Starting phenix.real_space_refine on Fri Mar 22 16:40:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5m3f_4147/03_2024/5m3f_4147.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5m3f_4147/03_2024/5m3f_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5m3f_4147/03_2024/5m3f_4147.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5m3f_4147/03_2024/5m3f_4147.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5m3f_4147/03_2024/5m3f_4147.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5m3f_4147/03_2024/5m3f_4147.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Residue "A ARG 347": "NH1" <-> "NH2" Residue "A PHE 1472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1063": "NH1" <-> "NH2" Residue "C TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 95": "OD1" <-> "OD2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/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: 17.16, per 1000 atoms: 0.50 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.93 Conformation dependent library (CDL) restraints added in 5.5 seconds 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: 10.70 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: 15.52 Time building geometry restraints manager: 14.05 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: 98.20 - 106.36: 1261 106.36 - 114.52: 20629 114.52 - 122.68: 21373 122.68 - 130.83: 3802 130.83 - 138.99: 139 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: 9 1.36 - 2.25: 79 2.25 - 3.13: 27643 3.13 - 4.02: 81237 4.02 - 4.90: 153054 Warning: very small nonbonded interaction distances. Nonbonded interactions: 262022 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=" CE1 TYR B1005 " pdb=" ND1 HIS N 170 " model vdw 1.197 3.420 ... (remaining 262017 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 0.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 4.780 Check model and map are aligned: 0.500 Set scattering table: 0.310 Process input model: 99.150 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.300 ------------------------------------------------------------------------------- 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 : 0.006 0.095 34788 Z= 0.418 Angle : 0.893 13.992 47204 Z= 0.539 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.034 0.003 TRP B 143 HIS 0.014 0.002 HIS B1082 PHE 0.028 0.003 PHE B 895 TYR 0.030 0.002 TYR B 671 ARG 0.008 0.001 ARG E 26 *********************** 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 fitting. rotamer outliers: 42 poor density : 918 time to evaluate : 3.841 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: 0.5218 time to fit residues: 766.9232 Evaluate side-chains 532 residues out of total 3693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 522 time to evaluate : 3.760 ------------------------------------------------------------------------------- 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 348 optimal weight: 8.9990 chunk 313 optimal weight: 9.9990 chunk 173 optimal weight: 9.9990 chunk 106 optimal weight: 8.9990 chunk 211 optimal weight: 10.0000 chunk 167 optimal weight: 10.0000 chunk 323 optimal weight: 5.9990 chunk 125 optimal weight: 20.0000 chunk 196 optimal weight: 1.9990 chunk 240 optimal weight: 2.9990 chunk 375 optimal weight: 0.4980 overall best weight: 4.0988 ------------------------------------------------------------------------------- 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 785 GLN 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 646 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 ASN B 715 ASN ** B 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 975 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 979 GLN ** 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 C 323 ASN F 59 GLN H 83 GLN I 44 ASN J 23 ASN K 106 GLN L 53 HIS N 51 GLN ** D 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 56 ASN G 126 GLN G 150 HIS Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 34788 Z= 0.327 Angle : 0.715 8.057 47204 Z= 0.379 Chirality : 0.048 0.228 5274 Planarity : 0.006 0.067 5937 Dihedral : 11.594 73.328 5081 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.65 % Favored : 96.20 % Rotamer: Outliers : 2.46 % Allowed : 9.02 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.12), residues: 4109 helix: -1.89 (0.13), residues: 1228 sheet: -1.05 (0.18), residues: 683 loop : -1.05 (0.12), residues: 2198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 143 HIS 0.010 0.002 HIS A1453 PHE 0.027 0.002 PHE B 895 TYR 0.024 0.002 TYR H 95 ARG 0.008 0.001 ARG G 40 *********************** 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 668 residues out of total 3693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 577 time to evaluate : 3.959 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 2 ASP cc_start: 0.7951 (t0) cc_final: 0.7691 (m-30) REVERT: A 33 THR cc_start: 0.7031 (p) cc_final: 0.6456 (m) REVERT: A 130 ILE cc_start: 0.8011 (mp) cc_final: 0.7745 (mt) REVERT: A 348 LYS cc_start: 0.8472 (mttt) cc_final: 0.8093 (tttt) REVERT: A 460 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7529 (mt) REVERT: A 592 GLN cc_start: 0.7966 (OUTLIER) cc_final: 0.7749 (mp10) REVERT: A 600 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.8309 (ttm) REVERT: A 606 ARG cc_start: 0.8234 (ttt180) cc_final: 0.7867 (ttt90) REVERT: A 804 GLU cc_start: 0.7433 (mp0) cc_final: 0.7174 (tt0) REVERT: A 1026 GLN cc_start: 0.8335 (tt0) cc_final: 0.7668 (tp-100) REVERT: A 1060 GLU cc_start: 0.7686 (tm-30) cc_final: 0.7425 (tm-30) REVERT: A 1100 LYS cc_start: 0.8198 (tptm) cc_final: 0.7765 (ttmt) REVERT: A 1238 MET cc_start: 0.8150 (mtp) cc_final: 0.7322 (ttm) REVERT: A 1297 PHE cc_start: 0.7464 (m-80) cc_final: 0.7130 (m-80) REVERT: A 1572 ARG cc_start: 0.8268 (ttm-80) cc_final: 0.7407 (tpm170) REVERT: A 1624 LYS cc_start: 0.8506 (mttt) cc_final: 0.7904 (mmmt) REVERT: B 54 GLU cc_start: 0.7377 (mt-10) cc_final: 0.7099 (mm-30) REVERT: B 164 MET cc_start: 0.8260 (ttt) cc_final: 0.8016 (ttt) REVERT: B 187 SER cc_start: 0.9061 (t) cc_final: 0.8846 (m) REVERT: B 255 ASP cc_start: 0.8120 (p0) cc_final: 0.7083 (t70) REVERT: B 288 ILE cc_start: 0.7944 (mp) cc_final: 0.7667 (mp) REVERT: B 314 LYS cc_start: 0.6040 (mttt) cc_final: 0.5602 (mtpp) REVERT: B 316 ARG cc_start: 0.7804 (mmm160) cc_final: 0.6706 (mtt90) REVERT: B 348 GLU cc_start: 0.8439 (tp30) cc_final: 0.8065 (mt-10) REVERT: B 448 ARG cc_start: 0.7333 (ttm110) cc_final: 0.6840 (mtt180) REVERT: B 493 PHE cc_start: 0.7689 (t80) cc_final: 0.7257 (t80) REVERT: B 517 VAL cc_start: 0.9238 (m) cc_final: 0.8928 (t) REVERT: B 602 LYS cc_start: 0.8637 (tttt) cc_final: 0.8352 (tptt) REVERT: B 623 ASP cc_start: 0.8374 (p0) cc_final: 0.7729 (m-30) REVERT: B 661 GLU cc_start: 0.7363 (tt0) cc_final: 0.6723 (mp0) REVERT: B 789 ILE cc_start: 0.9169 (mt) cc_final: 0.8915 (pt) REVERT: B 803 MET cc_start: 0.8053 (ttp) cc_final: 0.7830 (ttt) REVERT: B 808 LYS cc_start: 0.8062 (tttt) cc_final: 0.7738 (tttt) REVERT: B 883 GLU cc_start: 0.8374 (tp30) cc_final: 0.8066 (tt0) REVERT: B 884 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8285 (tp30) REVERT: B 913 ILE cc_start: 0.9145 (mm) cc_final: 0.8853 (mt) REVERT: B 958 MET cc_start: 0.8457 (tpp) cc_final: 0.8233 (mtt) REVERT: B 998 GLU cc_start: 0.8690 (tt0) cc_final: 0.8393 (tm-30) REVERT: B 1013 MET cc_start: 0.8526 (mtp) cc_final: 0.8311 (mtp) REVERT: B 1115 GLN cc_start: 0.8410 (mm-40) cc_final: 0.8095 (tm-30) REVERT: B 1126 VAL cc_start: 0.9085 (t) cc_final: 0.8864 (p) REVERT: C 47 LEU cc_start: 0.8274 (tt) cc_final: 0.7921 (pp) REVERT: C 168 LYS cc_start: 0.7805 (mmtt) cc_final: 0.7147 (mtpt) REVERT: C 174 ARG cc_start: 0.7898 (mtt180) cc_final: 0.7356 (ptt-90) REVERT: C 201 GLU cc_start: 0.8425 (pt0) cc_final: 0.7808 (tt0) REVERT: C 283 GLU cc_start: 0.7668 (tm-30) cc_final: 0.7392 (tm-30) REVERT: C 312 GLU cc_start: 0.8083 (tt0) cc_final: 0.7781 (mm-30) REVERT: E 36 GLU cc_start: 0.6615 (mt-10) cc_final: 0.6096 (mt-10) REVERT: E 81 GLU cc_start: 0.6893 (tp30) cc_final: 0.6429 (mm-30) REVERT: E 106 GLN cc_start: 0.6219 (tp40) cc_final: 0.5983 (tt0) REVERT: E 127 ILE cc_start: 0.7678 (pt) cc_final: 0.7324 (tp) REVERT: E 215 MET cc_start: 0.8180 (mmt) cc_final: 0.7979 (mmm) REVERT: F 61 HIS cc_start: 0.7127 (t-90) cc_final: 0.6367 (t-90) REVERT: F 109 VAL cc_start: 0.8301 (p) cc_final: 0.7946 (m) REVERT: F 119 ARG cc_start: 0.7658 (mmt180) cc_final: 0.7176 (mtp85) REVERT: H 88 SER cc_start: 0.8383 (p) cc_final: 0.8095 (m) REVERT: J 39 LEU cc_start: 0.9049 (mt) cc_final: 0.8804 (mp) REVERT: J 61 LEU cc_start: 0.9025 (mt) cc_final: 0.8786 (mt) REVERT: J 68 LYS cc_start: 0.8002 (mmtp) cc_final: 0.7284 (ttpt) REVERT: K 45 GLU cc_start: 0.6855 (mt-10) cc_final: 0.6582 (pt0) REVERT: K 132 GLU cc_start: 0.8489 (tp30) cc_final: 0.8054 (tm-30) REVERT: L 28 LYS cc_start: 0.8169 (mttp) cc_final: 0.7515 (mmtm) REVERT: N 41 ASN cc_start: 0.0075 (OUTLIER) cc_final: -0.0283 (t0) REVERT: N 90 MET cc_start: 0.4261 (mtm) cc_final: 0.3219 (tpt) REVERT: N 167 LYS cc_start: 0.3624 (OUTLIER) cc_final: 0.2922 (mttp) REVERT: G 62 MET cc_start: 0.5047 (tmm) cc_final: 0.4797 (tmm) REVERT: G 71 MET cc_start: 0.4393 (tmm) cc_final: 0.2773 (mmt) outliers start: 91 outliers final: 51 residues processed: 633 average time/residue: 0.4559 time to fit residues: 466.1855 Evaluate side-chains 532 residues out of total 3693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 476 time to evaluate : 3.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 112 SER 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 600 MET Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 953 GLU Chi-restraints excluded: chain A residue 1087 GLU Chi-restraints excluded: chain A residue 1136 VAL Chi-restraints excluded: chain A residue 1162 ASN 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 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 234 ILE Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 672 MET Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 900 THR Chi-restraints excluded: chain B residue 994 ASP 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 C residue 73 SER Chi-restraints excluded: chain C residue 222 VAL 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 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 41 ASN 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 G residue 35 SER Chi-restraints excluded: chain G residue 105 ILE 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 208 optimal weight: 3.9990 chunk 116 optimal weight: 10.0000 chunk 312 optimal weight: 9.9990 chunk 255 optimal weight: 7.9990 chunk 103 optimal weight: 8.9990 chunk 375 optimal weight: 7.9990 chunk 405 optimal weight: 9.9990 chunk 334 optimal weight: 5.9990 chunk 372 optimal weight: 6.9990 chunk 128 optimal weight: 10.0000 chunk 301 optimal weight: 30.0000 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 76 GLN ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 HIS ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 694 GLN ** A1141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 GLN B 686 HIS ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 975 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 979 GLN B 999 GLN ** B1038 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** C 301 ASN I 44 ASN D 29 GLN G 23 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 34788 Z= 0.454 Angle : 0.773 9.777 47204 Z= 0.404 Chirality : 0.050 0.202 5274 Planarity : 0.006 0.081 5937 Dihedral : 11.484 73.471 5071 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.48 % Favored : 94.38 % Rotamer: Outliers : 3.66 % Allowed : 11.21 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.12), residues: 4109 helix: -1.40 (0.13), residues: 1250 sheet: -0.97 (0.19), residues: 693 loop : -1.26 (0.12), residues: 2166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP B 143 HIS 0.013 0.002 HIS A 603 PHE 0.026 0.003 PHE B 545 TYR 0.025 0.003 TYR A1034 ARG 0.009 0.001 ARG A 230 *********************** 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 666 residues out of total 3693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 531 time to evaluate : 3.556 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: symmetry clash REVERT: A 239 PHE cc_start: 0.7643 (m-80) cc_final: 0.7393 (m-80) REVERT: A 348 LYS cc_start: 0.8529 (mttt) cc_final: 0.8145 (tttt) REVERT: A 606 ARG cc_start: 0.8255 (ttt180) cc_final: 0.7915 (ttt90) REVERT: A 786 TYR cc_start: 0.8366 (p90) cc_final: 0.8069 (p90) REVERT: A 804 GLU cc_start: 0.7484 (mp0) cc_final: 0.7195 (tt0) REVERT: A 1026 GLN cc_start: 0.8518 (tt0) cc_final: 0.7952 (tp-100) REVERT: A 1060 GLU cc_start: 0.7932 (tm-30) cc_final: 0.7558 (tm-30) REVERT: A 1100 LYS cc_start: 0.8110 (tptm) cc_final: 0.7686 (ttmt) REVERT: A 1120 TYR cc_start: 0.6457 (p90) cc_final: 0.5343 (p90) REVERT: A 1238 MET cc_start: 0.8181 (mtp) cc_final: 0.7566 (ttm) REVERT: A 1256 LYS cc_start: 0.7079 (pttm) cc_final: 0.6541 (tptp) REVERT: A 1572 ARG cc_start: 0.8284 (ttm-80) cc_final: 0.7432 (tpm170) REVERT: A 1624 LYS cc_start: 0.8615 (mttt) cc_final: 0.8046 (mmmt) REVERT: B 54 GLU cc_start: 0.7282 (mt-10) cc_final: 0.7050 (mm-30) REVERT: B 164 MET cc_start: 0.8266 (ttt) cc_final: 0.8064 (ttt) REVERT: B 185 GLU cc_start: 0.8757 (mp0) cc_final: 0.8501 (mp0) REVERT: B 255 ASP cc_start: 0.8167 (p0) cc_final: 0.6835 (t70) REVERT: B 314 LYS cc_start: 0.6362 (mttt) cc_final: 0.5896 (mtpp) REVERT: B 316 ARG cc_start: 0.8010 (mmm160) cc_final: 0.6715 (mtt90) REVERT: B 348 GLU cc_start: 0.8574 (tp30) cc_final: 0.8081 (mt-10) REVERT: B 448 ARG cc_start: 0.7099 (ttm110) cc_final: 0.6622 (mtt180) REVERT: B 493 PHE cc_start: 0.7923 (t80) cc_final: 0.7542 (t80) REVERT: B 517 VAL cc_start: 0.9186 (m) cc_final: 0.8969 (t) REVERT: B 602 LYS cc_start: 0.8750 (tttt) cc_final: 0.8396 (tptt) REVERT: B 623 ASP cc_start: 0.8468 (p0) cc_final: 0.7818 (m-30) REVERT: B 717 TYR cc_start: 0.7934 (m-10) cc_final: 0.7714 (m-80) REVERT: B 803 MET cc_start: 0.8066 (ttp) cc_final: 0.7568 (ttt) REVERT: B 808 LYS cc_start: 0.8149 (tttt) cc_final: 0.7875 (tttt) REVERT: B 847 TYR cc_start: 0.8062 (m-80) cc_final: 0.7774 (m-10) REVERT: B 998 GLU cc_start: 0.8643 (tt0) cc_final: 0.8297 (tm-30) REVERT: B 1013 MET cc_start: 0.8620 (mtp) cc_final: 0.8379 (mtp) REVERT: B 1073 GLU cc_start: 0.7795 (tm-30) cc_final: 0.7591 (tm-30) REVERT: B 1115 GLN cc_start: 0.8646 (mm-40) cc_final: 0.8156 (tm-30) REVERT: C 47 LEU cc_start: 0.8192 (tt) cc_final: 0.7941 (pp) REVERT: C 168 LYS cc_start: 0.8050 (mmtt) cc_final: 0.7424 (mtpt) REVERT: C 308 MET cc_start: 0.7260 (mtp) cc_final: 0.6871 (mtt) REVERT: E 12 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8180 (mp) REVERT: E 57 MET cc_start: 0.7160 (tmm) cc_final: 0.6742 (tmm) REVERT: E 81 GLU cc_start: 0.6933 (tp30) cc_final: 0.6439 (mm-30) REVERT: E 103 LYS cc_start: 0.6658 (mttt) cc_final: 0.6101 (mmtm) REVERT: E 159 ASP cc_start: 0.7766 (t0) cc_final: 0.7403 (t70) REVERT: E 187 TYR cc_start: 0.8255 (t80) cc_final: 0.7819 (t80) REVERT: F 61 HIS cc_start: 0.7074 (t-90) cc_final: 0.6402 (t-90) REVERT: F 109 VAL cc_start: 0.8501 (p) cc_final: 0.8222 (t) REVERT: F 119 ARG cc_start: 0.7552 (mmt180) cc_final: 0.7271 (mmm160) REVERT: H 52 GLN cc_start: 0.7949 (mm-40) cc_final: 0.7614 (mm-40) REVERT: I 11 LEU cc_start: 0.7249 (mt) cc_final: 0.6856 (mp) REVERT: I 37 TYR cc_start: 0.5237 (m-80) cc_final: 0.4846 (m-10) REVERT: J 39 LEU cc_start: 0.9069 (mt) cc_final: 0.8862 (mp) REVERT: J 68 LYS cc_start: 0.7992 (mmtp) cc_final: 0.7251 (tttt) REVERT: K 45 GLU cc_start: 0.6813 (mt-10) cc_final: 0.6554 (pt0) REVERT: K 82 LYS cc_start: 0.8798 (mmtp) cc_final: 0.8365 (mmtp) REVERT: K 132 GLU cc_start: 0.8523 (tp30) cc_final: 0.8028 (tm-30) REVERT: K 135 PHE cc_start: 0.8761 (t80) cc_final: 0.8367 (t80) REVERT: L 28 LYS cc_start: 0.8252 (mttp) cc_final: 0.7954 (mmmm) REVERT: M 18 GLN cc_start: 0.4133 (OUTLIER) cc_final: 0.2717 (tt0) REVERT: N 41 ASN cc_start: 0.1601 (OUTLIER) cc_final: 0.0247 (t0) REVERT: N 90 MET cc_start: 0.4375 (mtm) cc_final: 0.3279 (tpt) REVERT: G 15 ARG cc_start: 0.5871 (OUTLIER) cc_final: 0.5648 (mmt90) REVERT: G 61 VAL cc_start: 0.6483 (OUTLIER) cc_final: 0.6038 (p) REVERT: G 71 MET cc_start: 0.5612 (tmm) cc_final: 0.4533 (mmt) outliers start: 135 outliers final: 92 residues processed: 615 average time/residue: 0.4700 time to fit residues: 469.3655 Evaluate side-chains 555 residues out of total 3693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 458 time to evaluate : 3.770 ------------------------------------------------------------------------------- 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 234 ASP 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 570 THR Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 836 THR 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 968 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 1118 VAL Chi-restraints excluded: chain A residue 1136 VAL Chi-restraints excluded: chain A residue 1162 ASN Chi-restraints excluded: chain A residue 1163 GLU Chi-restraints excluded: chain A residue 1498 ILE Chi-restraints excluded: chain A residue 1505 ASP 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 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 72 VAL 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 524 SER Chi-restraints excluded: chain B residue 589 ASP Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 687 THR 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 994 ASP Chi-restraints excluded: chain B residue 1049 THR Chi-restraints excluded: chain B residue 1113 THR Chi-restraints excluded: chain B residue 1161 ASP 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 51 GLU Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 75 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 E residue 12 LEU Chi-restraints excluded: chain E residue 18 THR 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 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 50 ILE Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain K residue 69 ASP 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 M residue 57 ASN Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain N residue 41 ASN Chi-restraints excluded: chain N residue 89 ILE 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 15 ARG Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain G residue 108 THR 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 371 optimal weight: 7.9990 chunk 282 optimal weight: 7.9990 chunk 194 optimal weight: 9.9990 chunk 41 optimal weight: 0.7980 chunk 179 optimal weight: 6.9990 chunk 252 optimal weight: 0.9990 chunk 377 optimal weight: 40.0000 chunk 399 optimal weight: 5.9990 chunk 197 optimal weight: 0.9990 chunk 357 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN A 580 HIS ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 939 ASN ** A1141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 GLN ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 899 GLN ** B 975 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 999 GLN B1094 ASN ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 GLN E 113 GLN H 139 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 34788 Z= 0.171 Angle : 0.575 12.889 47204 Z= 0.302 Chirality : 0.044 0.237 5274 Planarity : 0.004 0.057 5937 Dihedral : 11.063 73.253 5065 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.36 % Favored : 96.50 % Rotamer: Outliers : 2.68 % Allowed : 13.14 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.12), residues: 4109 helix: -0.65 (0.14), residues: 1248 sheet: -0.73 (0.19), residues: 706 loop : -0.94 (0.13), residues: 2155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 79 HIS 0.005 0.001 HIS A 78 PHE 0.022 0.001 PHE C 36 TYR 0.020 0.001 TYR A 695 ARG 0.011 0.000 ARG B 429 *********************** 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 634 residues out of total 3693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 535 time to evaluate : 3.763 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 99 ARG cc_start: 0.7601 (ttp-170) cc_final: 0.7331 (mtm110) REVERT: A 348 LYS cc_start: 0.8289 (mttt) cc_final: 0.7931 (tttt) REVERT: A 460 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7557 (mt) REVERT: A 606 ARG cc_start: 0.8251 (ttt180) cc_final: 0.7936 (ttt90) REVERT: A 683 LYS cc_start: 0.8823 (mtmt) cc_final: 0.8496 (ttmt) REVERT: A 786 TYR cc_start: 0.8252 (p90) cc_final: 0.7917 (p90) REVERT: A 830 MET cc_start: 0.9041 (tpt) cc_final: 0.8646 (tpt) REVERT: A 1026 GLN cc_start: 0.8560 (tt0) cc_final: 0.7916 (tp-100) REVERT: A 1060 GLU cc_start: 0.7739 (tm-30) cc_final: 0.7328 (tm-30) REVERT: A 1081 ASN cc_start: 0.7014 (t0) cc_final: 0.6748 (t0) REVERT: A 1100 LYS cc_start: 0.8016 (tptm) cc_final: 0.7624 (ttmt) REVERT: A 1120 TYR cc_start: 0.6344 (p90) cc_final: 0.5213 (p90) REVERT: A 1238 MET cc_start: 0.8031 (mtp) cc_final: 0.7442 (ttm) REVERT: A 1572 ARG cc_start: 0.8236 (ttm-80) cc_final: 0.7504 (tpm170) REVERT: A 1624 LYS cc_start: 0.8482 (mttt) cc_final: 0.7974 (mmmt) REVERT: B 54 GLU cc_start: 0.7191 (mt-10) cc_final: 0.6945 (mm-30) REVERT: B 185 GLU cc_start: 0.8634 (mp0) cc_final: 0.8231 (mp0) REVERT: B 255 ASP cc_start: 0.8087 (p0) cc_final: 0.6812 (t70) REVERT: B 314 LYS cc_start: 0.6322 (mttt) cc_final: 0.5929 (mtpp) REVERT: B 316 ARG cc_start: 0.7787 (mmm160) cc_final: 0.6850 (ttm170) REVERT: B 348 GLU cc_start: 0.8497 (tp30) cc_final: 0.8101 (mt-10) REVERT: B 429 ARG cc_start: 0.7385 (ttm-80) cc_final: 0.7142 (mmp80) REVERT: B 448 ARG cc_start: 0.7014 (ttm110) cc_final: 0.6517 (mtt180) REVERT: B 493 PHE cc_start: 0.7658 (t80) cc_final: 0.7258 (t80) REVERT: B 517 VAL cc_start: 0.9142 (m) cc_final: 0.8917 (t) REVERT: B 602 LYS cc_start: 0.8655 (tttt) cc_final: 0.8303 (tptt) REVERT: B 623 ASP cc_start: 0.8301 (p0) cc_final: 0.7711 (m-30) REVERT: B 716 MET cc_start: 0.7585 (mtp) cc_final: 0.7060 (mtt) REVERT: B 717 TYR cc_start: 0.7870 (m-10) cc_final: 0.7654 (m-80) REVERT: B 808 LYS cc_start: 0.8134 (tttt) cc_final: 0.7899 (tttt) REVERT: B 847 TYR cc_start: 0.7899 (m-80) cc_final: 0.7653 (m-10) REVERT: B 998 GLU cc_start: 0.8560 (tt0) cc_final: 0.8132 (tm-30) REVERT: B 1013 MET cc_start: 0.8506 (mtp) cc_final: 0.8245 (mtp) REVERT: B 1115 GLN cc_start: 0.8442 (mm-40) cc_final: 0.8169 (tm-30) REVERT: C 168 LYS cc_start: 0.7879 (mmtt) cc_final: 0.7361 (mtpt) REVERT: C 308 MET cc_start: 0.7165 (mtp) cc_final: 0.6816 (mtt) REVERT: C 312 GLU cc_start: 0.7804 (tt0) cc_final: 0.7310 (tm-30) REVERT: E 81 GLU cc_start: 0.6984 (tp30) cc_final: 0.6504 (mm-30) REVERT: E 103 LYS cc_start: 0.6657 (mttt) cc_final: 0.6078 (mmtm) REVERT: E 155 ARG cc_start: 0.8240 (ttp80) cc_final: 0.7897 (ttp-170) REVERT: E 159 ASP cc_start: 0.7604 (t0) cc_final: 0.7283 (t70) REVERT: F 61 HIS cc_start: 0.7156 (t-90) cc_final: 0.6395 (t-90) REVERT: F 109 VAL cc_start: 0.8416 (p) cc_final: 0.8121 (t) REVERT: F 119 ARG cc_start: 0.7504 (mmt180) cc_final: 0.7057 (mtp85) REVERT: H 52 GLN cc_start: 0.7644 (mm-40) cc_final: 0.7418 (mm-40) REVERT: H 100 THR cc_start: 0.8887 (m) cc_final: 0.8656 (m) REVERT: I 11 LEU cc_start: 0.7134 (mt) cc_final: 0.6750 (mp) REVERT: I 37 TYR cc_start: 0.4921 (m-80) cc_final: 0.4536 (m-10) REVERT: J 68 LYS cc_start: 0.7950 (mmtp) cc_final: 0.7223 (ttpt) REVERT: K 45 GLU cc_start: 0.6788 (mt-10) cc_final: 0.6500 (pt0) REVERT: K 132 GLU cc_start: 0.8488 (tp30) cc_final: 0.7974 (tm-30) REVERT: K 133 SER cc_start: 0.8859 (t) cc_final: 0.8473 (m) REVERT: L 28 LYS cc_start: 0.8130 (mttp) cc_final: 0.7824 (mmmm) REVERT: M 18 GLN cc_start: 0.4311 (OUTLIER) cc_final: 0.2850 (tt0) REVERT: N 90 MET cc_start: 0.4278 (mtm) cc_final: 0.3299 (tpt) REVERT: G 15 ARG cc_start: 0.5875 (OUTLIER) cc_final: 0.5595 (mmt90) REVERT: G 49 LEU cc_start: 0.7745 (tp) cc_final: 0.7534 (tp) REVERT: G 61 VAL cc_start: 0.6525 (t) cc_final: 0.6165 (p) REVERT: G 71 MET cc_start: 0.5955 (tmm) cc_final: 0.4987 (mmt) outliers start: 99 outliers final: 59 residues processed: 600 average time/residue: 0.4660 time to fit residues: 453.9917 Evaluate side-chains 532 residues out of total 3693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 470 time to evaluate : 3.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 1020 GLN 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 1162 ASN Chi-restraints excluded: chain A residue 1163 GLU Chi-restraints excluded: chain A residue 1498 ILE Chi-restraints excluded: chain A residue 1505 ASP Chi-restraints excluded: chain A residue 1520 VAL Chi-restraints excluded: chain A residue 1543 SER Chi-restraints excluded: chain A residue 1585 ILE 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 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 302 LEU Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 899 GLN Chi-restraints excluded: chain B residue 994 ASP 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 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 134 THR 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 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 57 ASP Chi-restraints excluded: chain K residue 62 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 N residue 176 ASP Chi-restraints excluded: chain D residue 29 GLN Chi-restraints excluded: chain G residue 15 ARG Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 105 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 332 optimal weight: 5.9990 chunk 226 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 297 optimal weight: 50.0000 chunk 164 optimal weight: 10.0000 chunk 340 optimal weight: 5.9990 chunk 275 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 203 optimal weight: 6.9990 chunk 358 optimal weight: 8.9990 chunk 100 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 HIS A 634 ASN A 939 ASN A 998 HIS ** A1141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 ASN ** B 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 899 GLN ** 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 99 ASN N 41 ASN G 170 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.4445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.103 34788 Z= 0.477 Angle : 0.742 8.799 47204 Z= 0.385 Chirality : 0.049 0.205 5274 Planarity : 0.006 0.071 5937 Dihedral : 11.300 72.888 5064 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.28 % Favored : 93.62 % Rotamer: Outliers : 4.36 % Allowed : 13.73 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.12), residues: 4109 helix: -0.91 (0.14), residues: 1259 sheet: -0.69 (0.20), residues: 674 loop : -1.29 (0.13), residues: 2176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 143 HIS 0.011 0.002 HIS A 603 PHE 0.026 0.002 PHE B 545 TYR 0.029 0.002 TYR B1098 ARG 0.008 0.001 ARG A1003 *********************** 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 639 residues out of total 3693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 478 time to evaluate : 4.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ARG cc_start: 0.7890 (ttp-170) cc_final: 0.7396 (mtm180) REVERT: A 219 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8151 (tt) REVERT: A 348 LYS cc_start: 0.8512 (mttt) cc_final: 0.8134 (tttt) REVERT: A 460 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7664 (mt) REVERT: A 606 ARG cc_start: 0.8233 (ttt180) cc_final: 0.7900 (ttt90) REVERT: A 786 TYR cc_start: 0.8382 (p90) cc_final: 0.8013 (p90) REVERT: A 831 ASP cc_start: 0.8983 (p0) cc_final: 0.8730 (p0) REVERT: A 1026 GLN cc_start: 0.8580 (tt0) cc_final: 0.8053 (tp-100) REVERT: A 1060 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7394 (tm-30) REVERT: A 1100 LYS cc_start: 0.8273 (tptm) cc_final: 0.7693 (ttmt) REVERT: A 1120 TYR cc_start: 0.6675 (p90) cc_final: 0.5572 (p90) REVERT: A 1238 MET cc_start: 0.8135 (mtp) cc_final: 0.7580 (ttm) REVERT: A 1255 CYS cc_start: 0.6279 (OUTLIER) cc_final: 0.5872 (t) REVERT: A 1535 PHE cc_start: 0.7309 (OUTLIER) cc_final: 0.6458 (m-80) REVERT: A 1572 ARG cc_start: 0.8426 (ttm-80) cc_final: 0.7695 (tpm170) REVERT: A 1624 LYS cc_start: 0.8725 (mttt) cc_final: 0.8221 (mmmt) REVERT: B 20 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7442 (tt0) REVERT: B 185 GLU cc_start: 0.8714 (mp0) cc_final: 0.8094 (mp0) REVERT: B 314 LYS cc_start: 0.6520 (mttt) cc_final: 0.6026 (mtpp) REVERT: B 316 ARG cc_start: 0.7980 (mmm160) cc_final: 0.6964 (ttm170) REVERT: B 446 MET cc_start: 0.7703 (tmm) cc_final: 0.7334 (tmm) REVERT: B 448 ARG cc_start: 0.7073 (ttm110) cc_final: 0.6672 (mtt180) REVERT: B 493 PHE cc_start: 0.7782 (t80) cc_final: 0.7373 (t80) REVERT: B 513 LYS cc_start: 0.6905 (tttt) cc_final: 0.6472 (ttmm) REVERT: B 517 VAL cc_start: 0.9164 (m) cc_final: 0.8910 (t) REVERT: B 602 LYS cc_start: 0.8709 (tttt) cc_final: 0.8353 (tptt) REVERT: B 623 ASP cc_start: 0.8462 (p0) cc_final: 0.7722 (m-30) REVERT: B 661 GLU cc_start: 0.7389 (tt0) cc_final: 0.6745 (mp0) REVERT: B 767 ASN cc_start: 0.8772 (OUTLIER) cc_final: 0.8443 (t0) REVERT: B 847 TYR cc_start: 0.8049 (m-80) cc_final: 0.7751 (m-10) REVERT: B 998 GLU cc_start: 0.8543 (tt0) cc_final: 0.8300 (tm-30) REVERT: B 1013 MET cc_start: 0.8610 (mtp) cc_final: 0.8392 (mtp) REVERT: B 1094 ASN cc_start: 0.8841 (OUTLIER) cc_final: 0.8471 (m110) REVERT: B 1115 GLN cc_start: 0.8639 (mm-40) cc_final: 0.8178 (tm-30) REVERT: C 168 LYS cc_start: 0.8099 (mmtt) cc_final: 0.7481 (mtpt) REVERT: C 308 MET cc_start: 0.7371 (mtp) cc_final: 0.6685 (mtm) REVERT: C 312 GLU cc_start: 0.8157 (tt0) cc_final: 0.7506 (tm-30) REVERT: E 81 GLU cc_start: 0.7025 (tp30) cc_final: 0.6491 (mm-30) REVERT: E 103 LYS cc_start: 0.6890 (mttt) cc_final: 0.6196 (mmtm) REVERT: E 159 ASP cc_start: 0.7890 (t0) cc_final: 0.7530 (t70) REVERT: E 196 VAL cc_start: 0.9177 (OUTLIER) cc_final: 0.8972 (m) REVERT: F 61 HIS cc_start: 0.7085 (t-90) cc_final: 0.6395 (t-90) REVERT: F 109 VAL cc_start: 0.8523 (p) cc_final: 0.8252 (t) REVERT: F 119 ARG cc_start: 0.7533 (mmt180) cc_final: 0.7204 (mmm160) REVERT: H 52 GLN cc_start: 0.7928 (mm-40) cc_final: 0.7626 (mm-40) REVERT: I 11 LEU cc_start: 0.7492 (mt) cc_final: 0.7191 (mp) REVERT: J 68 LYS cc_start: 0.8018 (mmtp) cc_final: 0.7330 (ttpt) REVERT: K 45 GLU cc_start: 0.6848 (mt-10) cc_final: 0.6587 (pt0) REVERT: K 132 GLU cc_start: 0.8596 (tp30) cc_final: 0.8084 (tm-30) REVERT: L 28 LYS cc_start: 0.8144 (mttp) cc_final: 0.7904 (mtpp) REVERT: N 90 MET cc_start: 0.4868 (mtm) cc_final: 0.3620 (tpt) REVERT: G 71 MET cc_start: 0.6394 (tmm) cc_final: 0.6043 (mmt) outliers start: 161 outliers final: 112 residues processed: 595 average time/residue: 0.4632 time to fit residues: 445.4251 Evaluate side-chains 562 residues out of total 3693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 442 time to evaluate : 3.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU 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 219 LEU Chi-restraints excluded: chain A residue 234 ASP 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 396 ILE Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain A residue 704 ASP Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 818 THR Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 990 ILE Chi-restraints excluded: chain A residue 1020 GLN Chi-restraints excluded: chain A residue 1022 CYS 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 1162 ASN Chi-restraints excluded: chain A residue 1163 GLU Chi-restraints excluded: chain A residue 1255 CYS Chi-restraints excluded: chain A residue 1498 ILE Chi-restraints excluded: chain A residue 1505 ASP Chi-restraints excluded: chain A residue 1520 VAL Chi-restraints excluded: chain A residue 1521 THR Chi-restraints excluded: chain A residue 1535 PHE Chi-restraints excluded: chain A residue 1543 SER Chi-restraints excluded: chain A residue 1585 ILE 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 20 GLU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 57 ASP Chi-restraints excluded: chain B residue 65 VAL 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 234 ILE Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 255 ASP 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 428 VAL Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 633 THR 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 767 ASN 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 994 ASP Chi-restraints excluded: chain B residue 1046 VAL Chi-restraints excluded: chain B residue 1049 THR Chi-restraints excluded: chain B residue 1094 ASN Chi-restraints excluded: chain B residue 1113 THR Chi-restraints excluded: chain B residue 1161 ASP Chi-restraints excluded: chain B residue 1175 THR Chi-restraints excluded: chain B residue 1196 LEU Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 222 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 21 GLU 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 196 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain H residue 12 VAL 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 50 ILE Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain K residue 62 SER Chi-restraints excluded: chain K residue 69 ASP Chi-restraints excluded: chain L residue 35 SER 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 105 ILE Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 248 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 134 optimal weight: 8.9990 chunk 359 optimal weight: 9.9990 chunk 78 optimal weight: 2.9990 chunk 234 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 399 optimal weight: 1.9990 chunk 331 optimal weight: 6.9990 chunk 185 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 132 optimal weight: 5.9990 chunk 209 optimal weight: 10.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 HIS A 939 ASN ** A1141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1314 GLN ** B 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.4599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 34788 Z= 0.194 Angle : 0.576 13.848 47204 Z= 0.302 Chirality : 0.043 0.218 5274 Planarity : 0.004 0.050 5937 Dihedral : 11.012 73.214 5063 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.97 % Favored : 95.94 % Rotamer: Outliers : 3.22 % Allowed : 15.44 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.13), residues: 4109 helix: -0.43 (0.14), residues: 1252 sheet: -0.59 (0.20), residues: 682 loop : -1.07 (0.13), residues: 2175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 842 HIS 0.006 0.001 HIS A 106 PHE 0.025 0.001 PHE A 239 TYR 0.017 0.001 TYR A 478 ARG 0.007 0.000 ARG G 15 *********************** 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 620 residues out of total 3693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 501 time to evaluate : 3.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ARG cc_start: 0.7781 (ttp-170) cc_final: 0.7398 (mtm180) REVERT: A 348 LYS cc_start: 0.8306 (mttt) cc_final: 0.7927 (tttm) REVERT: A 606 ARG cc_start: 0.8229 (ttt180) cc_final: 0.7902 (ttt90) REVERT: A 683 LYS cc_start: 0.9005 (mtmt) cc_final: 0.8590 (ttmt) REVERT: A 786 TYR cc_start: 0.8263 (p90) cc_final: 0.7920 (p90) REVERT: A 831 ASP cc_start: 0.8965 (p0) cc_final: 0.8724 (p0) REVERT: A 1021 ARG cc_start: 0.8228 (ttp-170) cc_final: 0.7956 (tmt170) REVERT: A 1026 GLN cc_start: 0.8517 (tt0) cc_final: 0.7974 (tp-100) REVERT: A 1060 GLU cc_start: 0.7782 (tm-30) cc_final: 0.7346 (tm-30) REVERT: A 1081 ASN cc_start: 0.7128 (t0) cc_final: 0.6769 (t0) REVERT: A 1100 LYS cc_start: 0.8121 (tptm) cc_final: 0.7601 (ttmt) REVERT: A 1120 TYR cc_start: 0.6630 (p90) cc_final: 0.5552 (p90) REVERT: A 1238 MET cc_start: 0.8061 (mtp) cc_final: 0.7504 (ttm) REVERT: A 1255 CYS cc_start: 0.6321 (OUTLIER) cc_final: 0.5869 (t) REVERT: A 1572 ARG cc_start: 0.8431 (ttm-80) cc_final: 0.7607 (tpm170) REVERT: A 1624 LYS cc_start: 0.8644 (mttt) cc_final: 0.8099 (mmmt) REVERT: B 20 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7374 (tt0) REVERT: B 164 MET cc_start: 0.8151 (ttt) cc_final: 0.7920 (ttt) REVERT: B 185 GLU cc_start: 0.8645 (mp0) cc_final: 0.8139 (mp0) REVERT: B 314 LYS cc_start: 0.6409 (mttt) cc_final: 0.5962 (mtpp) REVERT: B 316 ARG cc_start: 0.7829 (mmm160) cc_final: 0.6862 (ttm170) REVERT: B 348 GLU cc_start: 0.8324 (tp30) cc_final: 0.8027 (mt-10) REVERT: B 446 MET cc_start: 0.7573 (tmm) cc_final: 0.7158 (tmm) REVERT: B 448 ARG cc_start: 0.7040 (ttm110) cc_final: 0.6641 (mtt180) REVERT: B 493 PHE cc_start: 0.7581 (t80) cc_final: 0.7315 (t80) REVERT: B 517 VAL cc_start: 0.9126 (m) cc_final: 0.8878 (t) REVERT: B 602 LYS cc_start: 0.8641 (tttt) cc_final: 0.8288 (tptt) REVERT: B 623 ASP cc_start: 0.8307 (p0) cc_final: 0.7687 (m-30) REVERT: B 661 GLU cc_start: 0.7312 (tt0) cc_final: 0.6663 (mp0) REVERT: B 847 TYR cc_start: 0.7936 (m-80) cc_final: 0.7660 (m-10) REVERT: B 944 GLN cc_start: 0.8914 (OUTLIER) cc_final: 0.7929 (mt0) REVERT: B 998 GLU cc_start: 0.8499 (tt0) cc_final: 0.8252 (tm-30) REVERT: B 1013 MET cc_start: 0.8536 (mtp) cc_final: 0.8273 (mtp) REVERT: B 1094 ASN cc_start: 0.8737 (OUTLIER) cc_final: 0.8411 (m110) REVERT: B 1115 GLN cc_start: 0.8600 (mm-40) cc_final: 0.8068 (tm-30) REVERT: C 168 LYS cc_start: 0.7996 (mmtt) cc_final: 0.7419 (mtpt) REVERT: C 295 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7822 (mmt90) REVERT: C 308 MET cc_start: 0.7203 (mtp) cc_final: 0.6638 (mtm) REVERT: C 312 GLU cc_start: 0.8038 (tt0) cc_final: 0.7449 (tm-30) REVERT: E 81 GLU cc_start: 0.7109 (tp30) cc_final: 0.6642 (mm-30) REVERT: E 155 ARG cc_start: 0.8369 (ttp80) cc_final: 0.8072 (ttp-170) REVERT: E 159 ASP cc_start: 0.7768 (t0) cc_final: 0.7424 (t70) REVERT: E 196 VAL cc_start: 0.9106 (OUTLIER) cc_final: 0.8896 (m) REVERT: F 61 HIS cc_start: 0.7038 (t-90) cc_final: 0.6302 (t-90) REVERT: F 109 VAL cc_start: 0.8443 (p) cc_final: 0.8172 (t) REVERT: F 119 ARG cc_start: 0.7450 (mmt180) cc_final: 0.7090 (mmm160) REVERT: H 41 ASP cc_start: 0.8100 (m-30) cc_final: 0.7862 (m-30) REVERT: I 11 LEU cc_start: 0.7365 (mt) cc_final: 0.7033 (mp) REVERT: J 39 LEU cc_start: 0.9058 (mt) cc_final: 0.8797 (mp) REVERT: J 68 LYS cc_start: 0.8063 (mmtp) cc_final: 0.7369 (ttpt) REVERT: K 45 GLU cc_start: 0.6911 (mt-10) cc_final: 0.6568 (pt0) REVERT: K 82 LYS cc_start: 0.8625 (mmtp) cc_final: 0.8111 (mttt) REVERT: K 132 GLU cc_start: 0.8557 (tp30) cc_final: 0.8017 (tm-30) REVERT: K 133 SER cc_start: 0.8875 (t) cc_final: 0.8674 (t) REVERT: L 28 LYS cc_start: 0.8055 (mttp) cc_final: 0.7784 (mtpp) REVERT: M 18 GLN cc_start: 0.4178 (OUTLIER) cc_final: 0.2321 (tt0) REVERT: N 90 MET cc_start: 0.4642 (mtm) cc_final: 0.3494 (tpt) REVERT: D 15 THR cc_start: 0.7655 (OUTLIER) cc_final: 0.7243 (m) REVERT: G 71 MET cc_start: 0.6666 (tmm) cc_final: 0.6248 (mmt) outliers start: 119 outliers final: 90 residues processed: 589 average time/residue: 0.4734 time to fit residues: 451.8324 Evaluate side-chains 570 residues out of total 3693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 472 time to evaluate : 3.576 ------------------------------------------------------------------------------- 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 234 ASP 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 423 LEU Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 822 THR Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 1020 GLN Chi-restraints excluded: chain A residue 1063 MET Chi-restraints excluded: chain A residue 1077 LEU Chi-restraints excluded: chain A residue 1162 ASN Chi-restraints excluded: chain A residue 1163 GLU Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1255 CYS Chi-restraints excluded: chain A residue 1498 ILE Chi-restraints excluded: chain A residue 1505 ASP 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 1585 ILE 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 20 GLU Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 57 ASP 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 302 LEU Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 687 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 994 ASP Chi-restraints excluded: chain B residue 1041 ASN Chi-restraints excluded: chain B residue 1088 LEU Chi-restraints excluded: chain B residue 1094 ASN Chi-restraints excluded: chain B residue 1113 THR Chi-restraints excluded: chain B residue 1196 LEU Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 295 ARG Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 115 ASN Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain H residue 12 VAL 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 H residue 131 ASN 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 57 ASP Chi-restraints excluded: chain K residue 62 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 M residue 57 ASN Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain N residue 89 ILE Chi-restraints excluded: chain N residue 153 VAL Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain D residue 29 GLN Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 248 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 385 optimal weight: 20.0000 chunk 45 optimal weight: 1.9990 chunk 227 optimal weight: 6.9990 chunk 291 optimal weight: 0.1980 chunk 226 optimal weight: 7.9990 chunk 336 optimal weight: 2.9990 chunk 223 optimal weight: 10.0000 chunk 398 optimal weight: 0.5980 chunk 249 optimal weight: 4.9990 chunk 242 optimal weight: 9.9990 chunk 183 optimal weight: 10.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 598 HIS ** B 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 128 ASN G 64 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.4826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 34788 Z= 0.190 Angle : 0.558 15.832 47204 Z= 0.289 Chirality : 0.043 0.209 5274 Planarity : 0.004 0.054 5937 Dihedral : 10.812 73.480 5063 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.77 % Favored : 95.13 % Rotamer: Outliers : 3.20 % Allowed : 15.95 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.13), residues: 4109 helix: -0.08 (0.15), residues: 1251 sheet: -0.47 (0.20), residues: 684 loop : -0.96 (0.13), residues: 2174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 13 HIS 0.008 0.001 HIS G 65 PHE 0.023 0.001 PHE A 239 TYR 0.016 0.001 TYR A 478 ARG 0.008 0.000 ARG B 429 *********************** 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 626 residues out of total 3693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 508 time to evaluate : 3.755 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 186 SER cc_start: 0.7375 (m) cc_final: 0.6953 (t) REVERT: A 348 LYS cc_start: 0.8149 (mttt) cc_final: 0.7797 (tttm) REVERT: A 424 MET cc_start: 0.7986 (mmm) cc_final: 0.7731 (mmm) REVERT: A 606 ARG cc_start: 0.8238 (ttt180) cc_final: 0.7931 (ttt90) REVERT: A 683 LYS cc_start: 0.8992 (mtmt) cc_final: 0.8592 (ttmt) REVERT: A 786 TYR cc_start: 0.8194 (p90) cc_final: 0.7825 (p90) REVERT: A 831 ASP cc_start: 0.8928 (p0) cc_final: 0.8692 (p0) REVERT: A 1021 ARG cc_start: 0.8198 (ttp-170) cc_final: 0.7926 (tmt170) REVERT: A 1026 GLN cc_start: 0.8367 (tt0) cc_final: 0.7828 (tp-100) REVERT: A 1060 GLU cc_start: 0.7773 (tm-30) cc_final: 0.7358 (tm-30) REVERT: A 1081 ASN cc_start: 0.7162 (t0) cc_final: 0.6756 (t0) REVERT: A 1100 LYS cc_start: 0.8080 (tptm) cc_final: 0.7449 (ttmt) REVERT: A 1106 LYS cc_start: 0.7738 (mttm) cc_final: 0.7507 (ttmm) REVERT: A 1238 MET cc_start: 0.8005 (mtp) cc_final: 0.7496 (ttm) REVERT: A 1255 CYS cc_start: 0.6308 (OUTLIER) cc_final: 0.5924 (t) REVERT: A 1535 PHE cc_start: 0.7325 (OUTLIER) cc_final: 0.6378 (m-80) REVERT: A 1565 GLU cc_start: 0.8071 (tp30) cc_final: 0.7735 (tp30) REVERT: A 1572 ARG cc_start: 0.8407 (ttm-80) cc_final: 0.7580 (tpm170) REVERT: A 1624 LYS cc_start: 0.8597 (mttt) cc_final: 0.8032 (mmmt) REVERT: B 20 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7386 (tt0) REVERT: B 164 MET cc_start: 0.8098 (ttt) cc_final: 0.7873 (ttt) REVERT: B 185 GLU cc_start: 0.8632 (mp0) cc_final: 0.8081 (mp0) REVERT: B 215 MET cc_start: 0.8335 (ptm) cc_final: 0.8069 (ptt) REVERT: B 314 LYS cc_start: 0.6485 (mttt) cc_final: 0.6106 (mtpp) REVERT: B 316 ARG cc_start: 0.7748 (mmm160) cc_final: 0.6867 (ttm170) REVERT: B 348 GLU cc_start: 0.8284 (tp30) cc_final: 0.7997 (mt-10) REVERT: B 446 MET cc_start: 0.7578 (tmm) cc_final: 0.7137 (tmm) REVERT: B 493 PHE cc_start: 0.7600 (t80) cc_final: 0.7245 (t80) REVERT: B 517 VAL cc_start: 0.9126 (m) cc_final: 0.8854 (t) REVERT: B 602 LYS cc_start: 0.8531 (tttt) cc_final: 0.8180 (tptt) REVERT: B 623 ASP cc_start: 0.8279 (p0) cc_final: 0.7705 (m-30) REVERT: B 661 GLU cc_start: 0.7304 (tt0) cc_final: 0.6688 (mp0) REVERT: B 847 TYR cc_start: 0.7951 (m-80) cc_final: 0.7690 (m-10) REVERT: B 944 GLN cc_start: 0.8917 (OUTLIER) cc_final: 0.7922 (mt0) REVERT: B 998 GLU cc_start: 0.8455 (tt0) cc_final: 0.8240 (tm-30) REVERT: B 1094 ASN cc_start: 0.8650 (OUTLIER) cc_final: 0.8236 (m110) REVERT: C 168 LYS cc_start: 0.7945 (mmtt) cc_final: 0.7375 (mtpt) REVERT: C 201 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8100 (pm20) REVERT: C 223 SER cc_start: 0.8057 (m) cc_final: 0.7755 (p) REVERT: C 308 MET cc_start: 0.7175 (mtp) cc_final: 0.5857 (mtm) REVERT: C 312 GLU cc_start: 0.7991 (tt0) cc_final: 0.7545 (tm-30) REVERT: E 81 GLU cc_start: 0.7197 (tp30) cc_final: 0.6699 (mm-30) REVERT: E 155 ARG cc_start: 0.8351 (ttp80) cc_final: 0.8063 (ttp-170) REVERT: E 159 ASP cc_start: 0.7709 (t0) cc_final: 0.7418 (t70) REVERT: E 187 TYR cc_start: 0.8267 (t80) cc_final: 0.7729 (t80) REVERT: E 196 VAL cc_start: 0.9065 (OUTLIER) cc_final: 0.8863 (m) REVERT: F 61 HIS cc_start: 0.6915 (t-90) cc_final: 0.6243 (t-90) REVERT: F 109 VAL cc_start: 0.8393 (p) cc_final: 0.8065 (t) REVERT: F 119 ARG cc_start: 0.7572 (mmt180) cc_final: 0.7353 (tpp-160) REVERT: H 41 ASP cc_start: 0.8098 (m-30) cc_final: 0.7862 (m-30) REVERT: I 11 LEU cc_start: 0.7280 (mt) cc_final: 0.6958 (mp) REVERT: J 36 LEU cc_start: 0.9264 (mt) cc_final: 0.8981 (mm) REVERT: J 39 LEU cc_start: 0.9045 (mt) cc_final: 0.8792 (mp) REVERT: J 68 LYS cc_start: 0.8053 (mmtp) cc_final: 0.7337 (ttpt) REVERT: K 45 GLU cc_start: 0.6897 (mt-10) cc_final: 0.6592 (pt0) REVERT: K 82 LYS cc_start: 0.8631 (mmtp) cc_final: 0.8104 (mttt) REVERT: K 132 GLU cc_start: 0.8533 (tp30) cc_final: 0.8029 (tm-30) REVERT: L 28 LYS cc_start: 0.8090 (mttp) cc_final: 0.7782 (mtpp) REVERT: N 90 MET cc_start: 0.4512 (mtm) cc_final: 0.3416 (tpt) REVERT: G 18 LYS cc_start: 0.5752 (OUTLIER) cc_final: 0.5273 (mmmt) REVERT: G 71 MET cc_start: 0.6629 (tmm) cc_final: 0.6304 (mmt) outliers start: 118 outliers final: 91 residues processed: 592 average time/residue: 0.4965 time to fit residues: 478.2781 Evaluate side-chains 580 residues out of total 3693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 481 time to evaluate : 3.846 ------------------------------------------------------------------------------- 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 234 ASP 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 423 LEU Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 704 ASP Chi-restraints excluded: chain A residue 713 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 896 THR Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 990 ILE Chi-restraints excluded: chain A residue 1020 GLN Chi-restraints excluded: chain A residue 1063 MET Chi-restraints excluded: chain A residue 1136 VAL Chi-restraints excluded: chain A residue 1163 GLU Chi-restraints excluded: chain A residue 1255 CYS Chi-restraints excluded: chain A residue 1498 ILE Chi-restraints excluded: chain A residue 1505 ASP Chi-restraints excluded: chain A residue 1520 VAL Chi-restraints excluded: chain A residue 1521 THR Chi-restraints excluded: chain A residue 1535 PHE Chi-restraints excluded: chain A residue 1543 SER Chi-restraints excluded: chain A residue 1585 ILE Chi-restraints excluded: chain A residue 1607 THR Chi-restraints excluded: chain A residue 1617 THR Chi-restraints excluded: chain B residue 20 GLU Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 57 ASP 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 255 ASP Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 377 MET Chi-restraints excluded: chain B residue 687 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 1089 GLN Chi-restraints excluded: chain B residue 1094 ASN Chi-restraints excluded: chain B residue 1113 THR Chi-restraints excluded: chain B residue 1160 GLU Chi-restraints excluded: chain B residue 1196 LEU Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 201 GLU 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 21 GLU Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 88 VAL 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 196 VAL Chi-restraints excluded: chain F residue 59 GLN Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain H residue 12 VAL 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 K residue 57 ASP Chi-restraints excluded: chain K residue 62 SER 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 57 ASN Chi-restraints excluded: chain M residue 66 THR 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 18 LYS Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 248 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 246 optimal weight: 4.9990 chunk 158 optimal weight: 7.9990 chunk 237 optimal weight: 5.9990 chunk 119 optimal weight: 20.0000 chunk 78 optimal weight: 9.9990 chunk 77 optimal weight: 0.1980 chunk 253 optimal weight: 9.9990 chunk 271 optimal weight: 20.0000 chunk 196 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 312 optimal weight: 9.9990 overall best weight: 4.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 840 ASN ** A1141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1115 GLN ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 GLN M 18 GLN G 119 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.5023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 34788 Z= 0.327 Angle : 0.635 15.339 47204 Z= 0.329 Chirality : 0.045 0.211 5274 Planarity : 0.005 0.058 5937 Dihedral : 10.954 73.079 5063 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.60 % Favored : 94.35 % Rotamer: Outliers : 3.74 % Allowed : 16.25 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.13), residues: 4109 helix: -0.25 (0.14), residues: 1249 sheet: -0.48 (0.20), residues: 678 loop : -1.11 (0.13), residues: 2182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 79 HIS 0.008 0.001 HIS A 603 PHE 0.022 0.002 PHE A 467 TYR 0.020 0.002 TYR B1098 ARG 0.013 0.001 ARG A1176 *********************** 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 623 residues out of total 3693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 485 time to evaluate : 3.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8173 (tt) REVERT: A 348 LYS cc_start: 0.8297 (mttt) cc_final: 0.7899 (tttm) REVERT: A 606 ARG cc_start: 0.8211 (ttt180) cc_final: 0.7889 (ttt90) REVERT: A 683 LYS cc_start: 0.9027 (mtmt) cc_final: 0.8594 (ttmt) REVERT: A 786 TYR cc_start: 0.8295 (p90) cc_final: 0.7920 (p90) REVERT: A 831 ASP cc_start: 0.9022 (p0) cc_final: 0.8752 (p0) REVERT: A 1021 ARG cc_start: 0.8313 (ttp-170) cc_final: 0.8053 (tmt170) REVERT: A 1026 GLN cc_start: 0.8466 (tt0) cc_final: 0.7935 (tp-100) REVERT: A 1060 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7341 (tm-30) REVERT: A 1081 ASN cc_start: 0.7510 (t0) cc_final: 0.7055 (t0) REVERT: A 1120 TYR cc_start: 0.6721 (p90) cc_final: 0.5761 (p90) REVERT: A 1163 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.6843 (pp20) REVERT: A 1238 MET cc_start: 0.8104 (mtp) cc_final: 0.7554 (ttm) REVERT: A 1255 CYS cc_start: 0.6210 (OUTLIER) cc_final: 0.5817 (t) REVERT: A 1535 PHE cc_start: 0.7355 (OUTLIER) cc_final: 0.6366 (m-80) REVERT: A 1572 ARG cc_start: 0.8385 (ttm-80) cc_final: 0.7554 (tpm170) REVERT: A 1624 LYS cc_start: 0.8683 (mttt) cc_final: 0.8157 (mmmt) REVERT: B 20 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7451 (tt0) REVERT: B 35 PHE cc_start: 0.8926 (m-80) cc_final: 0.8680 (m-80) REVERT: B 164 MET cc_start: 0.8238 (ttt) cc_final: 0.8007 (ttt) REVERT: B 185 GLU cc_start: 0.8655 (mp0) cc_final: 0.7999 (mp0) REVERT: B 314 LYS cc_start: 0.6484 (mttt) cc_final: 0.6242 (mtpp) REVERT: B 316 ARG cc_start: 0.7874 (mmm160) cc_final: 0.6941 (ttm170) REVERT: B 348 GLU cc_start: 0.8375 (tp30) cc_final: 0.8098 (mt-10) REVERT: B 392 ASP cc_start: 0.6584 (m-30) cc_final: 0.6293 (m-30) REVERT: B 432 ILE cc_start: 0.7656 (tt) cc_final: 0.7431 (pt) REVERT: B 446 MET cc_start: 0.7796 (tmm) cc_final: 0.7317 (tmm) REVERT: B 493 PHE cc_start: 0.7649 (t80) cc_final: 0.7263 (t80) REVERT: B 517 VAL cc_start: 0.9080 (m) cc_final: 0.8862 (t) REVERT: B 588 ILE cc_start: 0.8695 (mt) cc_final: 0.8483 (pt) REVERT: B 602 LYS cc_start: 0.8673 (tttt) cc_final: 0.8321 (tptt) REVERT: B 623 ASP cc_start: 0.8379 (p0) cc_final: 0.7848 (m-30) REVERT: B 661 GLU cc_start: 0.7496 (tt0) cc_final: 0.6763 (mp0) REVERT: B 847 TYR cc_start: 0.7976 (m-80) cc_final: 0.7720 (m-10) REVERT: B 899 GLN cc_start: 0.7206 (OUTLIER) cc_final: 0.5602 (mp10) REVERT: B 944 GLN cc_start: 0.8901 (OUTLIER) cc_final: 0.7930 (mt0) REVERT: B 998 GLU cc_start: 0.8487 (tt0) cc_final: 0.8230 (tm-30) REVERT: B 1014 TYR cc_start: 0.8810 (m-80) cc_final: 0.8261 (m-80) REVERT: B 1094 ASN cc_start: 0.8782 (OUTLIER) cc_final: 0.8409 (m110) REVERT: C 168 LYS cc_start: 0.8057 (mmtt) cc_final: 0.7453 (mtpt) REVERT: C 256 ILE cc_start: 0.8498 (mm) cc_final: 0.8289 (mm) REVERT: C 295 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.7781 (mmt90) REVERT: C 308 MET cc_start: 0.7337 (mtp) cc_final: 0.5903 (mtm) REVERT: C 312 GLU cc_start: 0.8093 (tt0) cc_final: 0.7600 (tm-30) REVERT: E 57 MET cc_start: 0.6887 (OUTLIER) cc_final: 0.6236 (tmm) REVERT: E 81 GLU cc_start: 0.7152 (tp30) cc_final: 0.6575 (mm-30) REVERT: E 155 ARG cc_start: 0.8458 (ttp80) cc_final: 0.8156 (ttp-170) REVERT: E 159 ASP cc_start: 0.7798 (t0) cc_final: 0.7446 (t70) REVERT: E 187 TYR cc_start: 0.8172 (t80) cc_final: 0.7679 (t80) REVERT: E 196 VAL cc_start: 0.9099 (OUTLIER) cc_final: 0.8895 (m) REVERT: F 61 HIS cc_start: 0.6724 (t-90) cc_final: 0.6044 (t-90) REVERT: F 103 MET cc_start: 0.8446 (OUTLIER) cc_final: 0.8139 (ttt) REVERT: F 109 VAL cc_start: 0.8638 (p) cc_final: 0.8141 (m) REVERT: F 119 ARG cc_start: 0.7649 (mmt180) cc_final: 0.7309 (mmm160) REVERT: H 41 ASP cc_start: 0.8201 (m-30) cc_final: 0.7921 (m-30) REVERT: I 11 LEU cc_start: 0.7389 (mt) cc_final: 0.7085 (mp) REVERT: J 36 LEU cc_start: 0.9289 (mt) cc_final: 0.9017 (mm) REVERT: J 68 LYS cc_start: 0.8183 (mmtp) cc_final: 0.7406 (ttpt) REVERT: K 45 GLU cc_start: 0.6969 (mt-10) cc_final: 0.6670 (pt0) REVERT: K 132 GLU cc_start: 0.8535 (tp30) cc_final: 0.8070 (tm-30) REVERT: L 28 LYS cc_start: 0.8121 (mttp) cc_final: 0.7811 (mtpp) REVERT: N 90 MET cc_start: 0.4625 (mtm) cc_final: 0.3558 (tpt) REVERT: D 15 THR cc_start: 0.8441 (OUTLIER) cc_final: 0.8121 (m) REVERT: G 18 LYS cc_start: 0.5790 (OUTLIER) cc_final: 0.5360 (mmmt) outliers start: 138 outliers final: 107 residues processed: 578 average time/residue: 0.4646 time to fit residues: 436.0809 Evaluate side-chains 581 residues out of total 3693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 460 time to evaluate : 3.740 ------------------------------------------------------------------------------- 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 98 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 234 ASP 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 423 LEU Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 704 ASP Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 822 THR Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 853 THR Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 990 ILE Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1020 GLN Chi-restraints excluded: chain A residue 1063 MET Chi-restraints excluded: chain A residue 1162 ASN Chi-restraints excluded: chain A residue 1163 GLU Chi-restraints excluded: chain A residue 1255 CYS Chi-restraints excluded: chain A residue 1498 ILE Chi-restraints excluded: chain A residue 1505 ASP Chi-restraints excluded: chain A residue 1520 VAL Chi-restraints excluded: chain A residue 1521 THR Chi-restraints excluded: chain A residue 1535 PHE Chi-restraints excluded: chain A residue 1543 SER Chi-restraints excluded: chain A residue 1585 ILE Chi-restraints excluded: chain A residue 1607 THR Chi-restraints excluded: chain A residue 1617 THR Chi-restraints excluded: chain B residue 20 GLU Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 57 ASP 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 234 ILE Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 265 ARG Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 377 MET Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 866 LEU Chi-restraints excluded: chain B residue 899 GLN 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 977 ILE Chi-restraints excluded: chain B residue 1094 ASN Chi-restraints excluded: chain B residue 1113 THR Chi-restraints excluded: chain B residue 1160 GLU Chi-restraints excluded: chain B residue 1196 LEU Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 295 ARG Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 57 MET Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 88 VAL 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 196 VAL Chi-restraints excluded: chain F residue 59 GLN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain H residue 12 VAL 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 50 ILE Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain K residue 69 ASP 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 57 ASN Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain N residue 89 ILE Chi-restraints excluded: chain N residue 153 VAL Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain D residue 29 GLN Chi-restraints excluded: chain G residue 18 LYS Chi-restraints excluded: chain G residue 105 ILE Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 119 HIS Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain G residue 248 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 362 optimal weight: 30.0000 chunk 381 optimal weight: 20.0000 chunk 347 optimal weight: 0.5980 chunk 370 optimal weight: 30.0000 chunk 223 optimal weight: 1.9990 chunk 161 optimal weight: 3.9990 chunk 291 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 chunk 335 optimal weight: 10.0000 chunk 350 optimal weight: 2.9990 chunk 369 optimal weight: 10.0000 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 886 ASN ** A1141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 598 HIS ** B 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.5120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 34788 Z= 0.208 Angle : 0.573 16.366 47204 Z= 0.297 Chirality : 0.043 0.228 5274 Planarity : 0.004 0.055 5937 Dihedral : 10.820 73.173 5063 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.60 % Favored : 95.35 % Rotamer: Outliers : 3.39 % Allowed : 16.93 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.13), residues: 4109 helix: -0.02 (0.15), residues: 1254 sheet: -0.47 (0.20), residues: 684 loop : -1.01 (0.13), residues: 2171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 79 HIS 0.020 0.001 HIS G 119 PHE 0.020 0.001 PHE A 239 TYR 0.019 0.001 TYR B 778 ARG 0.013 0.000 ARG A1176 *********************** 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 601 residues out of total 3693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 476 time to evaluate : 3.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 SER cc_start: 0.7370 (m) cc_final: 0.6940 (t) REVERT: A 348 LYS cc_start: 0.8172 (mttt) cc_final: 0.7823 (tttm) REVERT: A 606 ARG cc_start: 0.8249 (ttt180) cc_final: 0.7922 (ttt90) REVERT: A 683 LYS cc_start: 0.9000 (mtmt) cc_final: 0.8612 (ttmt) REVERT: A 786 TYR cc_start: 0.8254 (p90) cc_final: 0.7879 (p90) REVERT: A 831 ASP cc_start: 0.9049 (p0) cc_final: 0.8732 (p0) REVERT: A 1026 GLN cc_start: 0.8387 (tt0) cc_final: 0.7864 (tp-100) REVERT: A 1060 GLU cc_start: 0.7796 (tm-30) cc_final: 0.7315 (tm-30) REVERT: A 1081 ASN cc_start: 0.7471 (t0) cc_final: 0.7045 (t0) REVERT: A 1163 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.6761 (pp20) REVERT: A 1238 MET cc_start: 0.7995 (mtp) cc_final: 0.7533 (ttm) REVERT: A 1255 CYS cc_start: 0.6472 (OUTLIER) cc_final: 0.6066 (t) REVERT: A 1535 PHE cc_start: 0.7367 (OUTLIER) cc_final: 0.6380 (m-80) REVERT: A 1572 ARG cc_start: 0.8390 (ttm-80) cc_final: 0.7274 (tpm170) REVERT: A 1624 LYS cc_start: 0.8632 (mttt) cc_final: 0.8121 (mmmt) REVERT: B 20 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7411 (tt0) REVERT: B 35 PHE cc_start: 0.8892 (m-80) cc_final: 0.8638 (m-80) REVERT: B 185 GLU cc_start: 0.8591 (mp0) cc_final: 0.7981 (mp0) REVERT: B 215 MET cc_start: 0.8222 (ptt) cc_final: 0.7882 (ptt) REVERT: B 316 ARG cc_start: 0.7700 (mmm160) cc_final: 0.6836 (ttm170) REVERT: B 348 GLU cc_start: 0.8360 (tp30) cc_final: 0.8072 (mt-10) REVERT: B 392 ASP cc_start: 0.6651 (m-30) cc_final: 0.6289 (m-30) REVERT: B 429 ARG cc_start: 0.7998 (ttm-80) cc_final: 0.7794 (mmm-85) REVERT: B 432 ILE cc_start: 0.7600 (OUTLIER) cc_final: 0.7364 (pt) REVERT: B 446 MET cc_start: 0.7710 (tmm) cc_final: 0.7218 (tmm) REVERT: B 493 PHE cc_start: 0.7587 (t80) cc_final: 0.7221 (t80) REVERT: B 517 VAL cc_start: 0.9066 (m) cc_final: 0.8839 (t) REVERT: B 602 LYS cc_start: 0.8572 (tttt) cc_final: 0.8220 (tptt) REVERT: B 623 ASP cc_start: 0.8320 (p0) cc_final: 0.7781 (m-30) REVERT: B 661 GLU cc_start: 0.7466 (tt0) cc_final: 0.6733 (mp0) REVERT: B 680 GLU cc_start: 0.8541 (mt-10) cc_final: 0.6767 (tm-30) REVERT: B 847 TYR cc_start: 0.7918 (m-80) cc_final: 0.7618 (m-10) REVERT: B 899 GLN cc_start: 0.7204 (OUTLIER) cc_final: 0.5578 (mp10) REVERT: B 944 GLN cc_start: 0.8925 (OUTLIER) cc_final: 0.7947 (mt0) REVERT: B 998 GLU cc_start: 0.8457 (tt0) cc_final: 0.8202 (tm-30) REVERT: B 1014 TYR cc_start: 0.8784 (m-80) cc_final: 0.8259 (m-80) REVERT: B 1094 ASN cc_start: 0.8743 (OUTLIER) cc_final: 0.8393 (m110) REVERT: C 168 LYS cc_start: 0.8002 (mmtt) cc_final: 0.7425 (mtpt) REVERT: C 295 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7789 (mmt90) REVERT: C 308 MET cc_start: 0.7240 (mtp) cc_final: 0.5994 (mtm) REVERT: C 312 GLU cc_start: 0.8001 (tt0) cc_final: 0.7558 (tm-30) REVERT: E 57 MET cc_start: 0.6803 (OUTLIER) cc_final: 0.6179 (tmm) REVERT: E 81 GLU cc_start: 0.7163 (tp30) cc_final: 0.6595 (mm-30) REVERT: E 155 ARG cc_start: 0.8375 (ttp80) cc_final: 0.8093 (ttp-170) REVERT: E 159 ASP cc_start: 0.7726 (t0) cc_final: 0.7374 (t70) REVERT: E 187 TYR cc_start: 0.8153 (t80) cc_final: 0.7659 (t80) REVERT: E 196 VAL cc_start: 0.9074 (OUTLIER) cc_final: 0.8862 (m) REVERT: F 65 ARG cc_start: 0.6034 (ttp-170) cc_final: 0.5656 (ttp-110) REVERT: F 103 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.8149 (ttt) REVERT: F 109 VAL cc_start: 0.8637 (p) cc_final: 0.8329 (t) REVERT: F 119 ARG cc_start: 0.7567 (mmt180) cc_final: 0.7023 (mtp85) REVERT: I 11 LEU cc_start: 0.7306 (mt) cc_final: 0.6962 (mp) REVERT: J 36 LEU cc_start: 0.9271 (mt) cc_final: 0.9008 (mm) REVERT: J 68 LYS cc_start: 0.8198 (mmtp) cc_final: 0.7415 (ttpt) REVERT: K 45 GLU cc_start: 0.6930 (mt-10) cc_final: 0.6616 (pt0) REVERT: K 82 LYS cc_start: 0.8686 (mmtp) cc_final: 0.8241 (mptt) REVERT: K 132 GLU cc_start: 0.8534 (tp30) cc_final: 0.8077 (tm-30) REVERT: L 28 LYS cc_start: 0.8106 (mttp) cc_final: 0.7790 (mtpp) REVERT: N 90 MET cc_start: 0.4610 (mtm) cc_final: 0.3570 (tpt) REVERT: D 15 THR cc_start: 0.8525 (OUTLIER) cc_final: 0.8296 (m) REVERT: G 18 LYS cc_start: 0.5785 (OUTLIER) cc_final: 0.5270 (mmmt) outliers start: 125 outliers final: 99 residues processed: 564 average time/residue: 0.4606 time to fit residues: 423.0948 Evaluate side-chains 576 residues out of total 3693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 463 time to evaluate : 3.802 ------------------------------------------------------------------------------- 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 212 VAL Chi-restraints excluded: chain A residue 234 ASP 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 423 LEU Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 704 ASP Chi-restraints excluded: chain A residue 713 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 941 SER Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 990 ILE Chi-restraints excluded: chain A residue 1020 GLN Chi-restraints excluded: chain A residue 1063 MET Chi-restraints excluded: chain A residue 1142 ASP Chi-restraints excluded: chain A residue 1162 ASN Chi-restraints excluded: chain A residue 1163 GLU Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1255 CYS Chi-restraints excluded: chain A residue 1498 ILE Chi-restraints excluded: chain A residue 1505 ASP Chi-restraints excluded: chain A residue 1520 VAL Chi-restraints excluded: chain A residue 1521 THR Chi-restraints excluded: chain A residue 1535 PHE Chi-restraints excluded: chain A residue 1543 SER Chi-restraints excluded: chain A residue 1585 ILE 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 20 GLU Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 57 ASP 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 255 ASP Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 377 MET Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 689 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 944 GLN Chi-restraints excluded: chain B residue 946 ASP Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain B residue 1089 GLN Chi-restraints excluded: chain B residue 1094 ASN 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 47 LEU Chi-restraints excluded: chain C residue 51 GLU Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 151 THR Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 295 ARG Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 57 MET Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 88 VAL 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 196 VAL Chi-restraints excluded: chain F residue 59 GLN Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain H residue 12 VAL 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 H residue 131 ASN 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 52 THR Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 57 ASP 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 66 THR Chi-restraints excluded: chain N residue 89 ILE Chi-restraints excluded: chain N residue 153 VAL Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain G residue 18 LYS Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 169 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 243 optimal weight: 0.2980 chunk 392 optimal weight: 7.9990 chunk 239 optimal weight: 7.9990 chunk 186 optimal weight: 4.9990 chunk 272 optimal weight: 0.7980 chunk 411 optimal weight: 20.0000 chunk 378 optimal weight: 30.0000 chunk 327 optimal weight: 8.9990 chunk 34 optimal weight: 9.9990 chunk 253 optimal weight: 9.9990 chunk 200 optimal weight: 0.0370 overall best weight: 2.8262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 598 HIS ** B 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 GLN G 144 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.5231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 34788 Z= 0.224 Angle : 0.574 16.176 47204 Z= 0.296 Chirality : 0.043 0.234 5274 Planarity : 0.004 0.058 5937 Dihedral : 10.766 73.142 5063 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.23 % Favored : 94.72 % Rotamer: Outliers : 3.25 % Allowed : 17.04 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.13), residues: 4109 helix: 0.06 (0.15), residues: 1248 sheet: -0.45 (0.20), residues: 691 loop : -1.01 (0.13), residues: 2170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 79 HIS 0.014 0.001 HIS C 216 PHE 0.019 0.001 PHE A 239 TYR 0.018 0.001 TYR B 778 ARG 0.013 0.000 ARG A1176 ********************** 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 589 residues out of total 3693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 469 time to evaluate : 3.659 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 98 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8135 (tt) REVERT: A 186 SER cc_start: 0.7347 (m) cc_final: 0.6928 (t) REVERT: A 348 LYS cc_start: 0.8136 (mttt) cc_final: 0.7782 (tttm) REVERT: A 606 ARG cc_start: 0.8216 (ttt180) cc_final: 0.7897 (ttt90) REVERT: A 683 LYS cc_start: 0.8991 (mtmt) cc_final: 0.8621 (ttmt) REVERT: A 786 TYR cc_start: 0.8270 (p90) cc_final: 0.7873 (p90) REVERT: A 831 ASP cc_start: 0.9073 (p0) cc_final: 0.8864 (p0) REVERT: A 1026 GLN cc_start: 0.8370 (tt0) cc_final: 0.7843 (tp-100) REVERT: A 1060 GLU cc_start: 0.7794 (tm-30) cc_final: 0.7309 (tm-30) REVERT: A 1081 ASN cc_start: 0.7405 (t0) cc_final: 0.6984 (t0) REVERT: A 1238 MET cc_start: 0.8005 (mtp) cc_final: 0.7516 (ttm) REVERT: A 1255 CYS cc_start: 0.6305 (OUTLIER) cc_final: 0.5907 (t) REVERT: A 1295 ARG cc_start: 0.6848 (mmt180) cc_final: 0.6564 (mmm160) REVERT: A 1535 PHE cc_start: 0.7257 (OUTLIER) cc_final: 0.6203 (m-80) REVERT: A 1565 GLU cc_start: 0.8095 (tp30) cc_final: 0.7768 (tp30) REVERT: A 1572 ARG cc_start: 0.8449 (ttm-80) cc_final: 0.7319 (tpm170) REVERT: A 1624 LYS cc_start: 0.8632 (mttt) cc_final: 0.8108 (mmmt) REVERT: B 185 GLU cc_start: 0.8593 (mp0) cc_final: 0.7977 (mp0) REVERT: B 215 MET cc_start: 0.8169 (ptt) cc_final: 0.7876 (ptt) REVERT: B 316 ARG cc_start: 0.7743 (mmm160) cc_final: 0.7511 (tpt90) REVERT: B 348 GLU cc_start: 0.8360 (tp30) cc_final: 0.8066 (mt-10) REVERT: B 392 ASP cc_start: 0.6601 (m-30) cc_final: 0.6264 (m-30) REVERT: B 432 ILE cc_start: 0.7566 (OUTLIER) cc_final: 0.7340 (pt) REVERT: B 446 MET cc_start: 0.7716 (tmm) cc_final: 0.7227 (tmm) REVERT: B 493 PHE cc_start: 0.7606 (t80) cc_final: 0.7246 (t80) REVERT: B 517 VAL cc_start: 0.9057 (m) cc_final: 0.8848 (t) REVERT: B 602 LYS cc_start: 0.8569 (tttt) cc_final: 0.8217 (tptt) REVERT: B 623 ASP cc_start: 0.8316 (p0) cc_final: 0.7787 (m-30) REVERT: B 661 GLU cc_start: 0.7436 (tt0) cc_final: 0.6720 (mp0) REVERT: B 680 GLU cc_start: 0.8493 (mt-10) cc_final: 0.6751 (tm-30) REVERT: B 847 TYR cc_start: 0.7961 (m-80) cc_final: 0.7668 (m-10) REVERT: B 899 GLN cc_start: 0.7227 (OUTLIER) cc_final: 0.5651 (mp10) REVERT: B 944 GLN cc_start: 0.8911 (OUTLIER) cc_final: 0.7916 (mt0) REVERT: B 998 GLU cc_start: 0.8454 (tt0) cc_final: 0.8168 (tm-30) REVERT: B 1014 TYR cc_start: 0.8775 (m-80) cc_final: 0.8442 (m-80) REVERT: B 1094 ASN cc_start: 0.8742 (OUTLIER) cc_final: 0.8361 (m110) REVERT: C 168 LYS cc_start: 0.8013 (mmtt) cc_final: 0.7455 (mtpt) REVERT: C 295 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7816 (mmt90) REVERT: C 308 MET cc_start: 0.7252 (mtp) cc_final: 0.5913 (mtm) REVERT: C 312 GLU cc_start: 0.8024 (tt0) cc_final: 0.7565 (tm-30) REVERT: E 57 MET cc_start: 0.6841 (OUTLIER) cc_final: 0.6265 (tmm) REVERT: E 81 GLU cc_start: 0.7168 (tp30) cc_final: 0.6618 (mm-30) REVERT: E 155 ARG cc_start: 0.8402 (ttp80) cc_final: 0.8090 (ttp-170) REVERT: E 159 ASP cc_start: 0.7738 (t0) cc_final: 0.7381 (t70) REVERT: E 187 TYR cc_start: 0.8150 (t80) cc_final: 0.7651 (t80) REVERT: E 196 VAL cc_start: 0.9060 (OUTLIER) cc_final: 0.8858 (m) REVERT: F 65 ARG cc_start: 0.5987 (ttp-170) cc_final: 0.5566 (tmm160) REVERT: F 103 MET cc_start: 0.8436 (OUTLIER) cc_final: 0.8164 (ttt) REVERT: F 109 VAL cc_start: 0.8630 (p) cc_final: 0.8093 (m) REVERT: F 119 ARG cc_start: 0.7574 (mmt180) cc_final: 0.7140 (mtp85) REVERT: I 11 LEU cc_start: 0.7262 (mt) cc_final: 0.7043 (mp) REVERT: J 36 LEU cc_start: 0.9283 (mt) cc_final: 0.9029 (mm) REVERT: J 68 LYS cc_start: 0.8201 (mmtp) cc_final: 0.7408 (ttpt) REVERT: K 45 GLU cc_start: 0.6969 (mt-10) cc_final: 0.6663 (pt0) REVERT: K 82 LYS cc_start: 0.8717 (mmtp) cc_final: 0.8275 (mptt) REVERT: K 132 GLU cc_start: 0.8473 (tp30) cc_final: 0.8056 (tm-30) REVERT: L 28 LYS cc_start: 0.8155 (mttp) cc_final: 0.7890 (mtpp) REVERT: L 66 GLN cc_start: 0.8179 (tt0) cc_final: 0.7776 (mt0) REVERT: N 90 MET cc_start: 0.4813 (mtm) cc_final: 0.3685 (tpt) REVERT: D 15 THR cc_start: 0.8562 (OUTLIER) cc_final: 0.8326 (m) REVERT: G 18 LYS cc_start: 0.5869 (OUTLIER) cc_final: 0.5366 (mmmt) outliers start: 120 outliers final: 103 residues processed: 554 average time/residue: 0.4546 time to fit residues: 409.3251 Evaluate side-chains 578 residues out of total 3693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 462 time to evaluate : 3.669 ------------------------------------------------------------------------------- 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 98 LEU Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 234 ASP 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 423 LEU Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 565 SER Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 704 ASP Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 769 VAL 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 968 SER Chi-restraints excluded: chain A residue 990 ILE Chi-restraints excluded: chain A residue 1020 GLN Chi-restraints excluded: chain A residue 1063 MET Chi-restraints excluded: chain A residue 1162 ASN Chi-restraints excluded: chain A residue 1163 GLU Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1255 CYS Chi-restraints excluded: chain A residue 1498 ILE Chi-restraints excluded: chain A residue 1505 ASP Chi-restraints excluded: chain A residue 1520 VAL Chi-restraints excluded: chain A residue 1521 THR Chi-restraints excluded: chain A residue 1535 PHE Chi-restraints excluded: chain A residue 1543 SER Chi-restraints excluded: chain A residue 1585 ILE 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 57 ASP 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 255 ASP Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 302 LEU Chi-restraints excluded: chain B residue 377 MET Chi-restraints excluded: chain B residue 432 ILE Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain B residue 689 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 944 GLN Chi-restraints excluded: chain B residue 946 ASP Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain B residue 1046 VAL Chi-restraints excluded: chain B residue 1089 GLN Chi-restraints excluded: chain B residue 1094 ASN 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 47 LEU Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 295 ARG Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 57 MET Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 88 VAL 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 196 VAL Chi-restraints excluded: chain F residue 59 GLN Chi-restraints excluded: chain F residue 103 MET Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain H residue 12 VAL 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 H residue 131 ASN 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 52 THR Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 57 ASP Chi-restraints excluded: chain L residue 35 SER Chi-restraints excluded: chain L residue 61 THR Chi-restraints excluded: chain M residue 66 THR Chi-restraints excluded: chain N residue 89 ILE Chi-restraints excluded: chain N residue 153 VAL Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain D residue 29 GLN Chi-restraints excluded: chain G residue 18 LYS Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 144 HIS Chi-restraints excluded: chain G residue 169 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 413 random chunks: chunk 260 optimal weight: 7.9990 chunk 349 optimal weight: 4.9990 chunk 100 optimal weight: 10.0000 chunk 302 optimal weight: 9.9990 chunk 48 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 chunk 328 optimal weight: 9.9990 chunk 137 optimal weight: 0.9980 chunk 336 optimal weight: 9.9990 chunk 41 optimal weight: 0.6980 chunk 60 optimal weight: 7.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 598 HIS ** B 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 75 GLN D 30 HIS G 119 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.179214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.146827 restraints weight = 47223.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.145803 restraints weight = 67982.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.147042 restraints weight = 68521.863| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.5292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 34788 Z= 0.250 Angle : 0.588 16.291 47204 Z= 0.303 Chirality : 0.044 0.235 5274 Planarity : 0.004 0.056 5937 Dihedral : 10.765 73.130 5063 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.31 % Favored : 94.65 % Rotamer: Outliers : 3.39 % Allowed : 17.20 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.13), residues: 4109 helix: 0.07 (0.15), residues: 1247 sheet: -0.45 (0.20), residues: 686 loop : -1.03 (0.13), residues: 2176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 79 HIS 0.014 0.001 HIS G 144 PHE 0.019 0.001 PHE A 467 TYR 0.019 0.001 TYR B1098 ARG 0.012 0.000 ARG A1176 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8214.86 seconds wall clock time: 148 minutes 36.03 seconds (8916.03 seconds total)