Starting phenix.real_space_refine on Sat Mar 7 07:04:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6rqt_4985/03_2026/6rqt_4985.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rqt_4985/03_2026/6rqt_4985.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6rqt_4985/03_2026/6rqt_4985.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rqt_4985/03_2026/6rqt_4985.map" model { file = "/net/cci-nas-00/data/ceres_data/6rqt_4985/03_2026/6rqt_4985.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rqt_4985/03_2026/6rqt_4985.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.014 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: 6 Type Number sf(0) Gaussians Zn 6 6.06 5 P 32 5.49 5 S 192 5.16 5 C 25171 2.51 5 N 6861 2.21 5 O 7558 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39820 Number of models: 1 Model: "" Number of chains: 22 Chain: "T" Number of atoms: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 364 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "U" Number of atoms: 293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 293 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "A" Number of atoms: 11571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1466, 11571 Classifications: {'peptide': 1466} Link IDs: {'PTRANS': 59, 'TRANS': 1406} Chain breaks: 7 Chain: "B" Number of atoms: 9301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1170, 9301 Classifications: {'peptide': 1170} Link IDs: {'PTRANS': 59, 'TRANS': 1110} Chain breaks: 4 Chain: "C" Number of atoms: 2418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2418 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 19, 'TRANS': 284} Chain breaks: 1 Chain: "D" Number of atoms: 467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 467 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 3, 'TRANS': 55} Chain breaks: 1 Chain: "E" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1751 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 12, 'TRANS': 201} 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: "G" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1600 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 11, 'TRANS': 190} Chain breaks: 2 Chain: "H" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1075 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain breaks: 1 Chain: "I" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 472 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 3, 'TRANS': 60} 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: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 785 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain: "L" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 344 Classifications: {'peptide': 43} Modifications used: {'COO': 1} Link IDs: {'TRANS': 42} Chain: "M" Number of atoms: 3100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3100 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 20, 'TRANS': 371} Chain breaks: 2 Chain: "N" Number of atoms: 1070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1070 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 9, 'TRANS': 125} Chain breaks: 3 Chain: "O" Number of atoms: 3811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3811 Classifications: {'peptide': 463} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 13, 'TRANS': 449} Chain breaks: 2 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 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 1438 SG CYS A 102 66.174 111.496 29.449 1.00134.25 S ATOM 1463 SG CYS A 105 68.758 109.770 27.061 1.00125.68 S ATOM 2266 SG CYS A 233 70.503 112.479 28.832 1.00138.82 S ATOM 2288 SG CYS A 236 67.323 113.009 25.923 1.00128.29 S ATOM 1118 SG CYS A 62 63.193 63.201 50.586 1.00126.53 S ATOM 20809 SG CYS B1104 77.104 70.352 40.906 1.00103.26 S ATOM 20835 SG CYS B1107 75.752 73.677 41.530 1.00 96.18 S ATOM 20982 SG CYS B1128 73.462 69.899 41.474 1.00123.10 S ATOM 21010 SG CYS B1131 75.928 72.325 38.130 1.00111.40 S ATOM 29889 SG CYS I 33 31.910 146.308 76.107 1.00151.43 S ATOM 30212 SG CYS J 10 79.847 70.030 122.752 1.00 86.08 S ATOM 30498 SG CYS J 46 78.102 69.462 125.806 1.00 91.81 S ATOM 31544 SG CYS L 34 35.059 66.052 108.191 1.00149.28 S ATOM 31648 SG CYS L 48 34.232 65.092 103.963 1.00155.75 S Time building chain proxies: 8.50, per 1000 atoms: 0.21 Number of scatterers: 39820 At special positions: 0 Unit cell: (156.562, 177.791, 164.523, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 6 29.99 S 192 16.00 P 32 15.00 O 7558 8.00 N 6861 7.00 C 25171 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.33 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1701 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 105 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 236 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 102 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 233 " pdb=" ZN A1702 " pdb="ZN ZN A1702 " - pdb=" NE2 HIS A 75 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 62 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1131 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1104 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1107 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1128 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 33 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " Number of angles added : 12 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9288 Finding SS restraints... Secondary structure from input PDB file: 181 helices and 51 sheets defined 28.2% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 21 through 25 removed outlier: 3.523A pdb=" N ILE A 24 " --> pdb=" O ALA A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 43 removed outlier: 4.355A pdb=" N GLY A 42 " --> pdb=" O ASP A 39 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N HIS A 43 " --> pdb=" O ASN A 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 39 through 43' Processing helix chain 'A' and resid 51 through 55 removed outlier: 3.658A pdb=" N LEU A 54 " --> pdb=" O ASP A 51 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLY A 55 " --> pdb=" O LEU A 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 51 through 55' Processing helix chain 'A' and resid 68 through 72 removed outlier: 3.650A pdb=" N CYS A 72 " --> pdb=" O GLU A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 93 removed outlier: 3.790A pdb=" N ASN A 92 " --> pdb=" O LEU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 100 Processing helix chain 'A' and resid 111 through 122 Processing helix chain 'A' and resid 130 through 134 removed outlier: 4.113A pdb=" N TYR A 134 " --> pdb=" O ASP A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 180 removed outlier: 3.993A pdb=" N GLU A 180 " --> pdb=" O THR A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 200 removed outlier: 3.603A pdb=" N SER A 186 " --> pdb=" O LYS A 182 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU A 187 " --> pdb=" O SER A 183 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N ALA A 192 " --> pdb=" O TYR A 188 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE A 193 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA A 194 " --> pdb=" O ASP A 190 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS A 195 " --> pdb=" O MET A 191 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA A 196 " --> pdb=" O ALA A 192 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASP A 199 " --> pdb=" O LYS A 195 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY A 200 " --> pdb=" O ALA A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 218 Processing helix chain 'A' and resid 226 through 230 Processing helix chain 'A' and resid 265 through 270 removed outlier: 3.946A pdb=" N GLY A 268 " --> pdb=" O ARG A 265 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N PHE A 269 " --> pdb=" O VAL A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 328 removed outlier: 3.969A pdb=" N THR A 326 " --> pdb=" O ASN A 322 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A 327 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE A 328 " --> pdb=" O LEU A 324 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 322 through 328' Processing helix chain 'A' and resid 331 through 333 No H-bonds generated for 'chain 'A' and resid 331 through 333' Processing helix chain 'A' and resid 334 through 339 removed outlier: 3.926A pdb=" N VAL A 338 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE A 339 " --> pdb=" O LEU A 335 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 334 through 339' Processing helix chain 'A' and resid 351 through 355 removed outlier: 3.875A pdb=" N SER A 354 " --> pdb=" O LYS A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 398 removed outlier: 3.543A pdb=" N LEU A 385 " --> pdb=" O SER A 381 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N THR A 391 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU A 395 " --> pdb=" O THR A 391 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASP A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 405 removed outlier: 3.677A pdb=" N LYS A 405 " --> pdb=" O ASP A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 439 removed outlier: 3.518A pdb=" N MET A 424 " --> pdb=" O PHE A 420 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN A 425 " --> pdb=" O SER A 421 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ALA A 426 " --> pdb=" O ARG A 422 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N THR A 429 " --> pdb=" O ASN A 425 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL A 434 " --> pdb=" O ILE A 430 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN A 435 " --> pdb=" O GLN A 431 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA A 436 " --> pdb=" O ASN A 432 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE A 437 " --> pdb=" O ASP A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 461 Processing helix chain 'A' and resid 518 through 526 removed outlier: 3.595A pdb=" N ALA A 522 " --> pdb=" O GLU A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 558 removed outlier: 4.039A pdb=" N LEU A 557 " --> pdb=" O GLN A 553 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA A 558 " --> pdb=" O ARG A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 571 removed outlier: 3.646A pdb=" N HIS A 571 " --> pdb=" O VAL A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 625 removed outlier: 3.902A pdb=" N TYR A 624 " --> pdb=" O ASN A 620 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASN A 625 " --> pdb=" O THR A 621 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 620 through 625' Processing helix chain 'A' and resid 641 through 648 removed outlier: 3.639A pdb=" N GLU A 646 " --> pdb=" O ASN A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 657 removed outlier: 3.710A pdb=" N GLN A 656 " --> pdb=" O THR A 653 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N TYR A 657 " --> pdb=" O ASP A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 682 removed outlier: 3.523A pdb=" N THR A 681 " --> pdb=" O GLY A 677 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER A 682 " --> pdb=" O VAL A 678 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 677 through 682' Processing helix chain 'A' and resid 688 through 698 removed outlier: 3.953A pdb=" N ILE A 696 " --> pdb=" O TYR A 692 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR A 697 " --> pdb=" O GLN A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 736 removed outlier: 3.565A pdb=" N ILE A 732 " --> pdb=" O GLY A 728 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR A 733 " --> pdb=" O LYS A 729 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL A 735 " --> pdb=" O ILE A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 760 Processing helix chain 'A' and resid 793 through 801 removed outlier: 4.223A pdb=" N GLU A 799 " --> pdb=" O HIS A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 809 removed outlier: 4.460A pdb=" N VAL A 805 " --> pdb=" O TYR A 801 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA A 806 " --> pdb=" O GLY A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 821 removed outlier: 3.500A pdb=" N PHE A 817 " --> pdb=" O LEU A 813 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR A 818 " --> pdb=" O GLY A 814 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASN A 819 " --> pdb=" O ARG A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 846 removed outlier: 3.905A pdb=" N ILE A 846 " --> pdb=" O TRP A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 850 removed outlier: 3.505A pdb=" N SER A 850 " --> pdb=" O LEU A 847 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 847 through 850' Processing helix chain 'A' and resid 852 through 859 Processing helix chain 'A' and resid 872 through 880 removed outlier: 3.988A pdb=" N ARG A 878 " --> pdb=" O GLU A 874 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LEU A 879 " --> pdb=" O LEU A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 908 removed outlier: 4.234A pdb=" N THR A 904 " --> pdb=" O VAL A 900 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER A 905 " --> pdb=" O ASN A 901 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLN A 906 " --> pdb=" O ALA A 902 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL A 907 " --> pdb=" O ILE A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 923 Processing helix chain 'A' and resid 940 through 945 Processing helix chain 'A' and resid 975 through 979 Processing helix chain 'A' and resid 993 through 999 removed outlier: 3.545A pdb=" N CYS A 999 " --> pdb=" O TYR A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1008 removed outlier: 3.739A pdb=" N GLU A1004 " --> pdb=" O MET A1000 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLY A1005 " --> pdb=" O ALA A1001 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU A1006 " --> pdb=" O GLY A1002 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP A1008 " --> pdb=" O GLU A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1027 removed outlier: 3.558A pdb=" N THR A1024 " --> pdb=" O GLN A1020 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N LYS A1025 " --> pdb=" O ARG A1021 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN A1026 " --> pdb=" O CYS A1022 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU A1027 " --> pdb=" O LEU A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1060 removed outlier: 3.543A pdb=" N LYS A1059 " --> pdb=" O ASP A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1071 removed outlier: 3.868A pdb=" N CYS A1069 " --> pdb=" O GLN A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1081 Processing helix chain 'A' and resid 1082 through 1085 Processing helix chain 'A' and resid 1092 through 1109 removed outlier: 3.902A pdb=" N LYS A1100 " --> pdb=" O LYS A1096 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS A1103 " --> pdb=" O LYS A1099 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N TYR A1104 " --> pdb=" O LYS A1100 " (cutoff:3.500A) Processing helix chain 'A' and resid 1163 through 1177 removed outlier: 3.579A pdb=" N ARG A1167 " --> pdb=" O GLU A1163 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA A1168 " --> pdb=" O LYS A1164 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LEU A1169 " --> pdb=" O LYS A1165 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LEU A1172 " --> pdb=" O ALA A1168 " (cutoff:3.500A) Processing helix chain 'A' and resid 1185 through 1192 removed outlier: 3.745A pdb=" N SER A1190 " --> pdb=" O GLY A1186 " (cutoff:3.500A) Processing helix chain 'A' and resid 1194 through 1199 removed outlier: 3.927A pdb=" N GLN A1199 " --> pdb=" O GLU A1195 " (cutoff:3.500A) Processing helix chain 'A' and resid 1218 through 1228 removed outlier: 4.298A pdb=" N GLU A1224 " --> pdb=" O PRO A1220 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL A1226 " --> pdb=" O LEU A1222 " (cutoff:3.500A) Processing helix chain 'A' and resid 1247 through 1256 removed outlier: 4.012A pdb=" N ASP A1252 " --> pdb=" O ASP A1248 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N THR A1253 " --> pdb=" O GLU A1249 " (cutoff:3.500A) Processing helix chain 'A' and resid 1263 through 1265 No H-bonds generated for 'chain 'A' and resid 1263 through 1265' Processing helix chain 'A' and resid 1301 through 1306 Processing helix chain 'A' and resid 1309 through 1314 Processing helix chain 'A' and resid 1320 through 1337 removed outlier: 3.699A pdb=" N ALA A1328 " --> pdb=" O LEU A1324 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL A1330 " --> pdb=" O GLU A1326 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N LYS A1331 " --> pdb=" O ALA A1327 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLU A1332 " --> pdb=" O ALA A1328 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE A1333 " --> pdb=" O ILE A1329 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LYS A1335 " --> pdb=" O LYS A1331 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS A1337 " --> pdb=" O ILE A1333 " (cutoff:3.500A) Processing helix chain 'A' and resid 1440 through 1452 removed outlier: 3.598A pdb=" N ARG A1446 " --> pdb=" O VAL A1442 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE A1450 " --> pdb=" O ARG A1446 " (cutoff:3.500A) Processing helix chain 'A' and resid 1486 through 1494 removed outlier: 3.573A pdb=" N GLU A1490 " --> pdb=" O VAL A1486 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU A1491 " --> pdb=" O ASN A1487 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ILE A1492 " --> pdb=" O ILE A1488 " (cutoff:3.500A) Processing helix chain 'A' and resid 1545 through 1549 removed outlier: 3.580A pdb=" N ALA A1548 " --> pdb=" O ASP A1545 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N VAL A1549 " --> pdb=" O VAL A1546 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1545 through 1549' Processing helix chain 'A' and resid 1554 through 1558 Processing helix chain 'A' and resid 1565 through 1573 removed outlier: 4.121A pdb=" N VAL A1569 " --> pdb=" O GLU A1565 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE A1570 " --> pdb=" O ILE A1566 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER A1571 " --> pdb=" O ASN A1567 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR A1573 " --> pdb=" O VAL A1569 " (cutoff:3.500A) Processing helix chain 'A' and resid 1581 through 1589 removed outlier: 3.548A pdb=" N ILE A1585 " --> pdb=" O HIS A1581 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N MET A1589 " --> pdb=" O ILE A1585 " (cutoff:3.500A) Processing helix chain 'A' and resid 1608 through 1614 removed outlier: 4.006A pdb=" N LYS A1612 " --> pdb=" O SER A1608 " (cutoff:3.500A) Processing helix chain 'A' and resid 1636 through 1641 removed outlier: 3.565A pdb=" N ILE A1641 " --> pdb=" O PRO A1637 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 23 Processing helix chain 'B' and resid 35 through 40 removed outlier: 3.571A pdb=" N GLN B 39 " --> pdb=" O PHE B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 52 removed outlier: 3.737A pdb=" N ALA B 51 " --> pdb=" O GLY B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 59 removed outlier: 3.708A pdb=" N GLY B 58 " --> pdb=" O GLY B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 127 removed outlier: 3.760A pdb=" N ARG B 127 " --> pdb=" O PRO B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 183 removed outlier: 3.655A pdb=" N VAL B 181 " --> pdb=" O PRO B 177 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN B 182 " --> pdb=" O TYR B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 223 Processing helix chain 'B' and resid 273 through 277 Processing helix chain 'B' and resid 285 through 290 removed outlier: 4.203A pdb=" N PHE B 289 " --> pdb=" O ASP B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 310 removed outlier: 3.514A pdb=" N GLU B 307 " --> pdb=" O THR B 303 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N LEU B 308 " --> pdb=" O ASP B 304 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU B 309 " --> pdb=" O ARG B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 315 removed outlier: 3.545A pdb=" N LYS B 314 " --> pdb=" O LEU B 310 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS B 315 " --> pdb=" O ARG B 311 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 310 through 315' Processing helix chain 'B' and resid 322 through 328 Processing helix chain 'B' and resid 329 through 334 removed outlier: 3.787A pdb=" N LYS B 333 " --> pdb=" O TYR B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 355 removed outlier: 3.518A pdb=" N VAL B 349 " --> pdb=" O SER B 345 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLN B 351 " --> pdb=" O LEU B 347 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU B 352 " --> pdb=" O GLU B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 363 removed outlier: 3.743A pdb=" N LEU B 362 " --> pdb=" O LEU B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 386 removed outlier: 4.407A pdb=" N PHE B 371 " --> pdb=" O SER B 367 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG B 372 " --> pdb=" O GLN B 368 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N MET B 373 " --> pdb=" O ASP B 369 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE B 376 " --> pdb=" O ARG B 372 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS B 380 " --> pdb=" O PHE B 376 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU B 381 " --> pdb=" O MET B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 400 removed outlier: 3.948A pdb=" N GLN B 400 " --> pdb=" O THR B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 416 removed outlier: 3.759A pdb=" N LEU B 413 " --> pdb=" O TYR B 409 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LYS B 414 " --> pdb=" O GLY B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 425 removed outlier: 4.181A pdb=" N GLN B 422 " --> pdb=" O ASP B 418 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE B 425 " --> pdb=" O LEU B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 433 Processing helix chain 'B' and resid 443 through 448 Processing helix chain 'B' and resid 457 through 467 removed outlier: 4.339A pdb=" N TYR B 463 " --> pdb=" O SER B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 499 Processing helix chain 'B' and resid 508 through 512 removed outlier: 3.689A pdb=" N GLN B 511 " --> pdb=" O PHE B 508 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU B 512 " --> pdb=" O PHE B 509 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 508 through 512' Processing helix chain 'B' and resid 597 through 599 No H-bonds generated for 'chain 'B' and resid 597 through 599' Processing helix chain 'B' and resid 600 through 612 removed outlier: 3.673A pdb=" N ASP B 606 " --> pdb=" O LYS B 602 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LEU B 608 " --> pdb=" O ILE B 604 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ARG B 609 " --> pdb=" O ALA B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 635 removed outlier: 4.068A pdb=" N ARG B 634 " --> pdb=" O PRO B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 696 removed outlier: 3.534A pdb=" N ASN B 695 " --> pdb=" O THR B 692 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE B 696 " --> pdb=" O PRO B 693 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 692 through 696' Processing helix chain 'B' and resid 698 through 704 Processing helix chain 'B' and resid 706 through 710 removed outlier: 3.788A pdb=" N ASN B 710 " --> pdb=" O SER B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 714 Processing helix chain 'B' and resid 715 through 723 removed outlier: 3.566A pdb=" N CYS B 719 " --> pdb=" O ASN B 715 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N MET B 721 " --> pdb=" O TYR B 717 " (cutoff:3.500A) Processing helix chain 'B' and resid 754 through 759 removed outlier: 4.013A pdb=" N ASP B 758 " --> pdb=" O ALA B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 765 Processing helix chain 'B' and resid 791 through 795 Processing helix chain 'B' and resid 835 through 839 removed outlier: 4.119A pdb=" N GLU B 838 " --> pdb=" O GLU B 835 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LYS B 839 " --> pdb=" O TRP B 836 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 835 through 839' Processing helix chain 'B' and resid 960 through 969 removed outlier: 3.787A pdb=" N SER B 966 " --> pdb=" O MET B 962 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU B 967 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA B 968 " --> pdb=" O VAL B 964 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY B 969 " --> pdb=" O GLU B 965 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 1003 removed outlier: 3.592A pdb=" N GLN B 999 " --> pdb=" O TYR B 995 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU B1000 " --> pdb=" O PHE B 996 " (cutoff:3.500A) Processing helix chain 'B' and resid 1076 through 1082 removed outlier: 3.718A pdb=" N ILE B1080 " --> pdb=" O ARG B1076 " (cutoff:3.500A) Processing helix chain 'B' and resid 1085 through 1090 Processing helix chain 'B' and resid 1136 through 1138 No H-bonds generated for 'chain 'B' and resid 1136 through 1138' Processing helix chain 'B' and resid 1179 through 1193 removed outlier: 4.404A pdb=" N SER B1187 " --> pdb=" O LYS B1183 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER B1190 " --> pdb=" O ASP B1186 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N MET B1192 " --> pdb=" O GLU B1188 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY B1193 " --> pdb=" O LEU B1189 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 38 removed outlier: 3.771A pdb=" N LYS C 38 " --> pdb=" O GLU C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 67 removed outlier: 4.135A pdb=" N ALA C 66 " --> pdb=" O SER C 62 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE C 67 " --> pdb=" O ILE C 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 62 through 67' Processing helix chain 'C' and resid 97 through 102 removed outlier: 3.807A pdb=" N GLY C 102 " --> pdb=" O ALA C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 167 Processing helix chain 'C' and resid 216 through 220 Processing helix chain 'C' and resid 277 through 281 Processing helix chain 'C' and resid 313 through 318 Processing helix chain 'C' and resid 321 through 330 removed outlier: 3.668A pdb=" N GLU C 326 " --> pdb=" O LYS C 322 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N TYR C 327 " --> pdb=" O ASN C 323 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU C 328 " --> pdb=" O LYS C 324 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASN C 330 " --> pdb=" O GLU C 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 92 through 96 removed outlier: 3.623A pdb=" N ASP D 95 " --> pdb=" O ILE D 92 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N PHE D 96 " --> pdb=" O GLN D 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 92 through 96' Processing helix chain 'E' and resid 4 through 27 removed outlier: 3.696A pdb=" N LEU E 12 " --> pdb=" O ASN E 8 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N THR E 18 " --> pdb=" O ARG E 14 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL E 19 " --> pdb=" O ALA E 15 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS E 20 " --> pdb=" O PHE E 16 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU E 21 " --> pdb=" O ARG E 17 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL E 23 " --> pdb=" O VAL E 19 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS E 24 " --> pdb=" O LYS E 20 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY E 27 " --> pdb=" O VAL E 23 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 42 through 47 Processing helix chain 'E' and resid 54 through 58 removed outlier: 3.988A pdb=" N MET E 57 " --> pdb=" O GLN E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 70 Processing helix chain 'E' and resid 89 through 104 removed outlier: 3.694A pdb=" N MET E 93 " --> pdb=" O GLY E 89 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS E 94 " --> pdb=" O VAL E 90 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR E 95 " --> pdb=" O LYS E 91 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE E 98 " --> pdb=" O LYS E 94 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N HIS E 99 " --> pdb=" O THR E 95 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE E 100 " --> pdb=" O PHE E 96 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LYS E 103 " --> pdb=" O HIS E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 141 removed outlier: 3.988A pdb=" N VAL E 141 " --> pdb=" O ALA E 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 138 through 141' Processing helix chain 'E' and resid 160 through 169 Processing helix chain 'F' and resid 86 through 91 Processing helix chain 'F' and resid 92 through 103 removed outlier: 3.554A pdb=" N GLN F 100 " --> pdb=" O THR F 96 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET F 103 " --> pdb=" O LEU F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 126 removed outlier: 3.812A pdb=" N ILE F 120 " --> pdb=" O ASP F 116 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ALA F 121 " --> pdb=" O PRO F 117 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N MET F 122 " --> pdb=" O LEU F 118 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS F 123 " --> pdb=" O ARG F 119 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA F 126 " --> pdb=" O MET F 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 11 through 13 No H-bonds generated for 'chain 'G' and resid 11 through 13' Processing helix chain 'G' and resid 14 through 19 removed outlier: 4.115A pdb=" N LYS G 18 " --> pdb=" O ALA G 14 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS G 19 " --> pdb=" O ARG G 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 14 through 19' Processing helix chain 'G' and resid 56 through 61 removed outlier: 3.501A pdb=" N VAL G 61 " --> pdb=" O PRO G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 66 removed outlier: 3.527A pdb=" N HIS G 65 " --> pdb=" O VAL G 61 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU G 66 " --> pdb=" O MET G 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 61 through 66' Processing helix chain 'G' and resid 67 through 70 removed outlier: 3.659A pdb=" N VAL G 70 " --> pdb=" O ASN G 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 67 through 70' Processing helix chain 'G' and resid 148 through 152 Processing helix chain 'J' and resid 15 through 23 removed outlier: 3.954A pdb=" N GLU J 19 " --> pdb=" O GLY J 15 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER J 20 " --> pdb=" O ASP J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 32 through 37 removed outlier: 3.677A pdb=" N LEU J 36 " --> pdb=" O GLU J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 47 through 52 Processing helix chain 'K' and resid 51 through 54 removed outlier: 3.529A pdb=" N THR K 54 " --> pdb=" O THR K 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 51 through 54' Processing helix chain 'K' and resid 69 through 81 removed outlier: 3.785A pdb=" N GLY K 73 " --> pdb=" O ASP K 69 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ALA K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG K 77 " --> pdb=" O GLY K 73 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N TYR K 78 " --> pdb=" O ASN K 74 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N VAL K 79 " --> pdb=" O ALA K 75 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET K 81 " --> pdb=" O ARG K 77 " (cutoff:3.500A) Processing helix chain 'K' and resid 114 through 128 removed outlier: 3.792A pdb=" N LYS K 119 " --> pdb=" O ASP K 115 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY K 120 " --> pdb=" O ALA K 116 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP K 123 " --> pdb=" O LYS K 119 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET K 125 " --> pdb=" O LEU K 121 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP K 126 " --> pdb=" O LYS K 122 " (cutoff:3.500A) Processing helix chain 'K' and resid 129 through 134 removed outlier: 3.510A pdb=" N LYS K 134 " --> pdb=" O VAL K 130 " (cutoff:3.500A) Processing helix chain 'K' and resid 134 through 141 removed outlier: 3.891A pdb=" N LYS K 138 " --> pdb=" O LYS K 134 " (cutoff:3.500A) Processing helix chain 'M' and resid 140 through 145 Processing helix chain 'M' and resid 159 through 164 removed outlier: 3.544A pdb=" N ASP M 163 " --> pdb=" O ILE M 159 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER M 164 " --> pdb=" O ASP M 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 159 through 164' Processing helix chain 'M' and resid 209 through 214 removed outlier: 3.549A pdb=" N GLN M 214 " --> pdb=" O LYS M 210 " (cutoff:3.500A) Processing helix chain 'M' and resid 243 through 250 removed outlier: 4.127A pdb=" N LYS M 246 " --> pdb=" O VAL M 243 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ASP M 248 " --> pdb=" O LYS M 245 " (cutoff:3.500A) Processing helix chain 'M' and resid 259 through 266 removed outlier: 3.552A pdb=" N TYR M 264 " --> pdb=" O GLN M 260 " (cutoff:3.500A) Processing helix chain 'M' and resid 280 through 285 removed outlier: 3.823A pdb=" N GLU M 285 " --> pdb=" O THR M 281 " (cutoff:3.500A) Processing helix chain 'M' and resid 291 through 295 Processing helix chain 'M' and resid 308 through 313 removed outlier: 3.511A pdb=" N ARG M 312 " --> pdb=" O GLY M 308 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER M 313 " --> pdb=" O GLN M 309 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 308 through 313' Processing helix chain 'M' and resid 337 through 341 removed outlier: 3.764A pdb=" N ASP M 340 " --> pdb=" O MET M 337 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASN M 341 " --> pdb=" O HIS M 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 337 through 341' Processing helix chain 'M' and resid 346 through 351 Processing helix chain 'M' and resid 363 through 367 removed outlier: 3.764A pdb=" N VAL M 366 " --> pdb=" O LEU M 363 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LEU M 367 " --> pdb=" O PHE M 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 363 through 367' Processing helix chain 'M' and resid 377 through 381 removed outlier: 4.399A pdb=" N GLU M 380 " --> pdb=" O ALA M 377 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA M 381 " --> pdb=" O GLN M 378 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 377 through 381' Processing helix chain 'O' and resid 49 through 54 removed outlier: 3.659A pdb=" N ARG O 54 " --> pdb=" O ALA O 50 " (cutoff:3.500A) Processing helix chain 'O' and resid 89 through 100 removed outlier: 3.520A pdb=" N LEU O 93 " --> pdb=" O ASN O 89 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASN O 94 " --> pdb=" O ASP O 90 " (cutoff:3.500A) Processing helix chain 'O' and resid 115 through 121 removed outlier: 4.250A pdb=" N ILE O 119 " --> pdb=" O LEU O 115 " (cutoff:3.500A) Processing helix chain 'O' and resid 132 through 144 removed outlier: 3.751A pdb=" N TYR O 136 " --> pdb=" O THR O 132 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE O 137 " --> pdb=" O LEU O 133 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N CYS O 144 " --> pdb=" O ILE O 140 " (cutoff:3.500A) Processing helix chain 'O' and resid 154 through 161 removed outlier: 3.530A pdb=" N SER O 160 " --> pdb=" O MET O 156 " (cutoff:3.500A) Processing helix chain 'O' and resid 165 through 169 Processing helix chain 'O' and resid 173 through 180 removed outlier: 3.757A pdb=" N TYR O 178 " --> pdb=" O ASP O 174 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N PHE O 179 " --> pdb=" O MET O 175 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU O 180 " --> pdb=" O LEU O 176 " (cutoff:3.500A) Processing helix chain 'O' and resid 204 through 212 removed outlier: 4.001A pdb=" N LEU O 208 " --> pdb=" O THR O 204 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL O 209 " --> pdb=" O ARG O 205 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASN O 210 " --> pdb=" O ARG O 206 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR O 211 " --> pdb=" O LYS O 207 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR O 212 " --> pdb=" O LEU O 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 204 through 212' Processing helix chain 'O' and resid 214 through 222 removed outlier: 4.186A pdb=" N LEU O 218 " --> pdb=" O ASN O 214 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N TYR O 221 " --> pdb=" O LYS O 217 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N CYS O 222 " --> pdb=" O LEU O 218 " (cutoff:3.500A) Processing helix chain 'O' and resid 229 through 234 removed outlier: 4.444A pdb=" N LEU O 233 " --> pdb=" O ILE O 229 " (cutoff:3.500A) Processing helix chain 'O' and resid 235 through 246 removed outlier: 4.018A pdb=" N SER O 239 " --> pdb=" O GLU O 235 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE O 240 " --> pdb=" O LYS O 236 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU O 243 " --> pdb=" O SER O 239 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ASN O 246 " --> pdb=" O VAL O 242 " (cutoff:3.500A) Processing helix chain 'O' and resid 326 through 343 removed outlier: 4.062A pdb=" N THR O 330 " --> pdb=" O LYS O 326 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS O 331 " --> pdb=" O GLU O 327 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU O 332 " --> pdb=" O LEU O 328 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR O 337 " --> pdb=" O ASP O 333 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N LEU O 338 " --> pdb=" O SER O 334 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N THR O 341 " --> pdb=" O THR O 337 " (cutoff:3.500A) Processing helix chain 'O' and resid 348 through 352 removed outlier: 3.759A pdb=" N LEU O 352 " --> pdb=" O PRO O 349 " (cutoff:3.500A) Processing helix chain 'O' and resid 357 through 362 removed outlier: 3.858A pdb=" N PHE O 361 " --> pdb=" O GLY O 357 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN O 362 " --> pdb=" O VAL O 358 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 357 through 362' Processing helix chain 'O' and resid 365 through 370 Processing helix chain 'O' and resid 393 through 401 removed outlier: 3.624A pdb=" N ASP O 397 " --> pdb=" O LEU O 393 " (cutoff:3.500A) Processing helix chain 'O' and resid 415 through 423 removed outlier: 4.319A pdb=" N LYS O 419 " --> pdb=" O GLU O 415 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N SER O 420 " --> pdb=" O LYS O 416 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LEU O 421 " --> pdb=" O LYS O 417 " (cutoff:3.500A) Processing helix chain 'O' and resid 435 through 443 removed outlier: 4.002A pdb=" N ILE O 440 " --> pdb=" O ARG O 436 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE O 441 " --> pdb=" O THR O 437 " (cutoff:3.500A) Processing helix chain 'O' and resid 443 through 456 removed outlier: 3.871A pdb=" N VAL O 454 " --> pdb=" O LEU O 450 " (cutoff:3.500A) Processing helix chain 'O' and resid 475 through 481 Processing helix chain 'O' and resid 501 through 506 removed outlier: 4.066A pdb=" N PHE O 506 " --> pdb=" O LEU O 502 " (cutoff:3.500A) Processing helix chain 'O' and resid 523 through 527 removed outlier: 3.564A pdb=" N LEU O 526 " --> pdb=" O ASN O 523 " (cutoff:3.500A) Processing helix chain 'O' and resid 530 through 535 Processing helix chain 'O' and resid 543 through 551 removed outlier: 3.970A pdb=" N ASN O 548 " --> pdb=" O ILE O 544 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASN O 549 " --> pdb=" O GLU O 545 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLU O 550 " --> pdb=" O ASN O 546 " (cutoff:3.500A) Processing helix chain 'O' and resid 602 through 607 Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 17 Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 102 Processing sheet with id=AA3, first strand: chain 'A' and resid 243 through 244 removed outlier: 3.675A pdb=" N PHE A 252 " --> pdb=" O ARG A 244 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 475 through 476 removed outlier: 3.745A pdb=" N ILE B1069 " --> pdb=" O VAL A 476 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 479 through 481 removed outlier: 3.753A pdb=" N ALA A 479 " --> pdb=" O ARG B1047 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ARG B1047 " --> pdb=" O ALA A 479 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG A 481 " --> pdb=" O GLN B1045 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 484 through 487 removed outlier: 5.746A pdb=" N SER A 485 " --> pdb=" O LEU A 616 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 496 through 497 removed outlier: 3.503A pdb=" N VAL A 497 " --> pdb=" O ARG A 606 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 535 through 536 Processing sheet with id=AA9, first strand: chain 'A' and resid 586 through 589 removed outlier: 3.915A pdb=" N MET A 589 " --> pdb=" O MET A 601 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET A 601 " --> pdb=" O MET A 589 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 686 through 687 Processing sheet with id=AB2, first strand: chain 'A' and resid 750 through 751 removed outlier: 3.680A pdb=" N SER A 751 " --> pdb=" O VAL A 769 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1238 through 1239 removed outlier: 3.558A pdb=" N MET A1238 " --> pdb=" O THR A1521 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1267 through 1272 removed outlier: 3.683A pdb=" N ILE A1271 " --> pdb=" O HIS A1293 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N GLU A1471 " --> pdb=" O TYR A1460 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N TYR A1460 " --> pdb=" O GLU A1471 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LYS A1473 " --> pdb=" O THR A1458 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 142 through 145 Processing sheet with id=AB6, first strand: chain 'B' and resid 95 through 104 removed outlier: 3.894A pdb=" N SER B 144 " --> pdb=" O SER B 96 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LYS B 140 " --> pdb=" O GLU B 100 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N VAL B 102 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LEU B 138 " --> pdb=" O VAL B 102 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU B 154 " --> pdb=" O LEU B 141 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 194 through 196 removed outlier: 4.158A pdb=" N ILE B 199 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU B 202 " --> pdb=" O VAL B 486 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL B 486 " --> pdb=" O LEU B 202 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 206 through 208 Processing sheet with id=AB9, first strand: chain 'B' and resid 215 through 216 removed outlier: 4.843A pdb=" N ILE B 234 " --> pdb=" O LEU B 250 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL B 249 " --> pdb=" O ARG B 261 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG B 261 " --> pdb=" O VAL B 249 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 550 through 551 removed outlier: 3.592A pdb=" N LYS B 660 " --> pdb=" O TYR B 655 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 550 through 551 Processing sheet with id=AC3, first strand: chain 'B' and resid 594 through 596 removed outlier: 3.903A pdb=" N GLY B 594 " --> pdb=" O VAL B 586 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N CYS B 585 " --> pdb=" O LEU B 640 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N LEU B 642 " --> pdb=" O CYS B 585 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N GLN B 587 " --> pdb=" O LEU B 642 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLY B 639 " --> pdb=" O VAL B 629 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N VAL B 629 " --> pdb=" O GLY B 639 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU B 625 " --> pdb=" O PHE B 643 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 742 through 744 removed outlier: 3.917A pdb=" N GLY B 801 " --> pdb=" O ARG B 909 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ARG B 906 " --> pdb=" O ILE B 882 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N ILE B 882 " --> pdb=" O ARG B 906 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 926 through 931 removed outlier: 7.221A pdb=" N ILE B 789 " --> pdb=" O SER B 928 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LYS B 930 " --> pdb=" O ILE B 789 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE B 788 " --> pdb=" O ILE B 948 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ILE B 947 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA B 774 " --> pdb=" O ILE B 947 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE B 949 " --> pdb=" O ALA B 774 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 861 through 862 Processing sheet with id=AC7, first strand: chain 'B' and resid 1100 through 1103 removed outlier: 3.523A pdb=" N VAL B1103 " --> pdb=" O THR B1174 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N THR B1174 " --> pdb=" O VAL B1103 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 1114 through 1115 Processing sheet with id=AC9, first strand: chain 'B' and resid 1132 through 1134 Processing sheet with id=AD1, first strand: chain 'C' and resid 41 through 47 removed outlier: 6.277A pdb=" N ASN C 53 " --> pdb=" O SER C 45 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU C 230 " --> pdb=" O VAL C 294 " (cutoff:3.500A) removed outlier: 8.913A pdb=" N ASN C 296 " --> pdb=" O ARG C 228 " (cutoff:3.500A) removed outlier: 11.339A pdb=" N ARG C 228 " --> pdb=" O ASN C 296 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 168 through 169 removed outlier: 7.310A pdb=" N SER C 203 " --> pdb=" O PHE C 86 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE C 86 " --> pdb=" O SER C 203 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ILE C 209 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N ALA C 80 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N GLY C 211 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N VAL C 78 " --> pdb=" O GLY C 211 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL C 83 " --> pdb=" O PHE L 67 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE C 85 " --> pdb=" O VAL L 65 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL L 65 " --> pdb=" O PHE C 85 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 141 through 142 removed outlier: 3.578A pdb=" N ASN C 158 " --> pdb=" O THR C 141 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 161 through 162 removed outlier: 3.590A pdb=" N ALA C 194 " --> pdb=" O VAL C 162 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 21 through 24 removed outlier: 4.219A pdb=" N VAL D 21 " --> pdb=" O TYR G 46 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N HIS D 23 " --> pdb=" O ALA G 44 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 21 through 24 removed outlier: 4.219A pdb=" N VAL D 21 " --> pdb=" O TYR G 46 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N HIS D 23 " --> pdb=" O ALA G 44 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL G 39 " --> pdb=" O VAL G 124 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N CYS G 118 " --> pdb=" O LEU G 45 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR G 116 " --> pdb=" O VAL G 47 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLY G 83 " --> pdb=" O TYR G 123 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N TRP G 125 " --> pdb=" O VAL G 81 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N VAL G 81 " --> pdb=" O TRP G 125 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 60 through 62 removed outlier: 4.099A pdb=" N LEU E 78 " --> pdb=" O ALA E 62 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.558A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TYR E 208 " --> pdb=" O ARG E 200 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 84 through 85 Processing sheet with id=AE1, first strand: chain 'G' and resid 132 through 136 removed outlier: 3.653A pdb=" N PHE G 231 " --> pdb=" O LEU G 133 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 167 through 169 Processing sheet with id=AE3, first strand: chain 'G' and resid 235 through 237 removed outlier: 3.780A pdb=" N SER G 244 " --> pdb=" O HIS G 237 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 4 through 7 removed outlier: 6.215A pdb=" N ILE H 59 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA H 140 " --> pdb=" O GLY H 99 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY H 99 " --> pdb=" O ALA H 140 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TYR H 116 " --> pdb=" O MET H 123 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 10 through 16 removed outlier: 6.798A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 3 through 4 Processing sheet with id=AE7, first strand: chain 'K' and resid 48 through 50 removed outlier: 3.715A pdb=" N LEU K 50 " --> pdb=" O SER K 62 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N SER K 62 " --> pdb=" O LEU K 50 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ALA K 61 " --> pdb=" O ILE K 105 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE K 105 " --> pdb=" O ALA K 61 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE K 65 " --> pdb=" O LEU K 101 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN K 102 " --> pdb=" O SER K 92 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG K 104 " --> pdb=" O GLY K 90 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE K 88 " --> pdb=" O GLN K 106 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'L' and resid 29 through 30 Processing sheet with id=AE9, first strand: chain 'M' and resid 9 through 11 Processing sheet with id=AF1, first strand: chain 'M' and resid 23 through 24 Processing sheet with id=AF2, first strand: chain 'M' and resid 39 through 41 removed outlier: 3.645A pdb=" N HIS M 54 " --> pdb=" O ASP M 39 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'M' and resid 60 through 61 Processing sheet with id=AF4, first strand: chain 'M' and resid 64 through 65 Processing sheet with id=AF5, first strand: chain 'M' and resid 92 through 93 removed outlier: 3.596A pdb=" N VAL M 77 " --> pdb=" O ILE N 56 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N PHE M 81 " --> pdb=" O GLN N 52 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLN N 52 " --> pdb=" O PHE M 81 " (cutoff:3.500A) removed outlier: 9.218A pdb=" N PHE N 137 " --> pdb=" O VAL N 53 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N LEU N 55 " --> pdb=" O PHE N 137 " (cutoff:3.500A) removed outlier: 8.817A pdb=" N VAL N 139 " --> pdb=" O LEU N 55 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LYS N 57 " --> pdb=" O VAL N 139 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'M' and resid 343 through 344 removed outlier: 3.854A pdb=" N THR M 396 " --> pdb=" O ILE M 370 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ILE M 370 " --> pdb=" O THR M 396 " (cutoff:3.500A) 655 hydrogen bonds defined for protein. 1668 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.20 Time building geometry restraints manager: 4.43 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: 11849 1.33 - 1.45: 7436 1.45 - 1.58: 21002 1.58 - 1.70: 62 1.70 - 1.82: 305 Bond restraints: 40654 Sorted by residual: bond pdb=" C VAL B 121 " pdb=" N TYR B 122 " ideal model delta sigma weight residual 1.331 1.221 0.110 2.07e-02 2.33e+03 2.84e+01 bond pdb=" N ILE O 163 " pdb=" CA ILE O 163 " ideal model delta sigma weight residual 1.461 1.503 -0.042 1.31e-02 5.83e+03 1.02e+01 bond pdb=" N LEU B 476 " pdb=" CA LEU B 476 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.17e-02 7.31e+03 8.42e+00 bond pdb=" N LEU A 41 " pdb=" CA LEU A 41 " ideal model delta sigma weight residual 1.457 1.494 -0.036 1.29e-02 6.01e+03 7.98e+00 bond pdb=" N LYS A 919 " pdb=" CA LYS A 919 " ideal model delta sigma weight residual 1.454 1.491 -0.038 1.34e-02 5.57e+03 7.95e+00 ... (remaining 40649 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 52755 2.65 - 5.31: 1957 5.31 - 7.96: 273 7.96 - 10.62: 65 10.62 - 13.27: 5 Bond angle restraints: 55055 Sorted by residual: angle pdb=" C ILE O 163 " pdb=" N LEU O 164 " pdb=" CA LEU O 164 " ideal model delta sigma weight residual 120.68 133.95 -13.27 1.52e+00 4.33e-01 7.62e+01 angle pdb=" C GLU N 169 " pdb=" N HIS N 170 " pdb=" CA HIS N 170 " ideal model delta sigma weight residual 123.00 111.78 11.22 1.41e+00 5.03e-01 6.33e+01 angle pdb=" N ASN C 53 " pdb=" CA ASN C 53 " pdb=" C ASN C 53 " ideal model delta sigma weight residual 110.23 98.82 11.41 1.45e+00 4.76e-01 6.20e+01 angle pdb=" N ILE O 325 " pdb=" CA ILE O 325 " pdb=" C ILE O 325 " ideal model delta sigma weight residual 113.53 105.85 7.68 9.80e-01 1.04e+00 6.14e+01 angle pdb=" N LEU A 813 " pdb=" CA LEU A 813 " pdb=" C LEU A 813 " ideal model delta sigma weight residual 111.36 104.09 7.27 1.09e+00 8.42e-01 4.45e+01 ... (remaining 55050 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.92: 23961 29.92 - 59.83: 700 59.83 - 89.75: 61 89.75 - 119.67: 0 119.67 - 149.58: 2 Dihedral angle restraints: 24724 sinusoidal: 10378 harmonic: 14346 Sorted by residual: dihedral pdb=" C ASP B 784 " pdb=" N ASP B 784 " pdb=" CA ASP B 784 " pdb=" CB ASP B 784 " ideal model delta harmonic sigma weight residual -122.60 -138.24 15.64 0 2.50e+00 1.60e-01 3.92e+01 dihedral pdb=" CA ILE B 276 " pdb=" C ILE B 276 " pdb=" N LEU B 277 " pdb=" CA LEU B 277 " ideal model delta harmonic sigma weight residual 180.00 150.01 29.99 0 5.00e+00 4.00e-02 3.60e+01 dihedral pdb=" CA ASN B 950 " pdb=" C ASN B 950 " pdb=" N PRO B 951 " pdb=" CA PRO B 951 " ideal model delta harmonic sigma weight residual 180.00 150.13 29.87 0 5.00e+00 4.00e-02 3.57e+01 ... (remaining 24721 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 5626 0.110 - 0.220: 495 0.220 - 0.331: 43 0.331 - 0.441: 5 0.441 - 0.551: 4 Chirality restraints: 6173 Sorted by residual: chirality pdb=" C3' DA U 58 " pdb=" C4' DA U 58 " pdb=" O3' DA U 58 " pdb=" C2' DA U 58 " both_signs ideal model delta sigma weight residual False -2.66 -2.11 -0.55 2.00e-01 2.50e+01 7.59e+00 chirality pdb=" CA ASP B 784 " pdb=" N ASP B 784 " pdb=" C ASP B 784 " pdb=" CB ASP B 784 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 6.91e+00 chirality pdb=" CB ILE F 130 " pdb=" CA ILE F 130 " pdb=" CG1 ILE F 130 " pdb=" CG2 ILE F 130 " both_signs ideal model delta sigma weight residual False 2.64 2.19 0.45 2.00e-01 2.50e+01 5.15e+00 ... (remaining 6170 not shown) Planarity restraints: 6974 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU N 168 " 0.018 2.00e-02 2.50e+03 3.78e-02 1.43e+01 pdb=" C LEU N 168 " -0.065 2.00e-02 2.50e+03 pdb=" O LEU N 168 " 0.026 2.00e-02 2.50e+03 pdb=" N GLU N 169 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 617 " 0.023 2.00e-02 2.50e+03 2.90e-02 1.26e+01 pdb=" CG HIS A 617 " -0.062 2.00e-02 2.50e+03 pdb=" ND1 HIS A 617 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 HIS A 617 " 0.021 2.00e-02 2.50e+03 pdb=" CE1 HIS A 617 " 0.003 2.00e-02 2.50e+03 pdb=" NE2 HIS A 617 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 265 " 0.016 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C ARG B 265 " -0.058 2.00e-02 2.50e+03 pdb=" O ARG B 265 " 0.022 2.00e-02 2.50e+03 pdb=" N LYS B 266 " 0.019 2.00e-02 2.50e+03 ... (remaining 6971 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 371 2.53 - 3.12: 28954 3.12 - 3.72: 63552 3.72 - 4.31: 85360 4.31 - 4.90: 133023 Nonbonded interactions: 311260 Sorted by model distance: nonbonded pdb=" OE2 GLU N 169 " pdb=" N HIS N 170 " model vdw 1.938 3.120 nonbonded pdb=" O TYR A1306 " pdb=" OD1 ASP A1307 " model vdw 2.000 3.040 nonbonded pdb=" OG1 THR A 64 " pdb="ZN ZN A1702 " model vdw 2.115 2.230 nonbonded pdb=" N CYS J 46 " pdb="ZN ZN J 101 " model vdw 2.159 2.310 nonbonded pdb=" OD1 ASP L 50 " pdb="ZN ZN L 101 " model vdw 2.210 2.230 ... (remaining 311255 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.320 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: 0.030 Extract box with map and model: 0.530 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 41.870 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5883 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 : 0.008 0.271 40669 Z= 0.359 Angle : 1.217 34.251 55067 Z= 0.659 Chirality : 0.069 0.551 6173 Planarity : 0.008 0.076 6974 Dihedral : 13.878 149.581 15436 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.14 % Allowed : 14.84 % Favored : 85.02 % Rotamer: Outliers : 1.35 % Allowed : 9.60 % Favored : 89.05 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.39 (0.09), residues: 4839 helix: -4.56 (0.07), residues: 1201 sheet: -3.47 (0.20), residues: 485 loop : -3.38 (0.09), residues: 3153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG L 54 TYR 0.045 0.004 TYR H 93 PHE 0.034 0.004 PHE M 364 TRP 0.044 0.004 TRP B 836 HIS 0.036 0.004 HIS A 617 Details of bonding type rmsd covalent geometry : bond 0.00726 (40654) covalent geometry : angle 1.19523 (55055) hydrogen bonds : bond 0.33191 ( 651) hydrogen bonds : angle 12.21176 ( 1668) metal coordination : bond 0.17424 ( 15) metal coordination : angle 15.51167 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1198 residues out of total 4381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 1139 time to evaluate : 1.486 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: 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 10 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7331 (mp0) REVERT: A 117 ARG cc_start: 0.6766 (tpm-80) cc_final: 0.5815 (tpp80) REVERT: A 136 LEU cc_start: 0.8829 (mt) cc_final: 0.8035 (mm) REVERT: A 191 MET cc_start: 0.7295 (tpp) cc_final: 0.6918 (tmm) REVERT: A 366 ARG cc_start: 0.6783 (ttp80) cc_final: 0.6543 (ttt-90) REVERT: A 384 GLN cc_start: 0.5417 (tm-30) cc_final: 0.4845 (mt0) REVERT: A 471 MET cc_start: 0.3831 (mpt) cc_final: 0.3591 (ttp) REVERT: A 477 ASN cc_start: 0.7705 (t0) cc_final: 0.7222 (m110) REVERT: A 535 GLN cc_start: 0.6690 (mt0) cc_final: 0.6445 (mt0) REVERT: A 537 GLN cc_start: 0.7018 (pp30) cc_final: 0.6453 (mm-40) REVERT: A 549 MET cc_start: 0.6501 (mtp) cc_final: 0.6287 (mtt) REVERT: A 589 MET cc_start: 0.8601 (ttm) cc_final: 0.8306 (ttt) REVERT: A 590 ASN cc_start: 0.6591 (t0) cc_final: 0.6222 (t0) REVERT: A 596 HIS cc_start: 0.8382 (p90) cc_final: 0.7975 (p90) REVERT: A 600 MET cc_start: 0.7917 (tpp) cc_final: 0.7544 (tpp) REVERT: A 711 LYS cc_start: 0.6634 (pttp) cc_final: 0.6045 (mtmt) REVERT: A 712 ILE cc_start: 0.8501 (OUTLIER) cc_final: 0.8163 (tp) REVERT: A 824 THR cc_start: 0.8162 (t) cc_final: 0.7710 (m) REVERT: A 826 PHE cc_start: 0.7622 (t80) cc_final: 0.7391 (t80) REVERT: A 833 LEU cc_start: 0.7164 (mm) cc_final: 0.6691 (mm) REVERT: A 840 ASN cc_start: 0.7848 (p0) cc_final: 0.7648 (t0) REVERT: A 880 GLN cc_start: 0.6815 (pt0) cc_final: 0.6273 (mt0) REVERT: A 981 TYR cc_start: 0.6732 (t80) cc_final: 0.5843 (t80) REVERT: A 1000 MET cc_start: 0.7707 (mmp) cc_final: 0.7294 (tpp) REVERT: A 1006 LEU cc_start: 0.7279 (pt) cc_final: 0.6884 (mp) REVERT: A 1036 ASN cc_start: 0.7478 (m-40) cc_final: 0.7000 (t0) REVERT: A 1049 MET cc_start: 0.7133 (ttm) cc_final: 0.6797 (ttm) REVERT: A 1059 LYS cc_start: 0.7226 (mttt) cc_final: 0.6728 (tptt) REVERT: A 1070 LEU cc_start: 0.8769 (tt) cc_final: 0.8533 (tp) REVERT: A 1073 TYR cc_start: 0.4979 (p90) cc_final: 0.4563 (p90) REVERT: A 1099 LYS cc_start: 0.8307 (mmpt) cc_final: 0.8074 (tmmt) REVERT: A 1248 ASP cc_start: 0.8257 (m-30) cc_final: 0.7864 (m-30) REVERT: A 1260 LYS cc_start: 0.7371 (tmmt) cc_final: 0.7088 (ttmm) REVERT: A 1269 LYS cc_start: 0.5674 (pttp) cc_final: 0.5328 (mttt) REVERT: A 1473 LYS cc_start: 0.7022 (ttpt) cc_final: 0.6298 (mtpp) REVERT: A 1580 ARG cc_start: 0.7259 (mpp80) cc_final: 0.6008 (mtt-85) REVERT: A 1588 MET cc_start: 0.7683 (tpt) cc_final: 0.6342 (mtt) REVERT: A 1603 MET cc_start: 0.7841 (mtt) cc_final: 0.6213 (ptt) REVERT: B 90 TYR cc_start: 0.4826 (t80) cc_final: 0.4059 (m-10) REVERT: B 94 LYS cc_start: 0.5186 (tppp) cc_final: 0.4613 (tmtt) REVERT: B 100 GLU cc_start: 0.6158 (tm-30) cc_final: 0.5475 (tt0) REVERT: B 101 GLN cc_start: 0.7735 (tp40) cc_final: 0.7169 (tt0) REVERT: B 149 GLU cc_start: 0.5944 (pp20) cc_final: 0.5571 (mm-30) REVERT: B 261 ARG cc_start: 0.7398 (ttp80) cc_final: 0.6858 (ttp80) REVERT: B 275 MET cc_start: 0.5522 (ptm) cc_final: 0.5252 (ttm) REVERT: B 290 ASP cc_start: 0.6843 (t70) cc_final: 0.6583 (t0) REVERT: B 323 ARG cc_start: 0.5857 (mpt90) cc_final: 0.3592 (ttp-170) REVERT: B 425 ILE cc_start: 0.6879 (pt) cc_final: 0.6340 (mt) REVERT: B 543 ASN cc_start: 0.7296 (p0) cc_final: 0.7074 (p0) REVERT: B 674 ILE cc_start: 0.7692 (mm) cc_final: 0.7343 (tt) REVERT: B 720 GLN cc_start: 0.8072 (mm110) cc_final: 0.6547 (tm-30) REVERT: B 726 MET cc_start: 0.7661 (ttm) cc_final: 0.7429 (ttt) REVERT: B 744 LEU cc_start: 0.7265 (tm) cc_final: 0.6887 (tm) REVERT: B 803 MET cc_start: 0.6364 (ptt) cc_final: 0.5273 (ptt) REVERT: B 822 THR cc_start: 0.3176 (p) cc_final: 0.2925 (p) REVERT: B 840 LEU cc_start: 0.6877 (mm) cc_final: 0.6622 (mp) REVERT: B 853 GLU cc_start: 0.6635 (mt-10) cc_final: 0.6390 (tt0) REVERT: B 906 ARG cc_start: 0.8179 (ttm110) cc_final: 0.7614 (ttp-110) REVERT: B 934 ILE cc_start: 0.7511 (mm) cc_final: 0.7119 (mm) REVERT: B 935 ASP cc_start: 0.7443 (m-30) cc_final: 0.7093 (p0) REVERT: B 974 LEU cc_start: 0.5917 (tm) cc_final: 0.5666 (tt) REVERT: B 984 TRP cc_start: 0.4866 (m100) cc_final: 0.4289 (m100) REVERT: B 1070 ARG cc_start: 0.6087 (ttt-90) cc_final: 0.4270 (tmm-80) REVERT: B 1134 ARG cc_start: 0.6680 (mmt-90) cc_final: 0.4360 (mtt180) REVERT: C 31 TRP cc_start: 0.6664 (t-100) cc_final: 0.6268 (t-100) REVERT: C 132 ILE cc_start: 0.8943 (mm) cc_final: 0.8678 (mm) REVERT: C 139 LYS cc_start: 0.8445 (mttt) cc_final: 0.8083 (mttt) REVERT: C 155 GLU cc_start: 0.5901 (tm-30) cc_final: 0.5657 (mm-30) REVERT: C 237 GLN cc_start: 0.7055 (mt0) cc_final: 0.6604 (mp10) REVERT: C 315 PHE cc_start: 0.7854 (m-10) cc_final: 0.7521 (m-80) REVERT: C 329 LYS cc_start: 0.7588 (pptt) cc_final: 0.7297 (pptt) REVERT: D 45 ASP cc_start: 0.6819 (m-30) cc_final: 0.6209 (p0) REVERT: E 22 MET cc_start: 0.7392 (mtt) cc_final: 0.7184 (ttt) REVERT: E 34 GLU cc_start: 0.5824 (tm-30) cc_final: 0.5432 (mt-10) REVERT: E 42 PHE cc_start: 0.7720 (t80) cc_final: 0.7280 (t80) REVERT: E 61 GLN cc_start: 0.8418 (tt0) cc_final: 0.7799 (tm-30) REVERT: E 110 PHE cc_start: 0.6681 (m-10) cc_final: 0.6300 (t80) REVERT: E 208 TYR cc_start: 0.7071 (p90) cc_final: 0.6677 (p90) REVERT: F 71 GLU cc_start: 0.8531 (tm-30) cc_final: 0.7490 (tt0) REVERT: F 76 LYS cc_start: 0.7016 (pptt) cc_final: 0.6212 (tppt) REVERT: F 77 ASP cc_start: 0.7745 (m-30) cc_final: 0.7322 (m-30) REVERT: F 99 LEU cc_start: 0.6102 (OUTLIER) cc_final: 0.5789 (pp) REVERT: G 43 ILE cc_start: 0.6589 (OUTLIER) cc_final: 0.6241 (pt) REVERT: G 59 GLN cc_start: 0.7073 (tt0) cc_final: 0.6407 (tt0) REVERT: G 159 LYS cc_start: 0.4032 (tttp) cc_final: 0.3652 (mmtt) REVERT: H 135 LEU cc_start: 0.6812 (pp) cc_final: 0.5916 (mt) REVERT: I 44 ASN cc_start: 0.7765 (m-40) cc_final: 0.7113 (p0) REVERT: J 49 MET cc_start: 0.8339 (mmp) cc_final: 0.8089 (mmm) REVERT: J 68 LYS cc_start: 0.7169 (tmmm) cc_final: 0.6835 (mptt) REVERT: K 57 ASP cc_start: 0.5325 (m-30) cc_final: 0.5117 (t70) REVERT: L 30 ILE cc_start: 0.7771 (mp) cc_final: 0.7563 (tp) REVERT: L 33 GLU cc_start: 0.5597 (tp30) cc_final: 0.5281 (tp30) REVERT: L 37 LYS cc_start: 0.6794 (tmtm) cc_final: 0.6552 (ttmm) REVERT: M 263 TYR cc_start: 0.5128 (t80) cc_final: 0.4583 (t80) REVERT: M 277 VAL cc_start: 0.6049 (p) cc_final: 0.5704 (t) REVERT: N 78 THR cc_start: 0.4554 (t) cc_final: 0.4149 (m) REVERT: N 88 LYS cc_start: 0.5778 (tptt) cc_final: 0.5473 (ttmt) REVERT: N 89 ILE cc_start: 0.4222 (OUTLIER) cc_final: 0.3933 (mm) REVERT: O 127 GLU cc_start: 0.0593 (mt-10) cc_final: 0.0207 (tt0) REVERT: O 328 LEU cc_start: 0.2637 (mp) cc_final: 0.2235 (mt) REVERT: O 396 MET cc_start: -0.0962 (ttm) cc_final: -0.1476 (ptt) REVERT: O 467 MET cc_start: 0.2327 (mmp) cc_final: 0.1981 (mtm) outliers start: 59 outliers final: 11 residues processed: 1183 average time/residue: 0.2597 time to fit residues: 487.4921 Evaluate side-chains 650 residues out of total 4381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 635 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 785 ASP Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain G residue 43 ILE Chi-restraints excluded: chain N residue 89 ILE Chi-restraints excluded: chain N residue 169 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 432 optimal weight: 3.9990 chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 0.7980 chunk 455 optimal weight: 5.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.0370 chunk 470 optimal weight: 20.0000 overall best weight: 1.9062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 ASN A 60 ASN A 75 HIS A 92 ASN A 116 HIS A 224 HIS A 257 ASN A 344 ASN ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 458 GLN A 515 ASN A 537 GLN A 592 GLN A 634 ASN A 649 ASN A 693 GLN ** A 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 798 HIS A 939 ASN ** A 998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1047 GLN A1088 HIS ** A1113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1293 HIS A1315 ASN A1437 ASN A1567 ASN A1620 GLN ** B 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN B 110 ASN B 128 GLN B 168 ASN B 183 HIS B 224 ASN ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN ** B 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 555 GLN B 598 HIS B 711 GLN ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 748 GLN ** B 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1008 HIS B1041 ASN B1045 GLN ** B1058 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1094 ASN B1171 ASN D 38 GLN E 113 GLN ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 147 HIS E 153 HIS F 104 ASN G 8 ASN G 64 GLN G 65 HIS G 67 ASN ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 154 ASN G 160 ASN G 170 HIS G 235 ASN H 43 ASN I 19 ASN J 53 HIS K 70 HIS K 83 ASN ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 54 HIS M 75 GLN ** M 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 323 GLN N 37 ASN N 50 GLN N 51 GLN N 52 GLN ** N 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 117 GLN O 362 ASN O 478 GLN Total number of N/Q/H flips: 68 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.207567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.195146 restraints weight = 69560.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.194441 restraints weight = 102552.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.195117 restraints weight = 88583.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.194937 restraints weight = 70412.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.195226 restraints weight = 61580.561| |-----------------------------------------------------------------------------| r_work (final): 0.4433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5920 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.852 40669 Z= 0.212 Angle : 0.786 12.313 55067 Z= 0.404 Chirality : 0.048 0.273 6173 Planarity : 0.006 0.119 6974 Dihedral : 11.350 154.422 5697 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.39 % Favored : 89.54 % Rotamer: Outliers : 3.79 % Allowed : 15.20 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.45 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.76 (0.10), residues: 4839 helix: -3.90 (0.09), residues: 1312 sheet: -3.24 (0.19), residues: 543 loop : -2.91 (0.10), residues: 2984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B1130 TYR 0.029 0.002 TYR H 116 PHE 0.025 0.002 PHE O 361 TRP 0.023 0.002 TRP B 836 HIS 0.015 0.002 HIS A 617 Details of bonding type rmsd covalent geometry : bond 0.00353 (40654) covalent geometry : angle 0.77857 (55055) hydrogen bonds : bond 0.05269 ( 651) hydrogen bonds : angle 8.23510 ( 1668) metal coordination : bond 0.22042 ( 15) metal coordination : angle 7.25944 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 894 residues out of total 4381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 728 time to evaluate : 1.305 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 ILE cc_start: 0.6759 (OUTLIER) cc_final: 0.6396 (tt) REVERT: A 357 MET cc_start: 0.2788 (mtp) cc_final: 0.2348 (mtp) REVERT: A 390 LEU cc_start: 0.6678 (OUTLIER) cc_final: 0.6453 (mm) REVERT: A 427 PHE cc_start: 0.6027 (OUTLIER) cc_final: 0.5811 (m-80) REVERT: A 477 ASN cc_start: 0.7469 (t0) cc_final: 0.7190 (m-40) REVERT: A 494 GLU cc_start: 0.4939 (mt-10) cc_final: 0.4696 (mt-10) REVERT: A 649 ASN cc_start: 0.6117 (OUTLIER) cc_final: 0.5778 (m110) REVERT: A 824 THR cc_start: 0.8063 (OUTLIER) cc_final: 0.7623 (p) REVERT: A 871 ASP cc_start: 0.6522 (p0) cc_final: 0.6001 (p0) REVERT: A 981 TYR cc_start: 0.5900 (t80) cc_final: 0.5234 (t80) REVERT: A 1049 MET cc_start: 0.7106 (ttm) cc_final: 0.6898 (ttm) REVERT: A 1070 LEU cc_start: 0.8046 (tt) cc_final: 0.7760 (tp) REVERT: A 1073 TYR cc_start: 0.5824 (p90) cc_final: 0.5051 (p90) REVERT: A 1150 LYS cc_start: 0.7052 (pptt) cc_final: 0.6751 (tptt) REVERT: A 1225 ILE cc_start: 0.8990 (mm) cc_final: 0.8578 (tp) REVERT: A 1591 ARG cc_start: 0.7712 (ptp-170) cc_final: 0.6713 (ttt180) REVERT: A 1603 MET cc_start: 0.5805 (mtt) cc_final: 0.5548 (ttp) REVERT: B 73 ILE cc_start: 0.5463 (tt) cc_final: 0.4782 (mm) REVERT: B 90 TYR cc_start: 0.5286 (t80) cc_final: 0.4938 (m-80) REVERT: B 261 ARG cc_start: 0.7453 (ttp80) cc_final: 0.7008 (ttt-90) REVERT: B 270 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7459 (pp) REVERT: B 323 ARG cc_start: 0.5637 (mpt90) cc_final: 0.3689 (ttp-170) REVERT: B 372 ARG cc_start: 0.6898 (ttt-90) cc_final: 0.6562 (ttt90) REVERT: B 471 VAL cc_start: 0.8535 (OUTLIER) cc_final: 0.8326 (m) REVERT: B 543 ASN cc_start: 0.6458 (p0) cc_final: 0.5664 (p0) REVERT: B 614 GLU cc_start: 0.6222 (mm-30) cc_final: 0.6019 (mm-30) REVERT: B 720 GLN cc_start: 0.7170 (mm110) cc_final: 0.6784 (tm-30) REVERT: B 744 LEU cc_start: 0.7001 (OUTLIER) cc_final: 0.6494 (tm) REVERT: B 822 THR cc_start: 0.3578 (p) cc_final: 0.3273 (p) REVERT: B 840 LEU cc_start: 0.6723 (mm) cc_final: 0.6359 (mt) REVERT: B 878 GLU cc_start: 0.5690 (mm-30) cc_final: 0.5235 (mm-30) REVERT: B 931 TRP cc_start: 0.6076 (t-100) cc_final: 0.5800 (t-100) REVERT: B 934 ILE cc_start: 0.7647 (mm) cc_final: 0.6518 (mm) REVERT: B 935 ASP cc_start: 0.7862 (m-30) cc_final: 0.6796 (p0) REVERT: B 967 LEU cc_start: 0.7058 (OUTLIER) cc_final: 0.6807 (mt) REVERT: B 1134 ARG cc_start: 0.6519 (mmt-90) cc_final: 0.5449 (mtt180) REVERT: C 329 LYS cc_start: 0.7302 (pptt) cc_final: 0.7064 (pptt) REVERT: E 42 PHE cc_start: 0.6468 (t80) cc_final: 0.5789 (t80) REVERT: E 93 MET cc_start: 0.3058 (ppp) cc_final: 0.2617 (tpp) REVERT: E 116 ILE cc_start: 0.5318 (OUTLIER) cc_final: 0.4705 (tp) REVERT: E 173 SER cc_start: 0.7415 (m) cc_final: 0.7155 (p) REVERT: F 71 GLU cc_start: 0.7785 (tm-30) cc_final: 0.7187 (tt0) REVERT: F 76 LYS cc_start: 0.6510 (pptt) cc_final: 0.6012 (tppt) REVERT: F 100 GLN cc_start: 0.7843 (tm-30) cc_final: 0.7612 (tt0) REVERT: G 53 TYR cc_start: 0.5985 (m-80) cc_final: 0.5522 (m-10) REVERT: H 123 MET cc_start: 0.4573 (mmm) cc_final: 0.3781 (mmt) REVERT: H 135 LEU cc_start: 0.6034 (pp) cc_final: 0.5244 (mt) REVERT: I 44 ASN cc_start: 0.6872 (m-40) cc_final: 0.6656 (p0) REVERT: K 81 MET cc_start: 0.7674 (ppp) cc_final: 0.7397 (ppp) REVERT: K 142 MET cc_start: 0.6595 (tpt) cc_final: 0.6115 (tpt) REVERT: M 54 HIS cc_start: 0.4793 (OUTLIER) cc_final: 0.4342 (t70) REVERT: M 126 ASN cc_start: 0.1954 (OUTLIER) cc_final: 0.1693 (m110) REVERT: M 207 ILE cc_start: 0.7073 (mm) cc_final: 0.6824 (mt) REVERT: M 277 VAL cc_start: 0.5686 (p) cc_final: 0.5328 (t) REVERT: M 384 ILE cc_start: 0.0052 (OUTLIER) cc_final: -0.0329 (tt) REVERT: N 40 LEU cc_start: 0.3354 (OUTLIER) cc_final: 0.2977 (mp) REVERT: O 127 GLU cc_start: 0.3385 (mt-10) cc_final: 0.2952 (tt0) REVERT: O 167 LYS cc_start: 0.4232 (mttm) cc_final: 0.3472 (mttt) REVERT: O 514 PHE cc_start: 0.5718 (m-80) cc_final: 0.5315 (m-80) outliers start: 166 outliers final: 57 residues processed: 848 average time/residue: 0.2371 time to fit residues: 334.0741 Evaluate side-chains 645 residues out of total 4381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 574 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 427 PHE Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 649 ASN Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1033 SER Chi-restraints excluded: chain A residue 1071 ASP Chi-restraints excluded: chain A residue 1149 ASP Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1198 THR Chi-restraints excluded: chain A residue 1264 SER Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1315 ASN Chi-restraints excluded: chain A residue 1442 VAL Chi-restraints excluded: chain A residue 1568 ASN Chi-restraints excluded: chain A residue 1617 THR Chi-restraints excluded: chain A residue 1630 GLU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain B residue 492 ASN Chi-restraints excluded: chain B residue 595 TRP Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 740 LYS Chi-restraints excluded: chain B residue 744 LEU Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 967 LEU Chi-restraints excluded: chain B residue 1036 LEU Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 301 ASN Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 147 SER Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 131 VAL Chi-restraints excluded: chain L residue 62 LYS Chi-restraints excluded: chain M residue 54 HIS Chi-restraints excluded: chain M residue 126 ASN Chi-restraints excluded: chain M residue 329 LEU Chi-restraints excluded: chain M residue 384 ILE Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain O residue 133 LEU Chi-restraints excluded: chain O residue 348 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 358 optimal weight: 6.9990 chunk 263 optimal weight: 10.0000 chunk 455 optimal weight: 10.0000 chunk 137 optimal weight: 7.9990 chunk 456 optimal weight: 9.9990 chunk 338 optimal weight: 20.0000 chunk 311 optimal weight: 8.9990 chunk 290 optimal weight: 2.9990 chunk 394 optimal weight: 20.0000 chunk 268 optimal weight: 0.9990 chunk 81 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 HIS ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 ASN A 525 ASN A 610 ASN A 640 ASN ** A 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 738 ASN ** A 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1065 GLN ** A1113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1293 HIS A1315 ASN A1500 GLN A1503 HIS ** A1601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 ASN ** B 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 398 GLN B 422 GLN B 456 ASN B 462 GLN B 473 GLN ** B 544 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 547 HIS B 600 GLN B 686 HIS B 715 ASN ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 912 GLN B 950 ASN B1010 ASN ** B1058 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1094 ASN C 65 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 GLN D 38 GLN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 20 HIS G 23 GLN ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 16 GLN M 54 HIS M 126 ASN M 184 ASN ** N 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 152 GLN O 411 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.198415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.185910 restraints weight = 70640.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.185086 restraints weight = 111004.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.185891 restraints weight = 95490.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.186025 restraints weight = 65733.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.186184 restraints weight = 60036.321| |-----------------------------------------------------------------------------| r_work (final): 0.4329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6220 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.811 40669 Z= 0.283 Angle : 0.870 16.962 55067 Z= 0.448 Chirality : 0.051 0.278 6173 Planarity : 0.007 0.138 6974 Dihedral : 11.339 149.431 5680 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 18.69 Ramachandran Plot: Outliers : 0.02 % Allowed : 14.36 % Favored : 85.62 % Rotamer: Outliers : 5.42 % Allowed : 17.69 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.54 (0.10), residues: 4839 helix: -3.58 (0.10), residues: 1299 sheet: -3.20 (0.21), residues: 479 loop : -2.85 (0.10), residues: 3061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 648 TYR 0.035 0.003 TYR B 409 PHE 0.024 0.003 PHE A1472 TRP 0.033 0.003 TRP B 611 HIS 0.020 0.002 HIS M 54 Details of bonding type rmsd covalent geometry : bond 0.00577 (40654) covalent geometry : angle 0.86383 (55055) hydrogen bonds : bond 0.05216 ( 651) hydrogen bonds : angle 7.90493 ( 1668) metal coordination : bond 0.21025 ( 15) metal coordination : angle 7.11658 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 850 residues out of total 4381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 237 poor density : 613 time to evaluate : 1.471 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: symmetry clash revert: symmetry clash REVERT: A 136 LEU cc_start: 0.8011 (mm) cc_final: 0.7792 (mt) REVERT: A 230 ARG cc_start: 0.2991 (OUTLIER) cc_final: 0.1305 (mtm180) REVERT: A 261 ILE cc_start: 0.6955 (OUTLIER) cc_final: 0.6464 (tt) REVERT: A 390 LEU cc_start: 0.6738 (OUTLIER) cc_final: 0.6489 (mm) REVERT: A 477 ASN cc_start: 0.7406 (t0) cc_final: 0.7197 (m-40) REVERT: A 514 TYR cc_start: 0.6907 (OUTLIER) cc_final: 0.6570 (p90) REVERT: A 597 LYS cc_start: 0.7413 (pttm) cc_final: 0.7155 (pttm) REVERT: A 601 MET cc_start: 0.6129 (tpt) cc_final: 0.5928 (tpt) REVERT: A 711 LYS cc_start: 0.7134 (pttp) cc_final: 0.6876 (mtmt) REVERT: A 824 THR cc_start: 0.8353 (OUTLIER) cc_final: 0.7883 (m) REVERT: A 871 ASP cc_start: 0.6581 (p0) cc_final: 0.6321 (p0) REVERT: A 884 ARG cc_start: 0.5881 (mmp-170) cc_final: 0.5422 (ttp80) REVERT: A 1000 MET cc_start: 0.7517 (tpp) cc_final: 0.7256 (tpp) REVERT: A 1150 LYS cc_start: 0.7160 (pptt) cc_final: 0.6665 (tptt) REVERT: A 1178 LEU cc_start: 0.6974 (OUTLIER) cc_final: 0.6643 (mm) REVERT: A 1192 SER cc_start: 0.9101 (m) cc_final: 0.8419 (t) REVERT: A 1300 ASN cc_start: 0.6652 (p0) cc_final: 0.6379 (p0) REVERT: A 1591 ARG cc_start: 0.7478 (OUTLIER) cc_final: 0.6702 (ttt180) REVERT: B 35 PHE cc_start: 0.6796 (OUTLIER) cc_final: 0.5699 (p90) REVERT: B 101 GLN cc_start: 0.8005 (tt0) cc_final: 0.7641 (tt0) REVERT: B 261 ARG cc_start: 0.7681 (ttp80) cc_final: 0.7248 (ttt-90) REVERT: B 270 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7451 (pp) REVERT: B 277 LEU cc_start: 0.6325 (OUTLIER) cc_final: 0.6103 (tp) REVERT: B 323 ARG cc_start: 0.5886 (mpt90) cc_final: 0.3660 (ttp-170) REVERT: B 411 MET cc_start: 0.6930 (OUTLIER) cc_final: 0.6139 (mtp) REVERT: B 425 ILE cc_start: 0.6440 (OUTLIER) cc_final: 0.5979 (mt) REVERT: B 542 LEU cc_start: 0.6387 (OUTLIER) cc_final: 0.5877 (pp) REVERT: B 543 ASN cc_start: 0.7102 (p0) cc_final: 0.6802 (p0) REVERT: B 672 MET cc_start: 0.6655 (ppp) cc_final: 0.6343 (ppp) REVERT: B 720 GLN cc_start: 0.7564 (mm110) cc_final: 0.7047 (tm-30) REVERT: B 794 ASP cc_start: 0.7189 (t70) cc_final: 0.6703 (t0) REVERT: B 822 THR cc_start: 0.3585 (p) cc_final: 0.3274 (p) REVERT: B 840 LEU cc_start: 0.6667 (OUTLIER) cc_final: 0.6426 (mt) REVERT: B 878 GLU cc_start: 0.6425 (mm-30) cc_final: 0.5857 (mm-30) REVERT: B 935 ASP cc_start: 0.7697 (m-30) cc_final: 0.7092 (p0) REVERT: B 967 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.7524 (mt) REVERT: B 1134 ARG cc_start: 0.6284 (mmt-90) cc_final: 0.5244 (mtt180) REVERT: B 1194 ILE cc_start: 0.6687 (OUTLIER) cc_final: 0.6272 (mp) REVERT: C 321 LEU cc_start: 0.5862 (tt) cc_final: 0.5211 (tt) REVERT: E 42 PHE cc_start: 0.7090 (t80) cc_final: 0.6344 (t80) REVERT: E 116 ILE cc_start: 0.5802 (OUTLIER) cc_final: 0.5291 (tp) REVERT: E 149 LEU cc_start: 0.6659 (OUTLIER) cc_final: 0.6391 (mm) REVERT: E 177 ARG cc_start: 0.7271 (OUTLIER) cc_final: 0.5691 (ppt-90) REVERT: H 97 MET cc_start: 0.8013 (OUTLIER) cc_final: 0.7750 (mmm) REVERT: I 44 ASN cc_start: 0.6842 (m-40) cc_final: 0.6567 (p0) REVERT: M 54 HIS cc_start: 0.5783 (OUTLIER) cc_final: 0.5011 (t70) REVERT: M 178 LEU cc_start: 0.4520 (OUTLIER) cc_final: 0.3201 (mt) REVERT: M 263 TYR cc_start: 0.4018 (t80) cc_final: 0.3482 (t80) REVERT: M 384 ILE cc_start: 0.0318 (OUTLIER) cc_final: -0.0520 (tp) REVERT: M 397 MET cc_start: 0.2787 (mpp) cc_final: 0.1100 (mtt) REVERT: N 87 TYR cc_start: 0.5981 (m-10) cc_final: 0.5749 (m-10) REVERT: O 127 GLU cc_start: 0.4101 (mt-10) cc_final: 0.3448 (tt0) REVERT: O 167 LYS cc_start: 0.3961 (mttm) cc_final: 0.3129 (mttt) REVERT: O 457 ARG cc_start: 0.4320 (mtt90) cc_final: 0.4061 (mmt90) outliers start: 237 outliers final: 121 residues processed: 785 average time/residue: 0.2402 time to fit residues: 316.0450 Evaluate side-chains 656 residues out of total 4381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 512 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 585 ASP Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 942 GLN Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1033 SER Chi-restraints excluded: chain A residue 1149 ASP Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1198 THR Chi-restraints excluded: chain A residue 1239 THR Chi-restraints excluded: chain A residue 1264 SER Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1591 ARG Chi-restraints excluded: chain A residue 1630 GLU Chi-restraints excluded: chain A residue 1642 VAL Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 473 GLN Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain B residue 492 ASN Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 595 TRP Chi-restraints excluded: chain B residue 600 GLN Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 740 LYS Chi-restraints excluded: chain B residue 782 ASP Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 907 ILE Chi-restraints excluded: chain B residue 950 ASN Chi-restraints excluded: chain B residue 967 LEU Chi-restraints excluded: chain B residue 1000 LEU Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1036 LEU Chi-restraints excluded: chain B residue 1088 LEU Chi-restraints excluded: chain B residue 1113 THR Chi-restraints excluded: chain B residue 1117 VAL Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1128 CYS Chi-restraints excluded: chain B residue 1133 MET Chi-restraints excluded: chain B residue 1156 SER Chi-restraints excluded: chain B residue 1194 ILE Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 226 SER Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 177 ARG Chi-restraints excluded: chain E residue 184 VAL Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 40 LEU Chi-restraints excluded: chain H residue 97 MET Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 2 SER Chi-restraints excluded: chain K residue 65 ILE Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 72 LEU Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 131 VAL Chi-restraints excluded: chain L residue 62 LYS Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 54 HIS Chi-restraints excluded: chain M residue 143 ASP Chi-restraints excluded: chain M residue 178 LEU Chi-restraints excluded: chain M residue 251 THR Chi-restraints excluded: chain M residue 384 ILE Chi-restraints excluded: chain N residue 93 THR Chi-restraints excluded: chain O residue 348 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 446 optimal weight: 6.9990 chunk 449 optimal weight: 9.9990 chunk 226 optimal weight: 10.0000 chunk 182 optimal weight: 7.9990 chunk 42 optimal weight: 10.0000 chunk 420 optimal weight: 0.9980 chunk 127 optimal weight: 5.9990 chunk 369 optimal weight: 0.7980 chunk 204 optimal weight: 10.0000 chunk 314 optimal weight: 3.9990 chunk 348 optimal weight: 0.1980 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS A 60 ASN A 257 ASN ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1293 HIS A1299 ASN A1315 ASN ** A1601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 GLN ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 473 GLN ** B 544 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 912 GLN B 950 ASN ** B1008 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1094 ASN B1114 GLN C 65 ASN ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 216 HIS ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 153 HIS G 140 GLN ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 54 HIS ** N 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 170 HIS O 152 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.201629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.188604 restraints weight = 69694.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.187887 restraints weight = 102499.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.188541 restraints weight = 93880.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.188181 restraints weight = 72354.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.188438 restraints weight = 65918.170| |-----------------------------------------------------------------------------| r_work (final): 0.4357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6149 moved from start: 0.4351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 40669 Z= 0.152 Angle : 0.739 11.618 55067 Z= 0.378 Chirality : 0.047 0.221 6173 Planarity : 0.006 0.112 6974 Dihedral : 10.903 151.405 5678 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.02 % Allowed : 11.06 % Favored : 88.92 % Rotamer: Outliers : 5.14 % Allowed : 18.92 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.25 (0.11), residues: 4839 helix: -3.31 (0.11), residues: 1305 sheet: -2.94 (0.21), residues: 486 loop : -2.69 (0.11), residues: 3048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 648 TYR 0.028 0.002 TYR A 514 PHE 0.022 0.002 PHE M 132 TRP 0.025 0.002 TRP B 611 HIS 0.018 0.001 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00351 (40654) covalent geometry : angle 0.73465 (55055) hydrogen bonds : bond 0.04100 ( 651) hydrogen bonds : angle 7.40916 ( 1668) metal coordination : bond 0.00881 ( 15) metal coordination : angle 5.34115 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 807 residues out of total 4381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 225 poor density : 582 time to evaluate : 1.472 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.7303 (mm-30) cc_final: 0.6690 (mm-30) REVERT: A 230 ARG cc_start: 0.2723 (OUTLIER) cc_final: 0.1068 (mtm180) REVERT: A 261 ILE cc_start: 0.6904 (OUTLIER) cc_final: 0.6555 (tt) REVERT: A 477 ASN cc_start: 0.7536 (t0) cc_final: 0.7324 (m-40) REVERT: A 494 GLU cc_start: 0.5099 (mt-10) cc_final: 0.4860 (mt-10) REVERT: A 514 TYR cc_start: 0.7144 (OUTLIER) cc_final: 0.6590 (p90) REVERT: A 824 THR cc_start: 0.8407 (OUTLIER) cc_final: 0.7903 (m) REVERT: A 871 ASP cc_start: 0.6477 (p0) cc_final: 0.6139 (p0) REVERT: A 884 ARG cc_start: 0.5912 (mmp-170) cc_final: 0.5409 (ttp80) REVERT: A 1073 TYR cc_start: 0.5775 (p90) cc_final: 0.5022 (p90) REVERT: A 1150 LYS cc_start: 0.7048 (pptt) cc_final: 0.6674 (tptt) REVERT: A 1192 SER cc_start: 0.8985 (m) cc_final: 0.8352 (t) REVERT: A 1300 ASN cc_start: 0.6803 (p0) cc_final: 0.6294 (p0) REVERT: A 1591 ARG cc_start: 0.7419 (OUTLIER) cc_final: 0.6283 (ttt180) REVERT: A 1604 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7648 (pt0) REVERT: A 1615 TYR cc_start: 0.6711 (t80) cc_final: 0.5941 (t80) REVERT: B 35 PHE cc_start: 0.6636 (OUTLIER) cc_final: 0.5685 (p90) REVERT: B 101 GLN cc_start: 0.7919 (tt0) cc_final: 0.7464 (tt0) REVERT: B 161 LEU cc_start: 0.8929 (tm) cc_final: 0.8586 (tp) REVERT: B 261 ARG cc_start: 0.7498 (ttp80) cc_final: 0.7174 (ttt-90) REVERT: B 270 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7325 (pp) REVERT: B 277 LEU cc_start: 0.6456 (OUTLIER) cc_final: 0.6169 (tp) REVERT: B 323 ARG cc_start: 0.5762 (mpt90) cc_final: 0.3531 (ttp-170) REVERT: B 362 LEU cc_start: 0.8071 (mt) cc_final: 0.7791 (tt) REVERT: B 411 MET cc_start: 0.7071 (OUTLIER) cc_final: 0.6265 (mtp) REVERT: B 413 LEU cc_start: 0.7606 (OUTLIER) cc_final: 0.7346 (tp) REVERT: B 471 VAL cc_start: 0.8581 (OUTLIER) cc_final: 0.8360 (m) REVERT: B 543 ASN cc_start: 0.6909 (p0) cc_final: 0.6643 (p0) REVERT: B 672 MET cc_start: 0.6629 (ppp) cc_final: 0.6258 (ptp) REVERT: B 720 GLN cc_start: 0.7749 (mm110) cc_final: 0.7290 (tm-30) REVERT: B 744 LEU cc_start: 0.6861 (OUTLIER) cc_final: 0.6540 (tm) REVERT: B 794 ASP cc_start: 0.7173 (t70) cc_final: 0.6591 (t0) REVERT: B 822 THR cc_start: 0.3646 (p) cc_final: 0.3301 (p) REVERT: B 840 LEU cc_start: 0.6935 (mm) cc_final: 0.6724 (mt) REVERT: B 878 GLU cc_start: 0.6294 (mm-30) cc_final: 0.5761 (tp30) REVERT: B 935 ASP cc_start: 0.7673 (m-30) cc_final: 0.7028 (p0) REVERT: B 957 ARG cc_start: 0.7235 (mmt-90) cc_final: 0.6615 (mmm-85) REVERT: B 967 LEU cc_start: 0.7651 (OUTLIER) cc_final: 0.7367 (mt) REVERT: B 1008 HIS cc_start: 0.7231 (m90) cc_final: 0.6968 (m-70) REVERT: B 1134 ARG cc_start: 0.6516 (mmt-90) cc_final: 0.5245 (mtt180) REVERT: B 1194 ILE cc_start: 0.6653 (OUTLIER) cc_final: 0.6274 (mp) REVERT: C 68 ARG cc_start: 0.7438 (ttp80) cc_final: 0.6901 (ttp80) REVERT: C 329 LYS cc_start: 0.7352 (pptt) cc_final: 0.7008 (tmtt) REVERT: E 42 PHE cc_start: 0.6923 (t80) cc_final: 0.6126 (t80) REVERT: E 43 LYS cc_start: 0.7412 (OUTLIER) cc_final: 0.7169 (pttt) REVERT: E 116 ILE cc_start: 0.5706 (OUTLIER) cc_final: 0.5224 (tp) REVERT: F 120 ILE cc_start: 0.6563 (OUTLIER) cc_final: 0.5905 (mt) REVERT: G 53 TYR cc_start: 0.5770 (m-80) cc_final: 0.4924 (m-80) REVERT: H 45 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.6827 (pm20) REVERT: I 44 ASN cc_start: 0.6928 (m-40) cc_final: 0.6566 (p0) REVERT: J 7 CYS cc_start: 0.5438 (OUTLIER) cc_final: 0.4568 (t) REVERT: K 43 ASP cc_start: 0.7273 (p0) cc_final: 0.6920 (p0) REVERT: K 81 MET cc_start: 0.7836 (ppp) cc_final: 0.7535 (ppp) REVERT: L 38 LEU cc_start: 0.6585 (OUTLIER) cc_final: 0.6311 (pp) REVERT: M 54 HIS cc_start: 0.5485 (OUTLIER) cc_final: 0.3199 (t70) REVERT: M 148 ARG cc_start: 0.5800 (OUTLIER) cc_final: 0.5443 (mtm-85) REVERT: M 178 LEU cc_start: 0.4990 (OUTLIER) cc_final: 0.3445 (mt) REVERT: M 263 TYR cc_start: 0.3836 (t80) cc_final: 0.3269 (t80) REVERT: M 384 ILE cc_start: 0.0589 (OUTLIER) cc_final: -0.0387 (tp) REVERT: M 397 MET cc_start: 0.2791 (mpp) cc_final: 0.1038 (mtt) REVERT: N 40 LEU cc_start: 0.3489 (OUTLIER) cc_final: 0.2959 (mp) REVERT: O 127 GLU cc_start: 0.4214 (mt-10) cc_final: 0.3632 (tt0) REVERT: O 167 LYS cc_start: 0.3856 (mttm) cc_final: 0.3040 (mttt) REVERT: O 396 MET cc_start: -0.0100 (mmm) cc_final: -0.1978 (ptm) REVERT: O 606 MET cc_start: 0.3258 (tmm) cc_final: 0.2872 (tmm) outliers start: 225 outliers final: 123 residues processed: 743 average time/residue: 0.2348 time to fit residues: 292.8381 Evaluate side-chains 668 residues out of total 4381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 519 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 433 ASP Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 818 THR Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 943 ILE Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1033 SER Chi-restraints excluded: chain A residue 1149 ASP Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1198 THR Chi-restraints excluded: chain A residue 1225 ILE Chi-restraints excluded: chain A residue 1239 THR Chi-restraints excluded: chain A residue 1264 SER Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1315 ASN Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1442 VAL Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1538 VAL Chi-restraints excluded: chain A residue 1568 ASN Chi-restraints excluded: chain A residue 1589 MET Chi-restraints excluded: chain A residue 1591 ARG Chi-restraints excluded: chain A residue 1604 GLU Chi-restraints excluded: chain A residue 1611 MET Chi-restraints excluded: chain A residue 1630 GLU Chi-restraints excluded: chain A residue 1642 VAL Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 473 GLN Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain B residue 492 ASN Chi-restraints excluded: chain B residue 588 ILE Chi-restraints excluded: chain B residue 595 TRP Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 700 LEU Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 744 LEU Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 907 ILE Chi-restraints excluded: chain B residue 950 ASN Chi-restraints excluded: chain B residue 967 LEU Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1036 LEU Chi-restraints excluded: chain B residue 1093 LEU Chi-restraints excluded: chain B residue 1113 THR Chi-restraints excluded: chain B residue 1117 VAL Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1128 CYS Chi-restraints excluded: chain B residue 1131 CYS Chi-restraints excluded: chain B residue 1194 ILE Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 226 SER Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 187 TYR Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 116 TYR Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 44 TYR Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 131 VAL Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 53 HIS Chi-restraints excluded: chain L residue 62 LYS Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 54 HIS Chi-restraints excluded: chain M residue 148 ARG Chi-restraints excluded: chain M residue 178 LEU Chi-restraints excluded: chain M residue 251 THR Chi-restraints excluded: chain M residue 360 VAL Chi-restraints excluded: chain M residue 371 VAL Chi-restraints excluded: chain M residue 384 ILE Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 89 ILE Chi-restraints excluded: chain N residue 93 THR Chi-restraints excluded: chain N residue 166 LEU Chi-restraints excluded: chain O residue 73 ILE Chi-restraints excluded: chain O residue 348 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 262 optimal weight: 1.9990 chunk 206 optimal weight: 7.9990 chunk 90 optimal weight: 2.9990 chunk 155 optimal weight: 0.9990 chunk 441 optimal weight: 4.9990 chunk 50 optimal weight: 6.9990 chunk 265 optimal weight: 0.9990 chunk 204 optimal weight: 20.0000 chunk 52 optimal weight: 7.9990 chunk 293 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 649 ASN ** A 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 998 HIS ** A1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1293 HIS A1299 ASN A1500 GLN ** A1601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1629 ASN ** A1647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 HIS B 231 HIS B 243 GLN ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 473 GLN ** B 544 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 600 GLN ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1082 HIS B1094 ASN ** B1171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 216 HIS ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 GLN G 23 GLN ** G 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 ASN ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.202006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.188939 restraints weight = 70023.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.188170 restraints weight = 105827.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.188624 restraints weight = 92369.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.188782 restraints weight = 77473.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.188916 restraints weight = 64703.166| |-----------------------------------------------------------------------------| r_work (final): 0.4359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6149 moved from start: 0.4640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 40669 Z= 0.148 Angle : 0.713 10.148 55067 Z= 0.363 Chirality : 0.046 0.189 6173 Planarity : 0.005 0.110 6974 Dihedral : 10.684 151.101 5678 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.02 % Allowed : 12.13 % Favored : 87.85 % Rotamer: Outliers : 5.55 % Allowed : 19.79 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.08 (0.11), residues: 4839 helix: -3.17 (0.11), residues: 1331 sheet: -2.89 (0.21), residues: 490 loop : -2.55 (0.11), residues: 3018 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 59 TYR 0.027 0.002 TYR A 514 PHE 0.029 0.002 PHE C 314 TRP 0.046 0.002 TRP B 143 HIS 0.014 0.001 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00341 (40654) covalent geometry : angle 0.70981 (55055) hydrogen bonds : bond 0.03814 ( 651) hydrogen bonds : angle 7.15542 ( 1668) metal coordination : bond 0.00776 ( 15) metal coordination : angle 4.84280 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 798 residues out of total 4381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 243 poor density : 555 time to evaluate : 1.567 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: symmetry clash revert: symmetry clash REVERT: A 230 ARG cc_start: 0.2591 (OUTLIER) cc_final: 0.1100 (mtm180) REVERT: A 261 ILE cc_start: 0.6970 (OUTLIER) cc_final: 0.6643 (tt) REVERT: A 521 GLN cc_start: 0.7560 (tp-100) cc_final: 0.7026 (tp-100) REVERT: A 600 MET cc_start: 0.7293 (tpp) cc_final: 0.7069 (tpp) REVERT: A 633 MET cc_start: 0.8126 (ptp) cc_final: 0.7862 (ptp) REVERT: A 649 ASN cc_start: 0.6163 (OUTLIER) cc_final: 0.5632 (m110) REVERT: A 824 THR cc_start: 0.8471 (OUTLIER) cc_final: 0.7950 (m) REVERT: A 830 MET cc_start: 0.6678 (mmm) cc_final: 0.6373 (mmt) REVERT: A 833 LEU cc_start: 0.7731 (mm) cc_final: 0.7418 (mm) REVERT: A 871 ASP cc_start: 0.6535 (p0) cc_final: 0.6195 (p0) REVERT: A 884 ARG cc_start: 0.5945 (mmp-170) cc_final: 0.5368 (ttp80) REVERT: A 892 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7164 (pp) REVERT: A 1073 TYR cc_start: 0.5673 (p90) cc_final: 0.5264 (p90) REVERT: A 1089 LEU cc_start: 0.6883 (OUTLIER) cc_final: 0.6643 (mm) REVERT: A 1192 SER cc_start: 0.8995 (m) cc_final: 0.8346 (t) REVERT: A 1227 MET cc_start: 0.8873 (mtp) cc_final: 0.8607 (mtp) REVERT: A 1300 ASN cc_start: 0.6806 (p0) cc_final: 0.6599 (p0) REVERT: A 1439 MET cc_start: 0.4012 (mmm) cc_final: 0.3143 (mpp) REVERT: A 1591 ARG cc_start: 0.7453 (OUTLIER) cc_final: 0.6328 (ttt180) REVERT: A 1604 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7663 (pt0) REVERT: A 1611 MET cc_start: 0.7121 (OUTLIER) cc_final: 0.6601 (mtp) REVERT: A 1615 TYR cc_start: 0.6446 (t80) cc_final: 0.5811 (t80) REVERT: B 35 PHE cc_start: 0.6710 (OUTLIER) cc_final: 0.5601 (p90) REVERT: B 101 GLN cc_start: 0.7965 (tt0) cc_final: 0.7507 (tt0) REVERT: B 206 LEU cc_start: 0.6479 (OUTLIER) cc_final: 0.6207 (tm) REVERT: B 261 ARG cc_start: 0.7507 (ttp80) cc_final: 0.7124 (ttt-90) REVERT: B 270 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7381 (pp) REVERT: B 277 LEU cc_start: 0.6228 (OUTLIER) cc_final: 0.5945 (tp) REVERT: B 323 ARG cc_start: 0.5796 (mpt90) cc_final: 0.3557 (ttp-170) REVERT: B 373 MET cc_start: 0.8102 (tpt) cc_final: 0.7847 (tpt) REVERT: B 377 MET cc_start: 0.6334 (tpp) cc_final: 0.6058 (mmt) REVERT: B 411 MET cc_start: 0.7117 (OUTLIER) cc_final: 0.6827 (mpp) REVERT: B 425 ILE cc_start: 0.6080 (pt) cc_final: 0.5537 (tt) REVERT: B 461 MET cc_start: 0.7984 (mmt) cc_final: 0.7692 (mmt) REVERT: B 489 GLU cc_start: 0.5430 (OUTLIER) cc_final: 0.5134 (tt0) REVERT: B 542 LEU cc_start: 0.6348 (OUTLIER) cc_final: 0.6025 (pp) REVERT: B 672 MET cc_start: 0.6778 (ppp) cc_final: 0.6061 (ptp) REVERT: B 720 GLN cc_start: 0.7640 (mm110) cc_final: 0.7169 (tm-30) REVERT: B 744 LEU cc_start: 0.6841 (OUTLIER) cc_final: 0.6524 (tm) REVERT: B 794 ASP cc_start: 0.7092 (t70) cc_final: 0.6630 (t0) REVERT: B 822 THR cc_start: 0.3991 (p) cc_final: 0.3655 (p) REVERT: B 840 LEU cc_start: 0.6849 (OUTLIER) cc_final: 0.6604 (mt) REVERT: B 878 GLU cc_start: 0.6491 (mm-30) cc_final: 0.6118 (tp30) REVERT: B 882 ILE cc_start: 0.5608 (OUTLIER) cc_final: 0.5141 (mt) REVERT: B 935 ASP cc_start: 0.7425 (m-30) cc_final: 0.7006 (p0) REVERT: B 957 ARG cc_start: 0.7332 (mmt-90) cc_final: 0.6900 (mmm-85) REVERT: B 967 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7414 (mt) REVERT: B 1106 GLU cc_start: 0.6280 (OUTLIER) cc_final: 0.6062 (mp0) REVERT: B 1134 ARG cc_start: 0.6396 (mmt-90) cc_final: 0.5212 (mtt180) REVERT: B 1166 LYS cc_start: 0.7348 (tppt) cc_final: 0.6835 (tttm) REVERT: B 1194 ILE cc_start: 0.6627 (OUTLIER) cc_final: 0.6292 (mp) REVERT: C 34 GLU cc_start: 0.5003 (OUTLIER) cc_final: 0.4344 (tm-30) REVERT: C 54 PHE cc_start: 0.7312 (OUTLIER) cc_final: 0.4839 (m-80) REVERT: C 68 ARG cc_start: 0.7557 (ttp80) cc_final: 0.7267 (ttt-90) REVERT: C 329 LYS cc_start: 0.7387 (pptt) cc_final: 0.7011 (tmtt) REVERT: E 42 PHE cc_start: 0.6941 (t80) cc_final: 0.6075 (t80) REVERT: E 116 ILE cc_start: 0.5747 (OUTLIER) cc_final: 0.5294 (tp) REVERT: E 215 MET cc_start: 0.4704 (pp-130) cc_final: 0.3998 (pp-130) REVERT: F 120 ILE cc_start: 0.6582 (OUTLIER) cc_final: 0.5967 (mt) REVERT: G 53 TYR cc_start: 0.5761 (m-80) cc_final: 0.4931 (m-80) REVERT: G 76 LYS cc_start: 0.5060 (mptt) cc_final: 0.4076 (mtmt) REVERT: G 107 ILE cc_start: 0.7864 (OUTLIER) cc_final: 0.7648 (tt) REVERT: H 45 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.6967 (pm20) REVERT: I 44 ASN cc_start: 0.6976 (m-40) cc_final: 0.6569 (p0) REVERT: J 7 CYS cc_start: 0.5029 (OUTLIER) cc_final: 0.4232 (t) REVERT: K 43 ASP cc_start: 0.7299 (p0) cc_final: 0.6852 (p0) REVERT: L 38 LEU cc_start: 0.6455 (OUTLIER) cc_final: 0.6076 (pp) REVERT: M 178 LEU cc_start: 0.4928 (OUTLIER) cc_final: 0.3403 (mt) REVERT: M 263 TYR cc_start: 0.3469 (t80) cc_final: 0.3017 (t80) REVERT: M 384 ILE cc_start: 0.0488 (OUTLIER) cc_final: -0.0550 (tp) REVERT: M 397 MET cc_start: 0.2412 (mpp) cc_final: 0.0982 (mtt) REVERT: N 40 LEU cc_start: 0.3262 (OUTLIER) cc_final: 0.2691 (mp) REVERT: O 127 GLU cc_start: 0.4647 (mt-10) cc_final: 0.4154 (tt0) REVERT: O 167 LYS cc_start: 0.4337 (mttm) cc_final: 0.3856 (mttt) REVERT: O 385 MET cc_start: 0.5368 (mpp) cc_final: 0.4708 (mtt) REVERT: O 396 MET cc_start: -0.0314 (mmm) cc_final: -0.2069 (ptp) outliers start: 243 outliers final: 139 residues processed: 728 average time/residue: 0.2274 time to fit residues: 279.9082 Evaluate side-chains 671 residues out of total 4381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 499 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 649 ASN Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 818 THR Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 905 SER Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 943 ILE Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1033 SER Chi-restraints excluded: chain A residue 1063 MET Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1225 ILE Chi-restraints excluded: chain A residue 1239 THR Chi-restraints excluded: chain A residue 1264 SER Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1315 ASN Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1442 VAL Chi-restraints excluded: chain A residue 1486 VAL Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1538 VAL Chi-restraints excluded: chain A residue 1568 ASN Chi-restraints excluded: chain A residue 1589 MET Chi-restraints excluded: chain A residue 1591 ARG Chi-restraints excluded: chain A residue 1604 GLU Chi-restraints excluded: chain A residue 1611 MET Chi-restraints excluded: chain A residue 1630 GLU Chi-restraints excluded: chain A residue 1642 VAL Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain B residue 489 GLU Chi-restraints excluded: chain B residue 492 ASN Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 588 ILE Chi-restraints excluded: chain B residue 595 TRP Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 649 MET Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 697 LEU Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain B residue 725 THR Chi-restraints excluded: chain B residue 744 LEU Chi-restraints excluded: chain B residue 782 ASP Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 871 ILE Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 907 ILE Chi-restraints excluded: chain B residue 967 LEU Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1036 LEU Chi-restraints excluded: chain B residue 1093 LEU Chi-restraints excluded: chain B residue 1106 GLU Chi-restraints excluded: chain B residue 1113 THR Chi-restraints excluded: chain B residue 1117 VAL Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1128 CYS Chi-restraints excluded: chain B residue 1131 CYS Chi-restraints excluded: chain B residue 1133 MET Chi-restraints excluded: chain B residue 1156 SER Chi-restraints excluded: chain B residue 1194 ILE Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 54 PHE Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 226 SER Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 177 ARG Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 187 TYR Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 116 TYR Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 44 TYR Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 65 ILE Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 72 LEU Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 131 VAL Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 62 LYS Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain M residue 148 ARG Chi-restraints excluded: chain M residue 178 LEU Chi-restraints excluded: chain M residue 251 THR Chi-restraints excluded: chain M residue 360 VAL Chi-restraints excluded: chain M residue 371 VAL Chi-restraints excluded: chain M residue 384 ILE Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain N residue 69 SER Chi-restraints excluded: chain N residue 89 ILE Chi-restraints excluded: chain N residue 93 THR Chi-restraints excluded: chain N residue 166 LEU Chi-restraints excluded: chain O residue 73 ILE Chi-restraints excluded: chain O residue 348 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 165 optimal weight: 6.9990 chunk 73 optimal weight: 0.9980 chunk 286 optimal weight: 0.0370 chunk 177 optimal weight: 3.9990 chunk 385 optimal weight: 1.9990 chunk 126 optimal weight: 8.9990 chunk 140 optimal weight: 0.6980 chunk 352 optimal weight: 10.0000 chunk 450 optimal weight: 8.9990 chunk 258 optimal weight: 2.9990 chunk 388 optimal weight: 7.9990 overall best weight: 1.3462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 785 GLN A 942 GLN ** A1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1293 HIS A1299 ASN A1315 ASN ** A1525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1620 GLN A1629 ASN ** A1647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 HIS B 243 GLN ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 912 GLN B1094 ASN ** B1171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 18 GLN ** N 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.205479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.191795 restraints weight = 70393.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.191192 restraints weight = 97691.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.191916 restraints weight = 83556.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.191665 restraints weight = 70805.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.191910 restraints weight = 61140.336| |-----------------------------------------------------------------------------| r_work (final): 0.4389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6094 moved from start: 0.4887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 40669 Z= 0.124 Angle : 0.689 13.441 55067 Z= 0.348 Chirality : 0.045 0.180 6173 Planarity : 0.005 0.095 6974 Dihedral : 10.422 151.865 5676 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.29 % Favored : 89.69 % Rotamer: Outliers : 4.71 % Allowed : 21.07 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.87 (0.11), residues: 4839 helix: -2.93 (0.12), residues: 1327 sheet: -2.67 (0.21), residues: 493 loop : -2.47 (0.11), residues: 3019 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 743 TYR 0.026 0.002 TYR B 742 PHE 0.025 0.001 PHE M 132 TRP 0.031 0.002 TRP E 79 HIS 0.009 0.001 HIS A 617 Details of bonding type rmsd covalent geometry : bond 0.00286 (40654) covalent geometry : angle 0.68548 (55055) hydrogen bonds : bond 0.03500 ( 651) hydrogen bonds : angle 6.87417 ( 1668) metal coordination : bond 0.00767 ( 15) metal coordination : angle 4.94775 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 756 residues out of total 4381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 206 poor density : 550 time to evaluate : 1.510 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 230 ARG cc_start: 0.2921 (OUTLIER) cc_final: 0.1210 (mtm180) REVERT: A 261 ILE cc_start: 0.7083 (OUTLIER) cc_final: 0.6772 (tt) REVERT: A 335 LEU cc_start: 0.8664 (mm) cc_final: 0.8442 (mt) REVERT: A 521 GLN cc_start: 0.7507 (tp-100) cc_final: 0.7209 (tp-100) REVERT: A 744 MET cc_start: 0.7501 (mmt) cc_final: 0.7250 (mtt) REVERT: A 824 THR cc_start: 0.8311 (OUTLIER) cc_final: 0.7825 (m) REVERT: A 830 MET cc_start: 0.6561 (mmm) cc_final: 0.6169 (mmt) REVERT: A 833 LEU cc_start: 0.7607 (mm) cc_final: 0.7284 (mm) REVERT: A 871 ASP cc_start: 0.6440 (p0) cc_final: 0.6088 (p0) REVERT: A 884 ARG cc_start: 0.5685 (mmp-170) cc_final: 0.5133 (ttp80) REVERT: A 892 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7105 (pp) REVERT: A 953 GLU cc_start: 0.5466 (OUTLIER) cc_final: 0.4941 (pp20) REVERT: A 1073 TYR cc_start: 0.5614 (p90) cc_final: 0.5303 (p90) REVERT: A 1192 SER cc_start: 0.8903 (m) cc_final: 0.8286 (t) REVERT: A 1227 MET cc_start: 0.8866 (mtp) cc_final: 0.8560 (mtp) REVERT: A 1439 MET cc_start: 0.4105 (mmm) cc_final: 0.3252 (mpp) REVERT: A 1591 ARG cc_start: 0.7659 (OUTLIER) cc_final: 0.6372 (ttt180) REVERT: A 1604 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7589 (pt0) REVERT: A 1611 MET cc_start: 0.7090 (ttm) cc_final: 0.6680 (mtp) REVERT: B 35 PHE cc_start: 0.6764 (OUTLIER) cc_final: 0.5618 (p90) REVERT: B 46 ILE cc_start: 0.8606 (mm) cc_final: 0.8301 (mm) REVERT: B 164 MET cc_start: 0.6900 (pmm) cc_final: 0.6388 (pmm) REVERT: B 261 ARG cc_start: 0.7396 (ttp80) cc_final: 0.7105 (ttt-90) REVERT: B 277 LEU cc_start: 0.6107 (OUTLIER) cc_final: 0.5806 (tt) REVERT: B 323 ARG cc_start: 0.5739 (mpt90) cc_final: 0.3560 (ttp-170) REVERT: B 373 MET cc_start: 0.8013 (tpt) cc_final: 0.7660 (tpt) REVERT: B 377 MET cc_start: 0.6331 (tpp) cc_final: 0.5818 (mmm) REVERT: B 411 MET cc_start: 0.6760 (OUTLIER) cc_final: 0.5909 (mtp) REVERT: B 425 ILE cc_start: 0.6128 (pt) cc_final: 0.5544 (tt) REVERT: B 542 LEU cc_start: 0.6254 (OUTLIER) cc_final: 0.5935 (pp) REVERT: B 672 MET cc_start: 0.6755 (ppp) cc_final: 0.6021 (ptp) REVERT: B 744 LEU cc_start: 0.7048 (OUTLIER) cc_final: 0.6695 (tm) REVERT: B 822 THR cc_start: 0.3531 (p) cc_final: 0.3190 (p) REVERT: B 840 LEU cc_start: 0.6708 (mm) cc_final: 0.6501 (mt) REVERT: B 878 GLU cc_start: 0.6559 (mm-30) cc_final: 0.6236 (mm-30) REVERT: B 882 ILE cc_start: 0.5137 (OUTLIER) cc_final: 0.4824 (mt) REVERT: B 935 ASP cc_start: 0.7130 (m-30) cc_final: 0.6883 (p0) REVERT: B 957 ARG cc_start: 0.7138 (mmt-90) cc_final: 0.6920 (mmm-85) REVERT: B 967 LEU cc_start: 0.7549 (OUTLIER) cc_final: 0.7291 (mt) REVERT: B 1076 ARG cc_start: 0.7306 (tpm-80) cc_final: 0.6309 (ttp-170) REVERT: B 1126 VAL cc_start: 0.7632 (OUTLIER) cc_final: 0.7411 (m) REVERT: B 1134 ARG cc_start: 0.6307 (mmt-90) cc_final: 0.5144 (mtt180) REVERT: B 1166 LYS cc_start: 0.7362 (tppt) cc_final: 0.6791 (tttm) REVERT: C 34 GLU cc_start: 0.4766 (OUTLIER) cc_final: 0.4214 (tm-30) REVERT: C 54 PHE cc_start: 0.7230 (OUTLIER) cc_final: 0.5036 (m-80) REVERT: C 329 LYS cc_start: 0.7386 (pptt) cc_final: 0.6999 (tmtt) REVERT: E 42 PHE cc_start: 0.6667 (t80) cc_final: 0.5986 (t80) REVERT: E 116 ILE cc_start: 0.5861 (OUTLIER) cc_final: 0.5467 (tp) REVERT: E 149 LEU cc_start: 0.6360 (OUTLIER) cc_final: 0.6112 (mm) REVERT: E 171 LYS cc_start: 0.5439 (mmtt) cc_final: 0.5224 (mmtt) REVERT: E 215 MET cc_start: 0.4545 (pp-130) cc_final: 0.4009 (pp-130) REVERT: G 53 TYR cc_start: 0.5655 (m-80) cc_final: 0.4861 (m-80) REVERT: G 71 MET cc_start: 0.6537 (mmt) cc_final: 0.6244 (mmt) REVERT: H 45 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.6913 (pm20) REVERT: I 44 ASN cc_start: 0.6889 (m-40) cc_final: 0.6544 (p0) REVERT: J 7 CYS cc_start: 0.4652 (OUTLIER) cc_final: 0.3949 (t) REVERT: K 43 ASP cc_start: 0.7325 (p0) cc_final: 0.6931 (p0) REVERT: L 38 LEU cc_start: 0.6507 (OUTLIER) cc_final: 0.6289 (pp) REVERT: M 125 ARG cc_start: 0.4695 (mmt180) cc_final: 0.4327 (mpt180) REVERT: M 178 LEU cc_start: 0.4445 (OUTLIER) cc_final: 0.3474 (mt) REVERT: M 263 TYR cc_start: 0.3686 (t80) cc_final: 0.3209 (t80) REVERT: M 384 ILE cc_start: 0.0398 (OUTLIER) cc_final: -0.0177 (tt) REVERT: M 397 MET cc_start: 0.2454 (mpp) cc_final: 0.0956 (mtt) REVERT: N 40 LEU cc_start: 0.3150 (OUTLIER) cc_final: 0.2524 (mp) REVERT: O 127 GLU cc_start: 0.4268 (mt-10) cc_final: 0.3985 (tt0) REVERT: O 167 LYS cc_start: 0.4559 (mttm) cc_final: 0.4036 (mttt) REVERT: O 197 PHE cc_start: 0.4880 (m-80) cc_final: 0.4576 (t80) REVERT: O 385 MET cc_start: 0.5232 (mpp) cc_final: 0.4657 (mtt) REVERT: O 396 MET cc_start: -0.0593 (mmm) cc_final: -0.2128 (ptp) REVERT: O 514 PHE cc_start: 0.6118 (m-80) cc_final: 0.5807 (m-80) REVERT: O 606 MET cc_start: 0.3513 (tmm) cc_final: 0.3146 (tmm) outliers start: 206 outliers final: 134 residues processed: 698 average time/residue: 0.2376 time to fit residues: 277.5643 Evaluate side-chains 658 residues out of total 4381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 499 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 731 ILE Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 786 TYR Chi-restraints excluded: chain A residue 818 THR Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 905 SER Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 943 ILE Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 953 GLU Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1033 SER Chi-restraints excluded: chain A residue 1063 MET Chi-restraints excluded: chain A residue 1108 HIS Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1225 ILE Chi-restraints excluded: chain A residue 1239 THR Chi-restraints excluded: chain A residue 1264 SER Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1315 ASN Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1442 VAL Chi-restraints excluded: chain A residue 1486 VAL Chi-restraints excluded: chain A residue 1503 HIS Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1538 VAL Chi-restraints excluded: chain A residue 1568 ASN Chi-restraints excluded: chain A residue 1589 MET Chi-restraints excluded: chain A residue 1591 ARG Chi-restraints excluded: chain A residue 1604 GLU Chi-restraints excluded: chain A residue 1629 ASN Chi-restraints excluded: chain A residue 1630 GLU Chi-restraints excluded: chain A residue 1642 VAL Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 143 TRP Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 471 VAL Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain B residue 492 ASN Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 588 ILE Chi-restraints excluded: chain B residue 595 TRP Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 649 MET Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 744 LEU Chi-restraints excluded: chain B residue 782 ASP Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 962 MET Chi-restraints excluded: chain B residue 967 LEU Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1113 THR Chi-restraints excluded: chain B residue 1117 VAL Chi-restraints excluded: chain B residue 1125 THR Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1128 CYS Chi-restraints excluded: chain B residue 1131 CYS Chi-restraints excluded: chain B residue 1156 SER Chi-restraints excluded: chain B residue 1188 GLU Chi-restraints excluded: chain B residue 1196 LEU Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 54 PHE Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain E residue 7 ARG Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 187 TYR Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 200 ARG Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 116 TYR Chi-restraints excluded: chain H residue 130 ARG Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 44 TYR Chi-restraints excluded: chain K residue 50 LEU Chi-restraints excluded: chain K residue 65 ILE Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 72 LEU Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 131 VAL Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 53 HIS Chi-restraints excluded: chain L residue 62 LYS Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 148 ARG Chi-restraints excluded: chain M residue 178 LEU Chi-restraints excluded: chain M residue 251 THR Chi-restraints excluded: chain M residue 360 VAL Chi-restraints excluded: chain M residue 371 VAL Chi-restraints excluded: chain M residue 384 ILE Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain N residue 69 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 89 ILE Chi-restraints excluded: chain N residue 166 LEU Chi-restraints excluded: chain O residue 166 ILE Chi-restraints excluded: chain O residue 348 THR Chi-restraints excluded: chain O residue 371 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 78 optimal weight: 3.9990 chunk 76 optimal weight: 9.9990 chunk 67 optimal weight: 0.3980 chunk 371 optimal weight: 6.9990 chunk 53 optimal weight: 8.9990 chunk 238 optimal weight: 0.5980 chunk 456 optimal weight: 8.9990 chunk 107 optimal weight: 5.9990 chunk 217 optimal weight: 2.9990 chunk 402 optimal weight: 0.0030 chunk 28 optimal weight: 1.9990 overall best weight: 1.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1293 HIS A1299 ASN A1315 ASN ** A1525 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1629 ASN A1647 ASN B 183 HIS B 243 GLN ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 ASN ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1094 ASN C 161 HIS ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 HIS G 119 HIS ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 85 HIS O 390 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.206113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.193428 restraints weight = 70623.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.192723 restraints weight = 105220.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.193466 restraints weight = 93058.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.193003 restraints weight = 71490.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.193259 restraints weight = 64280.278| |-----------------------------------------------------------------------------| r_work (final): 0.4408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6053 moved from start: 0.5102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 40669 Z= 0.122 Angle : 0.679 11.522 55067 Z= 0.342 Chirality : 0.044 0.187 6173 Planarity : 0.005 0.093 6974 Dihedral : 10.273 152.057 5676 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.98 % Favored : 90.00 % Rotamer: Outliers : 4.50 % Allowed : 21.57 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.69 (0.11), residues: 4839 helix: -2.74 (0.12), residues: 1329 sheet: -2.58 (0.21), residues: 513 loop : -2.37 (0.11), residues: 2997 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B1076 TYR 0.029 0.001 TYR B 671 PHE 0.029 0.001 PHE O 473 TRP 0.034 0.002 TRP E 79 HIS 0.017 0.001 HIS B 183 Details of bonding type rmsd covalent geometry : bond 0.00278 (40654) covalent geometry : angle 0.67661 (55055) hydrogen bonds : bond 0.03307 ( 651) hydrogen bonds : angle 6.74712 ( 1668) metal coordination : bond 0.00647 ( 15) metal coordination : angle 4.28459 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 741 residues out of total 4381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 197 poor density : 544 time to evaluate : 1.457 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 72 CYS cc_start: 0.7500 (m) cc_final: 0.7082 (t) REVERT: A 230 ARG cc_start: 0.2584 (OUTLIER) cc_final: 0.1248 (mtm180) REVERT: A 261 ILE cc_start: 0.7067 (OUTLIER) cc_final: 0.6726 (tt) REVERT: A 335 LEU cc_start: 0.8576 (mm) cc_final: 0.8301 (mt) REVERT: A 521 GLN cc_start: 0.7510 (tp-100) cc_final: 0.7239 (tp-100) REVERT: A 600 MET cc_start: 0.6713 (mmt) cc_final: 0.6317 (mmt) REVERT: A 632 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8342 (pp20) REVERT: A 633 MET cc_start: 0.7899 (ptp) cc_final: 0.7693 (ptp) REVERT: A 824 THR cc_start: 0.8315 (OUTLIER) cc_final: 0.7829 (m) REVERT: A 830 MET cc_start: 0.6525 (mmm) cc_final: 0.5709 (mmt) REVERT: A 833 LEU cc_start: 0.7432 (mm) cc_final: 0.7216 (mm) REVERT: A 871 ASP cc_start: 0.6484 (p0) cc_final: 0.6108 (p0) REVERT: A 884 ARG cc_start: 0.5741 (mmp-170) cc_final: 0.5198 (ttp80) REVERT: A 953 GLU cc_start: 0.5473 (OUTLIER) cc_final: 0.4845 (pp20) REVERT: A 1073 TYR cc_start: 0.5765 (p90) cc_final: 0.5508 (p90) REVERT: A 1192 SER cc_start: 0.8868 (m) cc_final: 0.8236 (t) REVERT: A 1227 MET cc_start: 0.8852 (mtp) cc_final: 0.8596 (mtp) REVERT: A 1591 ARG cc_start: 0.7635 (OUTLIER) cc_final: 0.6458 (ttt180) REVERT: A 1604 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7608 (pt0) REVERT: A 1611 MET cc_start: 0.7193 (ttm) cc_final: 0.6769 (mtp) REVERT: A 1613 MET cc_start: 0.7116 (tpp) cc_final: 0.6626 (tmm) REVERT: B 35 PHE cc_start: 0.6753 (OUTLIER) cc_final: 0.5583 (p90) REVERT: B 46 ILE cc_start: 0.8548 (mm) cc_final: 0.8267 (mm) REVERT: B 261 ARG cc_start: 0.7417 (ttp80) cc_final: 0.7100 (ttt-90) REVERT: B 270 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7176 (pp) REVERT: B 277 LEU cc_start: 0.6269 (OUTLIER) cc_final: 0.6004 (tt) REVERT: B 323 ARG cc_start: 0.5709 (mpt90) cc_final: 0.3576 (ttp-170) REVERT: B 373 MET cc_start: 0.7983 (tpt) cc_final: 0.7628 (tpt) REVERT: B 377 MET cc_start: 0.6298 (tpp) cc_final: 0.5774 (mmm) REVERT: B 411 MET cc_start: 0.6828 (OUTLIER) cc_final: 0.6029 (mtp) REVERT: B 425 ILE cc_start: 0.6009 (pt) cc_final: 0.5450 (tt) REVERT: B 461 MET cc_start: 0.7831 (mmt) cc_final: 0.7623 (mmt) REVERT: B 672 MET cc_start: 0.6636 (ppp) cc_final: 0.6114 (ptt) REVERT: B 744 LEU cc_start: 0.7032 (OUTLIER) cc_final: 0.6700 (tm) REVERT: B 822 THR cc_start: 0.3187 (p) cc_final: 0.2806 (p) REVERT: B 840 LEU cc_start: 0.6639 (OUTLIER) cc_final: 0.6435 (mt) REVERT: B 878 GLU cc_start: 0.6427 (mm-30) cc_final: 0.6003 (mm-30) REVERT: B 882 ILE cc_start: 0.5406 (OUTLIER) cc_final: 0.5039 (mt) REVERT: B 967 LEU cc_start: 0.7468 (OUTLIER) cc_final: 0.7216 (mt) REVERT: B 1036 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8079 (mt) REVERT: B 1134 ARG cc_start: 0.6301 (mmt-90) cc_final: 0.5229 (mtt180) REVERT: B 1166 LYS cc_start: 0.7462 (tppt) cc_final: 0.7202 (tttm) REVERT: C 34 GLU cc_start: 0.4649 (OUTLIER) cc_final: 0.4159 (tm-30) REVERT: C 106 LEU cc_start: 0.8263 (mm) cc_final: 0.8009 (mm) REVERT: C 329 LYS cc_start: 0.7367 (pptt) cc_final: 0.6968 (tmtt) REVERT: D 38 GLN cc_start: 0.3703 (mp10) cc_final: 0.2287 (tt0) REVERT: E 42 PHE cc_start: 0.6421 (t80) cc_final: 0.5878 (t80) REVERT: E 116 ILE cc_start: 0.5746 (OUTLIER) cc_final: 0.5366 (tp) REVERT: E 149 LEU cc_start: 0.6485 (OUTLIER) cc_final: 0.6218 (mm) REVERT: E 150 VAL cc_start: 0.8485 (OUTLIER) cc_final: 0.8245 (t) REVERT: E 177 ARG cc_start: 0.7062 (OUTLIER) cc_final: 0.5760 (ptt-90) REVERT: G 53 TYR cc_start: 0.5722 (m-80) cc_final: 0.5430 (m-10) REVERT: H 45 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.6912 (pm20) REVERT: I 44 ASN cc_start: 0.6763 (m-40) cc_final: 0.6507 (p0) REVERT: J 7 CYS cc_start: 0.4909 (OUTLIER) cc_final: 0.4143 (t) REVERT: J 47 ARG cc_start: 0.7457 (mmm-85) cc_final: 0.7233 (mtp85) REVERT: K 43 ASP cc_start: 0.7674 (p0) cc_final: 0.7418 (p0) REVERT: K 137 GLU cc_start: 0.6863 (mp0) cc_final: 0.6061 (pm20) REVERT: L 38 LEU cc_start: 0.6538 (OUTLIER) cc_final: 0.6096 (pp) REVERT: M 178 LEU cc_start: 0.4409 (OUTLIER) cc_final: 0.3569 (mt) REVERT: M 263 TYR cc_start: 0.3666 (t80) cc_final: 0.3147 (t80) REVERT: M 384 ILE cc_start: 0.0259 (OUTLIER) cc_final: -0.0342 (tt) REVERT: M 397 MET cc_start: 0.2509 (mpp) cc_final: 0.1032 (mtt) REVERT: N 40 LEU cc_start: 0.3122 (OUTLIER) cc_final: 0.2227 (mp) REVERT: O 127 GLU cc_start: 0.4460 (mt-10) cc_final: 0.4202 (tt0) REVERT: O 197 PHE cc_start: 0.4714 (m-80) cc_final: 0.4500 (t80) REVERT: O 385 MET cc_start: 0.5217 (mpp) cc_final: 0.4602 (mtt) REVERT: O 396 MET cc_start: -0.1172 (mmm) cc_final: -0.1757 (ptp) REVERT: O 514 PHE cc_start: 0.6394 (m-80) cc_final: 0.5989 (m-80) REVERT: O 527 MET cc_start: -0.1305 (ttt) cc_final: -0.4477 (mmm) outliers start: 197 outliers final: 124 residues processed: 689 average time/residue: 0.2274 time to fit residues: 263.8769 Evaluate side-chains 646 residues out of total 4381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 495 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 632 GLU Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 786 TYR Chi-restraints excluded: chain A residue 818 THR Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 953 GLU Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1063 MET Chi-restraints excluded: chain A residue 1108 HIS Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1225 ILE Chi-restraints excluded: chain A residue 1239 THR Chi-restraints excluded: chain A residue 1270 VAL Chi-restraints excluded: chain A residue 1271 ILE Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1442 VAL Chi-restraints excluded: chain A residue 1486 VAL Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1538 VAL Chi-restraints excluded: chain A residue 1568 ASN Chi-restraints excluded: chain A residue 1579 PHE Chi-restraints excluded: chain A residue 1582 LEU Chi-restraints excluded: chain A residue 1589 MET Chi-restraints excluded: chain A residue 1591 ARG Chi-restraints excluded: chain A residue 1604 GLU Chi-restraints excluded: chain A residue 1628 ASP Chi-restraints excluded: chain A residue 1629 ASN Chi-restraints excluded: chain A residue 1630 GLU Chi-restraints excluded: chain A residue 1642 VAL Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 143 TRP Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 588 ILE Chi-restraints excluded: chain B residue 595 TRP Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain B residue 744 LEU Chi-restraints excluded: chain B residue 782 ASP Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 871 ILE Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 907 ILE Chi-restraints excluded: chain B residue 967 LEU Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1036 LEU Chi-restraints excluded: chain B residue 1093 LEU Chi-restraints excluded: chain B residue 1113 THR Chi-restraints excluded: chain B residue 1117 VAL Chi-restraints excluded: chain B residue 1125 THR Chi-restraints excluded: chain B residue 1128 CYS Chi-restraints excluded: chain B residue 1131 CYS Chi-restraints excluded: chain B residue 1156 SER Chi-restraints excluded: chain B residue 1196 LEU Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 313 ILE Chi-restraints excluded: chain E residue 7 ARG Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 177 ARG Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 187 TYR Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 44 TYR Chi-restraints excluded: chain K residue 65 ILE Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 72 LEU Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 131 VAL Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 53 HIS Chi-restraints excluded: chain L residue 62 LYS Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain M residue 148 ARG Chi-restraints excluded: chain M residue 178 LEU Chi-restraints excluded: chain M residue 251 THR Chi-restraints excluded: chain M residue 332 ILE Chi-restraints excluded: chain M residue 371 VAL Chi-restraints excluded: chain M residue 384 ILE Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain N residue 69 SER Chi-restraints excluded: chain N residue 89 ILE Chi-restraints excluded: chain O residue 73 ILE Chi-restraints excluded: chain O residue 166 ILE Chi-restraints excluded: chain O residue 348 THR Chi-restraints excluded: chain O residue 371 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 414 optimal weight: 0.9990 chunk 218 optimal weight: 6.9990 chunk 226 optimal weight: 10.0000 chunk 417 optimal weight: 10.0000 chunk 150 optimal weight: 6.9990 chunk 112 optimal weight: 10.0000 chunk 73 optimal weight: 0.9990 chunk 395 optimal weight: 9.9990 chunk 244 optimal weight: 0.0670 chunk 275 optimal weight: 9.9990 chunk 319 optimal weight: 5.9990 overall best weight: 3.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 ASN ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 950 GLN ** A1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1293 HIS A1299 ASN A1315 ASN ** A1601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1629 ASN ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 462 GLN ** B 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 912 GLN ** B 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1058 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1094 ASN ** B1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 54 HIS ** N 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.202445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.189589 restraints weight = 70924.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.188704 restraints weight = 112477.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.189359 restraints weight = 103455.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.188990 restraints weight = 82111.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.189395 restraints weight = 73116.985| |-----------------------------------------------------------------------------| r_work (final): 0.4366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6167 moved from start: 0.5314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 40669 Z= 0.159 Angle : 0.727 13.205 55067 Z= 0.368 Chirality : 0.047 0.223 6173 Planarity : 0.005 0.121 6974 Dihedral : 10.355 150.880 5673 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.02 % Allowed : 12.05 % Favored : 87.93 % Rotamer: Outliers : 4.84 % Allowed : 21.71 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.70 (0.11), residues: 4839 helix: -2.69 (0.12), residues: 1352 sheet: -2.62 (0.21), residues: 505 loop : -2.39 (0.11), residues: 2982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B1076 TYR 0.027 0.002 TYR J 21 PHE 0.030 0.002 PHE O 473 TRP 0.026 0.002 TRP E 79 HIS 0.009 0.001 HIS A 617 Details of bonding type rmsd covalent geometry : bond 0.00370 (40654) covalent geometry : angle 0.72447 (55055) hydrogen bonds : bond 0.03604 ( 651) hydrogen bonds : angle 6.79497 ( 1668) metal coordination : bond 0.00795 ( 15) metal coordination : angle 4.50059 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 735 residues out of total 4381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 212 poor density : 523 time to evaluate : 1.433 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 230 ARG cc_start: 0.2639 (OUTLIER) cc_final: 0.1253 (mtm180) REVERT: A 261 ILE cc_start: 0.7041 (OUTLIER) cc_final: 0.6724 (tt) REVERT: A 335 LEU cc_start: 0.8700 (mm) cc_final: 0.8432 (mp) REVERT: A 491 GLU cc_start: 0.6016 (pm20) cc_final: 0.5738 (pm20) REVERT: A 521 GLN cc_start: 0.7664 (tp-100) cc_final: 0.7388 (tp-100) REVERT: A 600 MET cc_start: 0.6969 (mmt) cc_final: 0.6358 (mmt) REVERT: A 632 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8254 (pp20) REVERT: A 633 MET cc_start: 0.7974 (ptp) cc_final: 0.7762 (ptp) REVERT: A 709 ARG cc_start: 0.2234 (OUTLIER) cc_final: -0.0856 (pmm150) REVERT: A 824 THR cc_start: 0.8254 (OUTLIER) cc_final: 0.7761 (m) REVERT: A 830 MET cc_start: 0.6812 (mmm) cc_final: 0.6384 (mmt) REVERT: A 833 LEU cc_start: 0.7495 (mm) cc_final: 0.7188 (mm) REVERT: A 871 ASP cc_start: 0.6588 (p0) cc_final: 0.6209 (p0) REVERT: A 884 ARG cc_start: 0.5395 (mmp-170) cc_final: 0.4926 (ttp80) REVERT: A 953 GLU cc_start: 0.5412 (OUTLIER) cc_final: 0.4844 (pp20) REVERT: A 1073 TYR cc_start: 0.5778 (p90) cc_final: 0.5450 (p90) REVERT: A 1178 LEU cc_start: 0.7195 (OUTLIER) cc_final: 0.6872 (mm) REVERT: A 1183 GLU cc_start: 0.6979 (OUTLIER) cc_final: 0.6262 (mp0) REVERT: A 1192 SER cc_start: 0.8894 (m) cc_final: 0.8138 (t) REVERT: A 1439 MET cc_start: 0.4234 (mmm) cc_final: 0.3750 (mpp) REVERT: A 1591 ARG cc_start: 0.7514 (OUTLIER) cc_final: 0.6389 (ttt180) REVERT: A 1604 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7638 (pt0) REVERT: A 1611 MET cc_start: 0.7017 (ttm) cc_final: 0.6748 (mtp) REVERT: B 35 PHE cc_start: 0.6704 (OUTLIER) cc_final: 0.5597 (p90) REVERT: B 161 LEU cc_start: 0.8852 (tm) cc_final: 0.8481 (tt) REVERT: B 205 MET cc_start: 0.6619 (mtm) cc_final: 0.6299 (mtt) REVERT: B 261 ARG cc_start: 0.7373 (ttp80) cc_final: 0.7100 (ttt-90) REVERT: B 268 GLU cc_start: 0.7373 (mp0) cc_final: 0.7034 (mp0) REVERT: B 270 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.7302 (pp) REVERT: B 277 LEU cc_start: 0.6140 (OUTLIER) cc_final: 0.5901 (tp) REVERT: B 323 ARG cc_start: 0.5973 (mpt90) cc_final: 0.3599 (ttp-170) REVERT: B 377 MET cc_start: 0.6406 (tpp) cc_final: 0.5860 (mmm) REVERT: B 411 MET cc_start: 0.6871 (OUTLIER) cc_final: 0.5992 (mtp) REVERT: B 672 MET cc_start: 0.6558 (ppp) cc_final: 0.6061 (ptp) REVERT: B 744 LEU cc_start: 0.7261 (OUTLIER) cc_final: 0.6883 (tm) REVERT: B 822 THR cc_start: 0.4011 (p) cc_final: 0.3744 (p) REVERT: B 840 LEU cc_start: 0.6807 (OUTLIER) cc_final: 0.6428 (mt) REVERT: B 882 ILE cc_start: 0.5981 (OUTLIER) cc_final: 0.5474 (mt) REVERT: B 967 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.7344 (mt) REVERT: B 1125 THR cc_start: 0.4450 (OUTLIER) cc_final: 0.4032 (p) REVERT: B 1134 ARG cc_start: 0.6671 (mmt-90) cc_final: 0.5416 (mtt180) REVERT: C 34 GLU cc_start: 0.4938 (OUTLIER) cc_final: 0.4371 (tm-30) REVERT: C 71 MET cc_start: 0.5199 (OUTLIER) cc_final: 0.4789 (mtt) REVERT: C 106 LEU cc_start: 0.8081 (mm) cc_final: 0.7876 (mm) REVERT: C 329 LYS cc_start: 0.7357 (pptt) cc_final: 0.6976 (tmtt) REVERT: D 90 LYS cc_start: 0.5318 (mmtt) cc_final: 0.4855 (mmtt) REVERT: E 42 PHE cc_start: 0.6722 (t80) cc_final: 0.6068 (t80) REVERT: E 149 LEU cc_start: 0.6545 (OUTLIER) cc_final: 0.6232 (mm) REVERT: F 85 MET cc_start: 0.6519 (tpt) cc_final: 0.6275 (tpt) REVERT: G 53 TYR cc_start: 0.5886 (m-80) cc_final: 0.5540 (m-10) REVERT: H 45 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.7062 (pm20) REVERT: H 135 LEU cc_start: 0.5570 (pt) cc_final: 0.4598 (mt) REVERT: J 7 CYS cc_start: 0.4667 (OUTLIER) cc_final: 0.3932 (t) REVERT: J 21 TYR cc_start: 0.5597 (t80) cc_final: 0.5158 (t80) REVERT: K 43 ASP cc_start: 0.7742 (p0) cc_final: 0.7517 (p0) REVERT: L 38 LEU cc_start: 0.6539 (OUTLIER) cc_final: 0.6333 (pp) REVERT: M 178 LEU cc_start: 0.4349 (OUTLIER) cc_final: 0.3378 (mt) REVERT: M 256 MET cc_start: 0.2479 (tpt) cc_final: 0.2238 (tpt) REVERT: M 263 TYR cc_start: 0.3978 (t80) cc_final: 0.3430 (t80) REVERT: M 384 ILE cc_start: 0.0314 (OUTLIER) cc_final: -0.0683 (tp) REVERT: M 397 MET cc_start: 0.2463 (mpp) cc_final: 0.1185 (mtt) REVERT: N 40 LEU cc_start: 0.3274 (OUTLIER) cc_final: 0.2274 (mp) REVERT: O 127 GLU cc_start: 0.4524 (mt-10) cc_final: 0.4186 (tt0) REVERT: O 238 ILE cc_start: 0.2362 (OUTLIER) cc_final: 0.2118 (tp) REVERT: O 385 MET cc_start: 0.5999 (mpp) cc_final: 0.5422 (mtt) REVERT: O 396 MET cc_start: -0.1192 (mmm) cc_final: -0.1655 (ptp) outliers start: 212 outliers final: 141 residues processed: 678 average time/residue: 0.2300 time to fit residues: 264.3141 Evaluate side-chains 665 residues out of total 4381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 495 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 632 GLU Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 671 GLN Chi-restraints excluded: chain A residue 709 ARG Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 786 TYR Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 818 THR Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 943 ILE Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 953 GLU Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1023 LEU Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1063 MET Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1183 GLU Chi-restraints excluded: chain A residue 1225 ILE Chi-restraints excluded: chain A residue 1239 THR Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1315 ASN Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1442 VAL Chi-restraints excluded: chain A residue 1486 VAL Chi-restraints excluded: chain A residue 1504 ILE Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1538 VAL Chi-restraints excluded: chain A residue 1568 ASN Chi-restraints excluded: chain A residue 1579 PHE Chi-restraints excluded: chain A residue 1582 LEU Chi-restraints excluded: chain A residue 1591 ARG Chi-restraints excluded: chain A residue 1604 GLU Chi-restraints excluded: chain A residue 1629 ASN Chi-restraints excluded: chain A residue 1630 GLU Chi-restraints excluded: chain A residue 1642 VAL Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 143 TRP Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 209 GLN Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain B residue 492 ASN Chi-restraints excluded: chain B residue 529 CYS Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 595 TRP Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 677 THR Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 744 LEU Chi-restraints excluded: chain B residue 782 ASP Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 907 ILE Chi-restraints excluded: chain B residue 967 LEU Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1036 LEU Chi-restraints excluded: chain B residue 1093 LEU Chi-restraints excluded: chain B residue 1113 THR Chi-restraints excluded: chain B residue 1125 THR Chi-restraints excluded: chain B residue 1128 CYS Chi-restraints excluded: chain B residue 1131 CYS Chi-restraints excluded: chain B residue 1156 SER Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 71 MET Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 313 ILE Chi-restraints excluded: chain E residue 7 ARG Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 177 ARG Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 187 TYR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 116 TYR Chi-restraints excluded: chain H residue 130 ARG Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 44 TYR Chi-restraints excluded: chain K residue 65 ILE Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 72 LEU Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 124 LEU Chi-restraints excluded: chain K residue 131 VAL Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 53 HIS Chi-restraints excluded: chain L residue 62 LYS Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain M residue 148 ARG Chi-restraints excluded: chain M residue 178 LEU Chi-restraints excluded: chain M residue 251 THR Chi-restraints excluded: chain M residue 332 ILE Chi-restraints excluded: chain M residue 360 VAL Chi-restraints excluded: chain M residue 371 VAL Chi-restraints excluded: chain M residue 384 ILE Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 89 ILE Chi-restraints excluded: chain N residue 93 THR Chi-restraints excluded: chain O residue 73 ILE Chi-restraints excluded: chain O residue 166 ILE Chi-restraints excluded: chain O residue 238 ILE Chi-restraints excluded: chain O residue 348 THR Chi-restraints excluded: chain O residue 371 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 443 optimal weight: 8.9990 chunk 159 optimal weight: 3.9990 chunk 392 optimal weight: 5.9990 chunk 310 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 391 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 12 optimal weight: 7.9990 chunk 438 optimal weight: 30.0000 chunk 262 optimal weight: 1.9990 chunk 301 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1293 HIS A1299 ASN A1315 ASN A1503 HIS ** A1601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1629 ASN ** B 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 GLN ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 HIS ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 950 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1094 ASN B1171 ASN ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 ASN ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.201757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.187398 restraints weight = 70975.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.186163 restraints weight = 87157.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.186362 restraints weight = 80933.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.186570 restraints weight = 74246.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.186683 restraints weight = 64558.978| |-----------------------------------------------------------------------------| r_work (final): 0.4326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6247 moved from start: 0.5518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 40669 Z= 0.162 Angle : 0.736 11.524 55067 Z= 0.372 Chirality : 0.047 0.297 6173 Planarity : 0.005 0.123 6974 Dihedral : 10.413 151.017 5673 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.02 % Allowed : 11.92 % Favored : 88.06 % Rotamer: Outliers : 4.57 % Allowed : 22.30 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.69 (0.11), residues: 4839 helix: -2.68 (0.12), residues: 1366 sheet: -2.58 (0.22), residues: 505 loop : -2.39 (0.11), residues: 2968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 200 TYR 0.027 0.002 TYR B 671 PHE 0.040 0.002 PHE B 706 TRP 0.027 0.002 TRP E 79 HIS 0.015 0.001 HIS C 297 Details of bonding type rmsd covalent geometry : bond 0.00380 (40654) covalent geometry : angle 0.73237 (55055) hydrogen bonds : bond 0.03655 ( 651) hydrogen bonds : angle 6.81308 ( 1668) metal coordination : bond 0.00802 ( 15) metal coordination : angle 4.67777 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 718 residues out of total 4381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 200 poor density : 518 time to evaluate : 0.989 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 230 ARG cc_start: 0.2725 (OUTLIER) cc_final: 0.1315 (mtm180) REVERT: A 261 ILE cc_start: 0.7107 (OUTLIER) cc_final: 0.6823 (tt) REVERT: A 335 LEU cc_start: 0.8716 (mm) cc_final: 0.8450 (mp) REVERT: A 521 GLN cc_start: 0.7653 (tp-100) cc_final: 0.7284 (tp-100) REVERT: A 600 MET cc_start: 0.6901 (mmt) cc_final: 0.6580 (mmt) REVERT: A 811 SER cc_start: 0.8297 (m) cc_final: 0.8012 (p) REVERT: A 824 THR cc_start: 0.8352 (OUTLIER) cc_final: 0.7832 (m) REVERT: A 871 ASP cc_start: 0.6719 (p0) cc_final: 0.6339 (p0) REVERT: A 884 ARG cc_start: 0.5376 (mmp-170) cc_final: 0.4812 (ttp80) REVERT: A 953 GLU cc_start: 0.5694 (OUTLIER) cc_final: 0.5147 (pp20) REVERT: A 1073 TYR cc_start: 0.5643 (p90) cc_final: 0.5316 (p90) REVERT: A 1183 GLU cc_start: 0.6980 (OUTLIER) cc_final: 0.6259 (mp0) REVERT: A 1192 SER cc_start: 0.8925 (m) cc_final: 0.8177 (t) REVERT: A 1225 ILE cc_start: 0.8849 (mm) cc_final: 0.8546 (tp) REVERT: A 1439 MET cc_start: 0.4492 (mmm) cc_final: 0.3910 (mpp) REVERT: A 1531 ASP cc_start: 0.7703 (t0) cc_final: 0.7390 (t0) REVERT: A 1591 ARG cc_start: 0.7601 (OUTLIER) cc_final: 0.6323 (ttt180) REVERT: A 1604 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7830 (pt0) REVERT: A 1611 MET cc_start: 0.7035 (ttm) cc_final: 0.6779 (mtp) REVERT: B 35 PHE cc_start: 0.6783 (OUTLIER) cc_final: 0.5664 (p90) REVERT: B 161 LEU cc_start: 0.8968 (tm) cc_final: 0.8652 (tt) REVERT: B 205 MET cc_start: 0.7004 (mtm) cc_final: 0.6544 (mtt) REVERT: B 261 ARG cc_start: 0.7391 (ttp80) cc_final: 0.7119 (ttt-90) REVERT: B 268 GLU cc_start: 0.7343 (mp0) cc_final: 0.7064 (mp0) REVERT: B 270 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7222 (pp) REVERT: B 277 LEU cc_start: 0.6223 (OUTLIER) cc_final: 0.5847 (tt) REVERT: B 323 ARG cc_start: 0.6109 (mpt90) cc_final: 0.3624 (ttp-170) REVERT: B 377 MET cc_start: 0.6275 (tpp) cc_final: 0.5904 (mmm) REVERT: B 672 MET cc_start: 0.6544 (ppp) cc_final: 0.6129 (ptp) REVERT: B 744 LEU cc_start: 0.7244 (OUTLIER) cc_final: 0.6805 (tm) REVERT: B 822 THR cc_start: 0.4030 (p) cc_final: 0.3759 (p) REVERT: B 840 LEU cc_start: 0.6719 (OUTLIER) cc_final: 0.6339 (mt) REVERT: B 882 ILE cc_start: 0.5924 (OUTLIER) cc_final: 0.5480 (mt) REVERT: B 967 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7246 (mt) REVERT: B 1125 THR cc_start: 0.4454 (OUTLIER) cc_final: 0.4023 (p) REVERT: B 1134 ARG cc_start: 0.6694 (mmt-90) cc_final: 0.5405 (mtt180) REVERT: C 34 GLU cc_start: 0.5096 (OUTLIER) cc_final: 0.4540 (tm-30) REVERT: C 315 PHE cc_start: 0.6635 (OUTLIER) cc_final: 0.6216 (t80) REVERT: C 329 LYS cc_start: 0.7270 (pptt) cc_final: 0.6931 (tmtt) REVERT: D 90 LYS cc_start: 0.5293 (mmtt) cc_final: 0.4915 (mmtt) REVERT: E 42 PHE cc_start: 0.6981 (t80) cc_final: 0.6289 (t80) REVERT: E 149 LEU cc_start: 0.6648 (OUTLIER) cc_final: 0.6315 (mm) REVERT: E 177 ARG cc_start: 0.7060 (OUTLIER) cc_final: 0.6077 (ptt-90) REVERT: F 85 MET cc_start: 0.6510 (tpt) cc_final: 0.6280 (tpt) REVERT: H 45 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.7116 (pm20) REVERT: H 135 LEU cc_start: 0.5772 (pt) cc_final: 0.4728 (mt) REVERT: J 7 CYS cc_start: 0.4243 (OUTLIER) cc_final: 0.3654 (t) REVERT: K 43 ASP cc_start: 0.7808 (p0) cc_final: 0.7541 (p0) REVERT: L 38 LEU cc_start: 0.6489 (OUTLIER) cc_final: 0.6260 (pp) REVERT: M 148 ARG cc_start: 0.6084 (OUTLIER) cc_final: 0.5661 (mtm-85) REVERT: M 178 LEU cc_start: 0.4535 (OUTLIER) cc_final: 0.3484 (mt) REVERT: M 263 TYR cc_start: 0.4066 (t80) cc_final: 0.3502 (t80) REVERT: M 384 ILE cc_start: 0.0332 (OUTLIER) cc_final: -0.0637 (tp) REVERT: M 397 MET cc_start: 0.2443 (mpp) cc_final: 0.1237 (mtt) REVERT: O 396 MET cc_start: -0.0697 (mmm) cc_final: -0.1171 (ptp) outliers start: 200 outliers final: 147 residues processed: 668 average time/residue: 0.2256 time to fit residues: 255.2512 Evaluate side-chains 662 residues out of total 4381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 490 time to evaluate : 1.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 671 GLN Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 786 TYR Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 818 THR Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 953 GLU Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 977 MET Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1063 MET Chi-restraints excluded: chain A residue 1108 HIS Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1183 GLU Chi-restraints excluded: chain A residue 1239 THR Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1315 ASN Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1442 VAL Chi-restraints excluded: chain A residue 1486 VAL Chi-restraints excluded: chain A residue 1503 HIS Chi-restraints excluded: chain A residue 1504 ILE Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1538 VAL Chi-restraints excluded: chain A residue 1566 ILE Chi-restraints excluded: chain A residue 1568 ASN Chi-restraints excluded: chain A residue 1579 PHE Chi-restraints excluded: chain A residue 1582 LEU Chi-restraints excluded: chain A residue 1591 ARG Chi-restraints excluded: chain A residue 1604 GLU Chi-restraints excluded: chain A residue 1629 ASN Chi-restraints excluded: chain A residue 1630 GLU Chi-restraints excluded: chain A residue 1642 VAL Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 143 TRP Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 209 GLN Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain B residue 492 ASN Chi-restraints excluded: chain B residue 529 CYS Chi-restraints excluded: chain B residue 541 LEU Chi-restraints excluded: chain B residue 595 TRP Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 677 THR Chi-restraints excluded: chain B residue 744 LEU Chi-restraints excluded: chain B residue 782 ASP Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 907 ILE Chi-restraints excluded: chain B residue 967 LEU Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain B residue 1000 LEU Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1036 LEU Chi-restraints excluded: chain B residue 1093 LEU Chi-restraints excluded: chain B residue 1113 THR Chi-restraints excluded: chain B residue 1125 THR Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1128 CYS Chi-restraints excluded: chain B residue 1131 CYS Chi-restraints excluded: chain B residue 1156 SER Chi-restraints excluded: chain B residue 1196 LEU Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 313 ILE Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain E residue 7 ARG Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 177 ARG Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 187 TYR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 130 ARG Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 44 TYR Chi-restraints excluded: chain K residue 65 ILE Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 72 LEU Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 124 LEU Chi-restraints excluded: chain K residue 131 VAL Chi-restraints excluded: chain L residue 38 LEU Chi-restraints excluded: chain L residue 53 HIS Chi-restraints excluded: chain L residue 62 LYS Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain M residue 148 ARG Chi-restraints excluded: chain M residue 178 LEU Chi-restraints excluded: chain M residue 251 THR Chi-restraints excluded: chain M residue 332 ILE Chi-restraints excluded: chain M residue 347 THR Chi-restraints excluded: chain M residue 360 VAL Chi-restraints excluded: chain M residue 371 VAL Chi-restraints excluded: chain M residue 384 ILE Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 89 ILE Chi-restraints excluded: chain N residue 93 THR Chi-restraints excluded: chain N residue 166 LEU Chi-restraints excluded: chain O residue 73 ILE Chi-restraints excluded: chain O residue 113 THR Chi-restraints excluded: chain O residue 166 ILE Chi-restraints excluded: chain O residue 348 THR Chi-restraints excluded: chain O residue 371 HIS Chi-restraints excluded: chain O residue 386 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 17 optimal weight: 9.9990 chunk 469 optimal weight: 2.9990 chunk 236 optimal weight: 2.9990 chunk 293 optimal weight: 1.9990 chunk 337 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 346 optimal weight: 5.9990 chunk 450 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 chunk 259 optimal weight: 9.9990 chunk 324 optimal weight: 10.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 ASN ** A 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1293 HIS A1299 ASN A1503 HIS ** A1620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1629 ASN ** B 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 GLN ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 950 ASN ** B1094 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.202021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.189430 restraints weight = 70809.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.188531 restraints weight = 115796.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.189209 restraints weight = 103675.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.188721 restraints weight = 80491.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.189201 restraints weight = 71632.925| |-----------------------------------------------------------------------------| r_work (final): 0.4362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6178 moved from start: 0.5663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 40669 Z= 0.150 Angle : 0.732 14.080 55067 Z= 0.369 Chirality : 0.047 0.295 6173 Planarity : 0.005 0.124 6974 Dihedral : 10.363 150.867 5671 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.02 % Allowed : 11.72 % Favored : 88.26 % Rotamer: Outliers : 4.27 % Allowed : 22.74 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.65 (0.11), residues: 4839 helix: -2.65 (0.12), residues: 1366 sheet: -2.50 (0.22), residues: 503 loop : -2.38 (0.11), residues: 2970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 200 TYR 0.028 0.002 TYR J 21 PHE 0.034 0.002 PHE B 706 TRP 0.049 0.002 TRP E 79 HIS 0.021 0.001 HIS C 297 Details of bonding type rmsd covalent geometry : bond 0.00353 (40654) covalent geometry : angle 0.72923 (55055) hydrogen bonds : bond 0.03552 ( 651) hydrogen bonds : angle 6.77226 ( 1668) metal coordination : bond 0.00755 ( 15) metal coordination : angle 4.55502 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9678 Ramachandran restraints generated. 4839 Oldfield, 0 Emsley, 4839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 695 residues out of total 4381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 508 time to evaluate : 1.519 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: symmetry clash REVERT: A 141 LEU cc_start: 0.5461 (OUTLIER) cc_final: 0.5128 (mp) REVERT: A 230 ARG cc_start: 0.2624 (OUTLIER) cc_final: 0.1192 (mtm180) REVERT: A 261 ILE cc_start: 0.7099 (OUTLIER) cc_final: 0.6863 (tt) REVERT: A 335 LEU cc_start: 0.8731 (mm) cc_final: 0.8457 (mp) REVERT: A 495 ILE cc_start: 0.6393 (mm) cc_final: 0.6187 (mm) REVERT: A 521 GLN cc_start: 0.7726 (tp-100) cc_final: 0.7385 (tp-100) REVERT: A 600 MET cc_start: 0.6920 (mmt) cc_final: 0.6451 (mmt) REVERT: A 633 MET cc_start: 0.7908 (ptp) cc_final: 0.7694 (ptp) REVERT: A 709 ARG cc_start: 0.2235 (OUTLIER) cc_final: -0.0922 (pmm150) REVERT: A 811 SER cc_start: 0.8300 (m) cc_final: 0.8018 (p) REVERT: A 824 THR cc_start: 0.8322 (OUTLIER) cc_final: 0.7805 (m) REVERT: A 830 MET cc_start: 0.6361 (mmt) cc_final: 0.6134 (mmt) REVERT: A 884 ARG cc_start: 0.5316 (mmp-170) cc_final: 0.4802 (ttp80) REVERT: A 953 GLU cc_start: 0.5823 (OUTLIER) cc_final: 0.5112 (pp20) REVERT: A 1073 TYR cc_start: 0.5602 (p90) cc_final: 0.5316 (p90) REVERT: A 1178 LEU cc_start: 0.7220 (OUTLIER) cc_final: 0.6856 (mm) REVERT: A 1183 GLU cc_start: 0.7029 (OUTLIER) cc_final: 0.6313 (mp0) REVERT: A 1192 SER cc_start: 0.8876 (m) cc_final: 0.8134 (t) REVERT: A 1439 MET cc_start: 0.4610 (mmm) cc_final: 0.3931 (mpp) REVERT: A 1531 ASP cc_start: 0.7695 (t0) cc_final: 0.7372 (t0) REVERT: A 1591 ARG cc_start: 0.7504 (OUTLIER) cc_final: 0.6260 (ttt180) REVERT: A 1604 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7786 (pt0) REVERT: A 1611 MET cc_start: 0.7058 (ttm) cc_final: 0.6809 (mtp) REVERT: B 35 PHE cc_start: 0.6738 (OUTLIER) cc_final: 0.5636 (p90) REVERT: B 161 LEU cc_start: 0.8979 (tm) cc_final: 0.8650 (tt) REVERT: B 205 MET cc_start: 0.7048 (mtm) cc_final: 0.6580 (mtt) REVERT: B 261 ARG cc_start: 0.7393 (ttp80) cc_final: 0.7107 (ttt-90) REVERT: B 268 GLU cc_start: 0.7512 (mp0) cc_final: 0.7232 (mp0) REVERT: B 270 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7267 (pp) REVERT: B 277 LEU cc_start: 0.6139 (OUTLIER) cc_final: 0.5796 (tt) REVERT: B 323 ARG cc_start: 0.6085 (mpt90) cc_final: 0.3669 (ttp-170) REVERT: B 439 ASN cc_start: 0.6369 (p0) cc_final: 0.5868 (p0) REVERT: B 672 MET cc_start: 0.6551 (ppp) cc_final: 0.6126 (ptp) REVERT: B 744 LEU cc_start: 0.7250 (OUTLIER) cc_final: 0.6918 (tm) REVERT: B 822 THR cc_start: 0.3789 (p) cc_final: 0.3512 (p) REVERT: B 840 LEU cc_start: 0.6617 (OUTLIER) cc_final: 0.6261 (mt) REVERT: B 882 ILE cc_start: 0.6083 (OUTLIER) cc_final: 0.5679 (mt) REVERT: B 967 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7317 (mt) REVERT: B 1125 THR cc_start: 0.4728 (OUTLIER) cc_final: 0.4299 (p) REVERT: B 1134 ARG cc_start: 0.6676 (mmt-90) cc_final: 0.5397 (mtt180) REVERT: C 34 GLU cc_start: 0.5043 (OUTLIER) cc_final: 0.4533 (tm-30) REVERT: C 315 PHE cc_start: 0.6648 (OUTLIER) cc_final: 0.5975 (t80) REVERT: C 329 LYS cc_start: 0.7195 (pptt) cc_final: 0.6885 (tmtt) REVERT: D 90 LYS cc_start: 0.5090 (mmtt) cc_final: 0.4740 (mmtt) REVERT: E 42 PHE cc_start: 0.6699 (t80) cc_final: 0.6095 (t80) REVERT: E 149 LEU cc_start: 0.6575 (OUTLIER) cc_final: 0.6172 (mm) REVERT: E 177 ARG cc_start: 0.7087 (OUTLIER) cc_final: 0.5871 (ptt-90) REVERT: G 76 LYS cc_start: 0.6257 (ptpt) cc_final: 0.6017 (pttt) REVERT: H 45 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7196 (pm20) REVERT: H 135 LEU cc_start: 0.5694 (pt) cc_final: 0.4715 (mt) REVERT: J 7 CYS cc_start: 0.4229 (OUTLIER) cc_final: 0.3653 (t) REVERT: K 43 ASP cc_start: 0.7775 (p0) cc_final: 0.7510 (p0) REVERT: M 178 LEU cc_start: 0.4408 (OUTLIER) cc_final: 0.3414 (mt) REVERT: M 263 TYR cc_start: 0.3841 (t80) cc_final: 0.3322 (t80) REVERT: M 384 ILE cc_start: 0.0400 (OUTLIER) cc_final: -0.0617 (tp) REVERT: M 397 MET cc_start: 0.2339 (mpp) cc_final: 0.1126 (mtt) REVERT: O 396 MET cc_start: -0.0854 (mmm) cc_final: -0.1215 (ptp) outliers start: 187 outliers final: 146 residues processed: 645 average time/residue: 0.2332 time to fit residues: 254.3218 Evaluate side-chains 658 residues out of total 4381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 486 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 476 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 641 GLU Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 671 GLN Chi-restraints excluded: chain A residue 709 ARG Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 786 TYR Chi-restraints excluded: chain A residue 793 ILE Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 818 THR Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 953 GLU Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 977 MET Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1044 THR Chi-restraints excluded: chain A residue 1063 MET Chi-restraints excluded: chain A residue 1108 HIS Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1183 GLU Chi-restraints excluded: chain A residue 1239 THR Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1442 VAL Chi-restraints excluded: chain A residue 1486 VAL Chi-restraints excluded: chain A residue 1503 HIS Chi-restraints excluded: chain A residue 1504 ILE Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1538 VAL Chi-restraints excluded: chain A residue 1566 ILE Chi-restraints excluded: chain A residue 1568 ASN Chi-restraints excluded: chain A residue 1579 PHE Chi-restraints excluded: chain A residue 1582 LEU Chi-restraints excluded: chain A residue 1591 ARG Chi-restraints excluded: chain A residue 1604 GLU Chi-restraints excluded: chain A residue 1630 GLU Chi-restraints excluded: chain A residue 1642 VAL Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 143 TRP Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 209 GLN Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 249 VAL Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 274 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain B residue 492 ASN Chi-restraints excluded: chain B residue 595 TRP Chi-restraints excluded: chain B residue 629 VAL Chi-restraints excluded: chain B residue 663 ILE Chi-restraints excluded: chain B residue 664 VAL Chi-restraints excluded: chain B residue 677 THR Chi-restraints excluded: chain B residue 744 LEU Chi-restraints excluded: chain B residue 782 ASP Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 871 ILE Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 907 ILE Chi-restraints excluded: chain B residue 950 ASN Chi-restraints excluded: chain B residue 967 LEU Chi-restraints excluded: chain B residue 977 ILE Chi-restraints excluded: chain B residue 1000 LEU Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1036 LEU Chi-restraints excluded: chain B residue 1093 LEU Chi-restraints excluded: chain B residue 1113 THR Chi-restraints excluded: chain B residue 1125 THR Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1128 CYS Chi-restraints excluded: chain B residue 1131 CYS Chi-restraints excluded: chain B residue 1156 SER Chi-restraints excluded: chain B residue 1196 LEU Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 313 ILE Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain E residue 7 ARG Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 177 ARG Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 187 TYR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 130 ARG Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 44 TYR Chi-restraints excluded: chain K residue 65 ILE Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 72 LEU Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 124 LEU Chi-restraints excluded: chain K residue 131 VAL Chi-restraints excluded: chain L residue 53 HIS Chi-restraints excluded: chain L residue 62 LYS Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain M residue 145 GLU Chi-restraints excluded: chain M residue 148 ARG Chi-restraints excluded: chain M residue 178 LEU Chi-restraints excluded: chain M residue 251 THR Chi-restraints excluded: chain M residue 332 ILE Chi-restraints excluded: chain M residue 360 VAL Chi-restraints excluded: chain M residue 371 VAL Chi-restraints excluded: chain M residue 384 ILE Chi-restraints excluded: chain N residue 89 ILE Chi-restraints excluded: chain N residue 93 THR Chi-restraints excluded: chain O residue 73 ILE Chi-restraints excluded: chain O residue 113 THR Chi-restraints excluded: chain O residue 166 ILE Chi-restraints excluded: chain O residue 348 THR Chi-restraints excluded: chain O residue 371 HIS Chi-restraints excluded: chain O residue 386 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 188 optimal weight: 4.9990 chunk 422 optimal weight: 7.9990 chunk 334 optimal weight: 6.9990 chunk 437 optimal weight: 9.9990 chunk 436 optimal weight: 10.0000 chunk 134 optimal weight: 6.9990 chunk 359 optimal weight: 9.9990 chunk 308 optimal weight: 5.9990 chunk 301 optimal weight: 8.9990 chunk 109 optimal weight: 4.9990 chunk 236 optimal weight: 3.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1293 HIS A1299 ASN A1315 ASN ** A1620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1094 ASN ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.201727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.188995 restraints weight = 71272.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.188148 restraints weight = 108946.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.188741 restraints weight = 98704.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.188488 restraints weight = 77970.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.188776 restraints weight = 70352.193| |-----------------------------------------------------------------------------| r_work (final): 0.4359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6190 moved from start: 0.5685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.135 40669 Z= 0.215 Angle : 0.834 59.200 55067 Z= 0.454 Chirality : 0.047 0.292 6173 Planarity : 0.006 0.204 6974 Dihedral : 10.368 150.849 5671 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.02 % Allowed : 11.92 % Favored : 88.06 % Rotamer: Outliers : 4.18 % Allowed : 22.81 % Favored : 73.01 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.66 (0.11), residues: 4839 helix: -2.65 (0.12), residues: 1366 sheet: -2.49 (0.22), residues: 503 loop : -2.39 (0.11), residues: 2970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 200 TYR 0.025 0.002 TYR A 514 PHE 0.030 0.002 PHE O 473 TRP 0.040 0.002 TRP E 79 HIS 0.267 0.003 HIS A1503 Details of bonding type rmsd covalent geometry : bond 0.00454 (40654) covalent geometry : angle 0.83115 (55055) hydrogen bonds : bond 0.03577 ( 651) hydrogen bonds : angle 6.77252 ( 1668) metal coordination : bond 0.00846 ( 15) metal coordination : angle 4.52529 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6539.94 seconds wall clock time: 114 minutes 53.90 seconds (6893.90 seconds total)