Starting phenix.real_space_refine on Tue Sep 15 12:26:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6rqt_4985/09_2026/6rqt_4985.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rqt_4985/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6rqt_4985/09_2026/6rqt_4985.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6rqt_4985/09_2026/6rqt_4985.cif" model { file = "/net/cci-nas-00/data/ceres_data/6rqt_4985/09_2026/6rqt_4985.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rqt_4985/09_2026/6rqt_4985.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6rqt_4985/09_2026/6rqt_4985.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rqt_4985/09_2026/6rqt_4985.map" } 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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: 7.53, per 1000 atoms: 0.19 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: 2.80 Conformation dependent library (CDL) restraints added in 1.3 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: 1.19 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: 8.19 Time building geometry restraints manager: 3.80 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=" C1' DT U 55 " pdb=" N1 DT U 55 " ideal model delta sigma weight residual 1.468 1.534 -0.066 1.40e-02 5.10e+03 2.20e+01 bond pdb=" C5' DA U 56 " pdb=" C4' DA U 56 " ideal model delta sigma weight residual 1.512 1.536 -0.024 7.00e-03 2.04e+04 1.19e+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=" O3' DA U 58 " pdb=" P DG U 59 " ideal model delta sigma weight residual 1.607 1.643 -0.036 1.20e-02 6.94e+03 9.24e+00 ... (remaining 40649 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 52756 2.65 - 5.31: 1956 5.31 - 7.96: 271 7.96 - 10.62: 67 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 - 0.124: 5795 0.124 - 0.249: 348 0.249 - 0.373: 24 0.373 - 0.497: 4 0.497 - 0.621: 2 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 -2.73 -2.11 -0.62 2.00e-01 2.50e+01 9.65e+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: 0.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.610 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 37.170 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5971 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= 0.366 Angle : 1.218 34.251 55067 Z= 0.663 Chirality : 0.069 0.621 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/Z covalent geometry : bond 0.00726 / 0.35 (40654) covalent geometry : angle 1.19626 / 0.66 (55055) hydrogen bonds : bond 0.33191 / 37.50 ( 651) hydrogen bonds : angle 12.21176 / 12.91 ( 1668) metal coordination : bond 0.17424 / 18.14 ( 15) metal coordination : angle 15.51167 / 25.26 ( 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 : 1.393 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: 0.2502 time to fit residues: 471.9303 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 : 1.053 ------------------------------------------------------------------------------- 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... A 26 ASN A 60 ASN A 75 HIS A 92 ASN A 116 HIS A 224 HIS A 257 ASN A 336 GLN A 344 ASN ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 458 GLN ** A 470 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 ASN A 525 ASN ** A 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 592 GLN A 634 ASN A 649 ASN A 693 GLN ** A 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 798 HIS A 939 ASN ** A 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1047 GLN A1088 HIS ** A1113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1293 HIS A1315 ASN A1320 GLN A1437 ASN ** A1447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1567 ASN ** A1620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN B 110 ASN B 128 GLN B 168 ASN 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 646 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** B1010 ASN B1041 ASN ** B1058 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1094 ASN B1171 ASN ** C 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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 83 ASN ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 54 HIS ** M 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 O 117 GLN O 362 ASN O 478 GLN Total number of N/Q/H flips: 66 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.207011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.194862 restraints weight = 69739.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.194041 restraints weight = 109941.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.194744 restraints weight = 92903.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.194486 restraints weight = 75174.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.194909 restraints weight = 65352.700| |-----------------------------------------------------------------------------| r_work (final): 0.4428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5957 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.849 40669 Z= 0.220 Angle : 0.835 15.492 55067 Z= 0.432 Chirality : 0.050 0.263 6173 Planarity : 0.007 0.129 6974 Dihedral : 11.678 154.178 5697 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 11.51 % Favored : 88.43 % Rotamer: Outliers : 3.61 % Allowed : 15.56 % Favored : 80.83 % 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: -4.82 (0.10), residues: 4839 helix: -3.99 (0.09), residues: 1270 sheet: -3.25 (0.20), residues: 527 loop : -2.97 (0.10), residues: 3042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 185 TYR 0.033 0.002 TYR B1005 PHE 0.027 0.002 PHE O 361 TRP 0.024 0.002 TRP B 836 HIS 0.016 0.002 HIS A 617 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (40654) covalent geometry : angle 0.82697 / 0.43 (55055) hydrogen bonds : bond 0.06380 / 7.13 ( 651) hydrogen bonds : angle 8.72942 / 8.83 ( 1668) metal coordination : bond 0.22014 / 11.15 ( 15) metal coordination : angle 8.01341 / 12.16 ( 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 877 residues out of total 4381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 719 time to evaluate : 1.254 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: 0.6781 (OUTLIER) cc_final: 0.6433 (tt) REVERT: A 357 MET cc_start: 0.2626 (mtp) cc_final: 0.2325 (mtp) REVERT: A 427 PHE cc_start: 0.6297 (OUTLIER) cc_final: 0.5757 (m-80) REVERT: A 433 ASP cc_start: 0.7584 (m-30) cc_final: 0.7171 (p0) REVERT: A 477 ASN cc_start: 0.7420 (t0) cc_final: 0.7111 (m-40) REVERT: A 613 THR cc_start: 0.7373 (OUTLIER) cc_final: 0.7094 (t) REVERT: A 649 ASN cc_start: 0.6081 (OUTLIER) cc_final: 0.5726 (m110) REVERT: A 824 THR cc_start: 0.8124 (OUTLIER) cc_final: 0.7711 (p) REVERT: A 826 PHE cc_start: 0.7426 (t80) cc_final: 0.7219 (t80) REVERT: A 871 ASP cc_start: 0.6368 (p0) cc_final: 0.5919 (p0) REVERT: A 981 TYR cc_start: 0.5867 (t80) cc_final: 0.5162 (t80) REVERT: A 1000 MET cc_start: 0.6763 (mmp) cc_final: 0.6394 (tpp) REVERT: A 1006 LEU cc_start: 0.6862 (pt) cc_final: 0.6477 (mp) REVERT: A 1070 LEU cc_start: 0.8047 (tt) cc_final: 0.7770 (tp) REVERT: A 1073 TYR cc_start: 0.5513 (p90) cc_final: 0.4677 (p90) REVERT: A 1150 LYS cc_start: 0.7088 (pptt) cc_final: 0.6690 (tptt) REVERT: A 1225 ILE cc_start: 0.8939 (mm) cc_final: 0.8522 (tp) REVERT: A 1485 MET cc_start: 0.7700 (mmp) cc_final: 0.7346 (mmp) REVERT: A 1591 ARG cc_start: 0.7682 (ptp-170) cc_final: 0.7172 (ptp90) REVERT: A 1603 MET cc_start: 0.5820 (mtt) cc_final: 0.5487 (ttp) REVERT: B 73 ILE cc_start: 0.5577 (tt) cc_final: 0.5160 (mm) REVERT: B 94 LYS cc_start: 0.4736 (tppp) cc_final: 0.4470 (tmtt) REVERT: B 194 PHE cc_start: 0.7243 (m-10) cc_final: 0.7025 (m-10) REVERT: B 261 ARG cc_start: 0.7435 (ttp80) cc_final: 0.6874 (ttt-90) REVERT: B 323 ARG cc_start: 0.5577 (mpt90) cc_final: 0.3649 (ttt180) REVERT: B 372 ARG cc_start: 0.6979 (ttt-90) cc_final: 0.6552 (ttt90) REVERT: B 541 LEU cc_start: 0.7486 (mm) cc_final: 0.7198 (mm) REVERT: B 543 ASN cc_start: 0.6869 (p0) cc_final: 0.6238 (p0) REVERT: B 697 LEU cc_start: 0.7521 (mm) cc_final: 0.7292 (mm) REVERT: B 720 GLN cc_start: 0.7329 (mm110) cc_final: 0.6955 (tm-30) REVERT: B 744 LEU cc_start: 0.7151 (OUTLIER) cc_final: 0.6631 (tm) REVERT: B 822 THR cc_start: 0.3628 (p) cc_final: 0.3346 (p) REVERT: B 840 LEU cc_start: 0.6764 (mm) cc_final: 0.6375 (mt) REVERT: B 931 TRP cc_start: 0.5962 (t-100) cc_final: 0.5733 (t-100) REVERT: B 934 ILE cc_start: 0.7514 (mm) cc_final: 0.6320 (mm) REVERT: B 935 ASP cc_start: 0.7841 (m-30) cc_final: 0.6714 (p0) REVERT: B 940 GLU cc_start: 0.6469 (mt-10) cc_final: 0.6258 (mt-10) REVERT: B 967 LEU cc_start: 0.7142 (OUTLIER) cc_final: 0.6829 (mt) REVERT: B 1134 ARG cc_start: 0.6441 (mmt-90) cc_final: 0.5451 (mtt180) REVERT: C 329 LYS cc_start: 0.7387 (pptt) cc_final: 0.7158 (pptt) REVERT: E 42 PHE cc_start: 0.6541 (t80) cc_final: 0.5850 (t80) REVERT: E 116 ILE cc_start: 0.5205 (OUTLIER) cc_final: 0.4772 (tp) REVERT: E 173 SER cc_start: 0.6997 (m) cc_final: 0.6743 (p) REVERT: F 71 GLU cc_start: 0.7775 (tm-30) cc_final: 0.7200 (tt0) REVERT: F 76 LYS cc_start: 0.6500 (pptt) cc_final: 0.5947 (tppt) REVERT: F 100 GLN cc_start: 0.7746 (tm-30) cc_final: 0.7423 (tt0) REVERT: G 53 TYR cc_start: 0.6143 (m-80) cc_final: 0.5827 (m-10) REVERT: H 135 LEU cc_start: 0.5785 (pp) cc_final: 0.5041 (mt) REVERT: I 44 ASN cc_start: 0.6846 (m-40) cc_final: 0.6642 (p0) REVERT: K 45 GLU cc_start: 0.7584 (tp30) cc_final: 0.7371 (mt-10) REVERT: K 81 MET cc_start: 0.7670 (ppp) cc_final: 0.7374 (ppp) REVERT: K 142 MET cc_start: 0.6489 (tpt) cc_final: 0.6141 (tpp) REVERT: L 67 PHE cc_start: 0.5353 (m-10) cc_final: 0.5020 (m-10) REVERT: M 54 HIS cc_start: 0.4717 (OUTLIER) cc_final: 0.4125 (t70) REVERT: M 126 ASN cc_start: 0.2115 (OUTLIER) cc_final: 0.1813 (m110) REVERT: M 277 VAL cc_start: 0.5556 (p) cc_final: 0.5078 (t) REVERT: M 384 ILE cc_start: 0.0024 (OUTLIER) cc_final: -0.0356 (tt) REVERT: O 127 GLU cc_start: 0.3421 (mt-10) cc_final: 0.2859 (tt0) REVERT: O 338 LEU cc_start: 0.2238 (tt) cc_final: 0.1973 (tp) REVERT: O 514 PHE cc_start: 0.5789 (m-80) cc_final: 0.5391 (m-80) outliers start: 158 outliers final: 58 residues processed: 832 average time/residue: 0.2221 time to fit residues: 307.5522 Evaluate side-chains 633 residues out of total 4381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 564 time to evaluate : 1.434 ------------------------------------------------------------------------------- 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 391 THR Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 427 PHE Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 613 THR 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 1133 LEU 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 1568 ASN Chi-restraints excluded: chain A residue 1617 THR Chi-restraints excluded: chain A residue 1630 GLU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 381 LEU 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 649 MET Chi-restraints excluded: chain B residue 663 ILE 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 809 VAL Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 967 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 222 VAL Chi-restraints excluded: chain C residue 300 PHE Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain G residue 69 LEU Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain I residue 2 SER Chi-restraints excluded: chain J residue 42 LYS Chi-restraints excluded: chain J residue 44 TYR 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 251 THR Chi-restraints excluded: chain M residue 329 LEU Chi-restraints excluded: chain M residue 384 ILE Chi-restraints excluded: chain N residue 52 GLN Chi-restraints excluded: chain N residue 152 LYS 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: 2.9990 chunk 263 optimal weight: 9.9990 chunk 455 optimal weight: 9.9990 chunk 137 optimal weight: 9.9990 chunk 456 optimal weight: 20.0000 chunk 338 optimal weight: 9.9990 chunk 311 optimal weight: 10.0000 chunk 290 optimal weight: 9.9990 chunk 394 optimal weight: 7.9990 chunk 268 optimal weight: 0.9990 chunk 81 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 HIS ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 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 A1320 GLN A1500 GLN ** A1601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1620 GLN ** B 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 456 ASN ** B 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 473 GLN ** B 544 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 547 HIS 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 B1045 GLN ** B1058 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1094 ASN C 65 ASN 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 65 HIS ** G 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 70 HIS K 99 ASN ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 16 GLN ** M 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 126 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.198018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.185855 restraints weight = 70827.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.184810 restraints weight = 104001.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.185419 restraints weight = 93708.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.184998 restraints weight = 75116.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.185311 restraints weight = 68396.935| |-----------------------------------------------------------------------------| r_work (final): 0.4325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6237 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.732 40669 Z= 0.307 Angle : 0.923 17.273 55067 Z= 0.475 Chirality : 0.053 0.353 6173 Planarity : 0.007 0.137 6974 Dihedral : 11.600 149.268 5678 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 19.04 Ramachandran Plot: Outliers : 0.04 % Allowed : 14.61 % Favored : 85.35 % Rotamer: Outliers : 5.32 % Allowed : 17.53 % Favored : 77.15 % 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: -4.70 (0.10), residues: 4839 helix: -3.76 (0.10), residues: 1313 sheet: -3.17 (0.21), residues: 473 loop : -2.95 (0.10), residues: 3053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 648 TYR 0.032 0.003 TYR B1005 PHE 0.027 0.003 PHE A1472 TRP 0.027 0.003 TRP C 31 HIS 0.017 0.002 HIS A 636 Details of bonding type rmsd/Z covalent geometry : bond 0.00652 / 0.28 (40654) covalent geometry : angle 0.91700 / 0.47 (55055) hydrogen bonds : bond 0.05767 / 6.33 ( 651) hydrogen bonds : angle 8.24815 / 8.49 ( 1668) metal coordination : bond 0.18978 / 9.60 ( 15) metal coordination : angle 7.14008 / 11.52 ( 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 828 residues out of total 4381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 233 poor density : 595 time to evaluate : 1.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 LEU cc_start: 0.8056 (mm) cc_final: 0.7846 (mt) REVERT: A 230 ARG cc_start: 0.2959 (OUTLIER) cc_final: 0.1251 (mtm180) REVERT: A 261 ILE cc_start: 0.7006 (OUTLIER) cc_final: 0.6452 (tt) REVERT: A 477 ASN cc_start: 0.7499 (t0) cc_final: 0.7201 (m-40) REVERT: A 494 GLU cc_start: 0.5133 (mt-10) cc_final: 0.4658 (mt-10) REVERT: A 514 TYR cc_start: 0.7129 (OUTLIER) cc_final: 0.6696 (p90) REVERT: A 711 LYS cc_start: 0.7066 (pttp) cc_final: 0.6863 (mttt) REVERT: A 824 THR cc_start: 0.8445 (OUTLIER) cc_final: 0.7862 (m) REVERT: A 830 MET cc_start: 0.6657 (mmm) cc_final: 0.6348 (mmt) REVERT: A 871 ASP cc_start: 0.6577 (p0) cc_final: 0.6207 (p0) REVERT: A 884 ARG cc_start: 0.5845 (mmp-170) cc_final: 0.5327 (ttp80) REVERT: A 981 TYR cc_start: 0.6547 (t80) cc_final: 0.6139 (t80) REVERT: A 1000 MET cc_start: 0.7768 (mmp) cc_final: 0.7390 (tpp) REVERT: A 1006 LEU cc_start: 0.7002 (pt) cc_final: 0.6178 (mp) REVERT: A 1150 LYS cc_start: 0.7227 (pptt) cc_final: 0.6689 (tptt) REVERT: A 1192 SER cc_start: 0.9040 (m) cc_final: 0.8151 (t) REVERT: A 1225 ILE cc_start: 0.9027 (mm) cc_final: 0.8583 (tp) REVERT: A 1591 ARG cc_start: 0.7648 (ptp-170) cc_final: 0.6711 (ttt180) REVERT: B 35 PHE cc_start: 0.6864 (OUTLIER) cc_final: 0.5870 (p90) REVERT: B 94 LYS cc_start: 0.5136 (tppp) cc_final: 0.4612 (tmtt) REVERT: B 261 ARG cc_start: 0.7678 (ttp80) cc_final: 0.7223 (ttt-90) REVERT: B 270 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7500 (pp) REVERT: B 323 ARG cc_start: 0.5919 (mpt90) cc_final: 0.3726 (ttp-170) REVERT: B 372 ARG cc_start: 0.6939 (ttt-90) cc_final: 0.6647 (ttt90) REVERT: B 542 LEU cc_start: 0.6275 (OUTLIER) cc_final: 0.5632 (pp) REVERT: B 543 ASN cc_start: 0.7017 (p0) cc_final: 0.6511 (p0) REVERT: B 672 MET cc_start: 0.7044 (ppp) cc_final: 0.6838 (ppp) REVERT: B 681 ILE cc_start: 0.8805 (OUTLIER) cc_final: 0.8344 (mt) REVERT: B 720 GLN cc_start: 0.7423 (mm110) cc_final: 0.7094 (tm-30) REVERT: B 783 MET cc_start: 0.3123 (mtt) cc_final: 0.2740 (mtt) REVERT: B 822 THR cc_start: 0.3585 (p) cc_final: 0.3319 (p) REVERT: B 840 LEU cc_start: 0.7114 (OUTLIER) cc_final: 0.6516 (mt) REVERT: B 878 GLU cc_start: 0.6369 (mm-30) cc_final: 0.6054 (mm-30) REVERT: B 934 ILE cc_start: 0.8096 (mm) cc_final: 0.7756 (mm) REVERT: B 935 ASP cc_start: 0.7831 (m-30) cc_final: 0.7156 (p0) REVERT: B 940 GLU cc_start: 0.6855 (mt-10) cc_final: 0.6644 (mt-10) REVERT: B 1134 ARG cc_start: 0.6393 (mmt-90) cc_final: 0.5429 (mtt180) REVERT: B 1194 ILE cc_start: 0.6888 (OUTLIER) cc_final: 0.6588 (mp) REVERT: C 68 ARG cc_start: 0.7456 (ttp80) cc_final: 0.7172 (ttt-90) REVERT: C 71 MET cc_start: 0.5566 (mmt) cc_final: 0.5179 (mtt) REVERT: E 42 PHE cc_start: 0.7121 (t80) cc_final: 0.6378 (t80) REVERT: E 93 MET cc_start: 0.2864 (ppp) cc_final: 0.2417 (tpp) REVERT: E 116 ILE cc_start: 0.5623 (OUTLIER) cc_final: 0.5054 (tp) REVERT: E 149 LEU cc_start: 0.6531 (OUTLIER) cc_final: 0.6322 (mm) REVERT: E 173 SER cc_start: 0.7217 (m) cc_final: 0.6902 (p) REVERT: F 76 LYS cc_start: 0.6455 (pptt) cc_final: 0.6255 (tppt) REVERT: F 120 ILE cc_start: 0.6845 (OUTLIER) cc_final: 0.6260 (mt) REVERT: G 54 LEU cc_start: 0.7689 (mp) cc_final: 0.7419 (mp) REVERT: H 98 TYR cc_start: 0.6137 (OUTLIER) cc_final: 0.5377 (t80) REVERT: H 135 LEU cc_start: 0.6681 (pp) cc_final: 0.5595 (mt) REVERT: I 44 ASN cc_start: 0.6934 (m-40) cc_final: 0.6688 (p0) REVERT: K 81 MET cc_start: 0.8009 (ppp) cc_final: 0.7673 (ppp) REVERT: K 142 MET cc_start: 0.7063 (tpt) cc_final: 0.6664 (tpp) REVERT: M 178 LEU cc_start: 0.4354 (OUTLIER) cc_final: 0.3427 (mt) REVERT: M 263 TYR cc_start: 0.4177 (t80) cc_final: 0.3684 (t80) REVERT: M 384 ILE cc_start: 0.0379 (OUTLIER) cc_final: -0.0126 (tt) REVERT: N 40 LEU cc_start: 0.3922 (OUTLIER) cc_final: 0.3328 (mp) REVERT: O 127 GLU cc_start: 0.3777 (mt-10) cc_final: 0.3320 (tt0) REVERT: O 167 LYS cc_start: 0.4030 (mttp) cc_final: 0.2931 (mttt) REVERT: O 606 MET cc_start: 0.4233 (tmm) cc_final: 0.4007 (tmm) outliers start: 233 outliers final: 122 residues processed: 757 average time/residue: 0.2228 time to fit residues: 283.1839 Evaluate side-chains 655 residues out of total 4381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 516 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 38 LEU Chi-restraints excluded: chain A residue 94 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 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 514 TYR Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 581 ILE 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 780 ILE Chi-restraints excluded: chain A residue 781 LEU 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 905 SER Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 947 LEU Chi-restraints excluded: chain A residue 962 SER 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 1083 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 1264 SER Chi-restraints excluded: chain A residue 1291 VAL Chi-restraints excluded: chain A residue 1518 VAL 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 132 SER Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 195 ILE 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 244 THR 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 309 LEU Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 377 MET Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 425 ILE 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 586 VAL Chi-restraints excluded: chain B residue 595 TRP Chi-restraints excluded: chain B residue 596 VAL 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 681 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 782 ASP Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 950 ASN Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 1036 LEU Chi-restraints excluded: chain B residue 1088 LEU Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1128 CYS Chi-restraints excluded: chain B residue 1194 ILE Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 226 SER Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 149 LEU 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 120 ILE Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain G residue 43 ILE 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 G residue 133 LEU Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 40 LEU Chi-restraints excluded: chain H residue 97 MET Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain I residue 2 SER Chi-restraints excluded: chain K residue 71 THR 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 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 329 LEU 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 93 THR Chi-restraints excluded: chain O residue 133 LEU Chi-restraints excluded: chain O residue 330 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: 20.0000 chunk 449 optimal weight: 5.9990 chunk 226 optimal weight: 10.0000 chunk 182 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 420 optimal weight: 3.9990 chunk 127 optimal weight: 0.0770 chunk 369 optimal weight: 10.0000 chunk 204 optimal weight: 5.9990 chunk 314 optimal weight: 7.9990 chunk 348 optimal weight: 0.0270 overall best weight: 2.8202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 257 ASN ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 ASN A 636 HIS ** 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 A1447 GLN A1503 HIS ** A1601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1620 GLN ** A1647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 45 HIS ** B 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 HIS ** B 231 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 462 GLN B 499 HIS ** 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 C 161 HIS C 216 HIS C 232 GLN ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 153 HIS G 23 GLN G 140 GLN ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 54 HIS ** M 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.201690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.188226 restraints weight = 70069.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.187580 restraints weight = 95790.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.188106 restraints weight = 84774.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.188089 restraints weight = 71231.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.188230 restraints weight = 59024.837| |-----------------------------------------------------------------------------| r_work (final): 0.4353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6177 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 40669 Z= 0.164 Angle : 0.775 13.888 55067 Z= 0.398 Chirality : 0.048 0.245 6173 Planarity : 0.006 0.134 6974 Dihedral : 11.222 150.279 5678 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.30 % Favored : 88.65 % Rotamer: Outliers : 4.96 % Allowed : 18.65 % Favored : 76.39 % 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: -4.49 (0.11), residues: 4839 helix: -3.50 (0.10), residues: 1321 sheet: -3.15 (0.20), residues: 505 loop : -2.81 (0.11), residues: 3013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 648 TYR 0.039 0.002 TYR B1005 PHE 0.038 0.002 PHE B 338 TRP 0.024 0.002 TRP B 611 HIS 0.015 0.001 HIS C 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (40654) covalent geometry : angle 0.76976 / 0.40 (55055) hydrogen bonds : bond 0.04568 / 5.06 ( 651) hydrogen bonds : angle 7.75207 / 8.01 ( 1668) metal coordination : bond 0.01512 / 1.47 ( 15) metal coordination : angle 6.33007 / 10.03 ( 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 787 residues out of total 4381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 217 poor density : 570 time to evaluate : 1.525 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 72 CYS cc_start: 0.7358 (m) cc_final: 0.7041 (t) REVERT: A 136 LEU cc_start: 0.8035 (mm) cc_final: 0.7788 (mt) REVERT: A 230 ARG cc_start: 0.2699 (OUTLIER) cc_final: 0.1022 (mtm180) REVERT: A 261 ILE cc_start: 0.6819 (OUTLIER) cc_final: 0.6460 (tt) REVERT: A 477 ASN cc_start: 0.7574 (t0) cc_final: 0.7284 (m-40) REVERT: A 514 TYR cc_start: 0.7062 (OUTLIER) cc_final: 0.6660 (p90) REVERT: A 590 ASN cc_start: 0.8040 (m-40) cc_final: 0.7675 (m-40) REVERT: A 597 LYS cc_start: 0.7011 (pttm) cc_final: 0.6745 (ptpt) REVERT: A 780 ILE cc_start: 0.6818 (OUTLIER) cc_final: 0.6590 (mp) REVERT: A 818 THR cc_start: 0.7614 (OUTLIER) cc_final: 0.7413 (m) REVERT: A 824 THR cc_start: 0.8310 (OUTLIER) cc_final: 0.7716 (m) REVERT: A 830 MET cc_start: 0.6688 (mmm) cc_final: 0.6183 (mmt) REVERT: A 871 ASP cc_start: 0.6446 (p0) cc_final: 0.6092 (p0) REVERT: A 884 ARG cc_start: 0.5866 (mmp-170) cc_final: 0.5253 (ttp80) REVERT: A 1000 MET cc_start: 0.7502 (mmp) cc_final: 0.6887 (tpp) REVERT: A 1006 LEU cc_start: 0.7030 (pt) cc_final: 0.6427 (mp) REVERT: A 1192 SER cc_start: 0.8981 (m) cc_final: 0.8278 (t) REVERT: A 1225 ILE cc_start: 0.9008 (mm) cc_final: 0.8573 (tp) REVERT: A 1591 ARG cc_start: 0.7655 (ptp-170) cc_final: 0.6917 (ttt180) REVERT: A 1604 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7552 (pt0) REVERT: B 35 PHE cc_start: 0.6866 (OUTLIER) cc_final: 0.5769 (p90) REVERT: B 91 LEU cc_start: 0.7014 (OUTLIER) cc_final: 0.6810 (pp) REVERT: B 94 LYS cc_start: 0.5280 (tppp) cc_final: 0.4405 (tmtt) REVERT: B 206 LEU cc_start: 0.6420 (OUTLIER) cc_final: 0.6110 (tm) REVERT: B 261 ARG cc_start: 0.7556 (ttp80) cc_final: 0.7130 (ttt-90) REVERT: B 270 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7310 (pp) REVERT: B 313 PHE cc_start: 0.6940 (t80) cc_final: 0.6560 (t80) REVERT: B 323 ARG cc_start: 0.5830 (mpt90) cc_final: 0.3612 (ttp-170) REVERT: B 542 LEU cc_start: 0.6162 (OUTLIER) cc_final: 0.5654 (pp) REVERT: B 543 ASN cc_start: 0.6940 (p0) cc_final: 0.6586 (p0) REVERT: B 672 MET cc_start: 0.6493 (ppp) cc_final: 0.6101 (ptp) REVERT: B 720 GLN cc_start: 0.7716 (mm110) cc_final: 0.7059 (tm-30) REVERT: B 822 THR cc_start: 0.3626 (p) cc_final: 0.3298 (p) REVERT: B 840 LEU cc_start: 0.6539 (mm) cc_final: 0.6295 (mt) REVERT: B 850 THR cc_start: 0.4601 (OUTLIER) cc_final: 0.4331 (m) REVERT: B 878 GLU cc_start: 0.6285 (mm-30) cc_final: 0.5928 (tt0) REVERT: B 934 ILE cc_start: 0.7958 (mm) cc_final: 0.7676 (mm) REVERT: B 935 ASP cc_start: 0.7790 (m-30) cc_final: 0.7055 (p0) REVERT: B 1094 ASN cc_start: 0.6391 (OUTLIER) cc_final: 0.6152 (t0) REVERT: B 1134 ARG cc_start: 0.6560 (mmt-90) cc_final: 0.5355 (mtt180) REVERT: B 1194 ILE cc_start: 0.6826 (OUTLIER) cc_final: 0.6443 (mp) REVERT: C 161 HIS cc_start: 0.7255 (m90) cc_final: 0.7028 (m170) REVERT: E 42 PHE cc_start: 0.6818 (t80) cc_final: 0.6090 (t80) REVERT: E 93 MET cc_start: 0.3283 (ppp) cc_final: 0.2800 (tpp) REVERT: E 116 ILE cc_start: 0.5576 (OUTLIER) cc_final: 0.5060 (tp) REVERT: E 177 ARG cc_start: 0.6985 (OUTLIER) cc_final: 0.6061 (ppt-90) REVERT: F 76 LYS cc_start: 0.6300 (pptt) cc_final: 0.6036 (tppt) REVERT: F 138 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7694 (mm) REVERT: G 53 TYR cc_start: 0.5710 (m-80) cc_final: 0.5405 (m-10) REVERT: G 54 LEU cc_start: 0.7008 (mp) cc_final: 0.6674 (tt) REVERT: H 45 GLU cc_start: 0.7000 (OUTLIER) cc_final: 0.6559 (pm20) REVERT: H 123 MET cc_start: 0.3984 (mmm) cc_final: 0.3576 (mtt) REVERT: H 135 LEU cc_start: 0.6628 (OUTLIER) cc_final: 0.5547 (mt) REVERT: I 44 ASN cc_start: 0.7079 (m-40) cc_final: 0.6719 (p0) REVERT: K 81 MET cc_start: 0.7928 (ppp) cc_final: 0.7554 (ppp) REVERT: K 142 MET cc_start: 0.7031 (tpt) cc_final: 0.6621 (tpp) REVERT: L 67 PHE cc_start: 0.5211 (m-10) cc_final: 0.4919 (m-10) REVERT: M 54 HIS cc_start: 0.4868 (OUTLIER) cc_final: 0.3966 (t70) REVERT: M 178 LEU cc_start: 0.4743 (OUTLIER) cc_final: 0.3199 (mt) REVERT: M 263 TYR cc_start: 0.3871 (t80) cc_final: 0.3298 (t80) REVERT: M 384 ILE cc_start: 0.0236 (OUTLIER) cc_final: -0.0485 (tp) REVERT: N 40 LEU cc_start: 0.3690 (OUTLIER) cc_final: 0.3207 (mp) REVERT: O 117 GLN cc_start: 0.2597 (OUTLIER) cc_final: 0.2383 (mm110) REVERT: O 127 GLU cc_start: 0.4043 (mt-10) cc_final: 0.3366 (tt0) REVERT: O 167 LYS cc_start: 0.4217 (mttp) cc_final: 0.3093 (mttt) outliers start: 217 outliers final: 116 residues processed: 725 average time/residue: 0.2279 time to fit residues: 278.3303 Evaluate side-chains 648 residues out of total 4381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 507 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 38 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 369 LEU Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 418 VAL 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 574 ASN Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 608 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 780 ILE 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 947 LEU Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 1009 THR Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1033 SER Chi-restraints excluded: chain A residue 1124 LEU 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 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 1447 GLN Chi-restraints excluded: chain A residue 1486 VAL Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1568 ASN 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 91 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 139 LEU 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 244 THR 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 319 HIS Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 419 GLU 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 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 740 LYS Chi-restraints excluded: chain B residue 809 VAL Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 907 ILE Chi-restraints excluded: chain B residue 974 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 1094 ASN 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 1194 ILE 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 185 VAL 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 87 SER Chi-restraints excluded: chain E residue 92 THR 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 177 ARG 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 130 ILE Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain G residue 43 ILE 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 116 THR Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 161 ASN Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain H residue 97 MET Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 130 ARG Chi-restraints excluded: chain H residue 135 LEU Chi-restraints excluded: chain J residue 44 TYR Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 72 LEU 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 53 HIS Chi-restraints excluded: chain L residue 62 LYS 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 329 LEU 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 93 THR Chi-restraints excluded: chain O residue 117 GLN Chi-restraints excluded: chain O residue 133 LEU 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: 2.9990 chunk 206 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 155 optimal weight: 0.0770 chunk 441 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 265 optimal weight: 1.9990 chunk 204 optimal weight: 1.9990 chunk 52 optimal weight: 10.0000 chunk 293 optimal weight: 10.0000 chunk 66 optimal weight: 9.9990 overall best weight: 1.1944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 590 ASN ** A 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 950 GLN ** A 998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 ASN ** A1062 HIS ** 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** A1629 ASN ** A1647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 HIS B 183 HIS B 231 HIS ** 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 912 GLN B1094 ASN C 65 ASN C 216 HIS ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 54 HIS ** M 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.204693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.192145 restraints weight = 70786.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.191054 restraints weight = 117439.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.191929 restraints weight = 102781.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.191831 restraints weight = 70257.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.192114 restraints weight = 67762.143| |-----------------------------------------------------------------------------| r_work (final): 0.4394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6099 moved from start: 0.4215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 40669 Z= 0.136 Angle : 0.728 12.196 55067 Z= 0.371 Chirality : 0.046 0.323 6173 Planarity : 0.005 0.106 6974 Dihedral : 10.904 150.470 5678 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.02 % Allowed : 11.18 % Favored : 88.80 % Rotamer: Outliers : 4.62 % Allowed : 20.09 % Favored : 75.30 % 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: -4.17 (0.11), residues: 4839 helix: -3.24 (0.11), residues: 1307 sheet: -2.93 (0.21), residues: 499 loop : -2.63 (0.11), residues: 3033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 648 TYR 0.025 0.002 TYR B1184 PHE 0.031 0.002 PHE K 135 TRP 0.034 0.002 TRP C 31 HIS 0.013 0.001 HIS C 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (40654) covalent geometry : angle 0.72368 / 0.37 (55055) hydrogen bonds : bond 0.04112 / 4.53 ( 651) hydrogen bonds : angle 7.43155 / 7.71 ( 1668) metal coordination : bond 0.00715 / 0.80 ( 15) metal coordination : angle 5.38352 / 8.75 ( 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 761 residues out of total 4381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 202 poor density : 559 time to evaluate : 1.395 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: A 72 CYS cc_start: 0.7650 (m) cc_final: 0.7058 (t) REVERT: A 79 ILE cc_start: 0.5330 (OUTLIER) cc_final: 0.5105 (tt) REVERT: A 230 ARG cc_start: 0.2596 (OUTLIER) cc_final: 0.1036 (mtm180) REVERT: A 261 ILE cc_start: 0.6806 (OUTLIER) cc_final: 0.6479 (tt) REVERT: A 477 ASN cc_start: 0.7542 (t0) cc_final: 0.7335 (m-40) REVERT: A 514 TYR cc_start: 0.6913 (OUTLIER) cc_final: 0.6635 (p90) REVERT: A 597 LYS cc_start: 0.6963 (pttm) cc_final: 0.6669 (ptpt) REVERT: A 824 THR cc_start: 0.8266 (OUTLIER) cc_final: 0.7721 (m) REVERT: A 830 MET cc_start: 0.6769 (mmm) cc_final: 0.6425 (mmm) REVERT: A 871 ASP cc_start: 0.6253 (p0) cc_final: 0.5900 (p0) REVERT: A 884 ARG cc_start: 0.5900 (mmp-170) cc_final: 0.5224 (ttp80) REVERT: A 892 LEU cc_start: 0.7886 (OUTLIER) cc_final: 0.7042 (pp) REVERT: A 1006 LEU cc_start: 0.7088 (pt) cc_final: 0.6416 (mp) REVERT: A 1073 TYR cc_start: 0.5590 (p90) cc_final: 0.4919 (p90) REVERT: A 1192 SER cc_start: 0.8965 (m) cc_final: 0.8344 (t) REVERT: A 1225 ILE cc_start: 0.8970 (mm) cc_final: 0.8564 (tp) REVERT: A 1591 ARG cc_start: 0.7552 (OUTLIER) cc_final: 0.6561 (ttt180) REVERT: A 1610 PHE cc_start: 0.5883 (m-10) cc_final: 0.5433 (m-80) REVERT: B 35 PHE cc_start: 0.6749 (OUTLIER) cc_final: 0.5716 (p90) REVERT: B 94 LYS cc_start: 0.5423 (tppp) cc_final: 0.4590 (tmtt) REVERT: B 127 ARG cc_start: 0.7640 (ptp90) cc_final: 0.7369 (mtm180) REVERT: B 206 LEU cc_start: 0.6484 (OUTLIER) cc_final: 0.6208 (tm) REVERT: B 261 ARG cc_start: 0.7443 (ttp80) cc_final: 0.7054 (ttt-90) REVERT: B 270 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7270 (pp) REVERT: B 297 VAL cc_start: 0.5468 (OUTLIER) cc_final: 0.5265 (t) REVERT: B 313 PHE cc_start: 0.6860 (t80) cc_final: 0.6497 (t80) REVERT: B 323 ARG cc_start: 0.5677 (mpt90) cc_final: 0.3561 (ttp-170) REVERT: B 542 LEU cc_start: 0.6066 (OUTLIER) cc_final: 0.5608 (pp) REVERT: B 543 ASN cc_start: 0.6927 (p0) cc_final: 0.6544 (p0) REVERT: B 672 MET cc_start: 0.6607 (ppp) cc_final: 0.5979 (ptp) REVERT: B 720 GLN cc_start: 0.7635 (mm110) cc_final: 0.6967 (tm-30) REVERT: B 744 LEU cc_start: 0.6710 (OUTLIER) cc_final: 0.6322 (tm) REVERT: B 822 THR cc_start: 0.3472 (p) cc_final: 0.3139 (p) REVERT: B 840 LEU cc_start: 0.6855 (mm) cc_final: 0.6621 (mt) REVERT: B 878 GLU cc_start: 0.6312 (mm-30) cc_final: 0.6076 (mm-30) REVERT: B 934 ILE cc_start: 0.7707 (mm) cc_final: 0.7475 (mm) REVERT: B 935 ASP cc_start: 0.7619 (m-30) cc_final: 0.6937 (p0) REVERT: B 1134 ARG cc_start: 0.6516 (mmt-90) cc_final: 0.5325 (mtt180) REVERT: B 1186 ASP cc_start: 0.6114 (p0) cc_final: 0.5854 (p0) REVERT: B 1194 ILE cc_start: 0.6636 (OUTLIER) cc_final: 0.6324 (mp) REVERT: C 329 LYS cc_start: 0.7280 (pptt) cc_final: 0.6982 (tmtt) REVERT: E 42 PHE cc_start: 0.6843 (t80) cc_final: 0.6035 (t80) REVERT: E 116 ILE cc_start: 0.5744 (OUTLIER) cc_final: 0.5279 (tp) REVERT: E 177 ARG cc_start: 0.6911 (OUTLIER) cc_final: 0.5267 (ppt-90) REVERT: F 76 LYS cc_start: 0.6338 (pptt) cc_final: 0.6024 (tppt) REVERT: F 138 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7601 (mm) REVERT: G 53 TYR cc_start: 0.5810 (m-80) cc_final: 0.5478 (m-10) REVERT: H 45 GLU cc_start: 0.7238 (OUTLIER) cc_final: 0.6783 (pm20) REVERT: H 123 MET cc_start: 0.4081 (mmm) cc_final: 0.3828 (mtt) REVERT: H 135 LEU cc_start: 0.6497 (OUTLIER) cc_final: 0.5390 (mt) REVERT: I 44 ASN cc_start: 0.6862 (m-40) cc_final: 0.6566 (p0) REVERT: J 21 TYR cc_start: 0.5673 (t80) cc_final: 0.5459 (t80) REVERT: K 43 ASP cc_start: 0.7121 (p0) cc_final: 0.6825 (p0) REVERT: K 81 MET cc_start: 0.7807 (ppp) cc_final: 0.7592 (ppp) REVERT: K 142 MET cc_start: 0.6881 (tpt) cc_final: 0.6439 (tpp) REVERT: L 38 LEU cc_start: 0.6326 (OUTLIER) cc_final: 0.6104 (pp) REVERT: M 54 HIS cc_start: 0.4622 (OUTLIER) cc_final: 0.4126 (t70) REVERT: M 125 ARG cc_start: 0.4618 (mmt180) cc_final: 0.4276 (mpt180) REVERT: M 178 LEU cc_start: 0.4419 (OUTLIER) cc_final: 0.3559 (mt) REVERT: M 263 TYR cc_start: 0.3445 (t80) cc_final: 0.3011 (t80) REVERT: M 384 ILE cc_start: 0.0486 (OUTLIER) cc_final: 0.0011 (tt) REVERT: M 397 MET cc_start: 0.2927 (mpp) cc_final: 0.0425 (mtt) REVERT: N 40 LEU cc_start: 0.3413 (OUTLIER) cc_final: 0.2980 (mp) REVERT: N 132 GLN cc_start: 0.5398 (tt0) cc_final: 0.5168 (tm-30) REVERT: O 127 GLU cc_start: 0.4144 (mt-10) cc_final: 0.3572 (tt0) REVERT: O 167 LYS cc_start: 0.4541 (mttp) cc_final: 0.3441 (mttt) REVERT: O 514 PHE cc_start: 0.5839 (m-80) cc_final: 0.5562 (m-80) REVERT: O 606 MET cc_start: 0.3740 (tmm) cc_final: 0.3358 (tmm) outliers start: 202 outliers final: 110 residues processed: 705 average time/residue: 0.2254 time to fit residues: 265.9326 Evaluate side-chains 645 residues out of total 4381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 511 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 369 LEU Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 581 ILE 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 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 809 VAL Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 952 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 1124 LEU Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1239 THR Chi-restraints excluded: chain A residue 1263 LEU 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 1503 HIS Chi-restraints excluded: chain A residue 1518 VAL Chi-restraints excluded: chain A residue 1566 ILE Chi-restraints excluded: chain A residue 1568 ASN Chi-restraints excluded: chain A residue 1591 ARG Chi-restraints excluded: chain A residue 1629 ASN Chi-restraints excluded: chain A residue 1630 GLU Chi-restraints excluded: chain A residue 1649 VAL Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 45 HIS Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 195 ILE 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 244 THR 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 297 VAL Chi-restraints excluded: chain B residue 319 HIS Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 419 GLU 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 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 703 LEU Chi-restraints excluded: chain B residue 740 LYS Chi-restraints excluded: chain B residue 744 LEU Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 907 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 1117 VAL Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1128 CYS Chi-restraints excluded: chain B residue 1194 ILE 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 222 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 92 THR 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 177 ARG 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 138 LEU Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 43 ILE 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 116 THR Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 161 ASN 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 H residue 135 LEU Chi-restraints excluded: chain J residue 44 TYR 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 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 M residue 54 HIS Chi-restraints excluded: chain M residue 178 LEU Chi-restraints excluded: chain M residue 251 THR Chi-restraints excluded: chain M residue 329 LEU 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 166 LEU 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: 8.9990 chunk 73 optimal weight: 0.8980 chunk 286 optimal weight: 0.0060 chunk 177 optimal weight: 10.0000 chunk 385 optimal weight: 8.9990 chunk 126 optimal weight: 7.9990 chunk 140 optimal weight: 9.9990 chunk 352 optimal weight: 10.0000 chunk 450 optimal weight: 9.9990 chunk 258 optimal weight: 10.0000 chunk 388 optimal weight: 9.9990 overall best weight: 5.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 HIS ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 748 ASN ** 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** ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1293 HIS A1299 ASN ** A1601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 HIS ** 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 600 GLN ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 950 ASN ** B1058 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1094 ASN C 65 ASN C 158 ASN ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 GLN G 119 HIS H 33 GLN ** K 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 18 GLN M 54 HIS ** M 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 170 HIS O 411 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.198336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.185029 restraints weight = 72586.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.183872 restraints weight = 125803.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.184705 restraints weight = 107317.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.184709 restraints weight = 76742.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.184955 restraints weight = 72123.555| |-----------------------------------------------------------------------------| r_work (final): 0.4315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6290 moved from start: 0.4577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 40669 Z= 0.231 Angle : 0.837 17.053 55067 Z= 0.426 Chirality : 0.050 0.247 6173 Planarity : 0.006 0.119 6974 Dihedral : 11.044 148.293 5678 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 17.86 Ramachandran Plot: Outliers : 0.02 % Allowed : 14.16 % Favored : 85.82 % Rotamer: Outliers : 5.55 % Allowed : 20.73 % Favored : 73.72 % 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: -4.27 (0.11), residues: 4839 helix: -3.26 (0.11), residues: 1317 sheet: -3.13 (0.20), residues: 501 loop : -2.69 (0.11), residues: 3021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 200 TYR 0.043 0.003 TYR B 742 PHE 0.033 0.002 PHE M 132 TRP 0.039 0.003 TRP B 143 HIS 0.021 0.002 HIS M 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.23 (40654) covalent geometry : angle 0.83222 / 0.43 (55055) hydrogen bonds : bond 0.04560 / 5.08 ( 651) hydrogen bonds : angle 7.52019 / 7.90 ( 1668) metal coordination : bond 0.01514 / 1.69 ( 15) metal coordination : angle 6.19649 / 10.08 ( 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 768 residues out of total 4381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 243 poor density : 525 time to evaluate : 1.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ILE cc_start: 0.5734 (OUTLIER) cc_final: 0.5501 (tt) REVERT: A 230 ARG cc_start: 0.2786 (OUTLIER) cc_final: 0.1249 (mtm180) REVERT: A 261 ILE cc_start: 0.7103 (OUTLIER) cc_final: 0.6650 (tt) REVERT: A 477 ASN cc_start: 0.7484 (t0) cc_final: 0.7269 (m-40) REVERT: A 632 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8089 (pp20) REVERT: A 633 MET cc_start: 0.8120 (ptp) cc_final: 0.7721 (ptp) REVERT: A 818 THR cc_start: 0.7882 (OUTLIER) cc_final: 0.7599 (m) REVERT: A 824 THR cc_start: 0.8347 (OUTLIER) cc_final: 0.7732 (m) REVERT: A 830 MET cc_start: 0.6780 (mmm) cc_final: 0.6095 (mmt) REVERT: A 871 ASP cc_start: 0.6569 (p0) cc_final: 0.6212 (p0) REVERT: A 884 ARG cc_start: 0.5890 (mmp-170) cc_final: 0.5233 (ttp80) REVERT: A 1006 LEU cc_start: 0.7063 (pt) cc_final: 0.6313 (mp) REVERT: A 1150 LYS cc_start: 0.7043 (pptt) cc_final: 0.6578 (tptt) REVERT: A 1192 SER cc_start: 0.9098 (m) cc_final: 0.8399 (t) REVERT: A 1225 ILE cc_start: 0.9039 (mm) cc_final: 0.8621 (tp) REVERT: A 1439 MET cc_start: 0.4117 (mmm) cc_final: 0.3219 (mpp) REVERT: A 1503 HIS cc_start: 0.7303 (OUTLIER) cc_final: 0.7095 (m170) REVERT: A 1591 ARG cc_start: 0.7585 (ptp-170) cc_final: 0.6494 (ttt180) REVERT: A 1604 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7719 (pt0) REVERT: B 35 PHE cc_start: 0.6937 (OUTLIER) cc_final: 0.5865 (p90) REVERT: B 94 LYS cc_start: 0.5098 (tppp) cc_final: 0.4794 (ttpp) REVERT: B 175 MET cc_start: 0.6189 (tpp) cc_final: 0.5922 (tpp) REVERT: B 206 LEU cc_start: 0.6596 (OUTLIER) cc_final: 0.6375 (tm) REVERT: B 261 ARG cc_start: 0.7882 (ttp80) cc_final: 0.7455 (ttt-90) REVERT: B 270 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7522 (pp) REVERT: B 323 ARG cc_start: 0.6015 (mpt90) cc_final: 0.3691 (ttp-170) REVERT: B 425 ILE cc_start: 0.6508 (OUTLIER) cc_final: 0.5589 (tt) REVERT: B 542 LEU cc_start: 0.6312 (OUTLIER) cc_final: 0.5986 (pp) REVERT: B 543 ASN cc_start: 0.7054 (p0) cc_final: 0.6830 (p0) REVERT: B 672 MET cc_start: 0.6796 (ppp) cc_final: 0.6150 (ptp) REVERT: B 681 ILE cc_start: 0.8709 (OUTLIER) cc_final: 0.8384 (mt) REVERT: B 720 GLN cc_start: 0.7775 (mm110) cc_final: 0.6883 (tm-30) REVERT: B 725 THR cc_start: 0.8057 (OUTLIER) cc_final: 0.7834 (t) REVERT: B 744 LEU cc_start: 0.6844 (OUTLIER) cc_final: 0.6506 (tm) REVERT: B 794 ASP cc_start: 0.7029 (t70) cc_final: 0.6639 (t0) REVERT: B 822 THR cc_start: 0.3661 (p) cc_final: 0.3353 (p) REVERT: B 840 LEU cc_start: 0.6985 (OUTLIER) cc_final: 0.6698 (mt) REVERT: B 878 GLU cc_start: 0.6456 (mm-30) cc_final: 0.6211 (mm-30) REVERT: B 934 ILE cc_start: 0.7943 (mm) cc_final: 0.7615 (mm) REVERT: B 935 ASP cc_start: 0.7653 (m-30) cc_final: 0.7030 (p0) REVERT: B 957 ARG cc_start: 0.7453 (mmm-85) cc_final: 0.7227 (mmm-85) REVERT: B 1106 GLU cc_start: 0.6680 (OUTLIER) cc_final: 0.6419 (mp0) REVERT: B 1134 ARG cc_start: 0.6374 (mmt-90) cc_final: 0.5175 (mtt180) REVERT: B 1186 ASP cc_start: 0.6271 (p0) cc_final: 0.5820 (p0) REVERT: B 1194 ILE cc_start: 0.6751 (OUTLIER) cc_final: 0.6396 (mp) REVERT: E 42 PHE cc_start: 0.7170 (t80) cc_final: 0.6422 (t80) REVERT: E 116 ILE cc_start: 0.5801 (OUTLIER) cc_final: 0.5312 (tp) REVERT: E 149 LEU cc_start: 0.6472 (OUTLIER) cc_final: 0.6149 (mm) REVERT: E 177 ARG cc_start: 0.7113 (OUTLIER) cc_final: 0.6059 (ppt-90) REVERT: F 120 ILE cc_start: 0.6621 (OUTLIER) cc_final: 0.6033 (mt) REVERT: F 138 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7966 (mm) REVERT: G 53 TYR cc_start: 0.6010 (m-80) cc_final: 0.5695 (m-10) REVERT: H 45 GLU cc_start: 0.7143 (OUTLIER) cc_final: 0.6616 (pm20) REVERT: H 123 MET cc_start: 0.4015 (mmm) cc_final: 0.3487 (mtt) REVERT: I 44 ASN cc_start: 0.7053 (m-40) cc_final: 0.6642 (p0) REVERT: K 43 ASP cc_start: 0.7283 (p0) cc_final: 0.6954 (p0) REVERT: K 81 MET cc_start: 0.8023 (ppp) cc_final: 0.7465 (ppp) REVERT: K 142 MET cc_start: 0.6969 (tpt) cc_final: 0.6083 (tpt) REVERT: M 178 LEU cc_start: 0.5070 (OUTLIER) cc_final: 0.3494 (mt) REVERT: M 263 TYR cc_start: 0.4021 (t80) cc_final: 0.3387 (t80) REVERT: M 384 ILE cc_start: 0.0569 (OUTLIER) cc_final: -0.0413 (tp) REVERT: M 397 MET cc_start: 0.2549 (mpp) cc_final: 0.0881 (mtt) REVERT: N 40 LEU cc_start: 0.3742 (OUTLIER) cc_final: 0.3041 (mp) REVERT: O 127 GLU cc_start: 0.4200 (mt-10) cc_final: 0.3770 (tt0) REVERT: O 167 LYS cc_start: 0.4285 (mttp) cc_final: 0.3187 (mttt) REVERT: O 396 MET cc_start: -0.0059 (mmm) cc_final: -0.2369 (ptm) outliers start: 243 outliers final: 150 residues processed: 703 average time/residue: 0.2235 time to fit residues: 264.8851 Evaluate side-chains 670 residues out of total 4381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 492 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 220 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 391 THR Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 447 THR Chi-restraints excluded: chain A residue 471 MET 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 585 ASP Chi-restraints excluded: chain A residue 589 MET Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 632 GLU 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 769 VAL Chi-restraints excluded: chain A residue 781 LEU 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 833 LEU Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 905 SER Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 942 GLN 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 1027 LEU Chi-restraints excluded: chain A residue 1033 SER Chi-restraints excluded: chain A residue 1124 LEU Chi-restraints excluded: chain A residue 1142 ASP Chi-restraints excluded: chain A residue 1178 LEU 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 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 1604 GLU Chi-restraints excluded: chain A residue 1611 MET Chi-restraints excluded: chain A residue 1622 LEU 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 45 HIS 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 195 ILE 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 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 425 ILE 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 542 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 681 ILE Chi-restraints excluded: chain B residue 700 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 740 LYS Chi-restraints excluded: chain B residue 744 LEU Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 907 ILE Chi-restraints excluded: chain B residue 950 ASN Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1036 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 1194 ILE Chi-restraints excluded: chain C residue 56 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 185 VAL 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 267 VAL Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 92 THR 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 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 120 ILE Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 43 ILE 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 116 THR Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain G residue 161 ASN Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 40 LEU 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 I residue 2 SER Chi-restraints excluded: chain J residue 44 TYR 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 28 LYS Chi-restraints excluded: chain L residue 53 HIS Chi-restraints excluded: chain L residue 62 LYS Chi-restraints excluded: chain M residue 23 VAL Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain M residue 178 LEU Chi-restraints excluded: chain M residue 251 THR Chi-restraints excluded: chain M residue 347 THR 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 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 Chi-restraints excluded: chain O residue 455 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 78 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 371 optimal weight: 8.9990 chunk 53 optimal weight: 0.9990 chunk 238 optimal weight: 0.8980 chunk 456 optimal weight: 20.0000 chunk 107 optimal weight: 9.9990 chunk 217 optimal weight: 0.8980 chunk 402 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 60 ASN ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 636 HIS ** A 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1062 HIS ** 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** A1629 ASN ** A1647 ASN ** 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** B 912 GLN B1094 ASN B1114 GLN ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 ASN ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 HIS ** C 296 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** ** M 75 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 = 0.4529 r_free = 0.4529 target = 0.203976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.191239 restraints weight = 70836.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.190369 restraints weight = 105926.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.191049 restraints weight = 97167.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.190804 restraints weight = 70830.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.191151 restraints weight = 69405.663| |-----------------------------------------------------------------------------| r_work (final): 0.4384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6132 moved from start: 0.4728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 40669 Z= 0.131 Angle : 0.722 13.543 55067 Z= 0.366 Chirality : 0.046 0.248 6173 Planarity : 0.005 0.104 6974 Dihedral : 10.721 149.722 5678 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.02 % Favored : 89.94 % Rotamer: Outliers : 4.14 % Allowed : 22.39 % Favored : 73.47 % 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: -4.04 (0.11), residues: 4839 helix: -3.08 (0.11), residues: 1331 sheet: -2.86 (0.20), residues: 517 loop : -2.55 (0.11), residues: 2991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 134 TYR 0.023 0.002 TYR J 21 PHE 0.032 0.002 PHE A 771 TRP 0.031 0.002 TRP B 143 HIS 0.021 0.001 HIS C 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (40654) covalent geometry : angle 0.71830 / 0.37 (55055) hydrogen bonds : bond 0.03754 / 4.18 ( 651) hydrogen bonds : angle 7.15825 / 7.52 ( 1668) metal coordination : bond 0.00840 / 1.00 ( 15) metal coordination : angle 5.04018 / 8.28 ( 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 731 residues out of total 4381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 550 time to evaluate : 1.463 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 59 ARG cc_start: 0.6481 (ttt180) cc_final: 0.6175 (ttm170) REVERT: A 230 ARG cc_start: 0.2831 (OUTLIER) cc_final: 0.1084 (mtm180) REVERT: A 261 ILE cc_start: 0.7016 (OUTLIER) cc_final: 0.6677 (tt) REVERT: A 477 ASN cc_start: 0.7796 (t0) cc_final: 0.7543 (m-40) REVERT: A 632 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.8110 (pp20) REVERT: A 633 MET cc_start: 0.7957 (ptp) cc_final: 0.7543 (ptp) REVERT: A 824 THR cc_start: 0.8314 (OUTLIER) cc_final: 0.7823 (m) REVERT: A 830 MET cc_start: 0.6737 (mmm) cc_final: 0.6041 (mmt) REVERT: A 871 ASP cc_start: 0.6128 (p0) cc_final: 0.5776 (p0) REVERT: A 884 ARG cc_start: 0.5748 (mmp-170) cc_final: 0.5168 (ttp80) REVERT: A 892 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7113 (pp) REVERT: A 953 GLU cc_start: 0.5907 (OUTLIER) cc_final: 0.5294 (pp20) REVERT: A 1006 LEU cc_start: 0.7170 (pt) cc_final: 0.6486 (mp) REVERT: A 1073 TYR cc_start: 0.5625 (p90) cc_final: 0.5249 (p90) REVERT: A 1147 PHE cc_start: 0.6984 (t80) cc_final: 0.6742 (t80) REVERT: A 1192 SER cc_start: 0.9039 (m) cc_final: 0.8484 (t) REVERT: A 1225 ILE cc_start: 0.8973 (mm) cc_final: 0.8543 (tp) REVERT: A 1439 MET cc_start: 0.4216 (mmm) cc_final: 0.3318 (mpp) REVERT: A 1591 ARG cc_start: 0.7528 (OUTLIER) cc_final: 0.6487 (ttt180) REVERT: A 1604 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7670 (pt0) REVERT: A 1615 TYR cc_start: 0.6555 (t80) cc_final: 0.5828 (t80) REVERT: B 35 PHE cc_start: 0.6811 (OUTLIER) cc_final: 0.5637 (p90) REVERT: B 94 LYS cc_start: 0.5240 (tppp) cc_final: 0.4996 (ttpp) REVERT: B 101 GLN cc_start: 0.8122 (tm-30) cc_final: 0.7711 (tm-30) REVERT: B 127 ARG cc_start: 0.7624 (ptp90) cc_final: 0.7344 (mtm180) REVERT: B 133 TYR cc_start: 0.6281 (t80) cc_final: 0.5135 (t80) REVERT: B 164 MET cc_start: 0.6859 (pmm) cc_final: 0.6406 (pmm) REVERT: B 206 LEU cc_start: 0.6450 (OUTLIER) cc_final: 0.6151 (tm) REVERT: B 261 ARG cc_start: 0.7532 (ttp80) cc_final: 0.7104 (ttt-90) REVERT: B 270 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7239 (pp) REVERT: B 313 PHE cc_start: 0.6860 (t80) cc_final: 0.6571 (t80) REVERT: B 323 ARG cc_start: 0.5706 (mpt90) cc_final: 0.3530 (ttp-170) REVERT: B 543 ASN cc_start: 0.6908 (p0) cc_final: 0.6703 (p0) REVERT: B 672 MET cc_start: 0.6696 (ppp) cc_final: 0.6163 (ptp) REVERT: B 720 GLN cc_start: 0.7832 (mm110) cc_final: 0.7163 (tm-30) REVERT: B 822 THR cc_start: 0.3612 (p) cc_final: 0.3259 (p) REVERT: B 878 GLU cc_start: 0.6385 (mm-30) cc_final: 0.6105 (mm-30) REVERT: B 935 ASP cc_start: 0.7451 (m-30) cc_final: 0.6904 (p0) REVERT: B 1106 GLU cc_start: 0.6477 (OUTLIER) cc_final: 0.6121 (mp0) REVERT: B 1125 THR cc_start: 0.4119 (OUTLIER) cc_final: 0.3706 (p) REVERT: B 1134 ARG cc_start: 0.6477 (mmt-90) cc_final: 0.5250 (mtt180) REVERT: B 1166 LYS cc_start: 0.7303 (tppt) cc_final: 0.6801 (tttm) REVERT: B 1194 ILE cc_start: 0.6669 (OUTLIER) cc_final: 0.6346 (mp) REVERT: C 34 GLU cc_start: 0.4940 (OUTLIER) cc_final: 0.4357 (tm-30) REVERT: C 329 LYS cc_start: 0.7147 (pptt) cc_final: 0.6854 (tmtt) REVERT: E 42 PHE cc_start: 0.6665 (t80) cc_final: 0.5936 (t80) REVERT: E 116 ILE cc_start: 0.5824 (OUTLIER) cc_final: 0.5482 (tp) REVERT: E 177 ARG cc_start: 0.7009 (OUTLIER) cc_final: 0.5255 (ppt-90) REVERT: G 53 TYR cc_start: 0.5947 (m-80) cc_final: 0.5642 (m-10) REVERT: G 134 GLU cc_start: 0.5956 (OUTLIER) cc_final: 0.3637 (tp30) REVERT: H 45 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6896 (pm20) REVERT: H 123 MET cc_start: 0.4005 (mmm) cc_final: 0.3533 (mtt) REVERT: H 130 ARG cc_start: 0.6143 (OUTLIER) cc_final: 0.5760 (mtm-85) REVERT: I 44 ASN cc_start: 0.6881 (m-40) cc_final: 0.6502 (p0) REVERT: I 56 PHE cc_start: 0.6191 (m-80) cc_final: 0.5963 (m-80) REVERT: K 43 ASP cc_start: 0.7237 (p0) cc_final: 0.6888 (p0) REVERT: K 91 TYR cc_start: 0.7507 (p90) cc_final: 0.7295 (p90) REVERT: K 142 MET cc_start: 0.6727 (tpt) cc_final: 0.5850 (tpt) REVERT: L 38 LEU cc_start: 0.6263 (OUTLIER) cc_final: 0.5904 (pp) REVERT: M 178 LEU cc_start: 0.4582 (OUTLIER) cc_final: 0.3581 (mt) REVERT: M 263 TYR cc_start: 0.3453 (t80) cc_final: 0.3004 (t80) REVERT: M 384 ILE cc_start: 0.0446 (OUTLIER) cc_final: -0.0092 (tt) REVERT: M 397 MET cc_start: 0.2480 (mpp) cc_final: 0.0703 (mtt) REVERT: N 40 LEU cc_start: 0.3490 (OUTLIER) cc_final: 0.2998 (mp) REVERT: N 87 TYR cc_start: 0.5983 (m-10) cc_final: 0.5739 (m-10) REVERT: O 127 GLU cc_start: 0.4401 (mt-10) cc_final: 0.4103 (tt0) REVERT: O 167 LYS cc_start: 0.4548 (mttp) cc_final: 0.3476 (mttt) REVERT: O 396 MET cc_start: -0.1007 (mmm) cc_final: -0.2513 (ptm) REVERT: O 606 MET cc_start: 0.3331 (tmm) cc_final: 0.2844 (tmm) outliers start: 181 outliers final: 114 residues processed: 683 average time/residue: 0.2254 time to fit residues: 259.6028 Evaluate side-chains 641 residues out of total 4381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 503 time to evaluate : 1.057 ------------------------------------------------------------------------------- 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 369 LEU Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 632 GLU Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 727 THR 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 809 VAL Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 892 LEU 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 960 MET Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 977 MET Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1033 SER Chi-restraints excluded: chain A residue 1108 HIS Chi-restraints excluded: chain A residue 1124 LEU Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1239 THR 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 1518 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 1622 LEU Chi-restraints excluded: chain A residue 1629 ASN Chi-restraints excluded: chain A residue 1630 GLU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 35 PHE Chi-restraints excluded: chain B residue 45 HIS Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 195 ILE 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 319 HIS Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 419 GLU Chi-restraints excluded: chain B residue 480 GLN 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 703 LEU Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain B residue 740 LYS Chi-restraints excluded: chain B residue 782 ASP Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1036 LEU Chi-restraints excluded: chain B residue 1106 GLU 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 1194 ILE 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 185 VAL Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain E residue 7 ARG Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 177 ARG Chi-restraints excluded: chain E residue 187 TYR Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 43 ILE 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 G residue 133 LEU Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain H residue 30 SER 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 44 TYR 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 M residue 44 LYS 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 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 166 LEU 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: 7.9990 chunk 218 optimal weight: 2.9990 chunk 226 optimal weight: 7.9990 chunk 417 optimal weight: 4.9990 chunk 150 optimal weight: 5.9990 chunk 112 optimal weight: 0.9980 chunk 73 optimal weight: 6.9990 chunk 395 optimal weight: 20.0000 chunk 244 optimal weight: 0.8980 chunk 275 optimal weight: 9.9990 chunk 319 optimal weight: 1.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 383 ASN ** 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** ** A 998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1047 GLN ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1293 HIS A1299 ASN ** A1601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1647 ASN ** 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 711 GLN ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1058 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1094 ASN ** C 161 HIS ** 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** ** M 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.202652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.190226 restraints weight = 70815.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.189203 restraints weight = 113674.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.189796 restraints weight = 99313.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.189525 restraints weight = 77744.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.189914 restraints weight = 71586.258| |-----------------------------------------------------------------------------| r_work (final): 0.4369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6171 moved from start: 0.4864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 40669 Z= 0.150 Angle : 0.730 13.288 55067 Z= 0.369 Chirality : 0.047 0.246 6173 Planarity : 0.005 0.100 6974 Dihedral : 10.635 149.099 5678 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.02 % Allowed : 11.57 % Favored : 88.41 % Rotamer: Outliers : 4.16 % Allowed : 22.85 % 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: -3.98 (0.11), residues: 4839 helix: -3.00 (0.11), residues: 1346 sheet: -2.81 (0.20), residues: 522 loop : -2.52 (0.11), residues: 2971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A1559 TYR 0.028 0.002 TYR A 514 PHE 0.028 0.002 PHE O 473 TRP 0.046 0.002 TRP B 143 HIS 0.010 0.001 HIS A 617 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (40654) covalent geometry : angle 0.72686 / 0.37 (55055) hydrogen bonds : bond 0.03717 / 4.15 ( 651) hydrogen bonds : angle 7.08213 / 7.40 ( 1668) metal coordination : bond 0.00754 / 0.80 ( 15) metal coordination : angle 4.91376 / 8.17 ( 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 684 residues out of total 4381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 502 time to evaluate : 1.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 CYS cc_start: 0.7757 (m) cc_final: 0.7126 (t) REVERT: A 230 ARG cc_start: 0.2464 (OUTLIER) cc_final: 0.1020 (mtm180) REVERT: A 261 ILE cc_start: 0.7071 (OUTLIER) cc_final: 0.6699 (tt) REVERT: A 477 ASN cc_start: 0.7782 (t0) cc_final: 0.7558 (m-40) REVERT: A 632 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8130 (pp20) REVERT: A 824 THR cc_start: 0.8274 (OUTLIER) cc_final: 0.7701 (m) REVERT: A 830 MET cc_start: 0.6801 (mmm) cc_final: 0.6096 (mmt) REVERT: A 871 ASP cc_start: 0.6419 (p0) cc_final: 0.6045 (p0) REVERT: A 884 ARG cc_start: 0.5793 (mmp-170) cc_final: 0.5210 (ttp80) REVERT: A 953 GLU cc_start: 0.5952 (OUTLIER) cc_final: 0.5309 (pp20) REVERT: A 1006 LEU cc_start: 0.7231 (pt) cc_final: 0.6496 (mp) REVERT: A 1073 TYR cc_start: 0.5657 (p90) cc_final: 0.5322 (p90) REVERT: A 1147 PHE cc_start: 0.7156 (t80) cc_final: 0.6920 (t80) REVERT: A 1192 SER cc_start: 0.8986 (m) cc_final: 0.8423 (t) REVERT: A 1225 ILE cc_start: 0.8988 (mm) cc_final: 0.8559 (tp) REVERT: A 1439 MET cc_start: 0.4172 (mmm) cc_final: 0.3279 (mpp) REVERT: A 1591 ARG cc_start: 0.7488 (OUTLIER) cc_final: 0.6493 (ttt180) REVERT: A 1604 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7774 (pt0) REVERT: B 35 PHE cc_start: 0.6836 (OUTLIER) cc_final: 0.5675 (p90) REVERT: B 94 LYS cc_start: 0.5316 (tppp) cc_final: 0.4973 (ttpp) REVERT: B 127 ARG cc_start: 0.7685 (ptp90) cc_final: 0.7347 (mtm180) REVERT: B 206 LEU cc_start: 0.6534 (OUTLIER) cc_final: 0.6203 (tm) REVERT: B 261 ARG cc_start: 0.7614 (ttp80) cc_final: 0.7274 (ttt-90) REVERT: B 270 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7330 (pp) REVERT: B 277 LEU cc_start: 0.6363 (OUTLIER) cc_final: 0.6029 (tp) REVERT: B 313 PHE cc_start: 0.6780 (t80) cc_final: 0.6510 (t80) REVERT: B 323 ARG cc_start: 0.5830 (mpt90) cc_final: 0.3611 (ttp-170) REVERT: B 413 LEU cc_start: 0.7833 (tp) cc_final: 0.7409 (mt) REVERT: B 542 LEU cc_start: 0.6143 (OUTLIER) cc_final: 0.5884 (pp) REVERT: B 672 MET cc_start: 0.6793 (ppp) cc_final: 0.6200 (ptp) REVERT: B 720 GLN cc_start: 0.7807 (mm110) cc_final: 0.7145 (tm-30) REVERT: B 822 THR cc_start: 0.3689 (p) cc_final: 0.3328 (p) REVERT: B 935 ASP cc_start: 0.7577 (m-30) cc_final: 0.6991 (p0) REVERT: B 1106 GLU cc_start: 0.6528 (OUTLIER) cc_final: 0.6255 (mp0) REVERT: B 1125 THR cc_start: 0.4185 (OUTLIER) cc_final: 0.3734 (p) REVERT: B 1134 ARG cc_start: 0.6481 (mmt-90) cc_final: 0.5283 (mtt180) REVERT: B 1166 LYS cc_start: 0.7351 (tppt) cc_final: 0.6857 (tttm) REVERT: B 1194 ILE cc_start: 0.6686 (OUTLIER) cc_final: 0.6374 (mp) REVERT: C 34 GLU cc_start: 0.4995 (OUTLIER) cc_final: 0.4426 (tm-30) REVERT: C 329 LYS cc_start: 0.7126 (pptt) cc_final: 0.6866 (tmtt) REVERT: E 116 ILE cc_start: 0.5933 (OUTLIER) cc_final: 0.5543 (tp) REVERT: E 177 ARG cc_start: 0.7041 (OUTLIER) cc_final: 0.5431 (ppt-90) REVERT: E 215 MET cc_start: 0.4760 (pp-130) cc_final: 0.4020 (pp-130) REVERT: F 120 ILE cc_start: 0.6501 (OUTLIER) cc_final: 0.5910 (mt) REVERT: G 53 TYR cc_start: 0.5962 (m-80) cc_final: 0.5629 (m-10) REVERT: G 76 LYS cc_start: 0.6328 (tptp) cc_final: 0.5947 (tptt) REVERT: G 134 GLU cc_start: 0.6090 (OUTLIER) cc_final: 0.4218 (tt0) REVERT: H 45 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.6934 (pm20) REVERT: H 123 MET cc_start: 0.3830 (mmm) cc_final: 0.3452 (mtt) REVERT: I 44 ASN cc_start: 0.6775 (m-40) cc_final: 0.6439 (p0) REVERT: I 56 PHE cc_start: 0.6491 (m-80) cc_final: 0.6186 (m-80) REVERT: K 43 ASP cc_start: 0.7404 (p0) cc_final: 0.6986 (p0) REVERT: K 142 MET cc_start: 0.6884 (tpt) cc_final: 0.5839 (tpt) REVERT: L 38 LEU cc_start: 0.6373 (OUTLIER) cc_final: 0.6016 (pp) REVERT: M 125 ARG cc_start: 0.4296 (mmt180) cc_final: 0.4041 (mpt180) REVERT: M 148 ARG cc_start: 0.5448 (OUTLIER) cc_final: 0.5140 (mtm-85) REVERT: M 178 LEU cc_start: 0.4453 (OUTLIER) cc_final: 0.3479 (mt) REVERT: M 263 TYR cc_start: 0.3865 (t80) cc_final: 0.3287 (t80) REVERT: M 384 ILE cc_start: 0.0444 (OUTLIER) cc_final: -0.0119 (tt) REVERT: M 397 MET cc_start: 0.2570 (mpp) cc_final: 0.0885 (mtt) REVERT: N 40 LEU cc_start: 0.3437 (OUTLIER) cc_final: 0.2822 (mp) REVERT: N 87 TYR cc_start: 0.6199 (m-10) cc_final: 0.5943 (m-10) REVERT: O 127 GLU cc_start: 0.4400 (mt-10) cc_final: 0.4134 (tt0) REVERT: O 167 LYS cc_start: 0.4713 (mttp) cc_final: 0.3582 (mttt) REVERT: O 396 MET cc_start: -0.0665 (mmm) cc_final: -0.2307 (ptm) REVERT: O 606 MET cc_start: 0.3578 (tmm) cc_final: 0.3142 (tmm) outliers start: 182 outliers final: 130 residues processed: 637 average time/residue: 0.2334 time to fit residues: 252.1278 Evaluate side-chains 645 residues out of total 4381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 489 time to evaluate : 1.392 ------------------------------------------------------------------------------- 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 369 LEU Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 608 LEU 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 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 809 VAL 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 946 LEU Chi-restraints excluded: chain A residue 953 GLU Chi-restraints excluded: chain A residue 960 MET Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 977 MET 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 1124 LEU Chi-restraints excluded: chain A residue 1178 LEU 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 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 1589 MET Chi-restraints excluded: chain A residue 1591 ARG Chi-restraints excluded: chain A residue 1604 GLU Chi-restraints excluded: chain A residue 1622 LEU 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 45 HIS Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 195 ILE 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 319 HIS Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 377 MET 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 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 716 MET Chi-restraints excluded: chain B residue 782 ASP Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 871 ILE Chi-restraints excluded: chain B residue 907 ILE Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1036 LEU Chi-restraints excluded: chain B residue 1106 GLU 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 1194 ILE Chi-restraints excluded: chain C residue 34 GLU 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 192 LEU Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain E residue 7 ARG Chi-restraints excluded: chain E residue 116 ILE 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 82 THR Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 43 ILE 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 116 THR Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 40 LEU 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 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 M residue 23 VAL Chi-restraints excluded: chain M residue 44 LYS 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 443 optimal weight: 9.9990 chunk 159 optimal weight: 9.9990 chunk 392 optimal weight: 0.0970 chunk 310 optimal weight: 9.9990 chunk 65 optimal weight: 4.9990 chunk 391 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 438 optimal weight: 20.0000 chunk 262 optimal weight: 7.9990 chunk 301 optimal weight: 0.0370 overall best weight: 2.0060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 ASN ** A 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1293 HIS A1299 ASN A1315 ASN ** A1601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1629 ASN ** A1647 ASN ** 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 684 ASN ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1082 HIS B1094 ASN ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 HIS ** 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** ** M 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.203707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.191691 restraints weight = 71034.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.190926 restraints weight = 110296.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.191540 restraints weight = 96838.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.191437 restraints weight = 68378.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.191634 restraints weight = 65751.380| |-----------------------------------------------------------------------------| r_work (final): 0.4388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6133 moved from start: 0.5039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 40669 Z= 0.137 Angle : 0.718 12.670 55067 Z= 0.363 Chirality : 0.046 0.242 6173 Planarity : 0.005 0.101 6974 Dihedral : 10.508 149.022 5678 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.54 % Favored : 89.44 % Rotamer: Outliers : 4.30 % Allowed : 22.94 % Favored : 72.76 % 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: -3.86 (0.11), residues: 4839 helix: -2.89 (0.12), residues: 1355 sheet: -2.75 (0.20), residues: 534 loop : -2.43 (0.11), residues: 2950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1559 TYR 0.030 0.002 TYR B 671 PHE 0.028 0.002 PHE O 473 TRP 0.037 0.002 TRP B 143 HIS 0.014 0.001 HIS C 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (40654) covalent geometry : angle 0.71454 / 0.36 (55055) hydrogen bonds : bond 0.03586 / 4.02 ( 651) hydrogen bonds : angle 6.94329 / 7.24 ( 1668) metal coordination : bond 0.00715 / 0.77 ( 15) metal coordination : angle 4.59350 / 7.68 ( 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 705 residues out of total 4381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 188 poor density : 517 time to evaluate : 1.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 ARG cc_start: 0.2824 (OUTLIER) cc_final: 0.1158 (mtm180) REVERT: A 261 ILE cc_start: 0.7012 (OUTLIER) cc_final: 0.6723 (tt) REVERT: A 632 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8126 (pp20) REVERT: A 641 GLU cc_start: 0.6993 (pp20) cc_final: 0.6748 (pm20) REVERT: A 824 THR cc_start: 0.8224 (OUTLIER) cc_final: 0.7693 (m) REVERT: A 827 THR cc_start: 0.8244 (t) cc_final: 0.7904 (m) REVERT: A 830 MET cc_start: 0.6758 (mmm) cc_final: 0.5958 (mmt) REVERT: A 871 ASP cc_start: 0.6208 (p0) cc_final: 0.5821 (p0) REVERT: A 884 ARG cc_start: 0.5476 (mmp-170) cc_final: 0.4891 (ttp80) REVERT: A 953 GLU cc_start: 0.6128 (OUTLIER) cc_final: 0.5471 (pp20) REVERT: A 1006 LEU cc_start: 0.7288 (pt) cc_final: 0.6668 (mp) REVERT: A 1073 TYR cc_start: 0.5531 (p90) cc_final: 0.5231 (p90) REVERT: A 1192 SER cc_start: 0.8964 (m) cc_final: 0.8445 (t) REVERT: A 1225 ILE cc_start: 0.8981 (mm) cc_final: 0.8558 (tp) REVERT: A 1591 ARG cc_start: 0.7452 (OUTLIER) cc_final: 0.6453 (ttt180) REVERT: A 1604 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7678 (pt0) REVERT: A 1615 TYR cc_start: 0.6325 (t80) cc_final: 0.5716 (t80) REVERT: B 35 PHE cc_start: 0.6783 (OUTLIER) cc_final: 0.5597 (p90) REVERT: B 94 LYS cc_start: 0.5684 (tppp) cc_final: 0.5281 (ttpp) REVERT: B 133 TYR cc_start: 0.6437 (t80) cc_final: 0.5179 (t80) REVERT: B 206 LEU cc_start: 0.6532 (OUTLIER) cc_final: 0.6253 (tm) REVERT: B 261 ARG cc_start: 0.7572 (ttp80) cc_final: 0.7259 (ttt-90) REVERT: B 270 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7315 (pp) REVERT: B 277 LEU cc_start: 0.6334 (OUTLIER) cc_final: 0.5911 (tt) REVERT: B 323 ARG cc_start: 0.5794 (mpt90) cc_final: 0.3626 (ttp-170) REVERT: B 411 MET cc_start: 0.6949 (pmm) cc_final: 0.6286 (pmm) REVERT: B 439 ASN cc_start: 0.6315 (p0) cc_final: 0.5795 (p0) REVERT: B 672 MET cc_start: 0.6680 (ppp) cc_final: 0.6112 (ptp) REVERT: B 681 ILE cc_start: 0.8406 (OUTLIER) cc_final: 0.8181 (mt) REVERT: B 720 GLN cc_start: 0.7801 (mm110) cc_final: 0.7094 (tm-30) REVERT: B 822 THR cc_start: 0.3640 (p) cc_final: 0.3284 (p) REVERT: B 935 ASP cc_start: 0.7401 (m-30) cc_final: 0.6894 (p0) REVERT: B 1106 GLU cc_start: 0.6485 (OUTLIER) cc_final: 0.6249 (mp0) REVERT: B 1125 THR cc_start: 0.4204 (OUTLIER) cc_final: 0.3822 (p) REVERT: B 1134 ARG cc_start: 0.6408 (mmt-90) cc_final: 0.5208 (mtt180) REVERT: B 1166 LYS cc_start: 0.7442 (tppt) cc_final: 0.6862 (tttm) REVERT: B 1194 ILE cc_start: 0.6761 (OUTLIER) cc_final: 0.6536 (mp) REVERT: C 34 GLU cc_start: 0.5018 (OUTLIER) cc_final: 0.4429 (tm-30) REVERT: C 315 PHE cc_start: 0.6770 (OUTLIER) cc_final: 0.6009 (t80) REVERT: C 329 LYS cc_start: 0.7129 (pptt) cc_final: 0.6827 (tmtt) REVERT: E 116 ILE cc_start: 0.5972 (OUTLIER) cc_final: 0.5531 (tp) REVERT: E 177 ARG cc_start: 0.7052 (OUTLIER) cc_final: 0.5420 (ppt-90) REVERT: E 215 MET cc_start: 0.4654 (pp-130) cc_final: 0.3992 (pp-130) REVERT: F 120 ILE cc_start: 0.6430 (OUTLIER) cc_final: 0.5906 (mt) REVERT: G 53 TYR cc_start: 0.6023 (m-80) cc_final: 0.5655 (m-10) REVERT: G 71 MET cc_start: 0.6529 (mmt) cc_final: 0.6318 (mmt) REVERT: G 76 LYS cc_start: 0.6519 (tptp) cc_final: 0.6050 (mttt) REVERT: G 134 GLU cc_start: 0.5900 (OUTLIER) cc_final: 0.4325 (tt0) REVERT: H 45 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.6997 (pm20) REVERT: H 123 MET cc_start: 0.3985 (mmm) cc_final: 0.3719 (mtt) REVERT: I 44 ASN cc_start: 0.6933 (m-40) cc_final: 0.6562 (p0) REVERT: I 56 PHE cc_start: 0.6475 (m-80) cc_final: 0.6209 (m-80) REVERT: K 43 ASP cc_start: 0.7469 (p0) cc_final: 0.7097 (p0) REVERT: K 142 MET cc_start: 0.6897 (tpt) cc_final: 0.5769 (tpt) REVERT: L 38 LEU cc_start: 0.6283 (OUTLIER) cc_final: 0.5942 (pp) REVERT: M 125 ARG cc_start: 0.4428 (mmt180) cc_final: 0.4107 (mpt180) REVERT: M 148 ARG cc_start: 0.5446 (OUTLIER) cc_final: 0.5138 (mtm-85) REVERT: M 178 LEU cc_start: 0.4206 (OUTLIER) cc_final: 0.3269 (mt) REVERT: M 263 TYR cc_start: 0.3771 (t80) cc_final: 0.3215 (t80) REVERT: M 384 ILE cc_start: 0.0412 (OUTLIER) cc_final: -0.0158 (tt) REVERT: M 397 MET cc_start: 0.2661 (mpp) cc_final: 0.1013 (mtt) REVERT: N 40 LEU cc_start: 0.3362 (OUTLIER) cc_final: 0.2723 (mp) REVERT: N 87 TYR cc_start: 0.6265 (m-10) cc_final: 0.6045 (m-10) REVERT: O 127 GLU cc_start: 0.4206 (mt-10) cc_final: 0.3984 (tt0) REVERT: O 167 LYS cc_start: 0.4938 (mttp) cc_final: 0.3781 (mttt) REVERT: O 396 MET cc_start: -0.0960 (mmm) cc_final: -0.2273 (ptm) REVERT: O 606 MET cc_start: 0.3742 (tmm) cc_final: 0.3402 (tmm) outliers start: 188 outliers final: 126 residues processed: 655 average time/residue: 0.2432 time to fit residues: 269.3644 Evaluate side-chains 636 residues out of total 4381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 483 time to evaluate : 1.567 ------------------------------------------------------------------------------- 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 418 VAL Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 514 TYR 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 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 809 VAL 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 946 LEU Chi-restraints excluded: chain A residue 953 GLU Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 977 MET Chi-restraints excluded: chain A residue 1027 LEU Chi-restraints excluded: chain A residue 1033 SER Chi-restraints excluded: chain A residue 1108 HIS Chi-restraints excluded: chain A residue 1124 LEU Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1239 THR 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 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 1591 ARG Chi-restraints excluded: chain A residue 1604 GLU Chi-restraints excluded: chain A residue 1622 LEU Chi-restraints excluded: chain A residue 1629 ASN 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 45 HIS Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 125 GLU Chi-restraints excluded: chain B residue 195 ILE 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 319 HIS Chi-restraints excluded: chain B residue 337 VAL 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 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 681 ILE Chi-restraints excluded: chain B residue 684 ASN Chi-restraints excluded: chain B residue 703 LEU Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 871 ILE Chi-restraints excluded: chain B residue 907 ILE Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1036 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 1125 THR Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1128 CYS Chi-restraints excluded: chain B residue 1194 ILE Chi-restraints excluded: chain C residue 34 GLU Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 185 VAL 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 C residue 315 PHE Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 116 ILE Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 177 ARG Chi-restraints excluded: chain E residue 187 TYR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 43 ILE 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 116 THR Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain H residue 30 SER 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 44 TYR 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 M residue 23 VAL Chi-restraints excluded: chain M residue 44 LYS 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 78 THR Chi-restraints excluded: chain N residue 89 ILE Chi-restraints excluded: chain N residue 166 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 17 optimal weight: 6.9990 chunk 469 optimal weight: 4.9990 chunk 236 optimal weight: 6.9990 chunk 293 optimal weight: 3.9990 chunk 337 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 346 optimal weight: 3.9990 chunk 450 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 259 optimal weight: 0.0870 chunk 324 optimal weight: 0.9990 overall best weight: 1.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 383 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** ** A 998 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1062 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1293 HIS A1299 ASN A1315 ASN A1500 GLN A1629 ASN ** A1647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 HIS ** 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 912 GLN B1094 ASN ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 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** ** M 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 390 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.204268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.191704 restraints weight = 70530.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.190939 restraints weight = 116221.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.191724 restraints weight = 101126.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.191560 restraints weight = 72632.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.191768 restraints weight = 62417.214| |-----------------------------------------------------------------------------| r_work (final): 0.4389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6122 moved from start: 0.5132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 40669 Z= 0.132 Angle : 0.717 12.275 55067 Z= 0.362 Chirality : 0.046 0.248 6173 Planarity : 0.005 0.098 6974 Dihedral : 10.425 149.072 5678 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.81 % Favored : 89.17 % Rotamer: Outliers : 3.79 % Allowed : 23.56 % Favored : 72.65 % 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: -3.76 (0.11), residues: 4839 helix: -2.78 (0.12), residues: 1347 sheet: -2.69 (0.21), residues: 536 loop : -2.39 (0.11), residues: 2956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 920 TYR 0.039 0.002 TYR B1184 PHE 0.041 0.002 PHE B 493 TRP 0.038 0.002 TRP B 143 HIS 0.009 0.001 HIS A 617 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (40654) covalent geometry : angle 0.71359 / 0.36 (55055) hydrogen bonds : bond 0.03515 / 3.91 ( 651) hydrogen bonds : angle 6.84357 / 7.13 ( 1668) metal coordination : bond 0.01150 / 1.38 ( 15) metal coordination : angle 5.08907 / 8.35 ( 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 680 residues out of total 4381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 514 time to evaluate : 1.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 ARG cc_start: 0.2795 (OUTLIER) cc_final: 0.1177 (mtm180) REVERT: A 261 ILE cc_start: 0.7028 (OUTLIER) cc_final: 0.6793 (tt) REVERT: A 590 ASN cc_start: 0.8445 (m-40) cc_final: 0.8106 (m110) REVERT: A 632 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.8120 (pp20) REVERT: A 824 THR cc_start: 0.8247 (OUTLIER) cc_final: 0.7693 (m) REVERT: A 827 THR cc_start: 0.8277 (t) cc_final: 0.7952 (m) REVERT: A 830 MET cc_start: 0.6516 (mmm) cc_final: 0.5756 (mmt) REVERT: A 871 ASP cc_start: 0.6349 (p0) cc_final: 0.5964 (p0) REVERT: A 884 ARG cc_start: 0.5444 (mmp-170) cc_final: 0.4908 (ttp80) REVERT: A 892 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7121 (pp) REVERT: A 953 GLU cc_start: 0.6117 (OUTLIER) cc_final: 0.5455 (pp20) REVERT: A 1006 LEU cc_start: 0.7232 (pt) cc_final: 0.6644 (mp) REVERT: A 1073 TYR cc_start: 0.5532 (p90) cc_final: 0.5241 (p90) REVERT: A 1192 SER cc_start: 0.8950 (m) cc_final: 0.8429 (t) REVERT: A 1225 ILE cc_start: 0.8982 (mm) cc_final: 0.8534 (tp) REVERT: A 1591 ARG cc_start: 0.7510 (OUTLIER) cc_final: 0.6295 (ttt180) REVERT: A 1604 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7688 (pt0) REVERT: B 35 PHE cc_start: 0.6792 (OUTLIER) cc_final: 0.5580 (p90) REVERT: B 94 LYS cc_start: 0.5660 (tppp) cc_final: 0.5237 (ttpp) REVERT: B 261 ARG cc_start: 0.7528 (ttp80) cc_final: 0.7251 (ttt-90) REVERT: B 268 GLU cc_start: 0.7370 (mp0) cc_final: 0.7105 (mp0) REVERT: B 270 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7162 (pp) REVERT: B 277 LEU cc_start: 0.6253 (OUTLIER) cc_final: 0.5897 (tt) REVERT: B 323 ARG cc_start: 0.5773 (mpt90) cc_final: 0.3614 (ttp-170) REVERT: B 411 MET cc_start: 0.6850 (pmm) cc_final: 0.6336 (pmm) REVERT: B 439 ASN cc_start: 0.6279 (p0) cc_final: 0.5778 (p0) REVERT: B 672 MET cc_start: 0.6663 (ppp) cc_final: 0.6124 (ptp) REVERT: B 720 GLN cc_start: 0.7816 (mm110) cc_final: 0.7071 (tm-30) REVERT: B 822 THR cc_start: 0.3581 (p) cc_final: 0.3229 (p) REVERT: B 935 ASP cc_start: 0.7328 (m-30) cc_final: 0.6893 (p0) REVERT: B 1106 GLU cc_start: 0.6434 (OUTLIER) cc_final: 0.6193 (mp0) REVERT: B 1125 THR cc_start: 0.4014 (OUTLIER) cc_final: 0.3587 (p) REVERT: B 1126 VAL cc_start: 0.7600 (OUTLIER) cc_final: 0.7312 (m) REVERT: B 1134 ARG cc_start: 0.6589 (mmt-90) cc_final: 0.5328 (mtt180) REVERT: B 1166 LYS cc_start: 0.7469 (tppt) cc_final: 0.7188 (tttm) REVERT: C 34 GLU cc_start: 0.4892 (OUTLIER) cc_final: 0.4384 (tm-30) REVERT: C 329 LYS cc_start: 0.7109 (pptt) cc_final: 0.6819 (tmtt) REVERT: D 90 LYS cc_start: 0.5252 (mmtt) cc_final: 0.4888 (mmtt) REVERT: E 116 ILE cc_start: 0.5944 (OUTLIER) cc_final: 0.5539 (tp) REVERT: E 177 ARG cc_start: 0.7096 (OUTLIER) cc_final: 0.6181 (ptt-90) REVERT: G 76 LYS cc_start: 0.6463 (tptp) cc_final: 0.5997 (mttt) REVERT: G 134 GLU cc_start: 0.5820 (OUTLIER) cc_final: 0.4334 (tt0) REVERT: H 45 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.7013 (pm20) REVERT: H 111 LEU cc_start: 0.4950 (OUTLIER) cc_final: 0.4381 (tt) REVERT: I 44 ASN cc_start: 0.6886 (m-40) cc_final: 0.6541 (p0) REVERT: I 56 PHE cc_start: 0.6445 (m-80) cc_final: 0.6123 (m-80) REVERT: K 43 ASP cc_start: 0.7490 (p0) cc_final: 0.7064 (p0) REVERT: K 142 MET cc_start: 0.6913 (tpt) cc_final: 0.5716 (tpt) REVERT: L 38 LEU cc_start: 0.6268 (OUTLIER) cc_final: 0.5897 (pp) REVERT: M 125 ARG cc_start: 0.4435 (mmt180) cc_final: 0.4144 (mpt180) REVERT: M 148 ARG cc_start: 0.5416 (OUTLIER) cc_final: 0.5145 (mtm-85) REVERT: M 178 LEU cc_start: 0.4216 (OUTLIER) cc_final: 0.3284 (mt) REVERT: M 263 TYR cc_start: 0.3724 (t80) cc_final: 0.3188 (t80) REVERT: M 384 ILE cc_start: 0.0452 (OUTLIER) cc_final: -0.0132 (tt) REVERT: M 397 MET cc_start: 0.2643 (mpp) cc_final: 0.1038 (mtt) REVERT: N 40 LEU cc_start: 0.3264 (OUTLIER) cc_final: 0.2677 (mp) REVERT: O 127 GLU cc_start: 0.4484 (mt-10) cc_final: 0.4186 (tt0) REVERT: O 167 LYS cc_start: 0.4790 (mttp) cc_final: 0.3701 (mttt) REVERT: O 197 PHE cc_start: 0.4783 (m-80) cc_final: 0.4494 (t80) REVERT: O 396 MET cc_start: -0.0978 (mmm) cc_final: -0.2244 (ptm) REVERT: O 606 MET cc_start: 0.3655 (tmm) cc_final: 0.3320 (tmm) outliers start: 166 outliers final: 124 residues processed: 640 average time/residue: 0.2336 time to fit residues: 253.2798 Evaluate side-chains 643 residues out of total 4381 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 494 time to evaluate : 1.525 ------------------------------------------------------------------------------- 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 418 VAL Chi-restraints excluded: chain A residue 424 MET Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 514 TYR Chi-restraints excluded: chain A residue 587 VAL 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 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 809 VAL Chi-restraints excluded: chain A residue 824 THR Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 892 LEU 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 962 SER Chi-restraints excluded: chain A residue 965 THR Chi-restraints excluded: chain A residue 977 MET 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 1124 LEU Chi-restraints excluded: chain A residue 1178 LEU Chi-restraints excluded: chain A residue 1239 THR 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 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 1591 ARG Chi-restraints excluded: chain A residue 1604 GLU Chi-restraints excluded: chain A residue 1622 LEU 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 45 HIS Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 125 GLU 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 319 HIS Chi-restraints excluded: chain B residue 377 MET 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 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 703 LEU Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain B residue 782 ASP Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 863 ASP Chi-restraints excluded: chain B residue 871 ILE Chi-restraints excluded: chain B residue 907 ILE Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1036 LEU Chi-restraints excluded: chain B residue 1106 GLU 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 C residue 34 GLU Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 116 ILE 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 130 ILE Chi-restraints excluded: chain G residue 39 VAL Chi-restraints excluded: chain G residue 43 ILE 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 116 THR Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain G residue 134 GLU Chi-restraints excluded: chain G residue 145 ILE Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain J residue 44 TYR 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 M residue 23 VAL Chi-restraints excluded: chain M residue 44 LYS 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 188 optimal weight: 0.0040 chunk 422 optimal weight: 7.9990 chunk 334 optimal weight: 10.0000 chunk 437 optimal weight: 0.0060 chunk 436 optimal weight: 6.9990 chunk 134 optimal weight: 3.9990 chunk 359 optimal weight: 10.0000 chunk 308 optimal weight: 9.9990 chunk 301 optimal weight: 5.9990 chunk 109 optimal weight: 0.0020 chunk 236 optimal weight: 7.9990 overall best weight: 2.0020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 617 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 753 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 998 HIS ** A1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1293 HIS A1299 ASN ** A1647 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 HIS ** 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** C 58 ASN ** C 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.203894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.191603 restraints weight = 70828.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.190951 restraints weight = 108700.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.191572 restraints weight = 97019.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.191314 restraints weight = 71852.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.191595 restraints weight = 67645.745| |-----------------------------------------------------------------------------| r_work (final): 0.4388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6132 moved from start: 0.5232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 40669 Z= 0.138 Angle : 0.714 12.126 55067 Z= 0.361 Chirality : 0.046 0.237 6173 Planarity : 0.005 0.101 6974 Dihedral : 10.386 148.779 5678 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.66 % Favored : 89.32 % Rotamer: Outliers : 3.82 % Allowed : 23.70 % Favored : 72.49 % 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: -3.71 (0.11), residues: 4839 helix: -2.71 (0.12), residues: 1351 sheet: -2.60 (0.21), residues: 546 loop : -2.38 (0.11), residues: 2942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 920 TYR 0.033 0.002 TYR B1184 PHE 0.035 0.002 PHE C 314 TRP 0.033 0.002 TRP B 143 HIS 0.009 0.001 HIS A 617 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (40654) covalent geometry : angle 0.71108 / 0.36 (55055) hydrogen bonds : bond 0.03496 / 3.89 ( 651) hydrogen bonds : angle 6.80053 / 7.09 ( 1668) metal coordination : bond 0.00657 / 0.67 ( 15) metal coordination : angle 4.60022 / 7.70 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6546.59 seconds wall clock time: 114 minutes 38.07 seconds (6878.07 seconds total)