Starting phenix.real_space_refine on Tue Feb 20 17:12:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rw9_10035/02_2024/6rw9_10035.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rw9_10035/02_2024/6rw9_10035.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rw9_10035/02_2024/6rw9_10035.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rw9_10035/02_2024/6rw9_10035.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rw9_10035/02_2024/6rw9_10035.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rw9_10035/02_2024/6rw9_10035.pdb" } resolution = 3.27 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 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: 4 Type Number sf(0) Gaussians S 305 5.16 5 C 55970 2.51 5 N 15350 2.21 5 O 17075 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 41": "NH1" <-> "NH2" Residue "A ARG 44": "NH1" <-> "NH2" Residue "A ARG 137": "NH1" <-> "NH2" Residue "A ARG 194": "NH1" <-> "NH2" Residue "A PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 266": "NH1" <-> "NH2" Residue "A ARG 304": "NH1" <-> "NH2" Residue "A ARG 449": "NH1" <-> "NH2" Residue "A ARG 493": "NH1" <-> "NH2" Residue "A ARG 578": "NH1" <-> "NH2" Residue "A ARG 682": "NH1" <-> "NH2" Residue "A ARG 736": "NH1" <-> "NH2" Residue "A ARG 861": "NH1" <-> "NH2" Residue "A ARG 886": "NH1" <-> "NH2" Residue "A TYR 1532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1695": "NH1" <-> "NH2" Residue "A ARG 1785": "NH1" <-> "NH2" Residue "A TYR 1836": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1914": "NH1" <-> "NH2" Residue "A ARG 2054": "NH1" <-> "NH2" Residue "A ARG 2151": "NH1" <-> "NH2" Residue "A ARG 2208": "NH1" <-> "NH2" Residue "A ARG 2255": "NH1" <-> "NH2" Residue "B ARG 41": "NH1" <-> "NH2" Residue "B ARG 44": "NH1" <-> "NH2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B ARG 194": "NH1" <-> "NH2" Residue "B PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 266": "NH1" <-> "NH2" Residue "B ARG 304": "NH1" <-> "NH2" Residue "B ARG 449": "NH1" <-> "NH2" Residue "B ARG 493": "NH1" <-> "NH2" Residue "B ARG 578": "NH1" <-> "NH2" Residue "B ARG 682": "NH1" <-> "NH2" Residue "B ARG 736": "NH1" <-> "NH2" Residue "B ARG 861": "NH1" <-> "NH2" Residue "B ARG 886": "NH1" <-> "NH2" Residue "B TYR 1532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1695": "NH1" <-> "NH2" Residue "B ARG 1785": "NH1" <-> "NH2" Residue "B TYR 1836": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1914": "NH1" <-> "NH2" Residue "B ARG 2054": "NH1" <-> "NH2" Residue "B ARG 2151": "NH1" <-> "NH2" Residue "B ARG 2208": "NH1" <-> "NH2" Residue "B ARG 2255": "NH1" <-> "NH2" Residue "C ARG 41": "NH1" <-> "NH2" Residue "C ARG 44": "NH1" <-> "NH2" Residue "C ARG 137": "NH1" <-> "NH2" Residue "C ARG 194": "NH1" <-> "NH2" Residue "C PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 266": "NH1" <-> "NH2" Residue "C ARG 304": "NH1" <-> "NH2" Residue "C ARG 449": "NH1" <-> "NH2" Residue "C ARG 493": "NH1" <-> "NH2" Residue "C ARG 578": "NH1" <-> "NH2" Residue "C ARG 682": "NH1" <-> "NH2" Residue "C ARG 736": "NH1" <-> "NH2" Residue "C ARG 861": "NH1" <-> "NH2" Residue "C ARG 886": "NH1" <-> "NH2" Residue "C TYR 1532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1695": "NH1" <-> "NH2" Residue "C ARG 1785": "NH1" <-> "NH2" Residue "C TYR 1836": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1914": "NH1" <-> "NH2" Residue "C ARG 2054": "NH1" <-> "NH2" Residue "C ARG 2151": "NH1" <-> "NH2" Residue "C ARG 2208": "NH1" <-> "NH2" Residue "C ARG 2255": "NH1" <-> "NH2" Residue "D ARG 41": "NH1" <-> "NH2" Residue "D ARG 44": "NH1" <-> "NH2" Residue "D ARG 137": "NH1" <-> "NH2" Residue "D ARG 194": "NH1" <-> "NH2" Residue "D PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 266": "NH1" <-> "NH2" Residue "D ARG 304": "NH1" <-> "NH2" Residue "D ARG 449": "NH1" <-> "NH2" Residue "D ARG 493": "NH1" <-> "NH2" Residue "D ARG 578": "NH1" <-> "NH2" Residue "D ARG 682": "NH1" <-> "NH2" Residue "D ARG 736": "NH1" <-> "NH2" Residue "D ARG 861": "NH1" <-> "NH2" Residue "D ARG 886": "NH1" <-> "NH2" Residue "D TYR 1532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 1695": "NH1" <-> "NH2" Residue "D ARG 1785": "NH1" <-> "NH2" Residue "D TYR 1836": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 1914": "NH1" <-> "NH2" Residue "D ARG 2054": "NH1" <-> "NH2" Residue "D ARG 2151": "NH1" <-> "NH2" Residue "D ARG 2208": "NH1" <-> "NH2" Residue "D ARG 2255": "NH1" <-> "NH2" Residue "E ARG 41": "NH1" <-> "NH2" Residue "E ARG 44": "NH1" <-> "NH2" Residue "E ARG 137": "NH1" <-> "NH2" Residue "E ARG 194": "NH1" <-> "NH2" Residue "E PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 266": "NH1" <-> "NH2" Residue "E ARG 304": "NH1" <-> "NH2" Residue "E ARG 449": "NH1" <-> "NH2" Residue "E ARG 493": "NH1" <-> "NH2" Residue "E ARG 578": "NH1" <-> "NH2" Residue "E ARG 682": "NH1" <-> "NH2" Residue "E ARG 736": "NH1" <-> "NH2" Residue "E ARG 861": "NH1" <-> "NH2" Residue "E ARG 886": "NH1" <-> "NH2" Residue "E TYR 1532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 1695": "NH1" <-> "NH2" Residue "E ARG 1785": "NH1" <-> "NH2" Residue "E TYR 1836": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 1914": "NH1" <-> "NH2" Residue "E ARG 2054": "NH1" <-> "NH2" Residue "E ARG 2151": "NH1" <-> "NH2" Residue "E ARG 2208": "NH1" <-> "NH2" Residue "E ARG 2255": "NH1" <-> "NH2" Time to flip residues: 0.20s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 88700 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 17740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2285, 17740 Classifications: {'peptide': 2285} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 57} Link IDs: {'CIS': 4, 'PCIS': 6, 'PTRANS': 93, 'TRANS': 2181} Chain breaks: 5 Unresolved non-hydrogen bonds: 202 Unresolved non-hydrogen angles: 240 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 12, 'ARG:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 101 Chain: "B" Number of atoms: 17740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2285, 17740 Classifications: {'peptide': 2285} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 57} Link IDs: {'CIS': 4, 'PCIS': 6, 'PTRANS': 93, 'TRANS': 2181} Chain breaks: 5 Unresolved non-hydrogen bonds: 202 Unresolved non-hydrogen angles: 240 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 12, 'ARG:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 101 Chain: "C" Number of atoms: 17740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2285, 17740 Classifications: {'peptide': 2285} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 57} Link IDs: {'CIS': 4, 'PCIS': 6, 'PTRANS': 93, 'TRANS': 2181} Chain breaks: 5 Unresolved non-hydrogen bonds: 202 Unresolved non-hydrogen angles: 240 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 12, 'ARG:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 101 Chain: "D" Number of atoms: 17740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2285, 17740 Classifications: {'peptide': 2285} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 57} Link IDs: {'CIS': 4, 'PCIS': 6, 'PTRANS': 93, 'TRANS': 2181} Chain breaks: 5 Unresolved non-hydrogen bonds: 202 Unresolved non-hydrogen angles: 240 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 12, 'ARG:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 101 Chain: "E" Number of atoms: 17740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2285, 17740 Classifications: {'peptide': 2285} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 57} Link IDs: {'CIS': 4, 'PCIS': 6, 'PTRANS': 93, 'TRANS': 2181} Chain breaks: 5 Unresolved non-hydrogen bonds: 202 Unresolved non-hydrogen angles: 240 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 12, 'ARG:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 101 Time building chain proxies: 33.90, per 1000 atoms: 0.38 Number of scatterers: 88700 At special positions: 0 Unit cell: (190.38, 189.24, 258.78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 305 16.00 O 17075 8.00 N 15350 7.00 C 55970 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 26.39 Conformation dependent library (CDL) restraints added in 13.2 seconds 22730 Ramachandran restraints generated. 11365 Oldfield, 0 Emsley, 11365 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 21550 Finding SS restraints... Secondary structure from input PDB file: 395 helices and 100 sheets defined 47.8% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.09 Creating SS restraints... Processing helix chain 'A' and resid 30 through 37 Processing helix chain 'A' and resid 43 through 70 removed outlier: 3.507A pdb=" N ALA A 47 " --> pdb=" O SER A 43 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN A 48 " --> pdb=" O ARG A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 80 Proline residue: A 74 - end of helix removed outlier: 3.704A pdb=" N LYS A 77 " --> pdb=" O PRO A 74 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N LYS A 78 " --> pdb=" O LEU A 75 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N MET A 80 " --> pdb=" O LYS A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 128 Processing helix chain 'A' and resid 138 through 143 Processing helix chain 'A' and resid 152 through 158 Processing helix chain 'A' and resid 162 through 179 removed outlier: 3.823A pdb=" N ALA A 173 " --> pdb=" O GLN A 169 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA A 176 " --> pdb=" O THR A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 191 Processing helix chain 'A' and resid 202 through 215 removed outlier: 3.516A pdb=" N ARG A 215 " --> pdb=" O ALA A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 222 removed outlier: 3.612A pdb=" N ASP A 221 " --> pdb=" O VAL A 218 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN A 222 " --> pdb=" O LEU A 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 218 through 222' Processing helix chain 'A' and resid 226 through 228 No H-bonds generated for 'chain 'A' and resid 226 through 228' Processing helix chain 'A' and resid 229 through 239 removed outlier: 3.533A pdb=" N LEU A 233 " --> pdb=" O LYS A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 250 removed outlier: 3.862A pdb=" N GLU A 250 " --> pdb=" O ASN A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 268 removed outlier: 3.905A pdb=" N GLU A 261 " --> pdb=" O GLY A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 277 Processing helix chain 'A' and resid 278 through 286 removed outlier: 3.937A pdb=" N TYR A 286 " --> pdb=" O LEU A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 302 removed outlier: 3.591A pdb=" N LEU A 296 " --> pdb=" O ASP A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.607A pdb=" N LEU A 408 " --> pdb=" O ASP A 404 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS A 410 " --> pdb=" O LYS A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 461 removed outlier: 3.947A pdb=" N LEU A 447 " --> pdb=" O PRO A 443 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ARG A 449 " --> pdb=" O ILE A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 470 removed outlier: 3.650A pdb=" N GLN A 468 " --> pdb=" O PRO A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 495 Processing helix chain 'A' and resid 499 through 507 Processing helix chain 'A' and resid 521 through 528 Processing helix chain 'A' and resid 531 through 535 Processing helix chain 'A' and resid 553 through 562 removed outlier: 4.138A pdb=" N VAL A 557 " --> pdb=" O PRO A 553 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU A 558 " --> pdb=" O ARG A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 577 removed outlier: 3.896A pdb=" N TRP A 570 " --> pdb=" O ASN A 566 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASN A 577 " --> pdb=" O LEU A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 605 removed outlier: 3.732A pdb=" N LEU A 592 " --> pdb=" O LYS A 588 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA A 602 " --> pdb=" O VAL A 598 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N HIS A 605 " --> pdb=" O LEU A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 616 Processing helix chain 'A' and resid 630 through 651 removed outlier: 3.607A pdb=" N ARG A 634 " --> pdb=" O ASP A 630 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN A 635 " --> pdb=" O GLY A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 663 Processing helix chain 'A' and resid 671 through 683 Processing helix chain 'A' and resid 692 through 706 removed outlier: 3.946A pdb=" N THR A 696 " --> pdb=" O LYS A 692 " (cutoff:3.500A) Proline residue: A 700 - end of helix Processing helix chain 'A' and resid 710 through 724 removed outlier: 3.613A pdb=" N LEU A 718 " --> pdb=" O GLY A 714 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG A 719 " --> pdb=" O GLU A 715 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN A 724 " --> pdb=" O TRP A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 740 Processing helix chain 'A' and resid 749 through 770 removed outlier: 3.687A pdb=" N PHE A 769 " --> pdb=" O VAL A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 780 Processing helix chain 'A' and resid 787 through 805 removed outlier: 3.915A pdb=" N ASN A 793 " --> pdb=" O THR A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 817 removed outlier: 3.580A pdb=" N VAL A 811 " --> pdb=" O GLN A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 830 Processing helix chain 'A' and resid 832 through 840 removed outlier: 3.645A pdb=" N ILE A 836 " --> pdb=" O SER A 832 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N GLN A 838 " --> pdb=" O GLU A 834 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 855 Processing helix chain 'A' and resid 857 through 868 removed outlier: 3.894A pdb=" N ARG A 861 " --> pdb=" O VAL A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 871 through 874 Processing helix chain 'A' and resid 875 through 882 Processing helix chain 'A' and resid 888 through 902 removed outlier: 3.981A pdb=" N LEU A 898 " --> pdb=" O ALA A 894 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLY A 902 " --> pdb=" O LEU A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 904 through 931 Proline residue: A 917 - end of helix removed outlier: 3.901A pdb=" N ARG A 928 " --> pdb=" O SER A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 947 removed outlier: 3.665A pdb=" N TRP A 943 " --> pdb=" O ARG A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 977 Processing helix chain 'A' and resid 984 through 989 Processing helix chain 'A' and resid 990 through 995 Processing helix chain 'A' and resid 1003 through 1015 removed outlier: 3.892A pdb=" N VAL A1009 " --> pdb=" O THR A1005 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU A1012 " --> pdb=" O GLY A1008 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N VAL A1013 " --> pdb=" O VAL A1009 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N TYR A1014 " --> pdb=" O SER A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1019 Processing helix chain 'A' and resid 1029 through 1039 removed outlier: 3.878A pdb=" N GLN A1038 " --> pdb=" O THR A1034 " (cutoff:3.500A) Processing helix chain 'A' and resid 1045 through 1065 removed outlier: 3.813A pdb=" N PHE A1053 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing helix chain 'A' and resid 1113 through 1116 removed outlier: 3.818A pdb=" N TRP A1116 " --> pdb=" O ALA A1113 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1113 through 1116' Processing helix chain 'A' and resid 1243 through 1247 Processing helix chain 'A' and resid 1574 through 1579 removed outlier: 4.060A pdb=" N ARG A1578 " --> pdb=" O GLN A1574 " (cutoff:3.500A) Processing helix chain 'A' and resid 1582 through 1587 Processing helix chain 'A' and resid 1588 through 1593 removed outlier: 3.726A pdb=" N GLN A1592 " --> pdb=" O SER A1588 " (cutoff:3.500A) Processing helix chain 'A' and resid 1738 through 1747 removed outlier: 3.599A pdb=" N PHE A1742 " --> pdb=" O ASN A1738 " (cutoff:3.500A) Processing helix chain 'A' and resid 1747 through 1759 removed outlier: 3.553A pdb=" N GLN A1759 " --> pdb=" O THR A1755 " (cutoff:3.500A) Processing helix chain 'A' and resid 1762 through 1771 removed outlier: 4.072A pdb=" N ARG A1768 " --> pdb=" O THR A1764 " (cutoff:3.500A) Processing helix chain 'A' and resid 1786 through 1791 Processing helix chain 'A' and resid 1804 through 1812 removed outlier: 3.885A pdb=" N VAL A1808 " --> pdb=" O ASP A1804 " (cutoff:3.500A) Processing helix chain 'A' and resid 1813 through 1838 removed outlier: 3.577A pdb=" N MET A1838 " --> pdb=" O LYS A1834 " (cutoff:3.500A) Processing helix chain 'A' and resid 1840 through 1859 Processing helix chain 'A' and resid 1874 through 1879 Processing helix chain 'A' and resid 1880 through 1896 removed outlier: 3.673A pdb=" N ALA A1884 " --> pdb=" O ASP A1880 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE A1887 " --> pdb=" O GLN A1883 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER A1896 " --> pdb=" O SER A1892 " (cutoff:3.500A) Processing helix chain 'A' and resid 1918 through 1937 Processing helix chain 'A' and resid 1983 through 2070 removed outlier: 3.991A pdb=" N ASP A1989 " --> pdb=" O PRO A1985 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A1994 " --> pdb=" O SER A1990 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N MET A2017 " --> pdb=" O ASP A2013 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN A2022 " --> pdb=" O SER A2018 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N SER A2031 " --> pdb=" O GLU A2027 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU A2037 " --> pdb=" O LEU A2033 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLN A2038 " --> pdb=" O ARG A2034 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LEU A2043 " --> pdb=" O ALA A2039 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP A2044 " --> pdb=" O LEU A2040 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS A2048 " --> pdb=" O ASP A2044 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA A2066 " --> pdb=" O ASP A2062 " (cutoff:3.500A) Processing helix chain 'A' and resid 2075 through 2092 removed outlier: 3.617A pdb=" N MET A2080 " --> pdb=" O GLU A2076 " (cutoff:3.500A) Processing helix chain 'A' and resid 2093 through 2105 removed outlier: 3.601A pdb=" N ALA A2101 " --> pdb=" O ASP A2097 " (cutoff:3.500A) Processing helix chain 'A' and resid 2120 through 2209 removed outlier: 3.596A pdb=" N ARG A2169 " --> pdb=" O GLU A2165 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N MET A2187 " --> pdb=" O THR A2183 " (cutoff:3.500A) Processing helix chain 'A' and resid 2212 through 2249 removed outlier: 3.607A pdb=" N TYR A2216 " --> pdb=" O ASN A2212 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP A2232 " --> pdb=" O TYR A2228 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU A2233 " --> pdb=" O ARG A2229 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA A2236 " --> pdb=" O ASP A2232 " (cutoff:3.500A) Processing helix chain 'A' and resid 2271 through 2290 Processing helix chain 'A' and resid 2302 through 2308 Processing helix chain 'A' and resid 2312 through 2317 Processing helix chain 'A' and resid 2348 through 2353 removed outlier: 3.532A pdb=" N ASN A2353 " --> pdb=" O LYS A2350 " (cutoff:3.500A) Processing helix chain 'A' and resid 2449 through 2457 removed outlier: 3.872A pdb=" N LEU A2453 " --> pdb=" O LYS A2449 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 37 Processing helix chain 'B' and resid 43 through 70 removed outlier: 3.507A pdb=" N ALA B 47 " --> pdb=" O SER B 43 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN B 48 " --> pdb=" O ARG B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 80 Proline residue: B 74 - end of helix removed outlier: 3.704A pdb=" N LYS B 77 " --> pdb=" O PRO B 74 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N LYS B 78 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N MET B 80 " --> pdb=" O LYS B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 128 Processing helix chain 'B' and resid 138 through 143 Processing helix chain 'B' and resid 152 through 158 Processing helix chain 'B' and resid 162 through 179 removed outlier: 3.823A pdb=" N ALA B 173 " --> pdb=" O GLN B 169 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA B 176 " --> pdb=" O THR B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 191 Processing helix chain 'B' and resid 202 through 215 removed outlier: 3.515A pdb=" N ARG B 215 " --> pdb=" O ALA B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 222 removed outlier: 3.612A pdb=" N ASP B 221 " --> pdb=" O VAL B 218 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN B 222 " --> pdb=" O LEU B 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 218 through 222' Processing helix chain 'B' and resid 226 through 228 No H-bonds generated for 'chain 'B' and resid 226 through 228' Processing helix chain 'B' and resid 229 through 239 removed outlier: 3.533A pdb=" N LEU B 233 " --> pdb=" O LYS B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 250 removed outlier: 3.862A pdb=" N GLU B 250 " --> pdb=" O ASN B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 268 removed outlier: 3.906A pdb=" N GLU B 261 " --> pdb=" O GLY B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 277 Processing helix chain 'B' and resid 278 through 286 removed outlier: 3.937A pdb=" N TYR B 286 " --> pdb=" O LEU B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 302 removed outlier: 3.592A pdb=" N LEU B 296 " --> pdb=" O ASP B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.606A pdb=" N LEU B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS B 410 " --> pdb=" O LYS B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 461 removed outlier: 3.948A pdb=" N LEU B 447 " --> pdb=" O PRO B 443 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ARG B 449 " --> pdb=" O ILE B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 470 removed outlier: 3.650A pdb=" N GLN B 468 " --> pdb=" O PRO B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 495 Processing helix chain 'B' and resid 499 through 507 Processing helix chain 'B' and resid 521 through 528 Processing helix chain 'B' and resid 531 through 535 Processing helix chain 'B' and resid 553 through 562 removed outlier: 4.138A pdb=" N VAL B 557 " --> pdb=" O PRO B 553 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU B 558 " --> pdb=" O ARG B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 577 removed outlier: 3.896A pdb=" N TRP B 570 " --> pdb=" O ASN B 566 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASN B 577 " --> pdb=" O LEU B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 605 removed outlier: 3.731A pdb=" N LEU B 592 " --> pdb=" O LYS B 588 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA B 602 " --> pdb=" O VAL B 598 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N HIS B 605 " --> pdb=" O LEU B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 616 Processing helix chain 'B' and resid 630 through 651 removed outlier: 3.606A pdb=" N ARG B 634 " --> pdb=" O ASP B 630 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN B 635 " --> pdb=" O GLY B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 663 Processing helix chain 'B' and resid 671 through 683 Processing helix chain 'B' and resid 692 through 706 removed outlier: 3.947A pdb=" N THR B 696 " --> pdb=" O LYS B 692 " (cutoff:3.500A) Proline residue: B 700 - end of helix Processing helix chain 'B' and resid 710 through 724 removed outlier: 3.613A pdb=" N LEU B 718 " --> pdb=" O GLY B 714 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG B 719 " --> pdb=" O GLU B 715 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN B 724 " --> pdb=" O TRP B 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 731 through 740 Processing helix chain 'B' and resid 749 through 770 removed outlier: 3.687A pdb=" N PHE B 769 " --> pdb=" O VAL B 765 " (cutoff:3.500A) Processing helix chain 'B' and resid 772 through 780 Processing helix chain 'B' and resid 787 through 805 removed outlier: 3.915A pdb=" N ASN B 793 " --> pdb=" O THR B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 817 removed outlier: 3.579A pdb=" N VAL B 811 " --> pdb=" O GLN B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 830 Processing helix chain 'B' and resid 832 through 840 removed outlier: 3.644A pdb=" N ILE B 836 " --> pdb=" O SER B 832 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N GLN B 838 " --> pdb=" O GLU B 834 " (cutoff:3.500A) Processing helix chain 'B' and resid 851 through 855 Processing helix chain 'B' and resid 857 through 868 removed outlier: 3.894A pdb=" N ARG B 861 " --> pdb=" O VAL B 857 " (cutoff:3.500A) Processing helix chain 'B' and resid 871 through 874 Processing helix chain 'B' and resid 875 through 882 Processing helix chain 'B' and resid 888 through 902 removed outlier: 3.981A pdb=" N LEU B 898 " --> pdb=" O ALA B 894 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLY B 902 " --> pdb=" O LEU B 898 " (cutoff:3.500A) Processing helix chain 'B' and resid 904 through 931 Proline residue: B 917 - end of helix removed outlier: 3.902A pdb=" N ARG B 928 " --> pdb=" O SER B 924 " (cutoff:3.500A) Processing helix chain 'B' and resid 939 through 947 removed outlier: 3.665A pdb=" N TRP B 943 " --> pdb=" O ARG B 939 " (cutoff:3.500A) Processing helix chain 'B' and resid 960 through 977 Processing helix chain 'B' and resid 984 through 989 Processing helix chain 'B' and resid 990 through 995 Processing helix chain 'B' and resid 1003 through 1015 removed outlier: 3.892A pdb=" N VAL B1009 " --> pdb=" O THR B1005 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU B1012 " --> pdb=" O GLY B1008 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N VAL B1013 " --> pdb=" O VAL B1009 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N TYR B1014 " --> pdb=" O SER B1010 " (cutoff:3.500A) Processing helix chain 'B' and resid 1016 through 1019 Processing helix chain 'B' and resid 1029 through 1039 removed outlier: 3.877A pdb=" N GLN B1038 " --> pdb=" O THR B1034 " (cutoff:3.500A) Processing helix chain 'B' and resid 1045 through 1065 removed outlier: 3.813A pdb=" N PHE B1053 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing helix chain 'B' and resid 1113 through 1116 removed outlier: 3.818A pdb=" N TRP B1116 " --> pdb=" O ALA B1113 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1113 through 1116' Processing helix chain 'B' and resid 1243 through 1247 Processing helix chain 'B' and resid 1574 through 1579 removed outlier: 4.060A pdb=" N ARG B1578 " --> pdb=" O GLN B1574 " (cutoff:3.500A) Processing helix chain 'B' and resid 1582 through 1587 Processing helix chain 'B' and resid 1588 through 1593 removed outlier: 3.726A pdb=" N GLN B1592 " --> pdb=" O SER B1588 " (cutoff:3.500A) Processing helix chain 'B' and resid 1738 through 1747 removed outlier: 3.600A pdb=" N PHE B1742 " --> pdb=" O ASN B1738 " (cutoff:3.500A) Processing helix chain 'B' and resid 1747 through 1759 removed outlier: 3.552A pdb=" N GLN B1759 " --> pdb=" O THR B1755 " (cutoff:3.500A) Processing helix chain 'B' and resid 1762 through 1771 removed outlier: 4.072A pdb=" N ARG B1768 " --> pdb=" O THR B1764 " (cutoff:3.500A) Processing helix chain 'B' and resid 1786 through 1791 Processing helix chain 'B' and resid 1804 through 1812 removed outlier: 3.884A pdb=" N VAL B1808 " --> pdb=" O ASP B1804 " (cutoff:3.500A) Processing helix chain 'B' and resid 1813 through 1838 removed outlier: 3.579A pdb=" N MET B1838 " --> pdb=" O LYS B1834 " (cutoff:3.500A) Processing helix chain 'B' and resid 1840 through 1859 Processing helix chain 'B' and resid 1874 through 1879 Processing helix chain 'B' and resid 1880 through 1896 removed outlier: 3.673A pdb=" N ALA B1884 " --> pdb=" O ASP B1880 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE B1887 " --> pdb=" O GLN B1883 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER B1896 " --> pdb=" O SER B1892 " (cutoff:3.500A) Processing helix chain 'B' and resid 1918 through 1937 Processing helix chain 'B' and resid 1983 through 2070 removed outlier: 3.992A pdb=" N ASP B1989 " --> pdb=" O PRO B1985 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU B1994 " --> pdb=" O SER B1990 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N MET B2017 " --> pdb=" O ASP B2013 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN B2022 " --> pdb=" O SER B2018 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N SER B2031 " --> pdb=" O GLU B2027 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU B2037 " --> pdb=" O LEU B2033 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLN B2038 " --> pdb=" O ARG B2034 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LEU B2043 " --> pdb=" O ALA B2039 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP B2044 " --> pdb=" O LEU B2040 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS B2048 " --> pdb=" O ASP B2044 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA B2066 " --> pdb=" O ASP B2062 " (cutoff:3.500A) Processing helix chain 'B' and resid 2075 through 2092 removed outlier: 3.618A pdb=" N MET B2080 " --> pdb=" O GLU B2076 " (cutoff:3.500A) Processing helix chain 'B' and resid 2093 through 2105 removed outlier: 3.602A pdb=" N ALA B2101 " --> pdb=" O ASP B2097 " (cutoff:3.500A) Processing helix chain 'B' and resid 2120 through 2209 removed outlier: 3.596A pdb=" N ARG B2169 " --> pdb=" O GLU B2165 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N MET B2187 " --> pdb=" O THR B2183 " (cutoff:3.500A) Processing helix chain 'B' and resid 2212 through 2249 removed outlier: 3.607A pdb=" N TYR B2216 " --> pdb=" O ASN B2212 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP B2232 " --> pdb=" O TYR B2228 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU B2233 " --> pdb=" O ARG B2229 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA B2236 " --> pdb=" O ASP B2232 " (cutoff:3.500A) Processing helix chain 'B' and resid 2271 through 2290 Processing helix chain 'B' and resid 2302 through 2308 Processing helix chain 'B' and resid 2312 through 2317 Processing helix chain 'B' and resid 2348 through 2353 removed outlier: 3.532A pdb=" N ASN B2353 " --> pdb=" O LYS B2350 " (cutoff:3.500A) Processing helix chain 'B' and resid 2449 through 2457 removed outlier: 3.871A pdb=" N LEU B2453 " --> pdb=" O LYS B2449 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 37 Processing helix chain 'C' and resid 43 through 70 removed outlier: 3.507A pdb=" N ALA C 47 " --> pdb=" O SER C 43 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN C 48 " --> pdb=" O ARG C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 80 Proline residue: C 74 - end of helix removed outlier: 3.704A pdb=" N LYS C 77 " --> pdb=" O PRO C 74 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N LYS C 78 " --> pdb=" O LEU C 75 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N MET C 80 " --> pdb=" O LYS C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 128 Processing helix chain 'C' and resid 138 through 143 Processing helix chain 'C' and resid 152 through 158 Processing helix chain 'C' and resid 162 through 179 removed outlier: 3.823A pdb=" N ALA C 173 " --> pdb=" O GLN C 169 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA C 176 " --> pdb=" O THR C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 191 Processing helix chain 'C' and resid 202 through 215 removed outlier: 3.514A pdb=" N ARG C 215 " --> pdb=" O ALA C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 222 removed outlier: 3.611A pdb=" N ASP C 221 " --> pdb=" O VAL C 218 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN C 222 " --> pdb=" O LEU C 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 218 through 222' Processing helix chain 'C' and resid 226 through 228 No H-bonds generated for 'chain 'C' and resid 226 through 228' Processing helix chain 'C' and resid 229 through 239 removed outlier: 3.533A pdb=" N LEU C 233 " --> pdb=" O LYS C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 250 removed outlier: 3.862A pdb=" N GLU C 250 " --> pdb=" O ASN C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 268 removed outlier: 3.906A pdb=" N GLU C 261 " --> pdb=" O GLY C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 277 Processing helix chain 'C' and resid 278 through 286 removed outlier: 3.937A pdb=" N TYR C 286 " --> pdb=" O LEU C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 302 removed outlier: 3.592A pdb=" N LEU C 296 " --> pdb=" O ASP C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 removed outlier: 3.607A pdb=" N LEU C 408 " --> pdb=" O ASP C 404 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS C 410 " --> pdb=" O LYS C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 461 removed outlier: 3.947A pdb=" N LEU C 447 " --> pdb=" O PRO C 443 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ARG C 449 " --> pdb=" O ILE C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 470 removed outlier: 3.649A pdb=" N GLN C 468 " --> pdb=" O PRO C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 495 Processing helix chain 'C' and resid 499 through 507 Processing helix chain 'C' and resid 521 through 528 Processing helix chain 'C' and resid 531 through 535 Processing helix chain 'C' and resid 553 through 562 removed outlier: 4.139A pdb=" N VAL C 557 " --> pdb=" O PRO C 553 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU C 558 " --> pdb=" O ARG C 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 577 removed outlier: 3.897A pdb=" N TRP C 570 " --> pdb=" O ASN C 566 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASN C 577 " --> pdb=" O LEU C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 605 removed outlier: 3.731A pdb=" N LEU C 592 " --> pdb=" O LYS C 588 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA C 602 " --> pdb=" O VAL C 598 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N HIS C 605 " --> pdb=" O LEU C 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 616 Processing helix chain 'C' and resid 630 through 651 removed outlier: 3.607A pdb=" N ARG C 634 " --> pdb=" O ASP C 630 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN C 635 " --> pdb=" O GLY C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 654 through 663 Processing helix chain 'C' and resid 671 through 683 Processing helix chain 'C' and resid 692 through 706 removed outlier: 3.947A pdb=" N THR C 696 " --> pdb=" O LYS C 692 " (cutoff:3.500A) Proline residue: C 700 - end of helix Processing helix chain 'C' and resid 710 through 724 removed outlier: 3.613A pdb=" N LEU C 718 " --> pdb=" O GLY C 714 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG C 719 " --> pdb=" O GLU C 715 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN C 724 " --> pdb=" O TRP C 720 " (cutoff:3.500A) Processing helix chain 'C' and resid 731 through 740 Processing helix chain 'C' and resid 749 through 770 removed outlier: 3.686A pdb=" N PHE C 769 " --> pdb=" O VAL C 765 " (cutoff:3.500A) Processing helix chain 'C' and resid 772 through 780 Processing helix chain 'C' and resid 787 through 805 removed outlier: 3.915A pdb=" N ASN C 793 " --> pdb=" O THR C 789 " (cutoff:3.500A) Processing helix chain 'C' and resid 807 through 817 removed outlier: 3.579A pdb=" N VAL C 811 " --> pdb=" O GLN C 807 " (cutoff:3.500A) Processing helix chain 'C' and resid 821 through 830 Processing helix chain 'C' and resid 832 through 840 removed outlier: 3.644A pdb=" N ILE C 836 " --> pdb=" O SER C 832 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N GLN C 838 " --> pdb=" O GLU C 834 " (cutoff:3.500A) Processing helix chain 'C' and resid 851 through 855 Processing helix chain 'C' and resid 857 through 868 removed outlier: 3.893A pdb=" N ARG C 861 " --> pdb=" O VAL C 857 " (cutoff:3.500A) Processing helix chain 'C' and resid 871 through 874 Processing helix chain 'C' and resid 875 through 882 Processing helix chain 'C' and resid 888 through 902 removed outlier: 3.980A pdb=" N LEU C 898 " --> pdb=" O ALA C 894 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLY C 902 " --> pdb=" O LEU C 898 " (cutoff:3.500A) Processing helix chain 'C' and resid 904 through 931 Proline residue: C 917 - end of helix removed outlier: 3.900A pdb=" N ARG C 928 " --> pdb=" O SER C 924 " (cutoff:3.500A) Processing helix chain 'C' and resid 939 through 947 removed outlier: 3.665A pdb=" N TRP C 943 " --> pdb=" O ARG C 939 " (cutoff:3.500A) Processing helix chain 'C' and resid 960 through 977 Processing helix chain 'C' and resid 984 through 989 Processing helix chain 'C' and resid 990 through 995 Processing helix chain 'C' and resid 1003 through 1015 removed outlier: 3.893A pdb=" N VAL C1009 " --> pdb=" O THR C1005 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU C1012 " --> pdb=" O GLY C1008 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N VAL C1013 " --> pdb=" O VAL C1009 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N TYR C1014 " --> pdb=" O SER C1010 " (cutoff:3.500A) Processing helix chain 'C' and resid 1016 through 1019 Processing helix chain 'C' and resid 1029 through 1039 removed outlier: 3.878A pdb=" N GLN C1038 " --> pdb=" O THR C1034 " (cutoff:3.500A) Processing helix chain 'C' and resid 1045 through 1065 removed outlier: 3.813A pdb=" N PHE C1053 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing helix chain 'C' and resid 1113 through 1116 removed outlier: 3.818A pdb=" N TRP C1116 " --> pdb=" O ALA C1113 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1113 through 1116' Processing helix chain 'C' and resid 1243 through 1247 Processing helix chain 'C' and resid 1574 through 1579 removed outlier: 4.059A pdb=" N ARG C1578 " --> pdb=" O GLN C1574 " (cutoff:3.500A) Processing helix chain 'C' and resid 1582 through 1587 Processing helix chain 'C' and resid 1588 through 1593 removed outlier: 3.726A pdb=" N GLN C1592 " --> pdb=" O SER C1588 " (cutoff:3.500A) Processing helix chain 'C' and resid 1738 through 1747 removed outlier: 3.599A pdb=" N PHE C1742 " --> pdb=" O ASN C1738 " (cutoff:3.500A) Processing helix chain 'C' and resid 1747 through 1759 removed outlier: 3.552A pdb=" N GLN C1759 " --> pdb=" O THR C1755 " (cutoff:3.500A) Processing helix chain 'C' and resid 1762 through 1771 removed outlier: 4.072A pdb=" N ARG C1768 " --> pdb=" O THR C1764 " (cutoff:3.500A) Processing helix chain 'C' and resid 1786 through 1791 Processing helix chain 'C' and resid 1804 through 1812 removed outlier: 3.884A pdb=" N VAL C1808 " --> pdb=" O ASP C1804 " (cutoff:3.500A) Processing helix chain 'C' and resid 1813 through 1838 removed outlier: 3.577A pdb=" N MET C1838 " --> pdb=" O LYS C1834 " (cutoff:3.500A) Processing helix chain 'C' and resid 1840 through 1859 Processing helix chain 'C' and resid 1874 through 1879 Processing helix chain 'C' and resid 1880 through 1896 removed outlier: 3.673A pdb=" N ALA C1884 " --> pdb=" O ASP C1880 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE C1887 " --> pdb=" O GLN C1883 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER C1896 " --> pdb=" O SER C1892 " (cutoff:3.500A) Processing helix chain 'C' and resid 1918 through 1937 Processing helix chain 'C' and resid 1983 through 2070 removed outlier: 3.991A pdb=" N ASP C1989 " --> pdb=" O PRO C1985 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU C1994 " --> pdb=" O SER C1990 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N MET C2017 " --> pdb=" O ASP C2013 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN C2022 " --> pdb=" O SER C2018 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N SER C2031 " --> pdb=" O GLU C2027 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU C2037 " --> pdb=" O LEU C2033 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLN C2038 " --> pdb=" O ARG C2034 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LEU C2043 " --> pdb=" O ALA C2039 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP C2044 " --> pdb=" O LEU C2040 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS C2048 " --> pdb=" O ASP C2044 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA C2066 " --> pdb=" O ASP C2062 " (cutoff:3.500A) Processing helix chain 'C' and resid 2075 through 2092 removed outlier: 3.618A pdb=" N MET C2080 " --> pdb=" O GLU C2076 " (cutoff:3.500A) Processing helix chain 'C' and resid 2093 through 2105 removed outlier: 3.602A pdb=" N ALA C2101 " --> pdb=" O ASP C2097 " (cutoff:3.500A) Processing helix chain 'C' and resid 2120 through 2209 removed outlier: 3.595A pdb=" N ARG C2169 " --> pdb=" O GLU C2165 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N MET C2187 " --> pdb=" O THR C2183 " (cutoff:3.500A) Processing helix chain 'C' and resid 2212 through 2249 removed outlier: 3.606A pdb=" N TYR C2216 " --> pdb=" O ASN C2212 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP C2232 " --> pdb=" O TYR C2228 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU C2233 " --> pdb=" O ARG C2229 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA C2236 " --> pdb=" O ASP C2232 " (cutoff:3.500A) Processing helix chain 'C' and resid 2271 through 2290 Processing helix chain 'C' and resid 2302 through 2308 Processing helix chain 'C' and resid 2312 through 2317 Processing helix chain 'C' and resid 2348 through 2353 removed outlier: 3.532A pdb=" N ASN C2353 " --> pdb=" O LYS C2350 " (cutoff:3.500A) Processing helix chain 'C' and resid 2449 through 2457 removed outlier: 3.871A pdb=" N LEU C2453 " --> pdb=" O LYS C2449 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 37 Processing helix chain 'D' and resid 43 through 70 removed outlier: 3.507A pdb=" N ALA D 47 " --> pdb=" O SER D 43 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN D 48 " --> pdb=" O ARG D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 80 Proline residue: D 74 - end of helix removed outlier: 3.705A pdb=" N LYS D 77 " --> pdb=" O PRO D 74 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N LYS D 78 " --> pdb=" O LEU D 75 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N MET D 80 " --> pdb=" O LYS D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 128 Processing helix chain 'D' and resid 138 through 143 Processing helix chain 'D' and resid 152 through 158 Processing helix chain 'D' and resid 162 through 179 removed outlier: 3.822A pdb=" N ALA D 173 " --> pdb=" O GLN D 169 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA D 176 " --> pdb=" O THR D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 191 Processing helix chain 'D' and resid 202 through 215 removed outlier: 3.516A pdb=" N ARG D 215 " --> pdb=" O ALA D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 222 removed outlier: 3.612A pdb=" N ASP D 221 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN D 222 " --> pdb=" O LEU D 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 218 through 222' Processing helix chain 'D' and resid 226 through 228 No H-bonds generated for 'chain 'D' and resid 226 through 228' Processing helix chain 'D' and resid 229 through 239 removed outlier: 3.533A pdb=" N LEU D 233 " --> pdb=" O LYS D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 250 removed outlier: 3.861A pdb=" N GLU D 250 " --> pdb=" O ASN D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 268 removed outlier: 3.906A pdb=" N GLU D 261 " --> pdb=" O GLY D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 277 Processing helix chain 'D' and resid 278 through 286 removed outlier: 3.937A pdb=" N TYR D 286 " --> pdb=" O LEU D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 302 removed outlier: 3.592A pdb=" N LEU D 296 " --> pdb=" O ASP D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 410 removed outlier: 3.607A pdb=" N LEU D 408 " --> pdb=" O ASP D 404 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS D 410 " --> pdb=" O LYS D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 443 through 461 removed outlier: 3.948A pdb=" N LEU D 447 " --> pdb=" O PRO D 443 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ARG D 449 " --> pdb=" O ILE D 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 470 removed outlier: 3.649A pdb=" N GLN D 468 " --> pdb=" O PRO D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 478 through 495 Processing helix chain 'D' and resid 499 through 507 Processing helix chain 'D' and resid 521 through 528 Processing helix chain 'D' and resid 531 through 535 Processing helix chain 'D' and resid 553 through 562 removed outlier: 4.138A pdb=" N VAL D 557 " --> pdb=" O PRO D 553 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU D 558 " --> pdb=" O ARG D 554 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 577 removed outlier: 3.896A pdb=" N TRP D 570 " --> pdb=" O ASN D 566 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASN D 577 " --> pdb=" O LEU D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 605 removed outlier: 3.731A pdb=" N LEU D 592 " --> pdb=" O LYS D 588 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA D 602 " --> pdb=" O VAL D 598 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N HIS D 605 " --> pdb=" O LEU D 601 " (cutoff:3.500A) Processing helix chain 'D' and resid 608 through 616 Processing helix chain 'D' and resid 630 through 651 removed outlier: 3.606A pdb=" N ARG D 634 " --> pdb=" O ASP D 630 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN D 635 " --> pdb=" O GLY D 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 654 through 663 Processing helix chain 'D' and resid 671 through 683 Processing helix chain 'D' and resid 692 through 706 removed outlier: 3.947A pdb=" N THR D 696 " --> pdb=" O LYS D 692 " (cutoff:3.500A) Proline residue: D 700 - end of helix Processing helix chain 'D' and resid 710 through 724 removed outlier: 3.613A pdb=" N LEU D 718 " --> pdb=" O GLY D 714 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG D 719 " --> pdb=" O GLU D 715 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN D 724 " --> pdb=" O TRP D 720 " (cutoff:3.500A) Processing helix chain 'D' and resid 731 through 740 Processing helix chain 'D' and resid 749 through 770 removed outlier: 3.687A pdb=" N PHE D 769 " --> pdb=" O VAL D 765 " (cutoff:3.500A) Processing helix chain 'D' and resid 772 through 780 Processing helix chain 'D' and resid 787 through 805 removed outlier: 3.915A pdb=" N ASN D 793 " --> pdb=" O THR D 789 " (cutoff:3.500A) Processing helix chain 'D' and resid 807 through 817 removed outlier: 3.580A pdb=" N VAL D 811 " --> pdb=" O GLN D 807 " (cutoff:3.500A) Processing helix chain 'D' and resid 821 through 830 Processing helix chain 'D' and resid 832 through 840 removed outlier: 3.645A pdb=" N ILE D 836 " --> pdb=" O SER D 832 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N GLN D 838 " --> pdb=" O GLU D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 851 through 855 Processing helix chain 'D' and resid 857 through 868 removed outlier: 3.893A pdb=" N ARG D 861 " --> pdb=" O VAL D 857 " (cutoff:3.500A) Processing helix chain 'D' and resid 871 through 874 Processing helix chain 'D' and resid 875 through 882 Processing helix chain 'D' and resid 888 through 902 removed outlier: 3.981A pdb=" N LEU D 898 " --> pdb=" O ALA D 894 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLY D 902 " --> pdb=" O LEU D 898 " (cutoff:3.500A) Processing helix chain 'D' and resid 904 through 931 Proline residue: D 917 - end of helix removed outlier: 3.900A pdb=" N ARG D 928 " --> pdb=" O SER D 924 " (cutoff:3.500A) Processing helix chain 'D' and resid 939 through 947 removed outlier: 3.665A pdb=" N TRP D 943 " --> pdb=" O ARG D 939 " (cutoff:3.500A) Processing helix chain 'D' and resid 960 through 977 Processing helix chain 'D' and resid 984 through 989 Processing helix chain 'D' and resid 990 through 995 Processing helix chain 'D' and resid 1003 through 1015 removed outlier: 3.892A pdb=" N VAL D1009 " --> pdb=" O THR D1005 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU D1012 " --> pdb=" O GLY D1008 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N VAL D1013 " --> pdb=" O VAL D1009 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N TYR D1014 " --> pdb=" O SER D1010 " (cutoff:3.500A) Processing helix chain 'D' and resid 1016 through 1019 Processing helix chain 'D' and resid 1029 through 1039 removed outlier: 3.876A pdb=" N GLN D1038 " --> pdb=" O THR D1034 " (cutoff:3.500A) Processing helix chain 'D' and resid 1045 through 1065 removed outlier: 3.813A pdb=" N PHE D1053 " --> pdb=" O LEU D1049 " (cutoff:3.500A) Processing helix chain 'D' and resid 1113 through 1116 removed outlier: 3.819A pdb=" N TRP D1116 " --> pdb=" O ALA D1113 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1113 through 1116' Processing helix chain 'D' and resid 1243 through 1247 Processing helix chain 'D' and resid 1574 through 1579 removed outlier: 4.059A pdb=" N ARG D1578 " --> pdb=" O GLN D1574 " (cutoff:3.500A) Processing helix chain 'D' and resid 1582 through 1587 Processing helix chain 'D' and resid 1588 through 1593 removed outlier: 3.725A pdb=" N GLN D1592 " --> pdb=" O SER D1588 " (cutoff:3.500A) Processing helix chain 'D' and resid 1738 through 1747 removed outlier: 3.601A pdb=" N PHE D1742 " --> pdb=" O ASN D1738 " (cutoff:3.500A) Processing helix chain 'D' and resid 1747 through 1759 removed outlier: 3.553A pdb=" N GLN D1759 " --> pdb=" O THR D1755 " (cutoff:3.500A) Processing helix chain 'D' and resid 1762 through 1771 removed outlier: 4.072A pdb=" N ARG D1768 " --> pdb=" O THR D1764 " (cutoff:3.500A) Processing helix chain 'D' and resid 1786 through 1791 Processing helix chain 'D' and resid 1804 through 1812 removed outlier: 3.885A pdb=" N VAL D1808 " --> pdb=" O ASP D1804 " (cutoff:3.500A) Processing helix chain 'D' and resid 1813 through 1838 removed outlier: 3.578A pdb=" N MET D1838 " --> pdb=" O LYS D1834 " (cutoff:3.500A) Processing helix chain 'D' and resid 1840 through 1859 Processing helix chain 'D' and resid 1874 through 1879 Processing helix chain 'D' and resid 1880 through 1896 removed outlier: 3.673A pdb=" N ALA D1884 " --> pdb=" O ASP D1880 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE D1887 " --> pdb=" O GLN D1883 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER D1896 " --> pdb=" O SER D1892 " (cutoff:3.500A) Processing helix chain 'D' and resid 1918 through 1937 Processing helix chain 'D' and resid 1983 through 2070 removed outlier: 3.991A pdb=" N ASP D1989 " --> pdb=" O PRO D1985 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU D1994 " --> pdb=" O SER D1990 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N MET D2017 " --> pdb=" O ASP D2013 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN D2022 " --> pdb=" O SER D2018 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N SER D2031 " --> pdb=" O GLU D2027 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU D2037 " --> pdb=" O LEU D2033 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLN D2038 " --> pdb=" O ARG D2034 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU D2043 " --> pdb=" O ALA D2039 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP D2044 " --> pdb=" O LEU D2040 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS D2048 " --> pdb=" O ASP D2044 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA D2066 " --> pdb=" O ASP D2062 " (cutoff:3.500A) Processing helix chain 'D' and resid 2075 through 2092 removed outlier: 3.617A pdb=" N MET D2080 " --> pdb=" O GLU D2076 " (cutoff:3.500A) Processing helix chain 'D' and resid 2093 through 2105 removed outlier: 3.602A pdb=" N ALA D2101 " --> pdb=" O ASP D2097 " (cutoff:3.500A) Processing helix chain 'D' and resid 2120 through 2209 removed outlier: 3.596A pdb=" N ARG D2169 " --> pdb=" O GLU D2165 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET D2187 " --> pdb=" O THR D2183 " (cutoff:3.500A) Processing helix chain 'D' and resid 2212 through 2249 removed outlier: 3.607A pdb=" N TYR D2216 " --> pdb=" O ASN D2212 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP D2232 " --> pdb=" O TYR D2228 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU D2233 " --> pdb=" O ARG D2229 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA D2236 " --> pdb=" O ASP D2232 " (cutoff:3.500A) Processing helix chain 'D' and resid 2271 through 2290 Processing helix chain 'D' and resid 2302 through 2308 Processing helix chain 'D' and resid 2312 through 2317 Processing helix chain 'D' and resid 2348 through 2353 removed outlier: 3.532A pdb=" N ASN D2353 " --> pdb=" O LYS D2350 " (cutoff:3.500A) Processing helix chain 'D' and resid 2449 through 2457 removed outlier: 3.871A pdb=" N LEU D2453 " --> pdb=" O LYS D2449 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 37 Processing helix chain 'E' and resid 43 through 70 removed outlier: 3.507A pdb=" N ALA E 47 " --> pdb=" O SER E 43 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN E 48 " --> pdb=" O ARG E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 80 Proline residue: E 74 - end of helix removed outlier: 3.704A pdb=" N LYS E 77 " --> pdb=" O PRO E 74 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N LYS E 78 " --> pdb=" O LEU E 75 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N MET E 80 " --> pdb=" O LYS E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 128 Processing helix chain 'E' and resid 138 through 143 Processing helix chain 'E' and resid 152 through 158 Processing helix chain 'E' and resid 162 through 179 removed outlier: 3.823A pdb=" N ALA E 173 " --> pdb=" O GLN E 169 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA E 176 " --> pdb=" O THR E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 191 Processing helix chain 'E' and resid 202 through 215 removed outlier: 3.516A pdb=" N ARG E 215 " --> pdb=" O ALA E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 218 through 222 removed outlier: 3.612A pdb=" N ASP E 221 " --> pdb=" O VAL E 218 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN E 222 " --> pdb=" O LEU E 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 218 through 222' Processing helix chain 'E' and resid 226 through 228 No H-bonds generated for 'chain 'E' and resid 226 through 228' Processing helix chain 'E' and resid 229 through 239 removed outlier: 3.533A pdb=" N LEU E 233 " --> pdb=" O LYS E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 241 through 250 removed outlier: 3.863A pdb=" N GLU E 250 " --> pdb=" O ASN E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 268 removed outlier: 3.906A pdb=" N GLU E 261 " --> pdb=" O GLY E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 277 Processing helix chain 'E' and resid 278 through 286 removed outlier: 3.938A pdb=" N TYR E 286 " --> pdb=" O LEU E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 289 through 302 removed outlier: 3.591A pdb=" N LEU E 296 " --> pdb=" O ASP E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 410 removed outlier: 3.607A pdb=" N LEU E 408 " --> pdb=" O ASP E 404 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS E 410 " --> pdb=" O LYS E 406 " (cutoff:3.500A) Processing helix chain 'E' and resid 443 through 461 removed outlier: 3.947A pdb=" N LEU E 447 " --> pdb=" O PRO E 443 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ARG E 449 " --> pdb=" O ILE E 445 " (cutoff:3.500A) Processing helix chain 'E' and resid 463 through 470 removed outlier: 3.649A pdb=" N GLN E 468 " --> pdb=" O PRO E 464 " (cutoff:3.500A) Processing helix chain 'E' and resid 478 through 495 Processing helix chain 'E' and resid 499 through 507 Processing helix chain 'E' and resid 521 through 528 Processing helix chain 'E' and resid 531 through 535 Processing helix chain 'E' and resid 553 through 562 removed outlier: 4.138A pdb=" N VAL E 557 " --> pdb=" O PRO E 553 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU E 558 " --> pdb=" O ARG E 554 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 577 removed outlier: 3.897A pdb=" N TRP E 570 " --> pdb=" O ASN E 566 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASN E 577 " --> pdb=" O LEU E 573 " (cutoff:3.500A) Processing helix chain 'E' and resid 588 through 605 removed outlier: 3.731A pdb=" N LEU E 592 " --> pdb=" O LYS E 588 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA E 602 " --> pdb=" O VAL E 598 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N HIS E 605 " --> pdb=" O LEU E 601 " (cutoff:3.500A) Processing helix chain 'E' and resid 608 through 616 Processing helix chain 'E' and resid 630 through 651 removed outlier: 3.607A pdb=" N ARG E 634 " --> pdb=" O ASP E 630 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN E 635 " --> pdb=" O GLY E 631 " (cutoff:3.500A) Processing helix chain 'E' and resid 654 through 663 Processing helix chain 'E' and resid 671 through 683 Processing helix chain 'E' and resid 692 through 706 removed outlier: 3.947A pdb=" N THR E 696 " --> pdb=" O LYS E 692 " (cutoff:3.500A) Proline residue: E 700 - end of helix Processing helix chain 'E' and resid 710 through 724 removed outlier: 3.612A pdb=" N LEU E 718 " --> pdb=" O GLY E 714 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG E 719 " --> pdb=" O GLU E 715 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN E 724 " --> pdb=" O TRP E 720 " (cutoff:3.500A) Processing helix chain 'E' and resid 731 through 740 Processing helix chain 'E' and resid 749 through 770 removed outlier: 3.687A pdb=" N PHE E 769 " --> pdb=" O VAL E 765 " (cutoff:3.500A) Processing helix chain 'E' and resid 772 through 780 Processing helix chain 'E' and resid 787 through 805 removed outlier: 3.915A pdb=" N ASN E 793 " --> pdb=" O THR E 789 " (cutoff:3.500A) Processing helix chain 'E' and resid 807 through 817 removed outlier: 3.580A pdb=" N VAL E 811 " --> pdb=" O GLN E 807 " (cutoff:3.500A) Processing helix chain 'E' and resid 821 through 830 Processing helix chain 'E' and resid 832 through 840 removed outlier: 3.645A pdb=" N ILE E 836 " --> pdb=" O SER E 832 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N GLN E 838 " --> pdb=" O GLU E 834 " (cutoff:3.500A) Processing helix chain 'E' and resid 851 through 855 Processing helix chain 'E' and resid 857 through 868 removed outlier: 3.893A pdb=" N ARG E 861 " --> pdb=" O VAL E 857 " (cutoff:3.500A) Processing helix chain 'E' and resid 871 through 874 Processing helix chain 'E' and resid 875 through 882 Processing helix chain 'E' and resid 888 through 902 removed outlier: 3.980A pdb=" N LEU E 898 " --> pdb=" O ALA E 894 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLY E 902 " --> pdb=" O LEU E 898 " (cutoff:3.500A) Processing helix chain 'E' and resid 904 through 931 Proline residue: E 917 - end of helix removed outlier: 3.900A pdb=" N ARG E 928 " --> pdb=" O SER E 924 " (cutoff:3.500A) Processing helix chain 'E' and resid 939 through 947 removed outlier: 3.665A pdb=" N TRP E 943 " --> pdb=" O ARG E 939 " (cutoff:3.500A) Processing helix chain 'E' and resid 960 through 977 Processing helix chain 'E' and resid 984 through 989 Processing helix chain 'E' and resid 990 through 995 Processing helix chain 'E' and resid 1003 through 1015 removed outlier: 3.892A pdb=" N VAL E1009 " --> pdb=" O THR E1005 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU E1012 " --> pdb=" O GLY E1008 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N VAL E1013 " --> pdb=" O VAL E1009 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N TYR E1014 " --> pdb=" O SER E1010 " (cutoff:3.500A) Processing helix chain 'E' and resid 1016 through 1019 Processing helix chain 'E' and resid 1029 through 1039 removed outlier: 3.878A pdb=" N GLN E1038 " --> pdb=" O THR E1034 " (cutoff:3.500A) Processing helix chain 'E' and resid 1045 through 1065 removed outlier: 3.813A pdb=" N PHE E1053 " --> pdb=" O LEU E1049 " (cutoff:3.500A) Processing helix chain 'E' and resid 1113 through 1116 removed outlier: 3.818A pdb=" N TRP E1116 " --> pdb=" O ALA E1113 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1113 through 1116' Processing helix chain 'E' and resid 1243 through 1247 Processing helix chain 'E' and resid 1574 through 1579 removed outlier: 4.060A pdb=" N ARG E1578 " --> pdb=" O GLN E1574 " (cutoff:3.500A) Processing helix chain 'E' and resid 1582 through 1587 Processing helix chain 'E' and resid 1588 through 1593 removed outlier: 3.726A pdb=" N GLN E1592 " --> pdb=" O SER E1588 " (cutoff:3.500A) Processing helix chain 'E' and resid 1738 through 1747 removed outlier: 3.600A pdb=" N PHE E1742 " --> pdb=" O ASN E1738 " (cutoff:3.500A) Processing helix chain 'E' and resid 1747 through 1759 removed outlier: 3.552A pdb=" N GLN E1759 " --> pdb=" O THR E1755 " (cutoff:3.500A) Processing helix chain 'E' and resid 1762 through 1771 removed outlier: 4.072A pdb=" N ARG E1768 " --> pdb=" O THR E1764 " (cutoff:3.500A) Processing helix chain 'E' and resid 1786 through 1791 Processing helix chain 'E' and resid 1804 through 1812 removed outlier: 3.885A pdb=" N VAL E1808 " --> pdb=" O ASP E1804 " (cutoff:3.500A) Processing helix chain 'E' and resid 1813 through 1838 removed outlier: 3.579A pdb=" N MET E1838 " --> pdb=" O LYS E1834 " (cutoff:3.500A) Processing helix chain 'E' and resid 1840 through 1859 Processing helix chain 'E' and resid 1874 through 1879 Processing helix chain 'E' and resid 1880 through 1896 removed outlier: 3.673A pdb=" N ALA E1884 " --> pdb=" O ASP E1880 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE E1887 " --> pdb=" O GLN E1883 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER E1896 " --> pdb=" O SER E1892 " (cutoff:3.500A) Processing helix chain 'E' and resid 1918 through 1937 Processing helix chain 'E' and resid 1983 through 2070 removed outlier: 3.991A pdb=" N ASP E1989 " --> pdb=" O PRO E1985 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU E1994 " --> pdb=" O SER E1990 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N MET E2017 " --> pdb=" O ASP E2013 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN E2022 " --> pdb=" O SER E2018 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N SER E2031 " --> pdb=" O GLU E2027 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU E2037 " --> pdb=" O LEU E2033 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLN E2038 " --> pdb=" O ARG E2034 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LEU E2043 " --> pdb=" O ALA E2039 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP E2044 " --> pdb=" O LEU E2040 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS E2048 " --> pdb=" O ASP E2044 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA E2066 " --> pdb=" O ASP E2062 " (cutoff:3.500A) Processing helix chain 'E' and resid 2075 through 2092 removed outlier: 3.618A pdb=" N MET E2080 " --> pdb=" O GLU E2076 " (cutoff:3.500A) Processing helix chain 'E' and resid 2093 through 2105 removed outlier: 3.601A pdb=" N ALA E2101 " --> pdb=" O ASP E2097 " (cutoff:3.500A) Processing helix chain 'E' and resid 2120 through 2209 removed outlier: 3.595A pdb=" N ARG E2169 " --> pdb=" O GLU E2165 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N MET E2187 " --> pdb=" O THR E2183 " (cutoff:3.500A) Processing helix chain 'E' and resid 2212 through 2249 removed outlier: 3.606A pdb=" N TYR E2216 " --> pdb=" O ASN E2212 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP E2232 " --> pdb=" O TYR E2228 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU E2233 " --> pdb=" O ARG E2229 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA E2236 " --> pdb=" O ASP E2232 " (cutoff:3.500A) Processing helix chain 'E' and resid 2271 through 2290 Processing helix chain 'E' and resid 2302 through 2308 Processing helix chain 'E' and resid 2312 through 2317 Processing helix chain 'E' and resid 2348 through 2353 removed outlier: 3.532A pdb=" N ASN E2353 " --> pdb=" O LYS E2350 " (cutoff:3.500A) Processing helix chain 'E' and resid 2449 through 2457 removed outlier: 3.871A pdb=" N LEU E2453 " --> pdb=" O LYS E2449 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 159 through 161 Processing sheet with id=AA2, first strand: chain 'A' and resid 317 through 323 removed outlier: 3.807A pdb=" N GLU A 332 " --> pdb=" O HIS A 438 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N HIS A 438 " --> pdb=" O GLU A 332 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 346 through 352 removed outlier: 6.692A pdb=" N GLN A 355 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE A 360 " --> pdb=" O TYR A 397 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 373 through 374 Processing sheet with id=AA5, first strand: chain 'A' and resid 544 through 545 removed outlier: 4.299A pdb=" N ILE A 544 " --> pdb=" O ILE A 585 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1067 through 1073 removed outlier: 6.784A pdb=" N ILE A1086 " --> pdb=" O VAL A1069 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLY A1071 " --> pdb=" O TRP A1084 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N TRP A1084 " --> pdb=" O GLY A1071 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N HIS A1073 " --> pdb=" O ASN A1082 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ASN A1082 " --> pdb=" O HIS A1073 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1106 through 1107 removed outlier: 3.578A pdb=" N GLN A1107 " --> pdb=" O ARG A1110 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1133 through 1137 Processing sheet with id=AA9, first strand: chain 'A' and resid 1196 through 1201 removed outlier: 4.966A pdb=" N ASN A1222 " --> pdb=" O GLN A1214 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1267 through 1268 Processing sheet with id=AB2, first strand: chain 'A' and resid 1271 through 1272 removed outlier: 3.672A pdb=" N THR A1530 " --> pdb=" O PHE A1520 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE A1520 " --> pdb=" O THR A1530 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE A1462 " --> pdb=" O PHE A1469 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1285 through 1293 removed outlier: 3.710A pdb=" N ILE A1303 " --> pdb=" O SER A1287 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ALA A1301 " --> pdb=" O GLY A1289 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N TYR A1291 " --> pdb=" O ILE A1299 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N ILE A1299 " --> pdb=" O TYR A1291 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N SER A1298 " --> pdb=" O SER A1500 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N SER A1500 " --> pdb=" O SER A1298 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N SER A1300 " --> pdb=" O LYS A1498 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LYS A1498 " --> pdb=" O SER A1300 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU A1302 " --> pdb=" O PHE A1496 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1547 through 1550 Processing sheet with id=AB5, first strand: chain 'A' and resid 1595 through 1596 Processing sheet with id=AB6, first strand: chain 'A' and resid 1602 through 1609 Processing sheet with id=AB7, first strand: chain 'A' and resid 1637 through 1643 removed outlier: 6.883A pdb=" N TYR A1627 " --> pdb=" O PRO A1638 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR A1640 " --> pdb=" O ILE A1625 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR A1678 " --> pdb=" O SER A1628 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1774 through 1776 Processing sheet with id=AB9, first strand: chain 'A' and resid 2109 through 2110 Processing sheet with id=AC1, first strand: chain 'A' and resid 2114 through 2115 Processing sheet with id=AC2, first strand: chain 'A' and resid 2294 through 2301 removed outlier: 5.690A pdb=" N THR A2467 " --> pdb=" O ILE A2368 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N ILE A2368 " --> pdb=" O THR A2467 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N CYS A2469 " --> pdb=" O ARG A2366 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N ARG A2366 " --> pdb=" O CYS A2469 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N VAL A2373 " --> pdb=" O ASP A2411 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 2343 through 2345 removed outlier: 4.541A pdb=" N ALA A2387 " --> pdb=" O LEU A2405 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 159 through 161 Processing sheet with id=AC5, first strand: chain 'B' and resid 317 through 323 removed outlier: 3.807A pdb=" N GLU B 332 " --> pdb=" O HIS B 438 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N HIS B 438 " --> pdb=" O GLU B 332 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 346 through 352 removed outlier: 6.691A pdb=" N GLN B 355 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE B 360 " --> pdb=" O TYR B 397 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 373 through 374 Processing sheet with id=AC8, first strand: chain 'B' and resid 544 through 545 removed outlier: 4.300A pdb=" N ILE B 544 " --> pdb=" O ILE B 585 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 1067 through 1073 removed outlier: 6.784A pdb=" N ILE B1086 " --> pdb=" O VAL B1069 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLY B1071 " --> pdb=" O TRP B1084 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N TRP B1084 " --> pdb=" O GLY B1071 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N HIS B1073 " --> pdb=" O ASN B1082 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ASN B1082 " --> pdb=" O HIS B1073 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 1106 through 1107 removed outlier: 3.578A pdb=" N GLN B1107 " --> pdb=" O ARG B1110 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1133 through 1137 Processing sheet with id=AD3, first strand: chain 'B' and resid 1196 through 1201 removed outlier: 4.967A pdb=" N ASN B1222 " --> pdb=" O GLN B1214 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1267 through 1268 Processing sheet with id=AD5, first strand: chain 'B' and resid 1271 through 1272 removed outlier: 3.672A pdb=" N THR B1530 " --> pdb=" O PHE B1520 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE B1520 " --> pdb=" O THR B1530 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE B1462 " --> pdb=" O PHE B1469 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1285 through 1293 removed outlier: 3.710A pdb=" N ILE B1303 " --> pdb=" O SER B1287 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ALA B1301 " --> pdb=" O GLY B1289 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N TYR B1291 " --> pdb=" O ILE B1299 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N ILE B1299 " --> pdb=" O TYR B1291 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N SER B1298 " --> pdb=" O SER B1500 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N SER B1500 " --> pdb=" O SER B1298 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N SER B1300 " --> pdb=" O LYS B1498 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LYS B1498 " --> pdb=" O SER B1300 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU B1302 " --> pdb=" O PHE B1496 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1547 through 1550 Processing sheet with id=AD8, first strand: chain 'B' and resid 1595 through 1596 Processing sheet with id=AD9, first strand: chain 'B' and resid 1602 through 1609 Processing sheet with id=AE1, first strand: chain 'B' and resid 1637 through 1643 removed outlier: 6.882A pdb=" N TYR B1627 " --> pdb=" O PRO B1638 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR B1640 " --> pdb=" O ILE B1625 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR B1678 " --> pdb=" O SER B1628 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 1774 through 1776 Processing sheet with id=AE3, first strand: chain 'B' and resid 2114 through 2115 Processing sheet with id=AE4, first strand: chain 'B' and resid 2294 through 2301 removed outlier: 5.689A pdb=" N THR B2467 " --> pdb=" O ILE B2368 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ILE B2368 " --> pdb=" O THR B2467 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N CYS B2469 " --> pdb=" O ARG B2366 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N ARG B2366 " --> pdb=" O CYS B2469 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N VAL B2373 " --> pdb=" O ASP B2411 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 2343 through 2345 removed outlier: 4.542A pdb=" N ALA B2387 " --> pdb=" O LEU B2405 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 159 through 161 Processing sheet with id=AE7, first strand: chain 'C' and resid 317 through 323 removed outlier: 3.807A pdb=" N GLU C 332 " --> pdb=" O HIS C 438 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N HIS C 438 " --> pdb=" O GLU C 332 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 346 through 352 removed outlier: 6.691A pdb=" N GLN C 355 " --> pdb=" O GLN C 351 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE C 360 " --> pdb=" O TYR C 397 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 373 through 374 Processing sheet with id=AF1, first strand: chain 'C' and resid 544 through 545 removed outlier: 4.299A pdb=" N ILE C 544 " --> pdb=" O ILE C 585 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1067 through 1073 removed outlier: 6.784A pdb=" N ILE C1086 " --> pdb=" O VAL C1069 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLY C1071 " --> pdb=" O TRP C1084 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N TRP C1084 " --> pdb=" O GLY C1071 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N HIS C1073 " --> pdb=" O ASN C1082 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ASN C1082 " --> pdb=" O HIS C1073 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 1106 through 1107 removed outlier: 3.578A pdb=" N GLN C1107 " --> pdb=" O ARG C1110 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 1133 through 1137 Processing sheet with id=AF5, first strand: chain 'C' and resid 1196 through 1201 removed outlier: 4.967A pdb=" N ASN C1222 " --> pdb=" O GLN C1214 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1267 through 1268 Processing sheet with id=AF7, first strand: chain 'C' and resid 1271 through 1272 removed outlier: 3.672A pdb=" N THR C1530 " --> pdb=" O PHE C1520 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE C1520 " --> pdb=" O THR C1530 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE C1462 " --> pdb=" O PHE C1469 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 1285 through 1293 removed outlier: 3.709A pdb=" N ILE C1303 " --> pdb=" O SER C1287 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ALA C1301 " --> pdb=" O GLY C1289 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N TYR C1291 " --> pdb=" O ILE C1299 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N ILE C1299 " --> pdb=" O TYR C1291 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N SER C1298 " --> pdb=" O SER C1500 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N SER C1500 " --> pdb=" O SER C1298 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N SER C1300 " --> pdb=" O LYS C1498 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LYS C1498 " --> pdb=" O SER C1300 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU C1302 " --> pdb=" O PHE C1496 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 1547 through 1550 Processing sheet with id=AG1, first strand: chain 'C' and resid 1595 through 1596 Processing sheet with id=AG2, first strand: chain 'C' and resid 1602 through 1609 Processing sheet with id=AG3, first strand: chain 'C' and resid 1637 through 1643 removed outlier: 6.883A pdb=" N TYR C1627 " --> pdb=" O PRO C1638 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR C1640 " --> pdb=" O ILE C1625 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR C1678 " --> pdb=" O SER C1628 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 1774 through 1776 Processing sheet with id=AG5, first strand: chain 'C' and resid 2114 through 2115 Processing sheet with id=AG6, first strand: chain 'C' and resid 2294 through 2301 removed outlier: 5.690A pdb=" N THR C2467 " --> pdb=" O ILE C2368 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ILE C2368 " --> pdb=" O THR C2467 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N CYS C2469 " --> pdb=" O ARG C2366 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N ARG C2366 " --> pdb=" O CYS C2469 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VAL C2373 " --> pdb=" O ASP C2411 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'C' and resid 2343 through 2345 removed outlier: 4.542A pdb=" N ALA C2387 " --> pdb=" O LEU C2405 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'D' and resid 159 through 161 Processing sheet with id=AG9, first strand: chain 'D' and resid 317 through 323 removed outlier: 3.808A pdb=" N GLU D 332 " --> pdb=" O HIS D 438 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N HIS D 438 " --> pdb=" O GLU D 332 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'D' and resid 346 through 352 removed outlier: 6.692A pdb=" N GLN D 355 " --> pdb=" O GLN D 351 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE D 360 " --> pdb=" O TYR D 397 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'D' and resid 373 through 374 Processing sheet with id=AH3, first strand: chain 'D' and resid 544 through 545 removed outlier: 4.300A pdb=" N ILE D 544 " --> pdb=" O ILE D 585 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'D' and resid 1067 through 1073 removed outlier: 6.785A pdb=" N ILE D1086 " --> pdb=" O VAL D1069 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLY D1071 " --> pdb=" O TRP D1084 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N TRP D1084 " --> pdb=" O GLY D1071 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N HIS D1073 " --> pdb=" O ASN D1082 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ASN D1082 " --> pdb=" O HIS D1073 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'D' and resid 1106 through 1107 removed outlier: 3.579A pdb=" N GLN D1107 " --> pdb=" O ARG D1110 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'D' and resid 1133 through 1137 Processing sheet with id=AH7, first strand: chain 'D' and resid 1196 through 1201 removed outlier: 4.968A pdb=" N ASN D1222 " --> pdb=" O GLN D1214 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'D' and resid 1267 through 1268 Processing sheet with id=AH9, first strand: chain 'D' and resid 1271 through 1272 removed outlier: 3.672A pdb=" N THR D1530 " --> pdb=" O PHE D1520 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE D1520 " --> pdb=" O THR D1530 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE D1462 " --> pdb=" O PHE D1469 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'D' and resid 1285 through 1293 removed outlier: 3.709A pdb=" N ILE D1303 " --> pdb=" O SER D1287 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ALA D1301 " --> pdb=" O GLY D1289 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N TYR D1291 " --> pdb=" O ILE D1299 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N ILE D1299 " --> pdb=" O TYR D1291 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N SER D1298 " --> pdb=" O SER D1500 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N SER D1500 " --> pdb=" O SER D1298 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N SER D1300 " --> pdb=" O LYS D1498 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LYS D1498 " --> pdb=" O SER D1300 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU D1302 " --> pdb=" O PHE D1496 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'D' and resid 1547 through 1550 Processing sheet with id=AI3, first strand: chain 'D' and resid 1595 through 1596 Processing sheet with id=AI4, first strand: chain 'D' and resid 1602 through 1609 Processing sheet with id=AI5, first strand: chain 'D' and resid 1637 through 1643 removed outlier: 6.883A pdb=" N TYR D1627 " --> pdb=" O PRO D1638 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR D1640 " --> pdb=" O ILE D1625 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR D1678 " --> pdb=" O SER D1628 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'D' and resid 1774 through 1776 Processing sheet with id=AI7, first strand: chain 'D' and resid 2114 through 2115 Processing sheet with id=AI8, first strand: chain 'D' and resid 2294 through 2301 removed outlier: 5.690A pdb=" N THR D2467 " --> pdb=" O ILE D2368 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ILE D2368 " --> pdb=" O THR D2467 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N CYS D2469 " --> pdb=" O ARG D2366 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N ARG D2366 " --> pdb=" O CYS D2469 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N VAL D2373 " --> pdb=" O ASP D2411 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'D' and resid 2343 through 2345 removed outlier: 4.542A pdb=" N ALA D2387 " --> pdb=" O LEU D2405 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'E' and resid 159 through 161 Processing sheet with id=AJ2, first strand: chain 'E' and resid 317 through 323 removed outlier: 3.807A pdb=" N GLU E 332 " --> pdb=" O HIS E 438 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N HIS E 438 " --> pdb=" O GLU E 332 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'E' and resid 346 through 352 removed outlier: 6.692A pdb=" N GLN E 355 " --> pdb=" O GLN E 351 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE E 360 " --> pdb=" O TYR E 397 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'E' and resid 373 through 374 Processing sheet with id=AJ5, first strand: chain 'E' and resid 544 through 545 removed outlier: 4.299A pdb=" N ILE E 544 " --> pdb=" O ILE E 585 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'E' and resid 1067 through 1073 removed outlier: 6.784A pdb=" N ILE E1086 " --> pdb=" O VAL E1069 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLY E1071 " --> pdb=" O TRP E1084 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N TRP E1084 " --> pdb=" O GLY E1071 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N HIS E1073 " --> pdb=" O ASN E1082 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ASN E1082 " --> pdb=" O HIS E1073 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'E' and resid 1106 through 1107 removed outlier: 3.579A pdb=" N GLN E1107 " --> pdb=" O ARG E1110 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'E' and resid 1133 through 1137 Processing sheet with id=AJ9, first strand: chain 'E' and resid 1196 through 1201 removed outlier: 4.966A pdb=" N ASN E1222 " --> pdb=" O GLN E1214 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'E' and resid 1267 through 1268 Processing sheet with id=AK2, first strand: chain 'E' and resid 1271 through 1272 removed outlier: 3.672A pdb=" N THR E1530 " --> pdb=" O PHE E1520 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE E1520 " --> pdb=" O THR E1530 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE E1462 " --> pdb=" O PHE E1469 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'E' and resid 1285 through 1293 removed outlier: 3.709A pdb=" N ILE E1303 " --> pdb=" O SER E1287 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ALA E1301 " --> pdb=" O GLY E1289 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N TYR E1291 " --> pdb=" O ILE E1299 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N ILE E1299 " --> pdb=" O TYR E1291 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N SER E1298 " --> pdb=" O SER E1500 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N SER E1500 " --> pdb=" O SER E1298 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N SER E1300 " --> pdb=" O LYS E1498 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LYS E1498 " --> pdb=" O SER E1300 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU E1302 " --> pdb=" O PHE E1496 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'E' and resid 1547 through 1550 Processing sheet with id=AK5, first strand: chain 'E' and resid 1595 through 1596 Processing sheet with id=AK6, first strand: chain 'E' and resid 1602 through 1609 Processing sheet with id=AK7, first strand: chain 'E' and resid 1637 through 1643 removed outlier: 6.883A pdb=" N TYR E1627 " --> pdb=" O PRO E1638 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR E1640 " --> pdb=" O ILE E1625 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR E1678 " --> pdb=" O SER E1628 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'E' and resid 1774 through 1776 Processing sheet with id=AK9, first strand: chain 'E' and resid 2294 through 2301 removed outlier: 5.689A pdb=" N THR E2467 " --> pdb=" O ILE E2368 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N ILE E2368 " --> pdb=" O THR E2467 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N CYS E2469 " --> pdb=" O ARG E2366 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N ARG E2366 " --> pdb=" O CYS E2469 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N VAL E2373 " --> pdb=" O ASP E2411 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'E' and resid 2343 through 2345 removed outlier: 4.542A pdb=" N ALA E2387 " --> pdb=" O LEU E2405 " (cutoff:3.500A) 4150 hydrogen bonds defined for protein. 11925 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: 47.99 Time building geometry restraints manager: 29.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 27836 1.34 - 1.45: 14518 1.45 - 1.57: 47476 1.57 - 1.69: 10 1.69 - 1.81: 550 Bond restraints: 90390 Sorted by residual: bond pdb=" C GLU D 422 " pdb=" N PRO D 423 " ideal model delta sigma weight residual 1.334 1.390 -0.056 2.34e-02 1.83e+03 5.80e+00 bond pdb=" C GLU B 422 " pdb=" N PRO B 423 " ideal model delta sigma weight residual 1.334 1.389 -0.055 2.34e-02 1.83e+03 5.59e+00 bond pdb=" C GLU E 422 " pdb=" N PRO E 423 " ideal model delta sigma weight residual 1.334 1.389 -0.055 2.34e-02 1.83e+03 5.56e+00 bond pdb=" C GLU C 422 " pdb=" N PRO C 423 " ideal model delta sigma weight residual 1.334 1.389 -0.055 2.34e-02 1.83e+03 5.56e+00 bond pdb=" C GLU A 422 " pdb=" N PRO A 423 " ideal model delta sigma weight residual 1.334 1.389 -0.055 2.34e-02 1.83e+03 5.56e+00 ... (remaining 90385 not shown) Histogram of bond angle deviations from ideal: 98.04 - 106.43: 2703 106.43 - 114.83: 53524 114.83 - 123.22: 61865 123.22 - 131.62: 4516 131.62 - 140.02: 247 Bond angle restraints: 122855 Sorted by residual: angle pdb=" C ASN A1629 " pdb=" N ASP A1630 " pdb=" CA ASP A1630 " ideal model delta sigma weight residual 121.70 133.45 -11.75 1.80e+00 3.09e-01 4.26e+01 angle pdb=" C ASN E1629 " pdb=" N ASP E1630 " pdb=" CA ASP E1630 " ideal model delta sigma weight residual 121.70 133.41 -11.71 1.80e+00 3.09e-01 4.23e+01 angle pdb=" C ASN B1629 " pdb=" N ASP B1630 " pdb=" CA ASP B1630 " ideal model delta sigma weight residual 121.70 133.41 -11.71 1.80e+00 3.09e-01 4.23e+01 angle pdb=" C ASN C1629 " pdb=" N ASP C1630 " pdb=" CA ASP C1630 " ideal model delta sigma weight residual 121.70 133.40 -11.70 1.80e+00 3.09e-01 4.22e+01 angle pdb=" C ASN D1629 " pdb=" N ASP D1630 " pdb=" CA ASP D1630 " ideal model delta sigma weight residual 121.70 133.36 -11.66 1.80e+00 3.09e-01 4.20e+01 ... (remaining 122850 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.21: 52109 16.21 - 32.41: 2148 32.41 - 48.62: 463 48.62 - 64.83: 10 64.83 - 81.03: 40 Dihedral angle restraints: 54770 sinusoidal: 21435 harmonic: 33335 Sorted by residual: dihedral pdb=" CA SER C1708 " pdb=" C SER C1708 " pdb=" N VAL C1709 " pdb=" CA VAL C1709 " ideal model delta harmonic sigma weight residual -180.00 -133.19 -46.81 0 5.00e+00 4.00e-02 8.77e+01 dihedral pdb=" CA SER E1708 " pdb=" C SER E1708 " pdb=" N VAL E1709 " pdb=" CA VAL E1709 " ideal model delta harmonic sigma weight residual -180.00 -133.20 -46.80 0 5.00e+00 4.00e-02 8.76e+01 dihedral pdb=" CA SER D1708 " pdb=" C SER D1708 " pdb=" N VAL D1709 " pdb=" CA VAL D1709 " ideal model delta harmonic sigma weight residual -180.00 -133.25 -46.75 0 5.00e+00 4.00e-02 8.74e+01 ... (remaining 54767 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 10895 0.065 - 0.130: 2674 0.130 - 0.196: 390 0.196 - 0.261: 96 0.261 - 0.326: 30 Chirality restraints: 14085 Sorted by residual: chirality pdb=" CB ILE E2093 " pdb=" CA ILE E2093 " pdb=" CG1 ILE E2093 " pdb=" CG2 ILE E2093 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" CB ILE B2093 " pdb=" CA ILE B2093 " pdb=" CG1 ILE B2093 " pdb=" CG2 ILE B2093 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" CB ILE D2093 " pdb=" CA ILE D2093 " pdb=" CG1 ILE D2093 " pdb=" CG2 ILE D2093 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.63e+00 ... (remaining 14082 not shown) Planarity restraints: 15950 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 720 " 0.030 2.00e-02 2.50e+03 2.54e-02 1.61e+01 pdb=" CG TRP B 720 " -0.066 2.00e-02 2.50e+03 pdb=" CD1 TRP B 720 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP B 720 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP B 720 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP B 720 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 720 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 720 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 720 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP B 720 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 720 " -0.030 2.00e-02 2.50e+03 2.53e-02 1.60e+01 pdb=" CG TRP D 720 " 0.066 2.00e-02 2.50e+03 pdb=" CD1 TRP D 720 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP D 720 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP D 720 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP D 720 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 720 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 720 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 720 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP D 720 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 720 " -0.030 2.00e-02 2.50e+03 2.53e-02 1.60e+01 pdb=" CG TRP E 720 " 0.066 2.00e-02 2.50e+03 pdb=" CD1 TRP E 720 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP E 720 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP E 720 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP E 720 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP E 720 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 720 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 720 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP E 720 " -0.005 2.00e-02 2.50e+03 ... (remaining 15947 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 21486 2.79 - 3.31: 81881 3.31 - 3.84: 147160 3.84 - 4.37: 170330 4.37 - 4.90: 290651 Nonbonded interactions: 711508 Sorted by model distance: nonbonded pdb=" O TYR D 245 " pdb=" OG1 THR D 249 " model vdw 2.258 2.440 nonbonded pdb=" O TYR E 245 " pdb=" OG1 THR E 249 " model vdw 2.258 2.440 nonbonded pdb=" O TYR C 245 " pdb=" OG1 THR C 249 " model vdw 2.259 2.440 nonbonded pdb=" O TYR B 245 " pdb=" OG1 THR B 249 " model vdw 2.259 2.440 nonbonded pdb=" O TYR A 245 " pdb=" OG1 THR A 249 " model vdw 2.259 2.440 ... (remaining 711503 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.460 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: 0.100 Extract box with map and model: 16.010 Check model and map are aligned: 1.000 Set scattering table: 0.600 Process input model: 195.800 Find NCS groups from input model: 4.380 Set up NCS constraints: 0.400 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 224.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 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 0.088 90390 Z= 0.507 Angle : 1.092 13.444 122855 Z= 0.584 Chirality : 0.060 0.326 14085 Planarity : 0.007 0.077 15950 Dihedral : 9.914 81.032 33220 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.73 % Favored : 93.22 % Rotamer: Outliers : 0.37 % Allowed : 2.66 % Favored : 96.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.05 % Cis-general : 0.18 % Twisted Proline : 1.01 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.60 (0.06), residues: 11365 helix: -2.18 (0.05), residues: 5060 sheet: -2.68 (0.11), residues: 1465 loop : -2.34 (0.08), residues: 4840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.004 TRP B 720 HIS 0.017 0.002 HIS C1815 PHE 0.030 0.003 PHE B1714 TYR 0.041 0.003 TYR A 496 ARG 0.018 0.001 ARG A1831 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22730 Ramachandran restraints generated. 11365 Oldfield, 0 Emsley, 11365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22730 Ramachandran restraints generated. 11365 Oldfield, 0 Emsley, 11365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2261 residues out of total 9715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 2226 time to evaluate : 8.955 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 505 MET cc_start: 0.7962 (mmt) cc_final: 0.7739 (mmm) REVERT: A 1032 MET cc_start: 0.6926 (mmm) cc_final: 0.6615 (mtp) REVERT: A 1734 PHE cc_start: 0.7941 (m-10) cc_final: 0.7714 (m-80) REVERT: A 1822 MET cc_start: 0.7322 (mtt) cc_final: 0.7032 (mtm) REVERT: B 1771 SER cc_start: 0.8441 (t) cc_final: 0.8046 (p) REVERT: C 505 MET cc_start: 0.7958 (mmt) cc_final: 0.7748 (mmm) REVERT: C 807 GLN cc_start: 0.6813 (tt0) cc_final: 0.6257 (mt0) REVERT: C 1765 GLU cc_start: 0.6445 (tp30) cc_final: 0.5755 (tp30) REVERT: C 1822 MET cc_start: 0.7158 (mtt) cc_final: 0.6877 (mtp) REVERT: C 2084 LEU cc_start: 0.8591 (tt) cc_final: 0.8353 (tp) REVERT: D 344 ASP cc_start: 0.6123 (p0) cc_final: 0.5858 (p0) REVERT: D 807 GLN cc_start: 0.7139 (tt0) cc_final: 0.6160 (mt0) REVERT: D 1822 MET cc_start: 0.7216 (mtt) cc_final: 0.6872 (mtm) REVERT: D 2233 LEU cc_start: 0.8732 (mt) cc_final: 0.8476 (mt) REVERT: E 707 GLN cc_start: 0.7814 (mp10) cc_final: 0.7572 (mp-120) REVERT: E 807 GLN cc_start: 0.6652 (tt0) cc_final: 0.5045 (tt0) REVERT: E 1822 MET cc_start: 0.7167 (mtt) cc_final: 0.6703 (mtp) REVERT: E 1826 ASP cc_start: 0.6403 (m-30) cc_final: 0.6187 (m-30) REVERT: E 2047 LYS cc_start: 0.7980 (tttt) cc_final: 0.7685 (ttmm) outliers start: 35 outliers final: 7 residues processed: 2251 average time/residue: 0.9548 time to fit residues: 3612.0731 Evaluate side-chains 1168 residues out of total 9715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1161 time to evaluate : 7.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain D residue 1126 VAL Chi-restraints excluded: chain D residue 1259 VAL Chi-restraints excluded: chain E residue 1126 VAL Chi-restraints excluded: chain E residue 1773 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1140 random chunks: chunk 962 optimal weight: 0.0770 chunk 864 optimal weight: 5.9990 chunk 479 optimal weight: 0.9980 chunk 295 optimal weight: 0.6980 chunk 582 optimal weight: 6.9990 chunk 461 optimal weight: 0.6980 chunk 893 optimal weight: 4.9990 chunk 345 optimal weight: 4.9990 chunk 543 optimal weight: 0.9980 chunk 665 optimal weight: 0.9990 chunk 1035 optimal weight: 8.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN A 155 ASN ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 ASN A 312 ASN ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 528 ASN A 533 ASN A 683 ASN A 807 GLN A 906 GLN ** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1055 GLN A1062 GLN A1188 ASN A1227 HIS A1264 ASN ** A1311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1617 HIS A1649 ASN A1710 ASN A1775 GLN A1811 ASN A2052 GLN A2200 GLN A2407 HIS A2463 HIS B 38 ASN B 155 ASN B 158 ASN B 222 ASN B 312 ASN B 528 ASN B 533 ASN B 683 ASN B 807 GLN B 906 GLN B 912 GLN ** B 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1028 GLN B1062 GLN B1188 ASN ** B1227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1260 ASN B1264 ASN ** B1311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1581 ASN B1617 HIS B1620 ASN B1649 ASN B1710 ASN B1811 ASN B2052 GLN B2200 GLN B2266 ASN B2394 ASN B2407 HIS B2463 HIS C 38 ASN C 155 ASN C 158 ASN C 222 ASN C 312 ASN ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 528 ASN C 533 ASN C 683 ASN C 906 GLN ** C 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1028 GLN C1188 ASN C1227 HIS C1260 ASN C1264 ASN ** C1311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1617 HIS C1620 ASN C1649 ASN C1710 ASN C1811 ASN C2170 GLN C2266 ASN C2353 ASN C2394 ASN C2407 HIS C2463 HIS D 38 ASN D 155 ASN D 158 ASN D 222 ASN D 312 ASN D 528 ASN D 533 ASN D 683 ASN D 906 GLN ** D 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 991 GLN D1028 GLN D1062 GLN D1188 ASN ** D1227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1264 ASN D1297 ASN ** D1311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1617 HIS D1620 ASN D1649 ASN D1710 ASN D2200 GLN D2266 ASN D2407 HIS D2463 HIS E 38 ASN E 155 ASN E 222 ASN E 312 ASN ** E 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 528 ASN ** E 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1028 GLN E1045 ASN E1051 ASN E1188 ASN ** E1227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1264 ASN ** E1311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1617 HIS E1620 ASN E1649 ASN E1710 ASN ** E1727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1775 GLN E2052 GLN E2200 GLN E2266 ASN E2407 HIS E2463 HIS Total number of N/Q/H flips: 119 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 90390 Z= 0.189 Angle : 0.681 12.867 122855 Z= 0.351 Chirality : 0.042 0.218 14085 Planarity : 0.005 0.057 15950 Dihedral : 5.871 36.605 12373 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.54 % Favored : 94.41 % Rotamer: Outliers : 1.97 % Allowed : 10.73 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.08), residues: 11365 helix: -0.15 (0.07), residues: 5075 sheet: -2.13 (0.12), residues: 1475 loop : -1.88 (0.09), residues: 4815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B1560 HIS 0.015 0.001 HIS E2344 PHE 0.030 0.002 PHE B2442 TYR 0.024 0.001 TYR E 376 ARG 0.007 0.001 ARG C1519 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22730 Ramachandran restraints generated. 11365 Oldfield, 0 Emsley, 11365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22730 Ramachandran restraints generated. 11365 Oldfield, 0 Emsley, 11365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1565 residues out of total 9715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 1379 time to evaluate : 9.206 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 396 HIS cc_start: 0.8075 (m90) cc_final: 0.7858 (m90) REVERT: A 450 LEU cc_start: 0.8858 (tt) cc_final: 0.8655 (tt) REVERT: B 678 LEU cc_start: 0.9144 (mt) cc_final: 0.8912 (mp) REVERT: B 1489 ARG cc_start: 0.7245 (tpm170) cc_final: 0.6651 (tpp-160) REVERT: C 27 MET cc_start: 0.8493 (mtt) cc_final: 0.8290 (mtt) REVERT: C 505 MET cc_start: 0.7870 (mmt) cc_final: 0.7666 (mmm) REVERT: C 715 GLU cc_start: 0.7064 (tt0) cc_final: 0.6832 (tt0) REVERT: D 318 VAL cc_start: 0.9000 (t) cc_final: 0.8751 (m) REVERT: D 1489 ARG cc_start: 0.7283 (tpm170) cc_final: 0.6691 (tpp-160) REVERT: D 2352 LEU cc_start: 0.8699 (mt) cc_final: 0.8446 (tt) REVERT: E 674 MET cc_start: 0.8272 (tpt) cc_final: 0.7788 (tpt) REVERT: E 1822 MET cc_start: 0.7239 (mtt) cc_final: 0.6999 (mtp) REVERT: E 1826 ASP cc_start: 0.6352 (m-30) cc_final: 0.6029 (m-30) outliers start: 186 outliers final: 97 residues processed: 1511 average time/residue: 0.7866 time to fit residues: 2069.2162 Evaluate side-chains 1149 residues out of total 9715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 1052 time to evaluate : 7.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 692 LYS Chi-restraints excluded: chain A residue 985 SER Chi-restraints excluded: chain A residue 1063 VAL Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain A residue 1279 ASN Chi-restraints excluded: chain A residue 1284 LEU Chi-restraints excluded: chain A residue 1292 THR Chi-restraints excluded: chain A residue 1535 VAL Chi-restraints excluded: chain A residue 1803 VAL Chi-restraints excluded: chain A residue 1956 ASP Chi-restraints excluded: chain A residue 2095 VAL Chi-restraints excluded: chain B residue 265 LYS Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain B residue 928 ARG Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1063 VAL Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1297 ASN Chi-restraints excluded: chain B residue 1503 ILE Chi-restraints excluded: chain B residue 1535 VAL Chi-restraints excluded: chain B residue 1803 VAL Chi-restraints excluded: chain B residue 1842 ASP Chi-restraints excluded: chain B residue 1860 ASP Chi-restraints excluded: chain B residue 1900 LEU Chi-restraints excluded: chain B residue 1962 SER Chi-restraints excluded: chain B residue 1989 ASP Chi-restraints excluded: chain B residue 2030 LEU Chi-restraints excluded: chain B residue 2089 LEU Chi-restraints excluded: chain B residue 2095 VAL Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 346 ILE Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain C residue 928 ARG Chi-restraints excluded: chain C residue 986 ASP Chi-restraints excluded: chain C residue 1063 VAL Chi-restraints excluded: chain C residue 1097 TYR Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain C residue 1476 ASP Chi-restraints excluded: chain C residue 1535 VAL Chi-restraints excluded: chain C residue 1654 LEU Chi-restraints excluded: chain C residue 1803 VAL Chi-restraints excluded: chain C residue 1922 LEU Chi-restraints excluded: chain C residue 1962 SER Chi-restraints excluded: chain C residue 2027 GLU Chi-restraints excluded: chain C residue 2085 SER Chi-restraints excluded: chain C residue 2095 VAL Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 571 GLN Chi-restraints excluded: chain D residue 764 LEU Chi-restraints excluded: chain D residue 928 ARG Chi-restraints excluded: chain D residue 1063 VAL Chi-restraints excluded: chain D residue 1118 ASP Chi-restraints excluded: chain D residue 1126 VAL Chi-restraints excluded: chain D residue 1259 VAL Chi-restraints excluded: chain D residue 1292 THR Chi-restraints excluded: chain D residue 1297 ASN Chi-restraints excluded: chain D residue 1503 ILE Chi-restraints excluded: chain D residue 1535 VAL Chi-restraints excluded: chain D residue 1798 ASP Chi-restraints excluded: chain D residue 1803 VAL Chi-restraints excluded: chain D residue 1824 LEU Chi-restraints excluded: chain D residue 1900 LEU Chi-restraints excluded: chain D residue 1956 ASP Chi-restraints excluded: chain D residue 2027 GLU Chi-restraints excluded: chain D residue 2095 VAL Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 68 MET Chi-restraints excluded: chain E residue 571 GLN Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain E residue 681 LEU Chi-restraints excluded: chain E residue 686 ILE Chi-restraints excluded: chain E residue 709 ASP Chi-restraints excluded: chain E residue 845 GLN Chi-restraints excluded: chain E residue 928 ARG Chi-restraints excluded: chain E residue 942 ILE Chi-restraints excluded: chain E residue 986 ASP Chi-restraints excluded: chain E residue 1001 LYS Chi-restraints excluded: chain E residue 1057 LEU Chi-restraints excluded: chain E residue 1097 TYR Chi-restraints excluded: chain E residue 1126 VAL Chi-restraints excluded: chain E residue 1468 LYS Chi-restraints excluded: chain E residue 1476 ASP Chi-restraints excluded: chain E residue 1535 VAL Chi-restraints excluded: chain E residue 1773 ILE Chi-restraints excluded: chain E residue 1842 ASP Chi-restraints excluded: chain E residue 1927 MET Chi-restraints excluded: chain E residue 2027 GLU Chi-restraints excluded: chain E residue 2147 SER Chi-restraints excluded: chain E residue 2168 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1140 random chunks: chunk 575 optimal weight: 8.9990 chunk 321 optimal weight: 0.9980 chunk 861 optimal weight: 0.0470 chunk 704 optimal weight: 0.9990 chunk 285 optimal weight: 2.9990 chunk 1037 optimal weight: 4.9990 chunk 1120 optimal weight: 0.2980 chunk 923 optimal weight: 0.9980 chunk 1028 optimal weight: 7.9990 chunk 353 optimal weight: 10.0000 chunk 832 optimal weight: 5.9990 overall best weight: 0.6680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 522 HIS ** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1620 ASN B 522 HIS B 683 ASN ** B 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 991 GLN ** B1055 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1227 HIS B2146 GLN C 144 GLN ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 683 ASN ** C 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1028 GLN C1055 GLN C1543 GLN C2146 GLN C2170 GLN C2200 GLN D 144 GLN D 473 HIS ** D 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1227 HIS D1297 ASN ** D2284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 158 ASN ** E 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 707 GLN E 914 GLN E1062 GLN ** E1227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2146 GLN E2162 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 90390 Z= 0.169 Angle : 0.632 13.464 122855 Z= 0.321 Chirality : 0.041 0.219 14085 Planarity : 0.004 0.052 15950 Dihedral : 5.399 34.973 12373 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.44 % Allowed : 12.75 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.08), residues: 11365 helix: 0.68 (0.07), residues: 5125 sheet: -1.67 (0.12), residues: 1525 loop : -1.66 (0.09), residues: 4715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E1084 HIS 0.008 0.001 HIS E2344 PHE 0.019 0.001 PHE D1520 TYR 0.026 0.001 TYR E 376 ARG 0.009 0.000 ARG E1519 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22730 Ramachandran restraints generated. 11365 Oldfield, 0 Emsley, 11365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22730 Ramachandran restraints generated. 11365 Oldfield, 0 Emsley, 11365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1394 residues out of total 9715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 1164 time to evaluate : 7.896 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 659 MET cc_start: 0.7782 (mmm) cc_final: 0.7373 (mmm) REVERT: A 1290 ASP cc_start: 0.7778 (t0) cc_final: 0.7543 (t0) REVERT: B 58 LYS cc_start: 0.9021 (ttpp) cc_final: 0.8352 (ttmm) REVERT: B 1560 TRP cc_start: 0.8170 (OUTLIER) cc_final: 0.6312 (p-90) REVERT: B 1654 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8257 (mt) REVERT: B 1658 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8718 (tm) REVERT: D 318 VAL cc_start: 0.9021 (t) cc_final: 0.8768 (m) REVERT: E 292 ASP cc_start: 0.6984 (m-30) cc_final: 0.6748 (m-30) REVERT: E 674 MET cc_start: 0.8353 (tpt) cc_final: 0.7798 (tpt) REVERT: E 1658 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8058 (tm) REVERT: E 2352 LEU cc_start: 0.8601 (mp) cc_final: 0.8069 (tt) outliers start: 230 outliers final: 117 residues processed: 1317 average time/residue: 0.7769 time to fit residues: 1803.9884 Evaluate side-chains 1135 residues out of total 9715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 1014 time to evaluate : 7.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1031 MET Chi-restraints excluded: chain A residue 1047 ASP Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain A residue 1284 LEU Chi-restraints excluded: chain A residue 1303 ILE Chi-restraints excluded: chain A residue 1535 VAL Chi-restraints excluded: chain A residue 1752 MET Chi-restraints excluded: chain A residue 1803 VAL Chi-restraints excluded: chain A residue 1956 ASP Chi-restraints excluded: chain A residue 1962 SER Chi-restraints excluded: chain A residue 2095 VAL Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 692 LYS Chi-restraints excluded: chain B residue 845 GLN Chi-restraints excluded: chain B residue 928 ARG Chi-restraints excluded: chain B residue 986 ASP Chi-restraints excluded: chain B residue 1047 ASP Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1185 THR Chi-restraints excluded: chain B residue 1279 ASN Chi-restraints excluded: chain B residue 1297 ASN Chi-restraints excluded: chain B residue 1476 ASP Chi-restraints excluded: chain B residue 1503 ILE Chi-restraints excluded: chain B residue 1535 VAL Chi-restraints excluded: chain B residue 1560 TRP Chi-restraints excluded: chain B residue 1653 LYS Chi-restraints excluded: chain B residue 1654 LEU Chi-restraints excluded: chain B residue 1658 LEU Chi-restraints excluded: chain B residue 1803 VAL Chi-restraints excluded: chain B residue 1824 LEU Chi-restraints excluded: chain B residue 1842 ASP Chi-restraints excluded: chain B residue 1860 ASP Chi-restraints excluded: chain B residue 1900 LEU Chi-restraints excluded: chain B residue 1921 LEU Chi-restraints excluded: chain B residue 2089 LEU Chi-restraints excluded: chain B residue 2095 VAL Chi-restraints excluded: chain B residue 2168 ILE Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 346 ILE Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain C residue 928 ARG Chi-restraints excluded: chain C residue 986 ASP Chi-restraints excluded: chain C residue 1039 LEU Chi-restraints excluded: chain C residue 1047 ASP Chi-restraints excluded: chain C residue 1057 LEU Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain C residue 1185 THR Chi-restraints excluded: chain C residue 1303 ILE Chi-restraints excluded: chain C residue 1304 LEU Chi-restraints excluded: chain C residue 1476 ASP Chi-restraints excluded: chain C residue 1519 ARG Chi-restraints excluded: chain C residue 1535 VAL Chi-restraints excluded: chain C residue 1551 THR Chi-restraints excluded: chain C residue 1653 LYS Chi-restraints excluded: chain C residue 1654 LEU Chi-restraints excluded: chain C residue 1803 VAL Chi-restraints excluded: chain C residue 1860 ASP Chi-restraints excluded: chain C residue 2027 GLU Chi-restraints excluded: chain C residue 2095 VAL Chi-restraints excluded: chain C residue 2168 ILE Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 571 GLN Chi-restraints excluded: chain D residue 573 LEU Chi-restraints excluded: chain D residue 928 ARG Chi-restraints excluded: chain D residue 986 ASP Chi-restraints excluded: chain D residue 1024 LEU Chi-restraints excluded: chain D residue 1118 ASP Chi-restraints excluded: chain D residue 1126 VAL Chi-restraints excluded: chain D residue 1185 THR Chi-restraints excluded: chain D residue 1259 VAL Chi-restraints excluded: chain D residue 1297 ASN Chi-restraints excluded: chain D residue 1503 ILE Chi-restraints excluded: chain D residue 1535 VAL Chi-restraints excluded: chain D residue 1551 THR Chi-restraints excluded: chain D residue 1587 LEU Chi-restraints excluded: chain D residue 1798 ASP Chi-restraints excluded: chain D residue 1803 VAL Chi-restraints excluded: chain D residue 1824 LEU Chi-restraints excluded: chain D residue 1860 ASP Chi-restraints excluded: chain D residue 1900 LEU Chi-restraints excluded: chain D residue 1956 ASP Chi-restraints excluded: chain D residue 2027 GLU Chi-restraints excluded: chain D residue 2095 VAL Chi-restraints excluded: chain D residue 2190 GLU Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 280 ASP Chi-restraints excluded: chain E residue 549 ASP Chi-restraints excluded: chain E residue 571 GLN Chi-restraints excluded: chain E residue 681 LEU Chi-restraints excluded: chain E residue 686 ILE Chi-restraints excluded: chain E residue 692 LYS Chi-restraints excluded: chain E residue 845 GLN Chi-restraints excluded: chain E residue 928 ARG Chi-restraints excluded: chain E residue 942 ILE Chi-restraints excluded: chain E residue 1049 LEU Chi-restraints excluded: chain E residue 1057 LEU Chi-restraints excluded: chain E residue 1126 VAL Chi-restraints excluded: chain E residue 1185 THR Chi-restraints excluded: chain E residue 1468 LYS Chi-restraints excluded: chain E residue 1476 ASP Chi-restraints excluded: chain E residue 1535 VAL Chi-restraints excluded: chain E residue 1551 THR Chi-restraints excluded: chain E residue 1625 ILE Chi-restraints excluded: chain E residue 1653 LYS Chi-restraints excluded: chain E residue 1658 LEU Chi-restraints excluded: chain E residue 1773 ILE Chi-restraints excluded: chain E residue 2027 GLU Chi-restraints excluded: chain E residue 2095 VAL Chi-restraints excluded: chain E residue 2168 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1140 random chunks: chunk 1024 optimal weight: 7.9990 chunk 779 optimal weight: 2.9990 chunk 538 optimal weight: 0.7980 chunk 114 optimal weight: 8.9990 chunk 494 optimal weight: 9.9990 chunk 696 optimal weight: 4.9990 chunk 1040 optimal weight: 0.0000 chunk 1101 optimal weight: 0.0980 chunk 543 optimal weight: 3.9990 chunk 986 optimal weight: 6.9990 chunk 296 optimal weight: 3.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 473 HIS A1028 GLN A1055 GLN ** A1311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1620 ASN B 473 HIS ** B 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 184 ASN C 473 HIS ** C 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 827 GLN ** C 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1055 GLN ** C1311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2146 GLN C2170 GLN D 184 ASN D 294 GLN ** D 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1288 HIS D1297 ASN ** D1311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 914 GLN E1227 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 90390 Z= 0.222 Angle : 0.620 13.748 122855 Z= 0.315 Chirality : 0.041 0.223 14085 Planarity : 0.004 0.046 15950 Dihedral : 5.155 32.362 12373 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 3.00 % Allowed : 13.35 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.08), residues: 11365 helix: 1.23 (0.08), residues: 5135 sheet: -1.51 (0.13), residues: 1495 loop : -1.45 (0.09), residues: 4735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B1560 HIS 0.005 0.001 HIS E2344 PHE 0.026 0.001 PHE E1520 TYR 0.022 0.001 TYR E1836 ARG 0.007 0.000 ARG E2181 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22730 Ramachandran restraints generated. 11365 Oldfield, 0 Emsley, 11365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22730 Ramachandran restraints generated. 11365 Oldfield, 0 Emsley, 11365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1322 residues out of total 9715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 283 poor density : 1039 time to evaluate : 7.935 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: A 1842 ASP cc_start: 0.7415 (OUTLIER) cc_final: 0.7132 (p0) REVERT: A 2435 ASP cc_start: 0.6708 (t0) cc_final: 0.6316 (t0) REVERT: B 1658 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8719 (tm) REVERT: B 2435 ASP cc_start: 0.6367 (t0) cc_final: 0.6077 (t0) REVERT: C 483 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8114 (tt) REVERT: C 674 MET cc_start: 0.8679 (tpt) cc_final: 0.8395 (tpt) REVERT: C 1172 TYR cc_start: 0.8206 (m-80) cc_final: 0.7904 (m-80) REVERT: C 1560 TRP cc_start: 0.8135 (OUTLIER) cc_final: 0.6220 (p-90) REVERT: D 318 VAL cc_start: 0.9008 (t) cc_final: 0.8783 (m) REVERT: E 674 MET cc_start: 0.8475 (tpt) cc_final: 0.7990 (tpt) REVERT: E 1658 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8175 (tm) REVERT: E 1822 MET cc_start: 0.7234 (mtp) cc_final: 0.6997 (mmm) REVERT: E 1826 ASP cc_start: 0.6552 (m-30) cc_final: 0.6334 (m-30) REVERT: E 1957 PRO cc_start: 0.9256 (Cg_endo) cc_final: 0.8975 (Cg_exo) REVERT: E 2352 LEU cc_start: 0.8582 (mp) cc_final: 0.8122 (tt) outliers start: 283 outliers final: 174 residues processed: 1235 average time/residue: 0.7647 time to fit residues: 1676.5262 Evaluate side-chains 1143 residues out of total 9715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 964 time to evaluate : 8.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 692 LYS Chi-restraints excluded: chain A residue 866 ASP Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1047 ASP Chi-restraints excluded: chain A residue 1063 VAL Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain A residue 1185 THR Chi-restraints excluded: chain A residue 1209 LEU Chi-restraints excluded: chain A residue 1279 ASN Chi-restraints excluded: chain A residue 1284 LEU Chi-restraints excluded: chain A residue 1303 ILE Chi-restraints excluded: chain A residue 1535 VAL Chi-restraints excluded: chain A residue 1717 LEU Chi-restraints excluded: chain A residue 1752 MET Chi-restraints excluded: chain A residue 1789 LEU Chi-restraints excluded: chain A residue 1803 VAL Chi-restraints excluded: chain A residue 1842 ASP Chi-restraints excluded: chain A residue 1956 ASP Chi-restraints excluded: chain A residue 1962 SER Chi-restraints excluded: chain A residue 2061 VAL Chi-restraints excluded: chain A residue 2093 ILE Chi-restraints excluded: chain A residue 2095 VAL Chi-restraints excluded: chain A residue 2389 PHE Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 571 GLN Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain B residue 845 GLN Chi-restraints excluded: chain B residue 866 ASP Chi-restraints excluded: chain B residue 1047 ASP Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1063 VAL Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1185 THR Chi-restraints excluded: chain B residue 1209 LEU Chi-restraints excluded: chain B residue 1279 ASN Chi-restraints excluded: chain B residue 1297 ASN Chi-restraints excluded: chain B residue 1304 LEU Chi-restraints excluded: chain B residue 1476 ASP Chi-restraints excluded: chain B residue 1503 ILE Chi-restraints excluded: chain B residue 1535 VAL Chi-restraints excluded: chain B residue 1550 THR Chi-restraints excluded: chain B residue 1560 TRP Chi-restraints excluded: chain B residue 1653 LYS Chi-restraints excluded: chain B residue 1654 LEU Chi-restraints excluded: chain B residue 1658 LEU Chi-restraints excluded: chain B residue 1717 LEU Chi-restraints excluded: chain B residue 1732 MET Chi-restraints excluded: chain B residue 1749 THR Chi-restraints excluded: chain B residue 1768 ARG Chi-restraints excluded: chain B residue 1803 VAL Chi-restraints excluded: chain B residue 1824 LEU Chi-restraints excluded: chain B residue 1842 ASP Chi-restraints excluded: chain B residue 1860 ASP Chi-restraints excluded: chain B residue 1921 LEU Chi-restraints excluded: chain B residue 1962 SER Chi-restraints excluded: chain B residue 1989 ASP Chi-restraints excluded: chain B residue 2089 LEU Chi-restraints excluded: chain B residue 2095 VAL Chi-restraints excluded: chain B residue 2168 ILE Chi-restraints excluded: chain B residue 2433 ASP Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 346 ILE Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 481 TYR Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain C residue 928 ARG Chi-restraints excluded: chain C residue 986 ASP Chi-restraints excluded: chain C residue 1047 ASP Chi-restraints excluded: chain C residue 1048 THR Chi-restraints excluded: chain C residue 1063 VAL Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain C residue 1185 THR Chi-restraints excluded: chain C residue 1279 ASN Chi-restraints excluded: chain C residue 1303 ILE Chi-restraints excluded: chain C residue 1304 LEU Chi-restraints excluded: chain C residue 1476 ASP Chi-restraints excluded: chain C residue 1535 VAL Chi-restraints excluded: chain C residue 1551 THR Chi-restraints excluded: chain C residue 1560 TRP Chi-restraints excluded: chain C residue 1594 LEU Chi-restraints excluded: chain C residue 1653 LYS Chi-restraints excluded: chain C residue 1654 LEU Chi-restraints excluded: chain C residue 1717 LEU Chi-restraints excluded: chain C residue 1752 MET Chi-restraints excluded: chain C residue 1798 ASP Chi-restraints excluded: chain C residue 1803 VAL Chi-restraints excluded: chain C residue 1825 LEU Chi-restraints excluded: chain C residue 1860 ASP Chi-restraints excluded: chain C residue 1962 SER Chi-restraints excluded: chain C residue 2027 GLU Chi-restraints excluded: chain C residue 2095 VAL Chi-restraints excluded: chain C residue 2168 ILE Chi-restraints excluded: chain C residue 2170 GLN Chi-restraints excluded: chain D residue 68 MET Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 294 GLN Chi-restraints excluded: chain D residue 571 GLN Chi-restraints excluded: chain D residue 573 LEU Chi-restraints excluded: chain D residue 764 LEU Chi-restraints excluded: chain D residue 986 ASP Chi-restraints excluded: chain D residue 1024 LEU Chi-restraints excluded: chain D residue 1047 ASP Chi-restraints excluded: chain D residue 1057 LEU Chi-restraints excluded: chain D residue 1075 THR Chi-restraints excluded: chain D residue 1118 ASP Chi-restraints excluded: chain D residue 1126 VAL Chi-restraints excluded: chain D residue 1185 THR Chi-restraints excluded: chain D residue 1209 LEU Chi-restraints excluded: chain D residue 1259 VAL Chi-restraints excluded: chain D residue 1279 ASN Chi-restraints excluded: chain D residue 1292 THR Chi-restraints excluded: chain D residue 1503 ILE Chi-restraints excluded: chain D residue 1535 VAL Chi-restraints excluded: chain D residue 1551 THR Chi-restraints excluded: chain D residue 1587 LEU Chi-restraints excluded: chain D residue 1594 LEU Chi-restraints excluded: chain D residue 1798 ASP Chi-restraints excluded: chain D residue 1803 VAL Chi-restraints excluded: chain D residue 1824 LEU Chi-restraints excluded: chain D residue 1860 ASP Chi-restraints excluded: chain D residue 1956 ASP Chi-restraints excluded: chain D residue 1962 SER Chi-restraints excluded: chain D residue 2027 GLU Chi-restraints excluded: chain D residue 2093 ILE Chi-restraints excluded: chain D residue 2095 VAL Chi-restraints excluded: chain D residue 2168 ILE Chi-restraints excluded: chain D residue 2190 GLU Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 241 SER Chi-restraints excluded: chain E residue 280 ASP Chi-restraints excluded: chain E residue 454 LEU Chi-restraints excluded: chain E residue 459 VAL Chi-restraints excluded: chain E residue 549 ASP Chi-restraints excluded: chain E residue 571 GLN Chi-restraints excluded: chain E residue 681 LEU Chi-restraints excluded: chain E residue 686 ILE Chi-restraints excluded: chain E residue 709 ASP Chi-restraints excluded: chain E residue 845 GLN Chi-restraints excluded: chain E residue 942 ILE Chi-restraints excluded: chain E residue 986 ASP Chi-restraints excluded: chain E residue 1012 LEU Chi-restraints excluded: chain E residue 1049 LEU Chi-restraints excluded: chain E residue 1057 LEU Chi-restraints excluded: chain E residue 1075 THR Chi-restraints excluded: chain E residue 1126 VAL Chi-restraints excluded: chain E residue 1185 THR Chi-restraints excluded: chain E residue 1279 ASN Chi-restraints excluded: chain E residue 1303 ILE Chi-restraints excluded: chain E residue 1304 LEU Chi-restraints excluded: chain E residue 1468 LYS Chi-restraints excluded: chain E residue 1476 ASP Chi-restraints excluded: chain E residue 1535 VAL Chi-restraints excluded: chain E residue 1551 THR Chi-restraints excluded: chain E residue 1576 ILE Chi-restraints excluded: chain E residue 1586 ILE Chi-restraints excluded: chain E residue 1653 LYS Chi-restraints excluded: chain E residue 1658 LEU Chi-restraints excluded: chain E residue 1717 LEU Chi-restraints excluded: chain E residue 2027 GLU Chi-restraints excluded: chain E residue 2070 GLU Chi-restraints excluded: chain E residue 2093 ILE Chi-restraints excluded: chain E residue 2168 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1140 random chunks: chunk 917 optimal weight: 0.9990 chunk 625 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 820 optimal weight: 5.9990 chunk 454 optimal weight: 10.0000 chunk 940 optimal weight: 6.9990 chunk 761 optimal weight: 0.9990 chunk 1 optimal weight: 10.0000 chunk 562 optimal weight: 0.8980 chunk 989 optimal weight: 3.9990 chunk 278 optimal weight: 7.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 351 GLN ** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 351 GLN ** B 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 ASN C 351 GLN C 522 HIS C 533 ASN C 827 GLN ** C 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1090 GLN ** C1311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 351 GLN D 522 HIS D 807 GLN ** D 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1028 GLN ** D1297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 222 ASN E 351 GLN ** E 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1028 GLN ** E1311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 90390 Z= 0.290 Angle : 0.637 11.592 122855 Z= 0.324 Chirality : 0.042 0.227 14085 Planarity : 0.004 0.078 15950 Dihedral : 5.098 32.150 12371 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 3.01 % Allowed : 14.49 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.08), residues: 11365 helix: 1.51 (0.08), residues: 5130 sheet: -1.40 (0.13), residues: 1505 loop : -1.36 (0.09), residues: 4730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B1560 HIS 0.006 0.001 HIS A1815 PHE 0.023 0.002 PHE A1180 TYR 0.026 0.001 TYR B 496 ARG 0.014 0.001 ARG B 554 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22730 Ramachandran restraints generated. 11365 Oldfield, 0 Emsley, 11365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22730 Ramachandran restraints generated. 11365 Oldfield, 0 Emsley, 11365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1290 residues out of total 9715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 284 poor density : 1006 time to evaluate : 7.911 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: A 1842 ASP cc_start: 0.7451 (OUTLIER) cc_final: 0.7029 (p0) REVERT: A 2148 GLU cc_start: 0.7023 (mm-30) cc_final: 0.6749 (mm-30) REVERT: A 2435 ASP cc_start: 0.6738 (t0) cc_final: 0.6330 (t0) REVERT: B 1658 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8641 (tm) REVERT: B 2435 ASP cc_start: 0.6727 (t0) cc_final: 0.6449 (t0) REVERT: C 483 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8186 (tt) REVERT: C 674 MET cc_start: 0.8640 (tpt) cc_final: 0.8351 (tpt) REVERT: C 1172 TYR cc_start: 0.8163 (m-80) cc_final: 0.7905 (m-80) REVERT: C 1560 TRP cc_start: 0.8125 (OUTLIER) cc_final: 0.6387 (p-90) REVERT: D 291 ASP cc_start: 0.7957 (p0) cc_final: 0.7714 (p0) REVERT: E 674 MET cc_start: 0.8521 (tpt) cc_final: 0.7976 (tpt) REVERT: E 1315 TYR cc_start: 0.5107 (m-80) cc_final: 0.4802 (m-80) REVERT: E 1489 ARG cc_start: 0.7383 (tpm170) cc_final: 0.7156 (tpm170) REVERT: E 1658 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8200 (tm) REVERT: E 1826 ASP cc_start: 0.6613 (m-30) cc_final: 0.6404 (m-30) REVERT: E 2352 LEU cc_start: 0.8666 (mp) cc_final: 0.8239 (tt) outliers start: 284 outliers final: 194 residues processed: 1205 average time/residue: 0.7586 time to fit residues: 1620.2159 Evaluate side-chains 1144 residues out of total 9715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 945 time to evaluate : 7.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 692 LYS Chi-restraints excluded: chain A residue 765 VAL Chi-restraints excluded: chain A residue 866 ASP Chi-restraints excluded: chain A residue 890 THR Chi-restraints excluded: chain A residue 986 ASP Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain A residue 1047 ASP Chi-restraints excluded: chain A residue 1063 VAL Chi-restraints excluded: chain A residue 1075 THR Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain A residue 1185 THR Chi-restraints excluded: chain A residue 1209 LEU Chi-restraints excluded: chain A residue 1279 ASN Chi-restraints excluded: chain A residue 1284 LEU Chi-restraints excluded: chain A residue 1303 ILE Chi-restraints excluded: chain A residue 1499 LEU Chi-restraints excluded: chain A residue 1535 VAL Chi-restraints excluded: chain A residue 1717 LEU Chi-restraints excluded: chain A residue 1752 MET Chi-restraints excluded: chain A residue 1789 LEU Chi-restraints excluded: chain A residue 1803 VAL Chi-restraints excluded: chain A residue 1842 ASP Chi-restraints excluded: chain A residue 1956 ASP Chi-restraints excluded: chain A residue 1962 SER Chi-restraints excluded: chain A residue 2061 VAL Chi-restraints excluded: chain A residue 2091 THR Chi-restraints excluded: chain A residue 2093 ILE Chi-restraints excluded: chain A residue 2095 VAL Chi-restraints excluded: chain A residue 2165 GLU Chi-restraints excluded: chain A residue 2185 THR Chi-restraints excluded: chain A residue 2389 PHE Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 481 TYR Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain B residue 571 GLN Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain B residue 692 LYS Chi-restraints excluded: chain B residue 845 GLN Chi-restraints excluded: chain B residue 874 ASP Chi-restraints excluded: chain B residue 890 THR Chi-restraints excluded: chain B residue 986 ASP Chi-restraints excluded: chain B residue 1047 ASP Chi-restraints excluded: chain B residue 1057 LEU Chi-restraints excluded: chain B residue 1063 VAL Chi-restraints excluded: chain B residue 1075 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1185 THR Chi-restraints excluded: chain B residue 1209 LEU Chi-restraints excluded: chain B residue 1279 ASN Chi-restraints excluded: chain B residue 1297 ASN Chi-restraints excluded: chain B residue 1503 ILE Chi-restraints excluded: chain B residue 1535 VAL Chi-restraints excluded: chain B residue 1550 THR Chi-restraints excluded: chain B residue 1560 TRP Chi-restraints excluded: chain B residue 1653 LYS Chi-restraints excluded: chain B residue 1654 LEU Chi-restraints excluded: chain B residue 1658 LEU Chi-restraints excluded: chain B residue 1717 LEU Chi-restraints excluded: chain B residue 1725 LEU Chi-restraints excluded: chain B residue 1749 THR Chi-restraints excluded: chain B residue 1803 VAL Chi-restraints excluded: chain B residue 1824 LEU Chi-restraints excluded: chain B residue 1842 ASP Chi-restraints excluded: chain B residue 1921 LEU Chi-restraints excluded: chain B residue 1962 SER Chi-restraints excluded: chain B residue 2061 VAL Chi-restraints excluded: chain B residue 2089 LEU Chi-restraints excluded: chain B residue 2095 VAL Chi-restraints excluded: chain B residue 2132 LEU Chi-restraints excluded: chain B residue 2168 ILE Chi-restraints excluded: chain B residue 2190 GLU Chi-restraints excluded: chain B residue 2433 ASP Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 346 ILE Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain C residue 866 ASP Chi-restraints excluded: chain C residue 986 ASP Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain C residue 1037 GLU Chi-restraints excluded: chain C residue 1047 ASP Chi-restraints excluded: chain C residue 1048 THR Chi-restraints excluded: chain C residue 1063 VAL Chi-restraints excluded: chain C residue 1075 THR Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain C residue 1185 THR Chi-restraints excluded: chain C residue 1259 VAL Chi-restraints excluded: chain C residue 1279 ASN Chi-restraints excluded: chain C residue 1303 ILE Chi-restraints excluded: chain C residue 1304 LEU Chi-restraints excluded: chain C residue 1476 ASP Chi-restraints excluded: chain C residue 1535 VAL Chi-restraints excluded: chain C residue 1551 THR Chi-restraints excluded: chain C residue 1560 TRP Chi-restraints excluded: chain C residue 1594 LEU Chi-restraints excluded: chain C residue 1653 LYS Chi-restraints excluded: chain C residue 1654 LEU Chi-restraints excluded: chain C residue 1717 LEU Chi-restraints excluded: chain C residue 1725 LEU Chi-restraints excluded: chain C residue 1798 ASP Chi-restraints excluded: chain C residue 1803 VAL Chi-restraints excluded: chain C residue 1825 LEU Chi-restraints excluded: chain C residue 1860 ASP Chi-restraints excluded: chain C residue 1962 SER Chi-restraints excluded: chain C residue 2027 GLU Chi-restraints excluded: chain C residue 2046 GLU Chi-restraints excluded: chain C residue 2061 VAL Chi-restraints excluded: chain C residue 2075 GLU Chi-restraints excluded: chain C residue 2093 ILE Chi-restraints excluded: chain C residue 2095 VAL Chi-restraints excluded: chain C residue 2138 LYS Chi-restraints excluded: chain D residue 68 MET Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 322 ILE Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 571 GLN Chi-restraints excluded: chain D residue 573 LEU Chi-restraints excluded: chain D residue 618 ILE Chi-restraints excluded: chain D residue 764 LEU Chi-restraints excluded: chain D residue 875 ILE Chi-restraints excluded: chain D residue 890 THR Chi-restraints excluded: chain D residue 986 ASP Chi-restraints excluded: chain D residue 1024 LEU Chi-restraints excluded: chain D residue 1047 ASP Chi-restraints excluded: chain D residue 1075 THR Chi-restraints excluded: chain D residue 1118 ASP Chi-restraints excluded: chain D residue 1126 VAL Chi-restraints excluded: chain D residue 1185 THR Chi-restraints excluded: chain D residue 1209 LEU Chi-restraints excluded: chain D residue 1259 VAL Chi-restraints excluded: chain D residue 1279 ASN Chi-restraints excluded: chain D residue 1292 THR Chi-restraints excluded: chain D residue 1503 ILE Chi-restraints excluded: chain D residue 1535 VAL Chi-restraints excluded: chain D residue 1594 LEU Chi-restraints excluded: chain D residue 1653 LYS Chi-restraints excluded: chain D residue 1798 ASP Chi-restraints excluded: chain D residue 1803 VAL Chi-restraints excluded: chain D residue 1824 LEU Chi-restraints excluded: chain D residue 1860 ASP Chi-restraints excluded: chain D residue 1962 SER Chi-restraints excluded: chain D residue 2093 ILE Chi-restraints excluded: chain D residue 2095 VAL Chi-restraints excluded: chain D residue 2190 GLU Chi-restraints excluded: chain D residue 2389 PHE Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 241 SER Chi-restraints excluded: chain E residue 280 ASP Chi-restraints excluded: chain E residue 454 LEU Chi-restraints excluded: chain E residue 459 VAL Chi-restraints excluded: chain E residue 462 MET Chi-restraints excluded: chain E residue 549 ASP Chi-restraints excluded: chain E residue 571 GLN Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain E residue 637 MET Chi-restraints excluded: chain E residue 681 LEU Chi-restraints excluded: chain E residue 686 ILE Chi-restraints excluded: chain E residue 709 ASP Chi-restraints excluded: chain E residue 845 GLN Chi-restraints excluded: chain E residue 942 ILE Chi-restraints excluded: chain E residue 986 ASP Chi-restraints excluded: chain E residue 1012 LEU Chi-restraints excluded: chain E residue 1075 THR Chi-restraints excluded: chain E residue 1118 ASP Chi-restraints excluded: chain E residue 1126 VAL Chi-restraints excluded: chain E residue 1185 THR Chi-restraints excluded: chain E residue 1209 LEU Chi-restraints excluded: chain E residue 1279 ASN Chi-restraints excluded: chain E residue 1450 VAL Chi-restraints excluded: chain E residue 1476 ASP Chi-restraints excluded: chain E residue 1535 VAL Chi-restraints excluded: chain E residue 1551 THR Chi-restraints excluded: chain E residue 1576 ILE Chi-restraints excluded: chain E residue 1653 LYS Chi-restraints excluded: chain E residue 1658 LEU Chi-restraints excluded: chain E residue 1717 LEU Chi-restraints excluded: chain E residue 1803 VAL Chi-restraints excluded: chain E residue 1962 SER Chi-restraints excluded: chain E residue 2027 GLU Chi-restraints excluded: chain E residue 2070 GLU Chi-restraints excluded: chain E residue 2093 ILE Chi-restraints excluded: chain E residue 2095 VAL Chi-restraints excluded: chain E residue 2168 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1140 random chunks: chunk 370 optimal weight: 3.9990 chunk 992 optimal weight: 8.9990 chunk 217 optimal weight: 10.0000 chunk 646 optimal weight: 0.6980 chunk 272 optimal weight: 3.9990 chunk 1102 optimal weight: 0.5980 chunk 915 optimal weight: 3.9990 chunk 510 optimal weight: 7.9990 chunk 91 optimal weight: 9.9990 chunk 364 optimal weight: 7.9990 chunk 579 optimal weight: 9.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN A 184 ASN ** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1203 GLN ** A1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1944 GLN B 184 ASN B 222 ASN ** B 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1028 GLN B1073 HIS ** B1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 222 ASN C 246 ASN C 533 ASN ** C 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 ASN ** D 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1888 HIS ** D2284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 222 ASN ** E 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 90390 Z= 0.316 Angle : 0.649 11.353 122855 Z= 0.330 Chirality : 0.042 0.234 14085 Planarity : 0.004 0.049 15950 Dihedral : 5.089 34.580 12371 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 3.16 % Allowed : 15.10 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.08), residues: 11365 helix: 1.60 (0.07), residues: 5140 sheet: -1.35 (0.13), residues: 1505 loop : -1.31 (0.09), residues: 4720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B1560 HIS 0.010 0.001 HIS B1888 PHE 0.023 0.002 PHE E1180 TYR 0.026 0.002 TYR A1836 ARG 0.015 0.001 ARG C1519 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22730 Ramachandran restraints generated. 11365 Oldfield, 0 Emsley, 11365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22730 Ramachandran restraints generated. 11365 Oldfield, 0 Emsley, 11365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1275 residues out of total 9715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 298 poor density : 977 time to evaluate : 7.963 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: A 77 LYS cc_start: 0.7419 (ptmt) cc_final: 0.7173 (ttmt) REVERT: A 1145 LEU cc_start: 0.8220 (tt) cc_final: 0.7999 (tp) REVERT: A 1210 ILE cc_start: 0.9163 (OUTLIER) cc_final: 0.8952 (mt) REVERT: A 1560 TRP cc_start: 0.8155 (OUTLIER) cc_final: 0.7545 (p-90) REVERT: A 1842 ASP cc_start: 0.7345 (OUTLIER) cc_final: 0.6909 (p0) REVERT: A 2435 ASP cc_start: 0.6864 (t0) cc_final: 0.6448 (t0) REVERT: B 454 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.9077 (mm) REVERT: B 1489 ARG cc_start: 0.7189 (tpm170) cc_final: 0.6959 (tpp-160) REVERT: B 1658 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8648 (tm) REVERT: B 2435 ASP cc_start: 0.6532 (t0) cc_final: 0.6308 (t0) REVERT: C 483 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8227 (tt) REVERT: C 624 MET cc_start: 0.6755 (tmm) cc_final: 0.6117 (tmm) REVERT: C 1172 TYR cc_start: 0.8177 (m-80) cc_final: 0.7827 (m-80) REVERT: C 2435 ASP cc_start: 0.6572 (t0) cc_final: 0.6226 (t0) REVERT: D 291 ASP cc_start: 0.7981 (p0) cc_final: 0.7736 (p0) REVERT: D 2435 ASP cc_start: 0.6559 (t0) cc_final: 0.6303 (t0) REVERT: E 291 ASP cc_start: 0.7301 (p0) cc_final: 0.6839 (p0) REVERT: E 674 MET cc_start: 0.8524 (tpt) cc_final: 0.8198 (tpt) REVERT: E 1002 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7741 (mtm-85) REVERT: E 1315 TYR cc_start: 0.4590 (m-80) cc_final: 0.4334 (m-80) REVERT: E 1489 ARG cc_start: 0.7376 (tpm170) cc_final: 0.7142 (tpm170) REVERT: E 1658 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8377 (tm) REVERT: E 1822 MET cc_start: 0.7231 (mtp) cc_final: 0.6857 (mmm) REVERT: E 2352 LEU cc_start: 0.8677 (mp) cc_final: 0.8293 (tt) outliers start: 298 outliers final: 212 residues processed: 1198 average time/residue: 0.8483 time to fit residues: 1818.2742 Evaluate side-chains 1143 residues out of total 9715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 923 time to evaluate : 7.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 ASP Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 549 ASP Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 692 LYS Chi-restraints excluded: chain A residue 765 VAL Chi-restraints excluded: chain A residue 866 ASP Chi-restraints excluded: chain A residue 890 THR Chi-restraints excluded: chain A residue 986 ASP Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain A residue 1047 ASP Chi-restraints excluded: chain A residue 1063 VAL Chi-restraints excluded: chain A residue 1075 THR Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain A residue 1185 THR Chi-restraints excluded: chain A residue 1209 LEU Chi-restraints excluded: chain A residue 1210 ILE Chi-restraints excluded: chain A residue 1279 ASN Chi-restraints excluded: chain A residue 1284 LEU Chi-restraints excluded: chain A residue 1303 ILE Chi-restraints excluded: chain A residue 1535 VAL Chi-restraints excluded: chain A residue 1560 TRP Chi-restraints excluded: chain A residue 1654 LEU Chi-restraints excluded: chain A residue 1717 LEU Chi-restraints excluded: chain A residue 1752 MET Chi-restraints excluded: chain A residue 1789 LEU Chi-restraints excluded: chain A residue 1803 VAL Chi-restraints excluded: chain A residue 1842 ASP Chi-restraints excluded: chain A residue 1956 ASP Chi-restraints excluded: chain A residue 1962 SER Chi-restraints excluded: chain A residue 2061 VAL Chi-restraints excluded: chain A residue 2091 THR Chi-restraints excluded: chain A residue 2093 ILE Chi-restraints excluded: chain A residue 2095 VAL Chi-restraints excluded: chain A residue 2165 GLU Chi-restraints excluded: chain A residue 2185 THR Chi-restraints excluded: chain A residue 2389 PHE Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 481 TYR Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain B residue 571 GLN Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain B residue 692 LYS Chi-restraints excluded: chain B residue 845 GLN Chi-restraints excluded: chain B residue 986 ASP Chi-restraints excluded: chain B residue 1047 ASP Chi-restraints excluded: chain B residue 1063 VAL Chi-restraints excluded: chain B residue 1075 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1185 THR Chi-restraints excluded: chain B residue 1209 LEU Chi-restraints excluded: chain B residue 1279 ASN Chi-restraints excluded: chain B residue 1297 ASN Chi-restraints excluded: chain B residue 1503 ILE Chi-restraints excluded: chain B residue 1535 VAL Chi-restraints excluded: chain B residue 1550 THR Chi-restraints excluded: chain B residue 1560 TRP Chi-restraints excluded: chain B residue 1653 LYS Chi-restraints excluded: chain B residue 1654 LEU Chi-restraints excluded: chain B residue 1658 LEU Chi-restraints excluded: chain B residue 1717 LEU Chi-restraints excluded: chain B residue 1749 THR Chi-restraints excluded: chain B residue 1768 ARG Chi-restraints excluded: chain B residue 1803 VAL Chi-restraints excluded: chain B residue 1824 LEU Chi-restraints excluded: chain B residue 1842 ASP Chi-restraints excluded: chain B residue 1921 LEU Chi-restraints excluded: chain B residue 1962 SER Chi-restraints excluded: chain B residue 2061 VAL Chi-restraints excluded: chain B residue 2073 SER Chi-restraints excluded: chain B residue 2089 LEU Chi-restraints excluded: chain B residue 2095 VAL Chi-restraints excluded: chain B residue 2132 LEU Chi-restraints excluded: chain B residue 2138 LYS Chi-restraints excluded: chain B residue 2168 ILE Chi-restraints excluded: chain B residue 2190 GLU Chi-restraints excluded: chain B residue 2433 ASP Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 346 ILE Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 549 ASP Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain C residue 866 ASP Chi-restraints excluded: chain C residue 986 ASP Chi-restraints excluded: chain C residue 1037 GLU Chi-restraints excluded: chain C residue 1047 ASP Chi-restraints excluded: chain C residue 1048 THR Chi-restraints excluded: chain C residue 1063 VAL Chi-restraints excluded: chain C residue 1075 THR Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain C residue 1185 THR Chi-restraints excluded: chain C residue 1197 LEU Chi-restraints excluded: chain C residue 1259 VAL Chi-restraints excluded: chain C residue 1279 ASN Chi-restraints excluded: chain C residue 1303 ILE Chi-restraints excluded: chain C residue 1304 LEU Chi-restraints excluded: chain C residue 1476 ASP Chi-restraints excluded: chain C residue 1535 VAL Chi-restraints excluded: chain C residue 1551 THR Chi-restraints excluded: chain C residue 1560 TRP Chi-restraints excluded: chain C residue 1594 LEU Chi-restraints excluded: chain C residue 1653 LYS Chi-restraints excluded: chain C residue 1654 LEU Chi-restraints excluded: chain C residue 1717 LEU Chi-restraints excluded: chain C residue 1798 ASP Chi-restraints excluded: chain C residue 1803 VAL Chi-restraints excluded: chain C residue 1825 LEU Chi-restraints excluded: chain C residue 1860 ASP Chi-restraints excluded: chain C residue 1962 SER Chi-restraints excluded: chain C residue 2027 GLU Chi-restraints excluded: chain C residue 2061 VAL Chi-restraints excluded: chain C residue 2075 GLU Chi-restraints excluded: chain C residue 2086 SER Chi-restraints excluded: chain C residue 2093 ILE Chi-restraints excluded: chain C residue 2095 VAL Chi-restraints excluded: chain C residue 2138 LYS Chi-restraints excluded: chain C residue 2168 ILE Chi-restraints excluded: chain C residue 2389 PHE Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 322 ILE Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 571 GLN Chi-restraints excluded: chain D residue 573 LEU Chi-restraints excluded: chain D residue 618 ILE Chi-restraints excluded: chain D residue 764 LEU Chi-restraints excluded: chain D residue 1024 LEU Chi-restraints excluded: chain D residue 1037 GLU Chi-restraints excluded: chain D residue 1047 ASP Chi-restraints excluded: chain D residue 1057 LEU Chi-restraints excluded: chain D residue 1075 THR Chi-restraints excluded: chain D residue 1118 ASP Chi-restraints excluded: chain D residue 1126 VAL Chi-restraints excluded: chain D residue 1185 THR Chi-restraints excluded: chain D residue 1209 LEU Chi-restraints excluded: chain D residue 1259 VAL Chi-restraints excluded: chain D residue 1279 ASN Chi-restraints excluded: chain D residue 1292 THR Chi-restraints excluded: chain D residue 1503 ILE Chi-restraints excluded: chain D residue 1535 VAL Chi-restraints excluded: chain D residue 1594 LEU Chi-restraints excluded: chain D residue 1653 LYS Chi-restraints excluded: chain D residue 1798 ASP Chi-restraints excluded: chain D residue 1803 VAL Chi-restraints excluded: chain D residue 1824 LEU Chi-restraints excluded: chain D residue 1860 ASP Chi-restraints excluded: chain D residue 1962 SER Chi-restraints excluded: chain D residue 2093 ILE Chi-restraints excluded: chain D residue 2095 VAL Chi-restraints excluded: chain D residue 2168 ILE Chi-restraints excluded: chain D residue 2190 GLU Chi-restraints excluded: chain D residue 2389 PHE Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 241 SER Chi-restraints excluded: chain E residue 414 ILE Chi-restraints excluded: chain E residue 454 LEU Chi-restraints excluded: chain E residue 459 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 549 ASP Chi-restraints excluded: chain E residue 571 GLN Chi-restraints excluded: chain E residue 615 LEU Chi-restraints excluded: chain E residue 637 MET Chi-restraints excluded: chain E residue 681 LEU Chi-restraints excluded: chain E residue 686 ILE Chi-restraints excluded: chain E residue 709 ASP Chi-restraints excluded: chain E residue 764 LEU Chi-restraints excluded: chain E residue 845 GLN Chi-restraints excluded: chain E residue 877 THR Chi-restraints excluded: chain E residue 942 ILE Chi-restraints excluded: chain E residue 986 ASP Chi-restraints excluded: chain E residue 1002 ARG Chi-restraints excluded: chain E residue 1047 ASP Chi-restraints excluded: chain E residue 1075 THR Chi-restraints excluded: chain E residue 1118 ASP Chi-restraints excluded: chain E residue 1126 VAL Chi-restraints excluded: chain E residue 1185 THR Chi-restraints excluded: chain E residue 1209 LEU Chi-restraints excluded: chain E residue 1279 ASN Chi-restraints excluded: chain E residue 1450 VAL Chi-restraints excluded: chain E residue 1476 ASP Chi-restraints excluded: chain E residue 1520 PHE Chi-restraints excluded: chain E residue 1535 VAL Chi-restraints excluded: chain E residue 1551 THR Chi-restraints excluded: chain E residue 1576 ILE Chi-restraints excluded: chain E residue 1653 LYS Chi-restraints excluded: chain E residue 1658 LEU Chi-restraints excluded: chain E residue 1717 LEU Chi-restraints excluded: chain E residue 1803 VAL Chi-restraints excluded: chain E residue 1962 SER Chi-restraints excluded: chain E residue 2027 GLU Chi-restraints excluded: chain E residue 2070 GLU Chi-restraints excluded: chain E residue 2093 ILE Chi-restraints excluded: chain E residue 2095 VAL Chi-restraints excluded: chain E residue 2132 LEU Chi-restraints excluded: chain E residue 2168 ILE Chi-restraints excluded: chain E residue 2233 LEU Chi-restraints excluded: chain E residue 2389 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1140 random chunks: chunk 1063 optimal weight: 10.0000 chunk 124 optimal weight: 7.9990 chunk 628 optimal weight: 0.2980 chunk 805 optimal weight: 4.9990 chunk 624 optimal weight: 0.5980 chunk 928 optimal weight: 4.9990 chunk 615 optimal weight: 1.9990 chunk 1098 optimal weight: 4.9990 chunk 687 optimal weight: 3.9990 chunk 669 optimal weight: 2.9990 chunk 507 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 ASN ** A 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1888 HIS B 246 ASN B 267 ASN ** B 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1103 HIS ** B1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2146 GLN C 222 ASN ** C1311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1581 ASN D 222 ASN D 246 ASN D 267 ASN ** D 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1249 HIS ** D1297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 177 GLN E 222 ASN ** E 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1051 ASN ** E1311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.4190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 90390 Z= 0.202 Angle : 0.611 12.696 122855 Z= 0.308 Chirality : 0.041 0.219 14085 Planarity : 0.004 0.066 15950 Dihedral : 4.934 36.180 12371 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 2.67 % Allowed : 15.99 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.08), residues: 11365 helix: 1.69 (0.07), residues: 5190 sheet: -1.20 (0.13), residues: 1505 loop : -1.26 (0.09), residues: 4670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B1560 HIS 0.008 0.001 HIS B1888 PHE 0.020 0.001 PHE D1520 TYR 0.029 0.001 TYR B1172 ARG 0.008 0.000 ARG C2181 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22730 Ramachandran restraints generated. 11365 Oldfield, 0 Emsley, 11365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22730 Ramachandran restraints generated. 11365 Oldfield, 0 Emsley, 11365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1280 residues out of total 9715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 252 poor density : 1028 time to evaluate : 7.926 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: A 77 LYS cc_start: 0.7406 (ptmt) cc_final: 0.7177 (ttmt) REVERT: A 291 ASP cc_start: 0.7717 (p0) cc_final: 0.7507 (p0) REVERT: A 1210 ILE cc_start: 0.9151 (OUTLIER) cc_final: 0.8911 (mt) REVERT: A 1315 TYR cc_start: 0.4926 (m-80) cc_final: 0.4701 (m-80) REVERT: A 1560 TRP cc_start: 0.8154 (OUTLIER) cc_final: 0.7642 (p-90) REVERT: A 1842 ASP cc_start: 0.7258 (OUTLIER) cc_final: 0.6836 (p0) REVERT: A 2435 ASP cc_start: 0.6754 (t0) cc_final: 0.6371 (t0) REVERT: B 454 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9090 (mm) REVERT: B 1489 ARG cc_start: 0.7053 (tpm170) cc_final: 0.6824 (tpp-160) REVERT: B 1658 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8611 (tm) REVERT: B 2435 ASP cc_start: 0.6654 (t0) cc_final: 0.6413 (t0) REVERT: C 624 MET cc_start: 0.6785 (tmm) cc_final: 0.6199 (tmm) REVERT: C 1172 TYR cc_start: 0.8088 (m-80) cc_final: 0.7835 (m-80) REVERT: C 2435 ASP cc_start: 0.6474 (t0) cc_final: 0.6079 (t0) REVERT: D 291 ASP cc_start: 0.7894 (p0) cc_final: 0.7671 (p0) REVERT: D 292 ASP cc_start: 0.7607 (m-30) cc_final: 0.7338 (m-30) REVERT: D 2435 ASP cc_start: 0.6652 (t0) cc_final: 0.6365 (t0) REVERT: E 674 MET cc_start: 0.8518 (tpt) cc_final: 0.8044 (tpt) REVERT: E 1002 ARG cc_start: 0.8064 (OUTLIER) cc_final: 0.7718 (mtm-85) REVERT: E 1315 TYR cc_start: 0.4877 (m-80) cc_final: 0.4577 (m-80) REVERT: E 1658 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8312 (tm) REVERT: E 2352 LEU cc_start: 0.8624 (mp) cc_final: 0.8281 (tt) outliers start: 252 outliers final: 190 residues processed: 1211 average time/residue: 0.8024 time to fit residues: 1736.4713 Evaluate side-chains 1151 residues out of total 9715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 954 time to evaluate : 8.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 692 LYS Chi-restraints excluded: chain A residue 765 VAL Chi-restraints excluded: chain A residue 986 ASP Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain A residue 1047 ASP Chi-restraints excluded: chain A residue 1075 THR Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain A residue 1185 THR Chi-restraints excluded: chain A residue 1209 LEU Chi-restraints excluded: chain A residue 1210 ILE Chi-restraints excluded: chain A residue 1279 ASN Chi-restraints excluded: chain A residue 1303 ILE Chi-restraints excluded: chain A residue 1499 LEU Chi-restraints excluded: chain A residue 1535 VAL Chi-restraints excluded: chain A residue 1560 TRP Chi-restraints excluded: chain A residue 1717 LEU Chi-restraints excluded: chain A residue 1752 MET Chi-restraints excluded: chain A residue 1789 LEU Chi-restraints excluded: chain A residue 1803 VAL Chi-restraints excluded: chain A residue 1842 ASP Chi-restraints excluded: chain A residue 2061 VAL Chi-restraints excluded: chain A residue 2093 ILE Chi-restraints excluded: chain A residue 2095 VAL Chi-restraints excluded: chain A residue 2165 GLU Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 571 GLN Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 692 LYS Chi-restraints excluded: chain B residue 845 GLN Chi-restraints excluded: chain B residue 890 THR Chi-restraints excluded: chain B residue 986 ASP Chi-restraints excluded: chain B residue 1047 ASP Chi-restraints excluded: chain B residue 1075 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1185 THR Chi-restraints excluded: chain B residue 1209 LEU Chi-restraints excluded: chain B residue 1279 ASN Chi-restraints excluded: chain B residue 1297 ASN Chi-restraints excluded: chain B residue 1476 ASP Chi-restraints excluded: chain B residue 1503 ILE Chi-restraints excluded: chain B residue 1535 VAL Chi-restraints excluded: chain B residue 1550 THR Chi-restraints excluded: chain B residue 1560 TRP Chi-restraints excluded: chain B residue 1653 LYS Chi-restraints excluded: chain B residue 1654 LEU Chi-restraints excluded: chain B residue 1658 LEU Chi-restraints excluded: chain B residue 1717 LEU Chi-restraints excluded: chain B residue 1732 MET Chi-restraints excluded: chain B residue 1768 ARG Chi-restraints excluded: chain B residue 1803 VAL Chi-restraints excluded: chain B residue 1824 LEU Chi-restraints excluded: chain B residue 1842 ASP Chi-restraints excluded: chain B residue 1921 LEU Chi-restraints excluded: chain B residue 1962 SER Chi-restraints excluded: chain B residue 2061 VAL Chi-restraints excluded: chain B residue 2089 LEU Chi-restraints excluded: chain B residue 2095 VAL Chi-restraints excluded: chain B residue 2132 LEU Chi-restraints excluded: chain B residue 2168 ILE Chi-restraints excluded: chain B residue 2421 ASP Chi-restraints excluded: chain B residue 2433 ASP Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 346 ILE Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain C residue 866 ASP Chi-restraints excluded: chain C residue 986 ASP Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain C residue 1037 GLU Chi-restraints excluded: chain C residue 1075 THR Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain C residue 1185 THR Chi-restraints excluded: chain C residue 1197 LEU Chi-restraints excluded: chain C residue 1259 VAL Chi-restraints excluded: chain C residue 1279 ASN Chi-restraints excluded: chain C residue 1303 ILE Chi-restraints excluded: chain C residue 1304 LEU Chi-restraints excluded: chain C residue 1476 ASP Chi-restraints excluded: chain C residue 1535 VAL Chi-restraints excluded: chain C residue 1551 THR Chi-restraints excluded: chain C residue 1560 TRP Chi-restraints excluded: chain C residue 1653 LYS Chi-restraints excluded: chain C residue 1717 LEU Chi-restraints excluded: chain C residue 1798 ASP Chi-restraints excluded: chain C residue 1803 VAL Chi-restraints excluded: chain C residue 1860 ASP Chi-restraints excluded: chain C residue 1962 SER Chi-restraints excluded: chain C residue 2027 GLU Chi-restraints excluded: chain C residue 2061 VAL Chi-restraints excluded: chain C residue 2093 ILE Chi-restraints excluded: chain C residue 2095 VAL Chi-restraints excluded: chain C residue 2168 ILE Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 322 ILE Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 571 GLN Chi-restraints excluded: chain D residue 573 LEU Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 618 ILE Chi-restraints excluded: chain D residue 1031 MET Chi-restraints excluded: chain D residue 1037 GLU Chi-restraints excluded: chain D residue 1047 ASP Chi-restraints excluded: chain D residue 1075 THR Chi-restraints excluded: chain D residue 1118 ASP Chi-restraints excluded: chain D residue 1126 VAL Chi-restraints excluded: chain D residue 1185 THR Chi-restraints excluded: chain D residue 1209 LEU Chi-restraints excluded: chain D residue 1259 VAL Chi-restraints excluded: chain D residue 1279 ASN Chi-restraints excluded: chain D residue 1292 THR Chi-restraints excluded: chain D residue 1503 ILE Chi-restraints excluded: chain D residue 1535 VAL Chi-restraints excluded: chain D residue 1551 THR Chi-restraints excluded: chain D residue 1587 LEU Chi-restraints excluded: chain D residue 1594 LEU Chi-restraints excluded: chain D residue 1653 LYS Chi-restraints excluded: chain D residue 1798 ASP Chi-restraints excluded: chain D residue 1803 VAL Chi-restraints excluded: chain D residue 1824 LEU Chi-restraints excluded: chain D residue 1860 ASP Chi-restraints excluded: chain D residue 1962 SER Chi-restraints excluded: chain D residue 2027 GLU Chi-restraints excluded: chain D residue 2093 ILE Chi-restraints excluded: chain D residue 2095 VAL Chi-restraints excluded: chain D residue 2165 GLU Chi-restraints excluded: chain D residue 2168 ILE Chi-restraints excluded: chain D residue 2190 GLU Chi-restraints excluded: chain D residue 2389 PHE Chi-restraints excluded: chain D residue 2420 ASN Chi-restraints excluded: chain E residue 241 SER Chi-restraints excluded: chain E residue 454 LEU Chi-restraints excluded: chain E residue 459 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 549 ASP Chi-restraints excluded: chain E residue 571 GLN Chi-restraints excluded: chain E residue 575 ILE Chi-restraints excluded: chain E residue 637 MET Chi-restraints excluded: chain E residue 681 LEU Chi-restraints excluded: chain E residue 686 ILE Chi-restraints excluded: chain E residue 692 LYS Chi-restraints excluded: chain E residue 709 ASP Chi-restraints excluded: chain E residue 764 LEU Chi-restraints excluded: chain E residue 845 GLN Chi-restraints excluded: chain E residue 986 ASP Chi-restraints excluded: chain E residue 1002 ARG Chi-restraints excluded: chain E residue 1037 GLU Chi-restraints excluded: chain E residue 1047 ASP Chi-restraints excluded: chain E residue 1075 THR Chi-restraints excluded: chain E residue 1118 ASP Chi-restraints excluded: chain E residue 1126 VAL Chi-restraints excluded: chain E residue 1185 THR Chi-restraints excluded: chain E residue 1209 LEU Chi-restraints excluded: chain E residue 1279 ASN Chi-restraints excluded: chain E residue 1450 VAL Chi-restraints excluded: chain E residue 1520 PHE Chi-restraints excluded: chain E residue 1535 VAL Chi-restraints excluded: chain E residue 1551 THR Chi-restraints excluded: chain E residue 1653 LYS Chi-restraints excluded: chain E residue 1658 LEU Chi-restraints excluded: chain E residue 1803 VAL Chi-restraints excluded: chain E residue 2027 GLU Chi-restraints excluded: chain E residue 2070 GLU Chi-restraints excluded: chain E residue 2084 LEU Chi-restraints excluded: chain E residue 2095 VAL Chi-restraints excluded: chain E residue 2132 LEU Chi-restraints excluded: chain E residue 2168 ILE Chi-restraints excluded: chain E residue 2233 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1140 random chunks: chunk 679 optimal weight: 1.9990 chunk 438 optimal weight: 0.7980 chunk 656 optimal weight: 1.9990 chunk 330 optimal weight: 0.9990 chunk 215 optimal weight: 5.9990 chunk 212 optimal weight: 20.0000 chunk 698 optimal weight: 0.3980 chunk 748 optimal weight: 0.9990 chunk 543 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 863 optimal weight: 5.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN ** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2146 GLN C 222 ASN C1249 HIS ** C1311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 ASN D 533 ASN D 910 GLN ** D 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1944 GLN ** D2284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 ASN ** E 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1249 HIS ** E1888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.4334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 90390 Z= 0.173 Angle : 0.607 11.920 122855 Z= 0.303 Chirality : 0.041 0.215 14085 Planarity : 0.004 0.043 15950 Dihedral : 4.809 36.391 12371 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.59 % Allowed : 16.44 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.08), residues: 11365 helix: 1.77 (0.07), residues: 5195 sheet: -1.07 (0.13), residues: 1505 loop : -1.22 (0.09), residues: 4665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP E1084 HIS 0.005 0.001 HIS E1888 PHE 0.022 0.001 PHE D1520 TYR 0.024 0.001 TYR B1172 ARG 0.009 0.000 ARG C2181 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22730 Ramachandran restraints generated. 11365 Oldfield, 0 Emsley, 11365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22730 Ramachandran restraints generated. 11365 Oldfield, 0 Emsley, 11365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1253 residues out of total 9715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 244 poor density : 1009 time to evaluate : 8.096 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: A 77 LYS cc_start: 0.7461 (ptmt) cc_final: 0.7207 (ttmt) REVERT: A 291 ASP cc_start: 0.7697 (p0) cc_final: 0.7479 (p0) REVERT: A 624 MET cc_start: 0.6952 (tmm) cc_final: 0.6454 (tmm) REVERT: A 1132 MET cc_start: 0.7807 (mtt) cc_final: 0.7478 (mtt) REVERT: A 1210 ILE cc_start: 0.9142 (OUTLIER) cc_final: 0.8885 (mt) REVERT: A 1315 TYR cc_start: 0.5002 (m-80) cc_final: 0.4797 (m-80) REVERT: A 1560 TRP cc_start: 0.8075 (OUTLIER) cc_final: 0.7718 (p-90) REVERT: A 1842 ASP cc_start: 0.7237 (OUTLIER) cc_final: 0.6831 (p0) REVERT: A 2435 ASP cc_start: 0.6742 (t0) cc_final: 0.6466 (t0) REVERT: B 454 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.9069 (mm) REVERT: B 2435 ASP cc_start: 0.6646 (t0) cc_final: 0.6409 (t0) REVERT: C 624 MET cc_start: 0.6770 (tmm) cc_final: 0.6168 (tmm) REVERT: C 1172 TYR cc_start: 0.8035 (m-80) cc_final: 0.7827 (m-80) REVERT: C 2435 ASP cc_start: 0.6454 (t0) cc_final: 0.6047 (t0) REVERT: D 291 ASP cc_start: 0.7784 (p0) cc_final: 0.7562 (p0) REVERT: D 624 MET cc_start: 0.7103 (tmm) cc_final: 0.6815 (tmm) REVERT: D 2435 ASP cc_start: 0.6611 (t0) cc_final: 0.6338 (t0) REVERT: E 291 ASP cc_start: 0.7271 (p0) cc_final: 0.6914 (p0) REVERT: E 674 MET cc_start: 0.8503 (tpt) cc_final: 0.8120 (tpt) REVERT: E 1002 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.7556 (mtm-85) REVERT: E 1315 TYR cc_start: 0.5059 (m-10) cc_final: 0.4800 (m-80) REVERT: E 1658 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8360 (tm) REVERT: E 2352 LEU cc_start: 0.8628 (mp) cc_final: 0.8274 (tt) outliers start: 244 outliers final: 190 residues processed: 1189 average time/residue: 0.7648 time to fit residues: 1603.9259 Evaluate side-chains 1151 residues out of total 9715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 955 time to evaluate : 7.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 618 ILE Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 692 LYS Chi-restraints excluded: chain A residue 986 ASP Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain A residue 1047 ASP Chi-restraints excluded: chain A residue 1075 THR Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain A residue 1185 THR Chi-restraints excluded: chain A residue 1210 ILE Chi-restraints excluded: chain A residue 1279 ASN Chi-restraints excluded: chain A residue 1303 ILE Chi-restraints excluded: chain A residue 1499 LEU Chi-restraints excluded: chain A residue 1535 VAL Chi-restraints excluded: chain A residue 1560 TRP Chi-restraints excluded: chain A residue 1717 LEU Chi-restraints excluded: chain A residue 1752 MET Chi-restraints excluded: chain A residue 1789 LEU Chi-restraints excluded: chain A residue 1803 VAL Chi-restraints excluded: chain A residue 1842 ASP Chi-restraints excluded: chain A residue 2061 VAL Chi-restraints excluded: chain A residue 2093 ILE Chi-restraints excluded: chain A residue 2095 VAL Chi-restraints excluded: chain A residue 2165 GLU Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 571 GLN Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain B residue 692 LYS Chi-restraints excluded: chain B residue 845 GLN Chi-restraints excluded: chain B residue 1047 ASP Chi-restraints excluded: chain B residue 1075 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1185 THR Chi-restraints excluded: chain B residue 1279 ASN Chi-restraints excluded: chain B residue 1297 ASN Chi-restraints excluded: chain B residue 1304 LEU Chi-restraints excluded: chain B residue 1476 ASP Chi-restraints excluded: chain B residue 1503 ILE Chi-restraints excluded: chain B residue 1535 VAL Chi-restraints excluded: chain B residue 1550 THR Chi-restraints excluded: chain B residue 1560 TRP Chi-restraints excluded: chain B residue 1717 LEU Chi-restraints excluded: chain B residue 1732 MET Chi-restraints excluded: chain B residue 1768 ARG Chi-restraints excluded: chain B residue 1803 VAL Chi-restraints excluded: chain B residue 1824 LEU Chi-restraints excluded: chain B residue 1921 LEU Chi-restraints excluded: chain B residue 1962 SER Chi-restraints excluded: chain B residue 2061 VAL Chi-restraints excluded: chain B residue 2089 LEU Chi-restraints excluded: chain B residue 2095 VAL Chi-restraints excluded: chain B residue 2132 LEU Chi-restraints excluded: chain B residue 2168 ILE Chi-restraints excluded: chain B residue 2190 GLU Chi-restraints excluded: chain B residue 2255 ARG Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 346 ILE Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain C residue 986 ASP Chi-restraints excluded: chain C residue 1031 MET Chi-restraints excluded: chain C residue 1037 GLU Chi-restraints excluded: chain C residue 1048 THR Chi-restraints excluded: chain C residue 1075 THR Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain C residue 1185 THR Chi-restraints excluded: chain C residue 1197 LEU Chi-restraints excluded: chain C residue 1259 VAL Chi-restraints excluded: chain C residue 1279 ASN Chi-restraints excluded: chain C residue 1304 LEU Chi-restraints excluded: chain C residue 1476 ASP Chi-restraints excluded: chain C residue 1535 VAL Chi-restraints excluded: chain C residue 1551 THR Chi-restraints excluded: chain C residue 1560 TRP Chi-restraints excluded: chain C residue 1650 THR Chi-restraints excluded: chain C residue 1653 LYS Chi-restraints excluded: chain C residue 1717 LEU Chi-restraints excluded: chain C residue 1798 ASP Chi-restraints excluded: chain C residue 1803 VAL Chi-restraints excluded: chain C residue 1825 LEU Chi-restraints excluded: chain C residue 1860 ASP Chi-restraints excluded: chain C residue 1962 SER Chi-restraints excluded: chain C residue 2027 GLU Chi-restraints excluded: chain C residue 2061 VAL Chi-restraints excluded: chain C residue 2086 SER Chi-restraints excluded: chain C residue 2093 ILE Chi-restraints excluded: chain C residue 2095 VAL Chi-restraints excluded: chain C residue 2168 ILE Chi-restraints excluded: chain C residue 2389 PHE Chi-restraints excluded: chain C residue 2420 ASN Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 322 ILE Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 571 GLN Chi-restraints excluded: chain D residue 573 LEU Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 618 ILE Chi-restraints excluded: chain D residue 890 THR Chi-restraints excluded: chain D residue 963 ASP Chi-restraints excluded: chain D residue 1037 GLU Chi-restraints excluded: chain D residue 1047 ASP Chi-restraints excluded: chain D residue 1075 THR Chi-restraints excluded: chain D residue 1118 ASP Chi-restraints excluded: chain D residue 1126 VAL Chi-restraints excluded: chain D residue 1185 THR Chi-restraints excluded: chain D residue 1209 LEU Chi-restraints excluded: chain D residue 1259 VAL Chi-restraints excluded: chain D residue 1279 ASN Chi-restraints excluded: chain D residue 1503 ILE Chi-restraints excluded: chain D residue 1535 VAL Chi-restraints excluded: chain D residue 1551 THR Chi-restraints excluded: chain D residue 1587 LEU Chi-restraints excluded: chain D residue 1594 LEU Chi-restraints excluded: chain D residue 1653 LYS Chi-restraints excluded: chain D residue 1717 LEU Chi-restraints excluded: chain D residue 1798 ASP Chi-restraints excluded: chain D residue 1803 VAL Chi-restraints excluded: chain D residue 1824 LEU Chi-restraints excluded: chain D residue 1860 ASP Chi-restraints excluded: chain D residue 1962 SER Chi-restraints excluded: chain D residue 2027 GLU Chi-restraints excluded: chain D residue 2093 ILE Chi-restraints excluded: chain D residue 2095 VAL Chi-restraints excluded: chain D residue 2165 GLU Chi-restraints excluded: chain D residue 2168 ILE Chi-restraints excluded: chain D residue 2389 PHE Chi-restraints excluded: chain D residue 2420 ASN Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 241 SER Chi-restraints excluded: chain E residue 412 THR Chi-restraints excluded: chain E residue 414 ILE Chi-restraints excluded: chain E residue 459 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 549 ASP Chi-restraints excluded: chain E residue 571 GLN Chi-restraints excluded: chain E residue 637 MET Chi-restraints excluded: chain E residue 681 LEU Chi-restraints excluded: chain E residue 686 ILE Chi-restraints excluded: chain E residue 692 LYS Chi-restraints excluded: chain E residue 709 ASP Chi-restraints excluded: chain E residue 830 ASN Chi-restraints excluded: chain E residue 845 GLN Chi-restraints excluded: chain E residue 986 ASP Chi-restraints excluded: chain E residue 1002 ARG Chi-restraints excluded: chain E residue 1037 GLU Chi-restraints excluded: chain E residue 1047 ASP Chi-restraints excluded: chain E residue 1075 THR Chi-restraints excluded: chain E residue 1118 ASP Chi-restraints excluded: chain E residue 1126 VAL Chi-restraints excluded: chain E residue 1185 THR Chi-restraints excluded: chain E residue 1279 ASN Chi-restraints excluded: chain E residue 1450 VAL Chi-restraints excluded: chain E residue 1476 ASP Chi-restraints excluded: chain E residue 1535 VAL Chi-restraints excluded: chain E residue 1551 THR Chi-restraints excluded: chain E residue 1653 LYS Chi-restraints excluded: chain E residue 1658 LEU Chi-restraints excluded: chain E residue 1803 VAL Chi-restraints excluded: chain E residue 1921 LEU Chi-restraints excluded: chain E residue 2027 GLU Chi-restraints excluded: chain E residue 2070 GLU Chi-restraints excluded: chain E residue 2084 LEU Chi-restraints excluded: chain E residue 2093 ILE Chi-restraints excluded: chain E residue 2095 VAL Chi-restraints excluded: chain E residue 2132 LEU Chi-restraints excluded: chain E residue 2147 SER Chi-restraints excluded: chain E residue 2168 ILE Chi-restraints excluded: chain E residue 2233 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1140 random chunks: chunk 999 optimal weight: 3.9990 chunk 1052 optimal weight: 10.0000 chunk 960 optimal weight: 1.9990 chunk 1023 optimal weight: 0.5980 chunk 616 optimal weight: 3.9990 chunk 446 optimal weight: 0.9980 chunk 804 optimal weight: 6.9990 chunk 314 optimal weight: 0.8980 chunk 925 optimal weight: 0.9980 chunk 968 optimal weight: 0.9990 chunk 1020 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN A 246 ASN A 323 ASN ** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN ** B 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 222 ASN D 222 ASN ** D 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 222 ASN E 267 ASN E 807 GLN ** E 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.4472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 90390 Z= 0.175 Angle : 0.609 11.514 122855 Z= 0.304 Chirality : 0.040 0.212 14085 Planarity : 0.004 0.045 15950 Dihedral : 4.701 36.397 12371 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.49 % Allowed : 16.72 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.08), residues: 11365 helix: 1.78 (0.07), residues: 5240 sheet: -0.89 (0.13), residues: 1580 loop : -1.24 (0.10), residues: 4545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E1084 HIS 0.005 0.001 HIS E1888 PHE 0.025 0.001 PHE D1520 TYR 0.022 0.001 TYR B1172 ARG 0.009 0.000 ARG B1489 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22730 Ramachandran restraints generated. 11365 Oldfield, 0 Emsley, 11365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22730 Ramachandran restraints generated. 11365 Oldfield, 0 Emsley, 11365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1237 residues out of total 9715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 235 poor density : 1002 time to evaluate : 8.738 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 77 LYS cc_start: 0.7346 (ptmt) cc_final: 0.7092 (ttmt) REVERT: A 291 ASP cc_start: 0.7701 (p0) cc_final: 0.7479 (p0) REVERT: A 624 MET cc_start: 0.7040 (tmm) cc_final: 0.6582 (tmm) REVERT: A 1132 MET cc_start: 0.7770 (mtt) cc_final: 0.7503 (mtt) REVERT: A 1210 ILE cc_start: 0.9127 (OUTLIER) cc_final: 0.8908 (mt) REVERT: A 1560 TRP cc_start: 0.8051 (OUTLIER) cc_final: 0.7682 (p-90) REVERT: A 1842 ASP cc_start: 0.7251 (p0) cc_final: 0.6880 (p0) REVERT: A 2435 ASP cc_start: 0.6981 (t0) cc_final: 0.6687 (t0) REVERT: B 214 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7572 (tp40) REVERT: B 454 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.9079 (mm) REVERT: B 2435 ASP cc_start: 0.6599 (t0) cc_final: 0.6346 (t0) REVERT: C 624 MET cc_start: 0.6727 (tmm) cc_final: 0.6103 (tmm) REVERT: C 1172 TYR cc_start: 0.8043 (m-80) cc_final: 0.7833 (m-80) REVERT: C 2435 ASP cc_start: 0.6540 (t0) cc_final: 0.6136 (t0) REVERT: D 27 MET cc_start: 0.8013 (mmt) cc_final: 0.7379 (tpp) REVERT: D 624 MET cc_start: 0.7031 (tmm) cc_final: 0.6750 (tmm) REVERT: E 674 MET cc_start: 0.8423 (tpt) cc_final: 0.8103 (tpt) REVERT: E 1315 TYR cc_start: 0.5001 (m-10) cc_final: 0.4722 (m-80) REVERT: E 1658 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8376 (tm) REVERT: E 2352 LEU cc_start: 0.8582 (mp) cc_final: 0.8251 (tt) outliers start: 235 outliers final: 189 residues processed: 1172 average time/residue: 0.7610 time to fit residues: 1589.8634 Evaluate side-chains 1140 residues out of total 9715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 946 time to evaluate : 7.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 549 ASP Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 692 LYS Chi-restraints excluded: chain A residue 986 ASP Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain A residue 1047 ASP Chi-restraints excluded: chain A residue 1075 THR Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain A residue 1185 THR Chi-restraints excluded: chain A residue 1209 LEU Chi-restraints excluded: chain A residue 1210 ILE Chi-restraints excluded: chain A residue 1279 ASN Chi-restraints excluded: chain A residue 1303 ILE Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain A residue 1499 LEU Chi-restraints excluded: chain A residue 1535 VAL Chi-restraints excluded: chain A residue 1560 TRP Chi-restraints excluded: chain A residue 1717 LEU Chi-restraints excluded: chain A residue 1752 MET Chi-restraints excluded: chain A residue 1789 LEU Chi-restraints excluded: chain A residue 1798 ASP Chi-restraints excluded: chain A residue 1803 VAL Chi-restraints excluded: chain A residue 2061 VAL Chi-restraints excluded: chain A residue 2093 ILE Chi-restraints excluded: chain A residue 2095 VAL Chi-restraints excluded: chain A residue 2165 GLU Chi-restraints excluded: chain A residue 2389 PHE Chi-restraints excluded: chain B residue 214 GLN Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain B residue 692 LYS Chi-restraints excluded: chain B residue 845 GLN Chi-restraints excluded: chain B residue 890 THR Chi-restraints excluded: chain B residue 1047 ASP Chi-restraints excluded: chain B residue 1075 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1185 THR Chi-restraints excluded: chain B residue 1279 ASN Chi-restraints excluded: chain B residue 1297 ASN Chi-restraints excluded: chain B residue 1503 ILE Chi-restraints excluded: chain B residue 1535 VAL Chi-restraints excluded: chain B residue 1550 THR Chi-restraints excluded: chain B residue 1560 TRP Chi-restraints excluded: chain B residue 1717 LEU Chi-restraints excluded: chain B residue 1732 MET Chi-restraints excluded: chain B residue 1803 VAL Chi-restraints excluded: chain B residue 1921 LEU Chi-restraints excluded: chain B residue 1962 SER Chi-restraints excluded: chain B residue 2061 VAL Chi-restraints excluded: chain B residue 2089 LEU Chi-restraints excluded: chain B residue 2095 VAL Chi-restraints excluded: chain B residue 2132 LEU Chi-restraints excluded: chain B residue 2168 ILE Chi-restraints excluded: chain B residue 2190 GLU Chi-restraints excluded: chain B residue 2420 ASN Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 346 ILE Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 618 ILE Chi-restraints excluded: chain C residue 676 VAL Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain C residue 1037 GLU Chi-restraints excluded: chain C residue 1047 ASP Chi-restraints excluded: chain C residue 1048 THR Chi-restraints excluded: chain C residue 1075 THR Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain C residue 1185 THR Chi-restraints excluded: chain C residue 1197 LEU Chi-restraints excluded: chain C residue 1259 VAL Chi-restraints excluded: chain C residue 1279 ASN Chi-restraints excluded: chain C residue 1304 LEU Chi-restraints excluded: chain C residue 1473 THR Chi-restraints excluded: chain C residue 1476 ASP Chi-restraints excluded: chain C residue 1492 LEU Chi-restraints excluded: chain C residue 1535 VAL Chi-restraints excluded: chain C residue 1551 THR Chi-restraints excluded: chain C residue 1560 TRP Chi-restraints excluded: chain C residue 1653 LYS Chi-restraints excluded: chain C residue 1717 LEU Chi-restraints excluded: chain C residue 1798 ASP Chi-restraints excluded: chain C residue 1803 VAL Chi-restraints excluded: chain C residue 1860 ASP Chi-restraints excluded: chain C residue 1962 SER Chi-restraints excluded: chain C residue 2027 GLU Chi-restraints excluded: chain C residue 2061 VAL Chi-restraints excluded: chain C residue 2093 ILE Chi-restraints excluded: chain C residue 2095 VAL Chi-restraints excluded: chain C residue 2168 ILE Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 322 ILE Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 549 ASP Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 618 ILE Chi-restraints excluded: chain D residue 890 THR Chi-restraints excluded: chain D residue 963 ASP Chi-restraints excluded: chain D residue 1024 LEU Chi-restraints excluded: chain D residue 1037 GLU Chi-restraints excluded: chain D residue 1047 ASP Chi-restraints excluded: chain D residue 1075 THR Chi-restraints excluded: chain D residue 1118 ASP Chi-restraints excluded: chain D residue 1126 VAL Chi-restraints excluded: chain D residue 1185 THR Chi-restraints excluded: chain D residue 1209 LEU Chi-restraints excluded: chain D residue 1259 VAL Chi-restraints excluded: chain D residue 1279 ASN Chi-restraints excluded: chain D residue 1503 ILE Chi-restraints excluded: chain D residue 1535 VAL Chi-restraints excluded: chain D residue 1551 THR Chi-restraints excluded: chain D residue 1560 TRP Chi-restraints excluded: chain D residue 1587 LEU Chi-restraints excluded: chain D residue 1594 LEU Chi-restraints excluded: chain D residue 1653 LYS Chi-restraints excluded: chain D residue 1717 LEU Chi-restraints excluded: chain D residue 1798 ASP Chi-restraints excluded: chain D residue 1803 VAL Chi-restraints excluded: chain D residue 1824 LEU Chi-restraints excluded: chain D residue 1860 ASP Chi-restraints excluded: chain D residue 1962 SER Chi-restraints excluded: chain D residue 2027 GLU Chi-restraints excluded: chain D residue 2093 ILE Chi-restraints excluded: chain D residue 2095 VAL Chi-restraints excluded: chain D residue 2165 GLU Chi-restraints excluded: chain D residue 2168 ILE Chi-restraints excluded: chain D residue 2190 GLU Chi-restraints excluded: chain D residue 2389 PHE Chi-restraints excluded: chain D residue 2417 LEU Chi-restraints excluded: chain D residue 2420 ASN Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 241 SER Chi-restraints excluded: chain E residue 412 THR Chi-restraints excluded: chain E residue 459 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 549 ASP Chi-restraints excluded: chain E residue 571 GLN Chi-restraints excluded: chain E residue 681 LEU Chi-restraints excluded: chain E residue 686 ILE Chi-restraints excluded: chain E residue 692 LYS Chi-restraints excluded: chain E residue 709 ASP Chi-restraints excluded: chain E residue 845 GLN Chi-restraints excluded: chain E residue 874 ASP Chi-restraints excluded: chain E residue 986 ASP Chi-restraints excluded: chain E residue 1037 GLU Chi-restraints excluded: chain E residue 1047 ASP Chi-restraints excluded: chain E residue 1075 THR Chi-restraints excluded: chain E residue 1118 ASP Chi-restraints excluded: chain E residue 1126 VAL Chi-restraints excluded: chain E residue 1185 THR Chi-restraints excluded: chain E residue 1279 ASN Chi-restraints excluded: chain E residue 1450 VAL Chi-restraints excluded: chain E residue 1476 ASP Chi-restraints excluded: chain E residue 1535 VAL Chi-restraints excluded: chain E residue 1551 THR Chi-restraints excluded: chain E residue 1560 TRP Chi-restraints excluded: chain E residue 1653 LYS Chi-restraints excluded: chain E residue 1658 LEU Chi-restraints excluded: chain E residue 1803 VAL Chi-restraints excluded: chain E residue 1921 LEU Chi-restraints excluded: chain E residue 2027 GLU Chi-restraints excluded: chain E residue 2070 GLU Chi-restraints excluded: chain E residue 2084 LEU Chi-restraints excluded: chain E residue 2093 ILE Chi-restraints excluded: chain E residue 2095 VAL Chi-restraints excluded: chain E residue 2147 SER Chi-restraints excluded: chain E residue 2168 ILE Chi-restraints excluded: chain E residue 2233 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1140 random chunks: chunk 672 optimal weight: 2.9990 chunk 1082 optimal weight: 0.9980 chunk 660 optimal weight: 4.9990 chunk 513 optimal weight: 4.9990 chunk 752 optimal weight: 3.9990 chunk 1135 optimal weight: 2.9990 chunk 1045 optimal weight: 0.9980 chunk 904 optimal weight: 6.9990 chunk 93 optimal weight: 0.8980 chunk 698 optimal weight: 1.9990 chunk 554 optimal weight: 0.6980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN A 533 ASN ** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1028 GLN ** A1107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN ** B 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2146 GLN C 222 ASN C1055 GLN C2170 GLN D 222 ASN ** D 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 910 GLN ** D 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 222 ASN ** E 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1888 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E2146 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.4547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 90390 Z= 0.190 Angle : 0.623 12.165 122855 Z= 0.310 Chirality : 0.041 0.212 14085 Planarity : 0.004 0.044 15950 Dihedral : 4.662 36.403 12371 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.22 % Allowed : 16.89 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.08), residues: 11365 helix: 1.83 (0.07), residues: 5230 sheet: -0.98 (0.13), residues: 1515 loop : -1.21 (0.09), residues: 4620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP E1084 HIS 0.007 0.001 HIS B 209 PHE 0.025 0.001 PHE D1520 TYR 0.022 0.001 TYR D1172 ARG 0.010 0.000 ARG C2181 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22730 Ramachandran restraints generated. 11365 Oldfield, 0 Emsley, 11365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22730 Ramachandran restraints generated. 11365 Oldfield, 0 Emsley, 11365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1184 residues out of total 9715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 975 time to evaluate : 8.033 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 77 LYS cc_start: 0.7355 (ptmt) cc_final: 0.7064 (ttmt) REVERT: A 291 ASP cc_start: 0.7700 (p0) cc_final: 0.7490 (p0) REVERT: A 624 MET cc_start: 0.7014 (tmm) cc_final: 0.6569 (tmm) REVERT: A 1132 MET cc_start: 0.7681 (mtt) cc_final: 0.7421 (mtt) REVERT: A 1210 ILE cc_start: 0.9108 (OUTLIER) cc_final: 0.8903 (mt) REVERT: A 1560 TRP cc_start: 0.8058 (OUTLIER) cc_final: 0.7633 (p-90) REVERT: A 1842 ASP cc_start: 0.7249 (p0) cc_final: 0.6881 (p0) REVERT: A 2435 ASP cc_start: 0.6773 (t0) cc_final: 0.6458 (t0) REVERT: B 214 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.7712 (tp40) REVERT: B 454 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.9080 (mm) REVERT: B 1822 MET cc_start: 0.7082 (mtm) cc_final: 0.6853 (mtp) REVERT: B 2435 ASP cc_start: 0.6584 (t0) cc_final: 0.6343 (t0) REVERT: C 624 MET cc_start: 0.6731 (tmm) cc_final: 0.6115 (tmm) REVERT: C 1172 TYR cc_start: 0.8070 (m-80) cc_final: 0.7851 (m-80) REVERT: C 2435 ASP cc_start: 0.6473 (t0) cc_final: 0.6110 (t0) REVERT: D 27 MET cc_start: 0.8003 (mmt) cc_final: 0.7365 (tpp) REVERT: D 624 MET cc_start: 0.7056 (tmm) cc_final: 0.6795 (tmm) REVERT: D 1822 MET cc_start: 0.7407 (mtp) cc_final: 0.7125 (mtp) REVERT: E 674 MET cc_start: 0.8494 (tpt) cc_final: 0.8123 (tpt) REVERT: E 1315 TYR cc_start: 0.4786 (m-10) cc_final: 0.4517 (m-80) REVERT: E 1658 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8393 (tm) REVERT: E 2352 LEU cc_start: 0.8586 (mp) cc_final: 0.8263 (tt) outliers start: 209 outliers final: 187 residues processed: 1126 average time/residue: 0.7602 time to fit residues: 1527.2569 Evaluate side-chains 1128 residues out of total 9715 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 936 time to evaluate : 7.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 692 LYS Chi-restraints excluded: chain A residue 986 ASP Chi-restraints excluded: chain A residue 988 LEU Chi-restraints excluded: chain A residue 1047 ASP Chi-restraints excluded: chain A residue 1075 THR Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain A residue 1185 THR Chi-restraints excluded: chain A residue 1209 LEU Chi-restraints excluded: chain A residue 1210 ILE Chi-restraints excluded: chain A residue 1279 ASN Chi-restraints excluded: chain A residue 1304 LEU Chi-restraints excluded: chain A residue 1499 LEU Chi-restraints excluded: chain A residue 1535 VAL Chi-restraints excluded: chain A residue 1560 TRP Chi-restraints excluded: chain A residue 1717 LEU Chi-restraints excluded: chain A residue 1752 MET Chi-restraints excluded: chain A residue 1789 LEU Chi-restraints excluded: chain A residue 1798 ASP Chi-restraints excluded: chain A residue 1803 VAL Chi-restraints excluded: chain A residue 2090 SER Chi-restraints excluded: chain A residue 2093 ILE Chi-restraints excluded: chain A residue 2095 VAL Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 214 GLN Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 346 ILE Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 571 GLN Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 604 VAL Chi-restraints excluded: chain B residue 692 LYS Chi-restraints excluded: chain B residue 845 GLN Chi-restraints excluded: chain B residue 890 THR Chi-restraints excluded: chain B residue 1047 ASP Chi-restraints excluded: chain B residue 1075 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1126 VAL Chi-restraints excluded: chain B residue 1185 THR Chi-restraints excluded: chain B residue 1297 ASN Chi-restraints excluded: chain B residue 1503 ILE Chi-restraints excluded: chain B residue 1535 VAL Chi-restraints excluded: chain B residue 1550 THR Chi-restraints excluded: chain B residue 1560 TRP Chi-restraints excluded: chain B residue 1717 LEU Chi-restraints excluded: chain B residue 1803 VAL Chi-restraints excluded: chain B residue 1824 LEU Chi-restraints excluded: chain B residue 1921 LEU Chi-restraints excluded: chain B residue 1962 SER Chi-restraints excluded: chain B residue 2061 VAL Chi-restraints excluded: chain B residue 2073 SER Chi-restraints excluded: chain B residue 2089 LEU Chi-restraints excluded: chain B residue 2095 VAL Chi-restraints excluded: chain B residue 2132 LEU Chi-restraints excluded: chain B residue 2168 ILE Chi-restraints excluded: chain B residue 2190 GLU Chi-restraints excluded: chain B residue 2420 ASN Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 346 ILE Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 604 VAL Chi-restraints excluded: chain C residue 771 LEU Chi-restraints excluded: chain C residue 1037 GLU Chi-restraints excluded: chain C residue 1047 ASP Chi-restraints excluded: chain C residue 1048 THR Chi-restraints excluded: chain C residue 1075 THR Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1126 VAL Chi-restraints excluded: chain C residue 1185 THR Chi-restraints excluded: chain C residue 1197 LEU Chi-restraints excluded: chain C residue 1259 VAL Chi-restraints excluded: chain C residue 1279 ASN Chi-restraints excluded: chain C residue 1304 LEU Chi-restraints excluded: chain C residue 1473 THR Chi-restraints excluded: chain C residue 1476 ASP Chi-restraints excluded: chain C residue 1492 LEU Chi-restraints excluded: chain C residue 1535 VAL Chi-restraints excluded: chain C residue 1551 THR Chi-restraints excluded: chain C residue 1560 TRP Chi-restraints excluded: chain C residue 1653 LYS Chi-restraints excluded: chain C residue 1717 LEU Chi-restraints excluded: chain C residue 1798 ASP Chi-restraints excluded: chain C residue 1803 VAL Chi-restraints excluded: chain C residue 1825 LEU Chi-restraints excluded: chain C residue 1860 ASP Chi-restraints excluded: chain C residue 1962 SER Chi-restraints excluded: chain C residue 2027 GLU Chi-restraints excluded: chain C residue 2061 VAL Chi-restraints excluded: chain C residue 2093 ILE Chi-restraints excluded: chain C residue 2095 VAL Chi-restraints excluded: chain C residue 2138 LYS Chi-restraints excluded: chain C residue 2168 ILE Chi-restraints excluded: chain C residue 2389 PHE Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 278 THR Chi-restraints excluded: chain D residue 322 ILE Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 549 ASP Chi-restraints excluded: chain D residue 604 VAL Chi-restraints excluded: chain D residue 618 ILE Chi-restraints excluded: chain D residue 890 THR Chi-restraints excluded: chain D residue 963 ASP Chi-restraints excluded: chain D residue 1037 GLU Chi-restraints excluded: chain D residue 1047 ASP Chi-restraints excluded: chain D residue 1075 THR Chi-restraints excluded: chain D residue 1118 ASP Chi-restraints excluded: chain D residue 1126 VAL Chi-restraints excluded: chain D residue 1185 THR Chi-restraints excluded: chain D residue 1209 LEU Chi-restraints excluded: chain D residue 1259 VAL Chi-restraints excluded: chain D residue 1279 ASN Chi-restraints excluded: chain D residue 1503 ILE Chi-restraints excluded: chain D residue 1535 VAL Chi-restraints excluded: chain D residue 1560 TRP Chi-restraints excluded: chain D residue 1587 LEU Chi-restraints excluded: chain D residue 1594 LEU Chi-restraints excluded: chain D residue 1653 LYS Chi-restraints excluded: chain D residue 1717 LEU Chi-restraints excluded: chain D residue 1798 ASP Chi-restraints excluded: chain D residue 1803 VAL Chi-restraints excluded: chain D residue 1824 LEU Chi-restraints excluded: chain D residue 1860 ASP Chi-restraints excluded: chain D residue 1962 SER Chi-restraints excluded: chain D residue 2027 GLU Chi-restraints excluded: chain D residue 2093 ILE Chi-restraints excluded: chain D residue 2095 VAL Chi-restraints excluded: chain D residue 2168 ILE Chi-restraints excluded: chain D residue 2190 GLU Chi-restraints excluded: chain D residue 2389 PHE Chi-restraints excluded: chain D residue 2420 ASN Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 241 SER Chi-restraints excluded: chain E residue 412 THR Chi-restraints excluded: chain E residue 459 VAL Chi-restraints excluded: chain E residue 474 VAL Chi-restraints excluded: chain E residue 549 ASP Chi-restraints excluded: chain E residue 571 GLN Chi-restraints excluded: chain E residue 681 LEU Chi-restraints excluded: chain E residue 686 ILE Chi-restraints excluded: chain E residue 692 LYS Chi-restraints excluded: chain E residue 709 ASP Chi-restraints excluded: chain E residue 764 LEU Chi-restraints excluded: chain E residue 845 GLN Chi-restraints excluded: chain E residue 874 ASP Chi-restraints excluded: chain E residue 986 ASP Chi-restraints excluded: chain E residue 1037 GLU Chi-restraints excluded: chain E residue 1047 ASP Chi-restraints excluded: chain E residue 1075 THR Chi-restraints excluded: chain E residue 1118 ASP Chi-restraints excluded: chain E residue 1126 VAL Chi-restraints excluded: chain E residue 1185 THR Chi-restraints excluded: chain E residue 1209 LEU Chi-restraints excluded: chain E residue 1279 ASN Chi-restraints excluded: chain E residue 1450 VAL Chi-restraints excluded: chain E residue 1520 PHE Chi-restraints excluded: chain E residue 1535 VAL Chi-restraints excluded: chain E residue 1551 THR Chi-restraints excluded: chain E residue 1560 TRP Chi-restraints excluded: chain E residue 1653 LYS Chi-restraints excluded: chain E residue 1658 LEU Chi-restraints excluded: chain E residue 1803 VAL Chi-restraints excluded: chain E residue 1921 LEU Chi-restraints excluded: chain E residue 2070 GLU Chi-restraints excluded: chain E residue 2084 LEU Chi-restraints excluded: chain E residue 2093 ILE Chi-restraints excluded: chain E residue 2095 VAL Chi-restraints excluded: chain E residue 2132 LEU Chi-restraints excluded: chain E residue 2147 SER Chi-restraints excluded: chain E residue 2168 ILE Chi-restraints excluded: chain E residue 2233 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1140 random chunks: chunk 718 optimal weight: 7.9990 chunk 963 optimal weight: 0.8980 chunk 277 optimal weight: 3.9990 chunk 833 optimal weight: 0.8980 chunk 133 optimal weight: 3.9990 chunk 251 optimal weight: 0.9990 chunk 905 optimal weight: 0.0870 chunk 379 optimal weight: 8.9990 chunk 930 optimal weight: 0.4980 chunk 114 optimal weight: 4.9990 chunk 166 optimal weight: 2.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN ** A 845 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2146 GLN ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 GLN B 827 GLN ** B 906 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1249 HIS ** B1311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1888 HIS C 222 ASN C1055 GLN D 222 ASN ** D 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1888 HIS ** 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 = 0.3484 r_free = 0.3484 target = 0.083499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.063635 restraints weight = 255529.208| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 3.71 r_work: 0.2869 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.4631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 90390 Z= 0.165 Angle : 0.618 12.381 122855 Z= 0.307 Chirality : 0.041 0.212 14085 Planarity : 0.004 0.045 15950 Dihedral : 4.607 36.680 12371 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.16 % Allowed : 17.19 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.08), residues: 11365 helix: 1.85 (0.07), residues: 5235 sheet: -0.84 (0.13), residues: 1585 loop : -1.20 (0.10), residues: 4545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E1084 HIS 0.005 0.001 HIS B 209 PHE 0.026 0.001 PHE D1520 TYR 0.021 0.001 TYR B1172 ARG 0.013 0.000 ARG B 215 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27316.59 seconds wall clock time: 477 minutes 40.79 seconds (28660.79 seconds total)