunk 189 optimal weight: 4.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 ASN ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 646 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 899 GLN ** B 975 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1094 ASN ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 ASN F 100 GLN I 44 ASN ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 23 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.186168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 99)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.152360 restraints weight = 45664.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.146855 restraints weight = 61585.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.148913 restraints weight = 60936.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.149848 restraints weight = 40168.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.150018 restraints weight = 34947.817| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.104 34814 Z= 0.260 Angle : 0.770 31.459 47231 Z= 0.375 Chirality : 0.048 0.226 5274 Planarity : 0.005 0.064 5937 Dihedral : 11.271 73.158 5066 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.67 % Favored : 95.18 % Rotamer: Outliers : 3.58 % Allowed : 12.19 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.53 (0.12), residues: 4109 helix: -0.93 (0.14), residues: 1244 sheet: -0.74 (0.19), residues: 701 loop : -1.08 (0.13), residues: 2164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 63 TYR 0.024 0.002 TYR B1098 PHE 0.029 0.002 PHE C 300 TRP 0.038 0.002 TRP E 79 HIS 0.010 0.002 HIS A 603 Details of bonding type rmsd covalent geometry : bond 0.00624 (34788) covalent geometry : angle 0.71304 (47204) hydrogen bonds : bond 0.04791 ( 1162) hydrogen bonds : angle 5.52482 ( 3226) metal coordination : bond 0.02543 ( 22) metal coordination : angle 12.20904 ( 27) Misc. bond : bond 0.00143 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8218 Ramachandran restraints generated. 4109 Oldfield, 0 Emsley, 4109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8218 Ramachandran restraints generated. 4109 Oldfield, 0 Emsley, 4109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 616 residues out of total 3693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 484 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 PHE cc_start: 0.7670 (m-80) cc_final: 0.7308 (m-80) REVERT: A 575 LYS cc_start: 0.8557 (mttp) cc_final: 0.8154 (mttp) REVERT: A 786 TYR cc_start: 0.8290 (p90) cc_final: 0.7833 (p90) REVERT: A 925 MET cc_start: 0.8352 (tpp) cc_final: 0.7917 (tpp) REVERT: A 928 MET cc_start: 0.8412 (mtm) cc_final: 0.8101 (mtp) REVERT: A 1026 GLN cc_start: 0.7902 (tt0) cc_final: 0.7565 (tp-100) REVERT: A 1120 TYR cc_start: 0.6197 (p90) cc_final: 0.5161 (p90) REVERT: A 1238 MET cc_start: 0.8046 (mtp) cc_final: 0.7395 (ttm) REVERT: A 1572 ARG cc_start: 0.7673 (tpm170) cc_final: 0.7297 (tpm170) REVERT: A 1603 MET cc_start: 0.8209 (ttm) cc_final: 0.7926 (ttp) REVERT: B 255 ASP cc_start: 0.7588 (p0) cc_final: 0.6802 (t0) REVERT: B 316 ARG cc_start: 0.7384 (mmm160) cc_final: 0.6342 (mtt90) REVERT: B 493 PHE cc_start: 0.7708 (t80) cc_final: 0.7411 (t80) REVERT: B 513 LYS cc_start: 0.7154 (tttt) cc_final: 0.6760 (ttmm) REVERT: B 517 VAL cc_start: 0.8975 (m) cc_final: 0.8711 (t) REVERT: B 835 GLU cc_start: 0.7935 (mp0) cc_final: 0.7729 (mp0) REVERT: B 913 ILE cc_start: 0.9404 (mm) cc_final: 0.9028 (mt) REVERT: B 916 LYS cc_start: 0.8574 (mttt) cc_final: 0.8238 (mtmm) REVERT: B 994 ASP cc_start: 0.8252 (t70) cc_final: 0.7883 (t70) REVERT: B 1013 MET cc_start: 0.8577 (mtp) cc_final: 0.8330 (mtp) REVERT: B 1075 GLU cc_start: 0.7906 (mp0) cc_final: 0.7355 (mp0) REVERT: B 1094 ASN cc_start: 0.8627 (OUTLIER) cc_final: 0.8267 (m110) REVERT: B 1125 THR cc_start: 0.8636 (OUTLIER) cc_final: 0.8325 (p) REVERT: E 103 LYS cc_start: 0.6382 (mttt) cc_final: 0.5896 (mmtm) REVERT: F 61 HIS cc_start: 0.6958 (t-90) cc_final: 0.6204 (t-90) REVERT: F 119 ARG cc_start: 0.7164 (mtp85) cc_final: 0.6373 (tpp80) REVERT: J 68 LYS cc_start: 0.7605 (OUTLIER) cc_final: 0.6909 (tttt) REVERT: K 82 LYS cc_start: 0.8776 (mmtp) cc_final: 0.8278 (mmtp) REVERT: M 18 GLN cc_start: 0.4584 (OUTLIER) cc_final: 0.2580 (tt0) REVERT: N 90 MET cc_start: 0.4665 (mtm) cc_final: 0.3231 (tpt) REVERT: G 61 VAL cc_start: 0.6836 (OUTLIER) cc_final: 0.6495 (m) REVERT: G 71 MET cc_start: 0.6022 (ppp) cc_final: 0.4939 (mmt) outliers start: 132 outliers final: 92 residues processed: 577 average time/residue: 0.1859 time to fit residues: 176.1863 Evaluate side-chains 538 residues out of total 3693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 441 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 72 CYS Chi-restraints excluded: chain A residue 90 PHE Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 953 GLU Chi-restraints excluded: chain A residue 1020 GLN Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain A residue 1063 MET Chi-restraints excluded: chain A residue 1136 VAL Chi-restraints excluded: chain A residue 1142 ASP Chi-restraints excluded: chain A residue 1498 ILE Chi-restraints excluded: chain A residue 1520 VAL Chi-restraints excluded: chain A residue 1521 THR Chi-restraints excluded: chain A residue 1543 SER Chi-restraints excluded: chain A residue 1559 ARG Chi-restraints excluded: chain A residue 1585 ILE Chi-restraints excluded: chain A residue 1601 GLN Chi-restraints excluded: chain A residue 1607 THR Chi-restraints excluded: chain A residue 1617 THR Chi-restraints excluded: chain A residue 1629 ASN Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 689 VAL Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 946 ASP Chi-restraints excluded: chain B residue 1094 ASN Chi-restraints excluded: chain B residue 1113 THR Chi-restraints excluded: chain B residue 1125 THR Chi-restraints excluded: chain B residue 1173 THR Chi-restraints excluded: chain B residue 1196 LEU Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain F residue 59 GLN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain H residue 33 GLN Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain I residue 33 CYS Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain J residue 45 CYS Chi-restraints excluded: chain J residue 68 LYS Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 111 THR Chi-restraints excluded: chain L residue 35 SER Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain M residue 18 GLN Chi-restraints excluded: chain N residue 89 ILE Chi-restraints excluded: chain N residue 153 VAL Chi-restraints excluded: chain G residue 35 SER Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 169 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 41 optimal weight: 0.7980 chunk 374 optimal weight: 30.0000 chunk 254 optimal weight: 9.9990 chunk 46 optimal weight: 1.9990 chunk 256 optimal weight: 8.9990 chunk 28 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 162 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 213 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 998 HIS A1141 GLN ** A1601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1662 ASN ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 598 HIS ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 975 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1115 GLN ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 GLN I 44 ASN ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.181572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.154376 restraints weight = 45849.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.153732 restraints weight = 81382.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.154432 restraints weight = 75990.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.154061 restraints weight = 53621.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.154496 restraints weight = 49260.102| |-----------------------------------------------------------------------------| r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.4368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 34814 Z= 0.120 Angle : 0.615 20.472 47231 Z= 0.304 Chirality : 0.043 0.229 5274 Planarity : 0.004 0.060 5937 Dihedral : 10.936 73.420 5065 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.58 % Favored : 96.33 % Rotamer: Outliers : 2.76 % Allowed : 13.71 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.11 (0.13), residues: 4109 helix: -0.43 (0.14), residues: 1253 sheet: -0.60 (0.19), residues: 703 loop : -0.88 (0.13), residues: 2153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 957 TYR 0.020 0.001 TYR A 478 PHE 0.016 0.001 PHE B 895 TRP 0.026 0.001 TRP A 842 HIS 0.007 0.001 HIS G 65 Details of bonding type rmsd covalent geometry : bond 0.00271 (34788) covalent geometry : angle 0.57766 (47204) hydrogen bonds : bond 0.03905 ( 1162) hydrogen bonds : angle 5.04373 ( 3226) metal coordination : bond 0.01450 ( 22) metal coordination : angle 8.89465 ( 27) Misc. bond : bond 0.00109 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8218 Ramachandran restraints generated. 4109 Oldfield, 0 Emsley, 4109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8218 Ramachandran restraints generated. 4109 Oldfield, 0 Emsley, 4109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 3693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 502 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 683 LYS cc_start: 0.8662 (mtpt) cc_final: 0.8338 (mtpt) REVERT: A 786 TYR cc_start: 0.8124 (p90) cc_final: 0.7740 (p90) REVERT: A 830 MET cc_start: 0.9093 (mmm) cc_final: 0.8868 (tpt) REVERT: A 832 ASP cc_start: 0.7745 (m-30) cc_final: 0.7545 (m-30) REVERT: A 925 MET cc_start: 0.7915 (tpp) cc_final: 0.7700 (tpp) REVERT: A 1026 GLN cc_start: 0.7724 (tt0) cc_final: 0.7246 (tp-100) REVERT: A 1238 MET cc_start: 0.7800 (mtp) cc_final: 0.7244 (ttm) REVERT: A 1572 ARG cc_start: 0.7579 (tpm170) cc_final: 0.7228 (tpm170) REVERT: A 1603 MET cc_start: 0.8060 (ttm) cc_final: 0.7732 (ttp) REVERT: B 255 ASP cc_start: 0.7426 (p0) cc_final: 0.6882 (t70) REVERT: B 316 ARG cc_start: 0.6844 (mmm160) cc_final: 0.6512 (ttm170) REVERT: B 493 PHE cc_start: 0.7470 (t80) cc_final: 0.7157 (t80) REVERT: B 517 VAL cc_start: 0.8706 (m) cc_final: 0.8479 (t) REVERT: B 716 MET cc_start: 0.7392 (OUTLIER) cc_final: 0.6937 (mtt) REVERT: B 913 ILE cc_start: 0.9326 (mm) cc_final: 0.8856 (mt) REVERT: B 916 LYS cc_start: 0.8510 (mttt) cc_final: 0.8162 (mtmm) REVERT: B 1013 MET cc_start: 0.8447 (mtp) cc_final: 0.8205 (mtp) REVERT: E 187 TYR cc_start: 0.8177 (t80) cc_final: 0.7868 (t80) REVERT: F 61 HIS cc_start: 0.6447 (t-90) cc_final: 0.5729 (t-90) REVERT: F 119 ARG cc_start: 0.7100 (mtp85) cc_final: 0.6194 (tpp80) REVERT: H 33 GLN cc_start: 0.8204 (OUTLIER) cc_final: 0.7821 (mm-40) REVERT: J 68 LYS cc_start: 0.7628 (OUTLIER) cc_final: 0.6790 (ttpt) REVERT: K 82 LYS cc_start: 0.8632 (mmtp) cc_final: 0.8393 (mmtp) REVERT: M 18 GLN cc_start: 0.4265 (OUTLIER) cc_final: 0.2473 (tt0) REVERT: N 90 MET cc_start: 0.4017 (mtm) cc_final: 0.3354 (tpt) REVERT: G 61 VAL cc_start: 0.7256 (t) cc_final: 0.6893 (m) REVERT: G 71 MET cc_start: 0.6185 (ppp) cc_final: 0.5746 (mmt) REVERT: G 125 TRP cc_start: 0.5353 (t-100) cc_final: 0.5093 (t-100) outliers start: 102 outliers final: 62 residues processed: 564 average time/residue: 0.1820 time to fit residues: 168.9288 Evaluate side-chains 515 residues out of total 3693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 449 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 72 CYS Chi-restraints excluded: chain A residue 90 PHE Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 1020 GLN Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain A residue 1077 LEU Chi-restraints excluded: chain A residue 1142 ASP Chi-restraints excluded: chain A residue 1498 ILE Chi-restraints excluded: chain A residue 1520 VAL Chi-restraints excluded: chain A residue 1543 SER Chi-restraints excluded: chain A residue 1559 ARG Chi-restraints excluded: chain A residue 1607 THR Chi-restraints excluded: chain A residue 1617 THR Chi-restraints excluded: chain A residue 1629 ASN Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 614 GLU Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 1089 GLN Chi-restraints excluded: chain B residue 1173 THR Chi-restraints excluded: chain B residue 1196 LEU Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain F residue 59 GLN Chi-restraints excluded: chain H residue 33 GLN Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain I residue 33 CYS Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain J residue 45 CYS Chi-restraints excluded: chain J residue 68 LYS Chi-restraints excluded: chain K residue 133 SER Chi-restraints excluded: chain L residue 35 SER Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain M residue 18 GLN Chi-restraints excluded: chain N residue 89 ILE Chi-restraints excluded: chain N residue 153 VAL Chi-restraints excluded: chain D residue 29 GLN Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 218 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 377 optimal weight: 9.9990 chunk 324 optimal weight: 9.9990 chunk 176 optimal weight: 9.9990 chunk 339 optimal weight: 0.1980 chunk 249 optimal weight: 6.9990 chunk 209 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 chunk 225 optimal weight: 0.0570 chunk 85 optimal weight: 10.0000 chunk 124 optimal weight: 0.9990 chunk 161 optimal weight: 7.9990 overall best weight: 1.6302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 HIS ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 939 ASN A1601 GLN ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 598 HIS ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 975 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 44 ASN ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 170 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.191168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.165938 restraints weight = 46138.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.165312 restraints weight = 75881.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.165902 restraints weight = 70612.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.165789 restraints weight = 47389.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.166171 restraints weight = 43310.793| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.4580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 34814 Z= 0.117 Angle : 0.590 16.330 47231 Z= 0.295 Chirality : 0.043 0.200 5274 Planarity : 0.004 0.057 5937 Dihedral : 10.803 74.836 5063 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.75 % Favored : 96.18 % Rotamer: Outliers : 2.87 % Allowed : 14.41 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (0.13), residues: 4109 helix: -0.12 (0.15), residues: 1255 sheet: -0.46 (0.19), residues: 694 loop : -0.74 (0.13), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1176 TYR 0.022 0.001 TYR A 478 PHE 0.017 0.001 PHE A 239 TRP 0.037 0.002 TRP E 79 HIS 0.005 0.001 HIS G 65 Details of bonding type rmsd covalent geometry : bond 0.00268 (34788) covalent geometry : angle 0.56419 (47204) hydrogen bonds : bond 0.03684 ( 1162) hydrogen bonds : angle 4.84706 ( 3226) metal coordination : bond 0.01266 ( 22) metal coordination : angle 7.29867 ( 27) Misc. bond : bond 0.00124 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8218 Ramachandran restraints generated. 4109 Oldfield, 0 Emsley, 4109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8218 Ramachandran restraints generated. 4109 Oldfield, 0 Emsley, 4109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 3693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 482 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 SER cc_start: 0.7403 (m) cc_final: 0.6987 (t) REVERT: A 672 ASP cc_start: 0.7426 (m-30) cc_final: 0.6460 (t0) REVERT: A 683 LYS cc_start: 0.8693 (mtpt) cc_final: 0.8328 (mtpt) REVERT: A 786 TYR cc_start: 0.8171 (p90) cc_final: 0.7796 (p90) REVERT: A 830 MET cc_start: 0.9044 (mmm) cc_final: 0.8692 (tpt) REVERT: A 925 MET cc_start: 0.8120 (tpp) cc_final: 0.7910 (tpp) REVERT: A 1026 GLN cc_start: 0.7734 (tt0) cc_final: 0.7229 (tp-100) REVERT: A 1238 MET cc_start: 0.7747 (mtp) cc_final: 0.7159 (ttm) REVERT: A 1572 ARG cc_start: 0.7587 (tpm170) cc_final: 0.7253 (tpm170) REVERT: B 255 ASP cc_start: 0.7387 (p0) cc_final: 0.6864 (t70) REVERT: B 316 ARG cc_start: 0.6836 (mmm160) cc_final: 0.6505 (ttm170) REVERT: B 493 PHE cc_start: 0.7490 (t80) cc_final: 0.7158 (t80) REVERT: B 517 VAL cc_start: 0.8744 (m) cc_final: 0.8529 (t) REVERT: B 913 ILE cc_start: 0.9328 (mm) cc_final: 0.8957 (mt) REVERT: B 916 LYS cc_start: 0.8643 (mttt) cc_final: 0.8188 (mtmm) REVERT: B 1013 MET cc_start: 0.8474 (mtp) cc_final: 0.8237 (mtp) REVERT: C 283 GLU cc_start: 0.7126 (tm-30) cc_final: 0.6890 (tm-30) REVERT: E 187 TYR cc_start: 0.8217 (t80) cc_final: 0.7885 (t80) REVERT: F 119 ARG cc_start: 0.7128 (mtp85) cc_final: 0.6340 (tpp80) REVERT: H 33 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.7801 (mm-40) REVERT: H 100 THR cc_start: 0.8958 (m) cc_final: 0.8633 (m) REVERT: K 82 LYS cc_start: 0.8693 (mmtp) cc_final: 0.8397 (mmtp) REVERT: K 89 CYS cc_start: 0.8812 (t) cc_final: 0.8253 (t) REVERT: M 18 GLN cc_start: 0.4485 (OUTLIER) cc_final: 0.2531 (tt0) REVERT: N 90 MET cc_start: 0.4138 (mtm) cc_final: 0.3437 (tpt) REVERT: G 61 VAL cc_start: 0.7305 (t) cc_final: 0.6936 (m) REVERT: G 71 MET cc_start: 0.6074 (ppp) cc_final: 0.5730 (mmt) REVERT: G 125 TRP cc_start: 0.5472 (t-100) cc_final: 0.5264 (t-100) REVERT: G 250 ILE cc_start: 0.1367 (OUTLIER) cc_final: -0.0037 (tp) outliers start: 106 outliers final: 82 residues processed: 555 average time/residue: 0.1832 time to fit residues: 166.5538 Evaluate side-chains 536 residues out of total 3693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 451 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 72 CYS Chi-restraints excluded: chain A residue 90 PHE Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 1020 GLN Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain A residue 1063 MET Chi-restraints excluded: chain A residue 1077 LEU Chi-restraints excluded: chain A residue 1136 VAL Chi-restraints excluded: chain A residue 1142 ASP Chi-restraints excluded: chain A residue 1163 GLU Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1498 ILE Chi-restraints excluded: chain A residue 1520 VAL Chi-restraints excluded: chain A residue 1521 THR Chi-restraints excluded: chain A residue 1543 SER Chi-restraints excluded: chain A residue 1559 ARG Chi-restraints excluded: chain A residue 1617 THR Chi-restraints excluded: chain A residue 1629 ASN Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 614 GLU Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 900 THR Chi-restraints excluded: chain B residue 946 ASP Chi-restraints excluded: chain B residue 1089 GLN Chi-restraints excluded: chain B residue 1094 ASN Chi-restraints excluded: chain B residue 1173 THR Chi-restraints excluded: chain B residue 1196 LEU Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 93 GLN Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain F residue 59 GLN Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain H residue 33 GLN Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain I residue 33 CYS Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain J residue 45 CYS Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain L residue 35 SER Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain M residue 18 GLN Chi-restraints excluded: chain N residue 89 ILE Chi-restraints excluded: chain N residue 153 VAL Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 250 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 84 optimal weight: 0.9990 chunk 408 optimal weight: 10.0000 chunk 364 optimal weight: 20.0000 chunk 143 optimal weight: 8.9990 chunk 180 optimal weight: 10.0000 chunk 268 optimal weight: 7.9990 chunk 213 optimal weight: 0.0570 chunk 256 optimal weight: 20.0000 chunk 234 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 338 optimal weight: 20.0000 overall best weight: 3.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 634 ASN ** A1601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 598 HIS ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 975 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 61 HIS ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 237 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.178356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.150829 restraints weight = 46008.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.149926 restraints weight = 86199.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.150685 restraints weight = 83256.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.150621 restraints weight = 53333.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.151102 restraints weight = 48795.387| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.4758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 34814 Z= 0.176 Angle : 0.631 16.604 47231 Z= 0.318 Chirality : 0.045 0.200 5274 Planarity : 0.005 0.065 5937 Dihedral : 10.887 76.120 5063 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.50 % Favored : 95.40 % Rotamer: Outliers : 3.06 % Allowed : 14.92 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.88 (0.13), residues: 4109 helix: -0.12 (0.15), residues: 1246 sheet: -0.47 (0.19), residues: 696 loop : -0.83 (0.13), residues: 2167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1176 TYR 0.053 0.002 TYR B1005 PHE 0.034 0.002 PHE A 223 TRP 0.041 0.002 TRP E 79 HIS 0.013 0.001 HIS N 170 Details of bonding type rmsd covalent geometry : bond 0.00419 (34788) covalent geometry : angle 0.60836 (47204) hydrogen bonds : bond 0.04010 ( 1162) hydrogen bonds : angle 4.93233 ( 3226) metal coordination : bond 0.01384 ( 22) metal coordination : angle 7.07628 ( 27) Misc. bond : bond 0.00265 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8218 Ramachandran restraints generated. 4109 Oldfield, 0 Emsley, 4109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8218 Ramachandran restraints generated. 4109 Oldfield, 0 Emsley, 4109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 3693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 465 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 424 MET cc_start: 0.7983 (mmm) cc_final: 0.7715 (mmm) REVERT: A 683 LYS cc_start: 0.8638 (mtpt) cc_final: 0.8308 (mtpt) REVERT: A 786 TYR cc_start: 0.8196 (p90) cc_final: 0.7791 (p90) REVERT: A 830 MET cc_start: 0.8845 (mmm) cc_final: 0.8641 (tpt) REVERT: A 925 MET cc_start: 0.8104 (tpp) cc_final: 0.7838 (tpp) REVERT: A 1026 GLN cc_start: 0.7686 (tt0) cc_final: 0.7324 (tp-100) REVERT: A 1238 MET cc_start: 0.7777 (mtp) cc_final: 0.7195 (ttm) REVERT: A 1572 ARG cc_start: 0.7612 (tpm170) cc_final: 0.7249 (tpm170) REVERT: B 255 ASP cc_start: 0.7462 (p0) cc_final: 0.6992 (t70) REVERT: B 316 ARG cc_start: 0.6886 (mmm160) cc_final: 0.6610 (ttm170) REVERT: B 493 PHE cc_start: 0.7432 (t80) cc_final: 0.7121 (t80) REVERT: B 517 VAL cc_start: 0.8701 (m) cc_final: 0.8468 (t) REVERT: B 680 GLU cc_start: 0.7685 (mt-10) cc_final: 0.7189 (tt0) REVERT: B 913 ILE cc_start: 0.9436 (mm) cc_final: 0.9129 (mt) REVERT: B 916 LYS cc_start: 0.8690 (mttt) cc_final: 0.8237 (mtmm) REVERT: B 958 MET cc_start: 0.8001 (mtt) cc_final: 0.7787 (mtt) REVERT: C 283 GLU cc_start: 0.7142 (tm-30) cc_final: 0.6888 (tm-30) REVERT: E 79 TRP cc_start: 0.6931 (t-100) cc_final: 0.6535 (m100) REVERT: E 187 TYR cc_start: 0.8071 (t80) cc_final: 0.7808 (t80) REVERT: F 119 ARG cc_start: 0.7105 (mtp85) cc_final: 0.6273 (tpp80) REVERT: H 100 THR cc_start: 0.9184 (m) cc_final: 0.8912 (m) REVERT: J 68 LYS cc_start: 0.7635 (OUTLIER) cc_final: 0.6808 (ttpt) REVERT: K 89 CYS cc_start: 0.8646 (t) cc_final: 0.8330 (t) REVERT: N 90 MET cc_start: 0.4300 (mtm) cc_final: 0.3628 (tpt) REVERT: G 250 ILE cc_start: 0.1399 (OUTLIER) cc_final: -0.0074 (tp) outliers start: 113 outliers final: 91 residues processed: 545 average time/residue: 0.1856 time to fit residues: 167.4121 Evaluate side-chains 544 residues out of total 3693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 451 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 72 CYS Chi-restraints excluded: chain A residue 90 PHE Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 1020 GLN Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain A residue 1063 MET Chi-restraints excluded: chain A residue 1077 LEU Chi-restraints excluded: chain A residue 1142 ASP Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1498 ILE Chi-restraints excluded: chain A residue 1520 VAL Chi-restraints excluded: chain A residue 1521 THR Chi-restraints excluded: chain A residue 1543 SER Chi-restraints excluded: chain A residue 1559 ARG Chi-restraints excluded: chain A residue 1617 THR Chi-restraints excluded: chain A residue 1629 ASN Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 429 ARG Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 677 THR Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain B residue 900 THR Chi-restraints excluded: chain B residue 946 ASP Chi-restraints excluded: chain B residue 1046 VAL Chi-restraints excluded: chain B residue 1088 LEU Chi-restraints excluded: chain B residue 1113 THR Chi-restraints excluded: chain B residue 1160 GLU Chi-restraints excluded: chain B residue 1173 THR Chi-restraints excluded: chain B residue 1196 LEU Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 93 GLN Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain F residue 59 GLN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain H residue 33 GLN Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain J residue 45 CYS Chi-restraints excluded: chain J residue 68 LYS Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 133 SER Chi-restraints excluded: chain L residue 35 SER Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain N residue 89 ILE Chi-restraints excluded: chain N residue 153 VAL Chi-restraints excluded: chain D residue 18 THR Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 250 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 327 optimal weight: 4.9990 chunk 312 optimal weight: 9.9990 chunk 133 optimal weight: 10.0000 chunk 334 optimal weight: 5.9990 chunk 144 optimal weight: 10.0000 chunk 104 optimal weight: 10.0000 chunk 125 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 232 optimal weight: 9.9990 chunk 55 optimal weight: 7.9990 chunk 172 optimal weight: 0.0570 overall best weight: 2.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 639 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1601 GLN ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 598 HIS ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 975 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 61 HIS ** K 64 GLN ** 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 = 0.4099 r_free = 0.4099 target = 0.188133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.166827 restraints weight = 46246.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.162005 restraints weight = 91753.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.157456 restraints weight = 62326.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.157035 restraints weight = 73805.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.157309 restraints weight = 55771.240| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.4935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 34814 Z= 0.147 Angle : 0.602 15.736 47231 Z= 0.304 Chirality : 0.044 0.256 5274 Planarity : 0.004 0.067 5937 Dihedral : 10.838 79.429 5063 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.06 % Favored : 95.86 % Rotamer: Outliers : 2.98 % Allowed : 15.41 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.13), residues: 4109 helix: 0.02 (0.15), residues: 1249 sheet: -0.38 (0.20), residues: 681 loop : -0.77 (0.13), residues: 2179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 560 TYR 0.037 0.002 TYR B1005 PHE 0.031 0.001 PHE A 223 TRP 0.022 0.002 TRP E 79 HIS 0.009 0.001 HIS F 61 Details of bonding type rmsd covalent geometry : bond 0.00346 (34788) covalent geometry : angle 0.58514 (47204) hydrogen bonds : bond 0.03779 ( 1162) hydrogen bonds : angle 4.81542 ( 3226) metal coordination : bond 0.01146 ( 22) metal coordination : angle 6.01724 ( 27) Misc. bond : bond 0.00213 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8218 Ramachandran restraints generated. 4109 Oldfield, 0 Emsley, 4109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8218 Ramachandran restraints generated. 4109 Oldfield, 0 Emsley, 4109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 3693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 473 time to evaluate : 1.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 SER cc_start: 0.7494 (m) cc_final: 0.7059 (t) REVERT: A 424 MET cc_start: 0.7988 (mmm) cc_final: 0.7765 (mmm) REVERT: A 478 TYR cc_start: 0.8661 (m-10) cc_final: 0.8437 (m-10) REVERT: A 683 LYS cc_start: 0.8707 (mtpt) cc_final: 0.8382 (mtpt) REVERT: A 786 TYR cc_start: 0.8276 (p90) cc_final: 0.7853 (p90) REVERT: A 925 MET cc_start: 0.8148 (tpp) cc_final: 0.7874 (tpp) REVERT: A 1026 GLN cc_start: 0.7785 (tt0) cc_final: 0.7454 (tp-100) REVERT: A 1106 LYS cc_start: 0.7798 (mttm) cc_final: 0.7517 (ttmm) REVERT: A 1238 MET cc_start: 0.7837 (mtp) cc_final: 0.7180 (ttm) REVERT: A 1572 ARG cc_start: 0.7636 (tpm170) cc_final: 0.7261 (tpm170) REVERT: B 215 MET cc_start: 0.8034 (ptt) cc_final: 0.7753 (ptt) REVERT: B 255 ASP cc_start: 0.7372 (p0) cc_final: 0.6934 (t70) REVERT: B 316 ARG cc_start: 0.7028 (mmm160) cc_final: 0.6532 (ttm170) REVERT: B 493 PHE cc_start: 0.7482 (t80) cc_final: 0.7195 (t80) REVERT: B 517 VAL cc_start: 0.8778 (m) cc_final: 0.8559 (t) REVERT: B 680 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7048 (tt0) REVERT: B 913 ILE cc_start: 0.9349 (mm) cc_final: 0.8907 (mt) REVERT: B 916 LYS cc_start: 0.8739 (mttt) cc_final: 0.8264 (mtmm) REVERT: B 944 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.7894 (mt0) REVERT: B 1013 MET cc_start: 0.8512 (mtp) cc_final: 0.8280 (mtm) REVERT: B 1014 TYR cc_start: 0.9125 (m-80) cc_final: 0.8713 (m-80) REVERT: C 283 GLU cc_start: 0.7202 (tm-30) cc_final: 0.6935 (tm-30) REVERT: E 187 TYR cc_start: 0.8192 (t80) cc_final: 0.7908 (t80) REVERT: F 119 ARG cc_start: 0.7157 (mtp85) cc_final: 0.6382 (tpp80) REVERT: H 33 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.7914 (mm110) REVERT: H 100 THR cc_start: 0.9170 (m) cc_final: 0.8882 (m) REVERT: J 58 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7653 (mm-30) REVERT: J 68 LYS cc_start: 0.7635 (OUTLIER) cc_final: 0.6764 (ttpt) REVERT: N 90 MET cc_start: 0.4578 (mtm) cc_final: 0.3472 (tpt) REVERT: G 52 MET cc_start: 0.8176 (mpp) cc_final: 0.7933 (mpp) REVERT: G 250 ILE cc_start: 0.1812 (OUTLIER) cc_final: 0.0237 (tp) outliers start: 110 outliers final: 89 residues processed: 546 average time/residue: 0.1866 time to fit residues: 166.3013 Evaluate side-chains 544 residues out of total 3693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 451 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 72 CYS Chi-restraints excluded: chain A residue 90 PHE Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 1020 GLN Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain A residue 1063 MET Chi-restraints excluded: chain A residue 1077 LEU Chi-restraints excluded: chain A residue 1142 ASP Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1498 ILE Chi-restraints excluded: chain A residue 1520 VAL Chi-restraints excluded: chain A residue 1521 THR Chi-restraints excluded: chain A residue 1543 SER Chi-restraints excluded: chain A residue 1559 ARG Chi-restraints excluded: chain A residue 1601 GLN Chi-restraints excluded: chain A residue 1607 THR Chi-restraints excluded: chain A residue 1617 THR Chi-restraints excluded: chain A residue 1629 ASN Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 614 GLU Chi-restraints excluded: chain B residue 677 THR Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 900 THR Chi-restraints excluded: chain B residue 944 GLN Chi-restraints excluded: chain B residue 946 ASP Chi-restraints excluded: chain B residue 1046 VAL Chi-restraints excluded: chain B residue 1113 THR Chi-restraints excluded: chain B residue 1124 SER Chi-restraints excluded: chain B residue 1160 GLU Chi-restraints excluded: chain B residue 1173 THR Chi-restraints excluded: chain B residue 1196 LEU Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 93 GLN Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain F residue 59 GLN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain H residue 33 GLN Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain J residue 45 CYS Chi-restraints excluded: chain J residue 68 LYS Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 133 SER Chi-restraints excluded: chain L residue 35 SER Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain N residue 89 ILE Chi-restraints excluded: chain N residue 153 VAL Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 250 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 309 optimal weight: 5.9990 chunk 367 optimal weight: 8.9990 chunk 379 optimal weight: 6.9990 chunk 85 optimal weight: 9.9990 chunk 185 optimal weight: 4.9990 chunk 261 optimal weight: 4.9990 chunk 277 optimal weight: 0.3980 chunk 173 optimal weight: 0.0980 chunk 20 optimal weight: 1.9990 chunk 76 optimal weight: 8.9990 chunk 247 optimal weight: 0.6980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 639 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 949 GLN ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 598 HIS ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 975 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 GLN F 61 HIS ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 128 ASN G 119 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.189515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.164094 restraints weight = 45920.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.162571 restraints weight = 82292.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.163218 restraints weight = 77133.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.162698 restraints weight = 50439.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.163131 restraints weight = 48147.580| |-----------------------------------------------------------------------------| r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.5079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 34814 Z= 0.116 Angle : 0.578 16.194 47231 Z= 0.292 Chirality : 0.043 0.192 5274 Planarity : 0.004 0.068 5937 Dihedral : 10.749 82.262 5063 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.82 % Favored : 96.15 % Rotamer: Outliers : 2.74 % Allowed : 15.87 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.13), residues: 4109 helix: 0.25 (0.15), residues: 1243 sheet: -0.34 (0.20), residues: 695 loop : -0.67 (0.13), residues: 2171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A1176 TYR 0.029 0.001 TYR B1005 PHE 0.030 0.001 PHE A 223 TRP 0.038 0.002 TRP E 79 HIS 0.009 0.001 HIS F 61 Details of bonding type rmsd covalent geometry : bond 0.00267 (34788) covalent geometry : angle 0.56261 (47204) hydrogen bonds : bond 0.03560 ( 1162) hydrogen bonds : angle 4.69548 ( 3226) metal coordination : bond 0.01078 ( 22) metal coordination : angle 5.51369 ( 27) Misc. bond : bond 0.00209 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8218 Ramachandran restraints generated. 4109 Oldfield, 0 Emsley, 4109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8218 Ramachandran restraints generated. 4109 Oldfield, 0 Emsley, 4109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 3693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 476 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 SER cc_start: 0.7269 (m) cc_final: 0.6909 (t) REVERT: A 467 PHE cc_start: 0.8094 (OUTLIER) cc_final: 0.7481 (t80) REVERT: A 683 LYS cc_start: 0.8626 (mtpt) cc_final: 0.8271 (mtpt) REVERT: A 786 TYR cc_start: 0.8149 (p90) cc_final: 0.7774 (p90) REVERT: A 925 MET cc_start: 0.8012 (tpp) cc_final: 0.7809 (tpp) REVERT: A 1026 GLN cc_start: 0.7712 (tt0) cc_final: 0.7364 (tp-100) REVERT: A 1106 LYS cc_start: 0.7796 (mttm) cc_final: 0.7501 (ttmm) REVERT: A 1238 MET cc_start: 0.7764 (mtp) cc_final: 0.7153 (ttm) REVERT: A 1535 PHE cc_start: 0.7371 (m-80) cc_final: 0.7164 (m-80) REVERT: A 1565 GLU cc_start: 0.7256 (tp30) cc_final: 0.6979 (tp30) REVERT: A 1572 ARG cc_start: 0.7568 (tpm170) cc_final: 0.7233 (tpm170) REVERT: A 1599 ASN cc_start: 0.7279 (p0) cc_final: 0.7051 (p0) REVERT: B 255 ASP cc_start: 0.7249 (p0) cc_final: 0.6881 (t70) REVERT: B 316 ARG cc_start: 0.6778 (mmm160) cc_final: 0.6550 (ttm170) REVERT: B 493 PHE cc_start: 0.7421 (t80) cc_final: 0.7144 (t80) REVERT: B 680 GLU cc_start: 0.7679 (mt-10) cc_final: 0.6735 (tm-30) REVERT: B 913 ILE cc_start: 0.9306 (mm) cc_final: 0.8896 (mt) REVERT: B 916 LYS cc_start: 0.8692 (mttt) cc_final: 0.8230 (mtmm) REVERT: B 944 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.7956 (mt0) REVERT: B 1014 TYR cc_start: 0.9168 (m-80) cc_final: 0.8781 (m-80) REVERT: C 283 GLU cc_start: 0.7072 (tm-30) cc_final: 0.6840 (tm-30) REVERT: E 187 TYR cc_start: 0.8097 (t80) cc_final: 0.7846 (t80) REVERT: F 119 ARG cc_start: 0.7048 (mtp85) cc_final: 0.6223 (tpp80) REVERT: H 33 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.7885 (mm110) REVERT: H 100 THR cc_start: 0.9132 (m) cc_final: 0.8875 (m) REVERT: N 90 MET cc_start: 0.3953 (mtm) cc_final: 0.3546 (tpt) REVERT: G 52 MET cc_start: 0.8102 (mpp) cc_final: 0.7867 (mpp) REVERT: G 250 ILE cc_start: 0.1685 (OUTLIER) cc_final: 0.0148 (tp) outliers start: 101 outliers final: 88 residues processed: 541 average time/residue: 0.1943 time to fit residues: 173.3531 Evaluate side-chains 544 residues out of total 3693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 452 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 ASP Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 72 CYS Chi-restraints excluded: chain A residue 90 PHE Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 797 LEU Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 1020 GLN Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain A residue 1063 MET Chi-restraints excluded: chain A residue 1077 LEU Chi-restraints excluded: chain A residue 1142 ASP Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1498 ILE Chi-restraints excluded: chain A residue 1520 VAL Chi-restraints excluded: chain A residue 1521 THR Chi-restraints excluded: chain A residue 1543 SER Chi-restraints excluded: chain A residue 1559 ARG Chi-restraints excluded: chain A residue 1607 THR Chi-restraints excluded: chain A residue 1617 THR Chi-restraints excluded: chain A residue 1629 ASN Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 614 GLU Chi-restraints excluded: chain B residue 677 THR Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 900 THR Chi-restraints excluded: chain B residue 944 GLN Chi-restraints excluded: chain B residue 946 ASP Chi-restraints excluded: chain B residue 1046 VAL Chi-restraints excluded: chain B residue 1088 LEU Chi-restraints excluded: chain B residue 1093 LEU Chi-restraints excluded: chain B residue 1124 SER Chi-restraints excluded: chain B residue 1160 GLU Chi-restraints excluded: chain B residue 1173 THR Chi-restraints excluded: chain B residue 1175 THR Chi-restraints excluded: chain B residue 1196 LEU Chi-restraints excluded: chain C residue 93 GLN Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain F residue 59 GLN Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain H residue 33 GLN Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain J residue 45 CYS Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 82 LYS Chi-restraints excluded: chain K residue 133 SER Chi-restraints excluded: chain L residue 35 SER Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain L residue 66 GLN Chi-restraints excluded: chain N residue 89 ILE Chi-restraints excluded: chain N residue 153 VAL Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 119 HIS Chi-restraints excluded: chain G residue 250 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 410 optimal weight: 0.5980 chunk 399 optimal weight: 8.9990 chunk 41 optimal weight: 0.9980 chunk 241 optimal weight: 0.7980 chunk 243 optimal weight: 0.9990 chunk 25 optimal weight: 9.9990 chunk 160 optimal weight: 0.5980 chunk 66 optimal weight: 0.0050 chunk 221 optimal weight: 0.9990 chunk 219 optimal weight: 4.9990 chunk 99 optimal weight: 0.1980 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 HIS A 949 GLN ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 975 HIS ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 61 HIS F 100 GLN ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.192629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.161457 restraints weight = 46237.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.156976 restraints weight = 52984.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.157851 restraints weight = 61010.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.158679 restraints weight = 45207.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.158897 restraints weight = 39013.789| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.5242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 34814 Z= 0.102 Angle : 0.567 16.668 47231 Z= 0.288 Chirality : 0.042 0.179 5274 Planarity : 0.004 0.061 5937 Dihedral : 10.627 85.933 5063 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.14 % Favored : 96.84 % Rotamer: Outliers : 1.87 % Allowed : 17.06 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.13), residues: 4109 helix: 0.53 (0.15), residues: 1238 sheet: -0.24 (0.20), residues: 682 loop : -0.57 (0.13), residues: 2189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A1176 TYR 0.028 0.001 TYR B1005 PHE 0.030 0.001 PHE A 223 TRP 0.026 0.001 TRP A 842 HIS 0.018 0.001 HIS G 119 Details of bonding type rmsd covalent geometry : bond 0.00221 (34788) covalent geometry : angle 0.55587 (47204) hydrogen bonds : bond 0.03327 ( 1162) hydrogen bonds : angle 4.51825 ( 3226) metal coordination : bond 0.00916 ( 22) metal coordination : angle 4.72960 ( 27) Misc. bond : bond 0.00190 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8218 Ramachandran restraints generated. 4109 Oldfield, 0 Emsley, 4109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8218 Ramachandran restraints generated. 4109 Oldfield, 0 Emsley, 4109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 3693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 498 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 467 PHE cc_start: 0.7957 (OUTLIER) cc_final: 0.7367 (t80) REVERT: A 683 LYS cc_start: 0.8595 (mtpt) cc_final: 0.8280 (mtpt) REVERT: A 786 TYR cc_start: 0.8160 (p90) cc_final: 0.7690 (p90) REVERT: A 1026 GLN cc_start: 0.7755 (tt0) cc_final: 0.7346 (tp-100) REVERT: A 1106 LYS cc_start: 0.7793 (mttm) cc_final: 0.7504 (ttmm) REVERT: A 1176 ARG cc_start: 0.8304 (mmm160) cc_final: 0.7313 (mmt180) REVERT: A 1238 MET cc_start: 0.7760 (mtp) cc_final: 0.7157 (ttm) REVERT: A 1572 ARG cc_start: 0.7523 (tpm170) cc_final: 0.7164 (tpm170) REVERT: B 255 ASP cc_start: 0.7278 (p0) cc_final: 0.6952 (t70) REVERT: B 316 ARG cc_start: 0.6972 (mmm160) cc_final: 0.6430 (ttm170) REVERT: B 493 PHE cc_start: 0.7384 (t80) cc_final: 0.7109 (t80) REVERT: B 680 GLU cc_start: 0.7809 (mt-10) cc_final: 0.6648 (tm-30) REVERT: B 916 LYS cc_start: 0.8704 (mttt) cc_final: 0.8188 (mtmm) REVERT: B 1014 TYR cc_start: 0.9101 (m-80) cc_final: 0.8808 (m-80) REVERT: C 283 GLU cc_start: 0.7373 (tm-30) cc_final: 0.7120 (tm-30) REVERT: E 32 GLN cc_start: 0.7359 (tp40) cc_final: 0.6599 (tt0) REVERT: E 187 TYR cc_start: 0.8185 (t80) cc_final: 0.7882 (t80) REVERT: F 119 ARG cc_start: 0.7008 (mtp85) cc_final: 0.6129 (tpp80) REVERT: H 33 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.7886 (mm110) REVERT: H 62 SER cc_start: 0.8785 (t) cc_final: 0.8268 (m) REVERT: J 58 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7710 (mm-30) REVERT: K 89 CYS cc_start: 0.8465 (t) cc_final: 0.8193 (t) REVERT: N 90 MET cc_start: 0.4664 (mtm) cc_final: 0.3230 (tpt) REVERT: G 250 ILE cc_start: 0.2177 (OUTLIER) cc_final: 0.0663 (tp) outliers start: 69 outliers final: 56 residues processed: 545 average time/residue: 0.1804 time to fit residues: 161.4043 Evaluate side-chains 524 residues out of total 3693 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 465 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 72 CYS Chi-restraints excluded: chain A residue 90 PHE Chi-restraints excluded: chain A residue 106 HIS Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 1020 GLN Chi-restraints excluded: chain A residue 1024 THR Chi-restraints excluded: chain A residue 1077 LEU Chi-restraints excluded: chain A residue 1142 ASP Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1520 VAL Chi-restraints excluded: chain A residue 1543 SER Chi-restraints excluded: chain A residue 1607 THR Chi-restraints excluded: chain A residue 1617 THR Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 524 SER Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 1093 LEU Chi-restraints excluded: chain B residue 1124 SER Chi-restraints excluded: chain B residue 1160 GLU Chi-restraints excluded: chain B residue 1173 THR Chi-restraints excluded: chain B residue 1196 LEU Chi-restraints excluded: chain C residue 93 GLN Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain F residue 76 LYS Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain H residue 33 GLN Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain I residue 36 ILE Chi-restraints excluded: chain J residue 45 CYS Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 82 LYS Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain N residue 153 VAL Chi-restraints excluded: chain D residue 29 GLN Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 250 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 40 optimal weight: 9.9990 chunk 211 optimal weight: 7.9990 chunk 325 optimal weight: 9.9990 chunk 80 optimal weight: 10.0000 chunk 341 optimal weight: 3.9990 chunk 116 optimal weight: 7.9990 chunk 71 optimal weight: 9.9990 chunk 162 optimal weight: 6.9990 chunk 334 optimal weight: 5.9990 chunk 293 optimal weight: 9.9990 chunk 229 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 ASN ** A1601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 61 HIS F 100 GLN ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 18 GLN D 81 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.182804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.159070 restraints weight = 46498.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.158120 restraints weight = 89927.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.158216 restraints weight = 83182.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.157399 restraints weight = 60269.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.157838 restraints weight = 53899.733| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.5284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 34814 Z= 0.288 Angle : 0.767 22.599 47231 Z= 0.384 Chirality : 0.049 0.192 5274 Planarity : 0.006 0.081 5937 Dihedral : 10.998 86.855 5063 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.52 % Favored : 94.40 % Rotamer: Outliers : 2.38 % Allowed : 17.04 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.98 (0.13), residues: 4109 helix: -0.15 (0.15), residues: 1255 sheet: -0.47 (0.20), residues: 662 loop : -0.94 (0.13), residues: 2192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A1176 TYR 0.030 0.002 TYR B 420 PHE 0.034 0.002 PHE A 223 TRP 0.060 0.003 TRP E 79 HIS 0.034 0.002 HIS A 106 Details of bonding type rmsd covalent geometry : bond 0.00687 (34788) covalent geometry : angle 0.74124 (47204) hydrogen bonds : bond 0.04645 ( 1162) hydrogen bonds : angle 5.11886 ( 3226) metal coordination : bond 0.01668 ( 22) metal coordination : angle 8.35464 ( 27) Misc. bond : bond 0.00172 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5005.27 seconds wall clock time: 87 minutes 39.43 seconds (5259.43 seconds total)