Starting phenix.real_space_refine on Fri Mar 6 15:10:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7woa_32646/03_2026/7woa_32646.cif Found real_map, /net/cci-nas-00/data/ceres_data/7woa_32646/03_2026/7woa_32646.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7woa_32646/03_2026/7woa_32646.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7woa_32646/03_2026/7woa_32646.map" model { file = "/net/cci-nas-00/data/ceres_data/7woa_32646/03_2026/7woa_32646.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7woa_32646/03_2026/7woa_32646.cif" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 134 5.16 5 C 20304 2.51 5 N 5321 2.21 5 O 6193 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31952 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 8338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1076, 8338 Classifications: {'peptide': 1076} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 53, 'TRANS': 1022} Chain breaks: 3 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 39 Chain: "C" Number of atoms: 8338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1076, 8338 Classifications: {'peptide': 1076} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 53, 'TRANS': 1022} Chain breaks: 3 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 39 Chain: "E" Number of atoms: 8338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1076, 8338 Classifications: {'peptide': 1076} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 53, 'TRANS': 1022} Chain breaks: 3 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 39 Chain: "D" Number of atoms: 1560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1560 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 12, 'TRANS': 191} Chain breaks: 2 Chain: "B" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1636 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 199} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "F" Number of atoms: 1560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1560 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 12, 'TRANS': 191} Chain breaks: 2 Chain: "G" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1636 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 199} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "E" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 7.04, per 1000 atoms: 0.22 Number of scatterers: 31952 At special positions: 0 Unit cell: (170.56, 194.34, 222.22, 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 134 16.00 O 6193 8.00 N 5321 7.00 C 20304 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=50, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 15 " - pdb=" SG CYS E 136 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 166 " distance=2.03 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 301 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 538 " - pdb=" SG CYS E 590 " distance=2.03 Simple disulfide: pdb=" SG CYS E 617 " - pdb=" SG CYS E 649 " distance=2.03 Simple disulfide: pdb=" SG CYS E 662 " - pdb=" SG CYS E 671 " distance=2.03 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 760 " distance=2.03 Simple disulfide: pdb=" SG CYS E 743 " - pdb=" SG CYS E 749 " distance=2.03 Simple disulfide: pdb=" SG CYS E1032 " - pdb=" SG CYS E1043 " distance=2.03 Simple disulfide: pdb=" SG CYS E1082 " - pdb=" SG CYS E1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 203 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 89 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 195 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 147 " - pdb=" SG CYS F 203 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 89 " distance=2.03 Simple disulfide: pdb=" SG CYS G 135 " - pdb=" SG CYS G 195 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 165 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 343 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 709 " " NAG A1309 " - " ASN A 717 " " NAG A1310 " - " ASN A 801 " " NAG A1311 " - " ASN A1074 " " NAG A1312 " - " ASN A1098 " " NAG A1313 " - " ASN A1134 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 165 " " NAG C1303 " - " ASN C 234 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C 343 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 709 " " NAG C1309 " - " ASN C 717 " " NAG C1310 " - " ASN C 801 " " NAG C1311 " - " ASN C1074 " " NAG C1312 " - " ASN C1098 " " NAG C1313 " - " ASN C1134 " " NAG E1301 " - " ASN E 61 " " NAG E1302 " - " ASN E 165 " " NAG E1303 " - " ASN E 234 " " NAG E1304 " - " ASN E 282 " " NAG E1305 " - " ASN E 331 " " NAG E1306 " - " ASN E 343 " " NAG E1307 " - " ASN E 616 " " NAG E1308 " - " ASN E 709 " " NAG E1309 " - " ASN E 717 " " NAG E1310 " - " ASN E 801 " " NAG E1311 " - " ASN E1074 " " NAG E1312 " - " ASN E1098 " " NAG E1313 " - " ASN E1134 " Time building additional restraints: 2.69 Conformation dependent library (CDL) restraints added in 1.4 seconds 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7578 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 67 sheets defined 18.5% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.833A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 407 Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.754A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.984A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.311A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 907 removed outlier: 3.616A pdb=" N ASN A 907 " --> pdb=" O ALA A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.539A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.835A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.815A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 386 through 390 removed outlier: 3.655A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 386 through 390' Processing helix chain 'C' and resid 403 through 407 removed outlier: 3.548A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.735A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.557A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 782 removed outlier: 3.705A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.506A pdb=" N ALA C 890 " --> pdb=" O THR C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 941 removed outlier: 4.360A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.517A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1031 removed outlier: 4.752A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 4.630A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 303 Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 365 through 371 removed outlier: 4.205A pdb=" N TYR E 369 " --> pdb=" O TYR E 365 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER E 371 " --> pdb=" O VAL E 367 " (cutoff:3.500A) Processing helix chain 'E' and resid 386 through 390 removed outlier: 3.758A pdb=" N LEU E 390 " --> pdb=" O LEU E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 409 Processing helix chain 'E' and resid 438 through 443 removed outlier: 3.800A pdb=" N SER E 443 " --> pdb=" O ASN E 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 737 through 743 Processing helix chain 'E' and resid 746 through 754 removed outlier: 3.582A pdb=" N LEU E 754 " --> pdb=" O SER E 750 " (cutoff:3.500A) Processing helix chain 'E' and resid 758 through 783 removed outlier: 3.604A pdb=" N GLN E 762 " --> pdb=" O SER E 758 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL E 781 " --> pdb=" O ASN E 777 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE E 782 " --> pdb=" O THR E 778 " (cutoff:3.500A) Processing helix chain 'E' and resid 816 through 826 Processing helix chain 'E' and resid 866 through 885 Processing helix chain 'E' and resid 897 through 910 removed outlier: 3.617A pdb=" N ILE E 909 " --> pdb=" O ARG E 905 " (cutoff:3.500A) Processing helix chain 'E' and resid 912 through 941 removed outlier: 4.327A pdb=" N LEU E 916 " --> pdb=" O THR E 912 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LYS E 921 " --> pdb=" O TYR E 917 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LEU E 922 " --> pdb=" O GLU E 918 " (cutoff:3.500A) Processing helix chain 'E' and resid 945 through 965 removed outlier: 3.562A pdb=" N GLN E 949 " --> pdb=" O LEU E 945 " (cutoff:3.500A) Processing helix chain 'E' and resid 966 through 968 No H-bonds generated for 'chain 'E' and resid 966 through 968' Processing helix chain 'E' and resid 976 through 984 Processing helix chain 'E' and resid 985 through 1033 Processing helix chain 'D' and resid 61 through 65 removed outlier: 3.849A pdb=" N GLN D 65 " --> pdb=" O GLN D 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 84 removed outlier: 3.678A pdb=" N PHE B 84 " --> pdb=" O PRO B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 128 removed outlier: 3.576A pdb=" N SER B 128 " --> pdb=" O GLN B 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 91 removed outlier: 4.051A pdb=" N THR F 91 " --> pdb=" O SER F 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 127 removed outlier: 3.607A pdb=" N LYS G 127 " --> pdb=" O ASP G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 183 through 188 removed outlier: 3.540A pdb=" N GLU G 188 " --> pdb=" O LYS G 184 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.595A pdb=" N VAL A 62 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER A 31 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.595A pdb=" N VAL A 62 " --> pdb=" O THR A 29 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER A 31 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR A 208 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.014A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU A 276 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 130 through 131 removed outlier: 3.662A pdb=" N THR A 167 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 151 through 154 removed outlier: 4.542A pdb=" N SER A 151 " --> pdb=" O HIS A 146 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 314 removed outlier: 3.528A pdb=" N VAL A 610 " --> pdb=" O ILE A 651 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 355 removed outlier: 3.661A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER A 514 " --> pdb=" O TYR A 396 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 379 through 380 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.922A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 538 through 542 removed outlier: 3.594A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.875A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 712 through 728 removed outlier: 6.811A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 712 through 728 removed outlier: 6.811A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.805A pdb=" N ILE A 788 " --> pdb=" O ASN E 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AB9, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.725A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.935A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 83 through 85 Processing sheet with id=AC3, first strand: chain 'C' and resid 119 through 121 Processing sheet with id=AC4, first strand: chain 'C' and resid 152 through 153 removed outlier: 6.778A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.227A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 325 through 326 removed outlier: 5.243A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N PHE C 565 " --> pdb=" O PHE E 43 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 396 through 402 Processing sheet with id=AC8, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.738A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 702 through 703 Processing sheet with id=AD2, first strand: chain 'C' and resid 712 through 715 Processing sheet with id=AD3, first strand: chain 'C' and resid 718 through 722 removed outlier: 6.931A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 725 through 728 removed outlier: 3.631A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.302A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 1081 through 1082 removed outlier: 5.262A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 27 through 29 removed outlier: 3.570A pdb=" N ALA E 27 " --> pdb=" O TRP E 64 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 36 through 37 removed outlier: 7.063A pdb=" N VAL E 36 " --> pdb=" O LEU E 223 " (cutoff:3.500A) removed outlier: 9.278A pdb=" N ALA E 222 " --> pdb=" O HIS E 207 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N HIS E 207 " --> pdb=" O ALA E 222 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ILE E 203 " --> pdb=" O LEU E 226 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU E 189 " --> pdb=" O THR E 208 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 48 through 51 removed outlier: 6.343A pdb=" N LEU E 276 " --> pdb=" O ALA E 288 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ALA E 288 " --> pdb=" O LEU E 276 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N LYS E 278 " --> pdb=" O THR E 286 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 54 through 55 Processing sheet with id=AE2, first strand: chain 'E' and resid 84 through 85 removed outlier: 3.904A pdb=" N ILE E 105 " --> pdb=" O GLN E 239 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY E 103 " --> pdb=" O LEU E 241 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE E 119 " --> pdb=" O TRP E 104 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE E 168 " --> pdb=" O VAL E 130 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 151 through 157 removed outlier: 4.430A pdb=" N SER E 151 " --> pdb=" O HIS E 146 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N HIS E 146 " --> pdb=" O SER E 151 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N MET E 153 " --> pdb=" O TYR E 144 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N GLY E 142 " --> pdb=" O SER E 155 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N LEU E 141 " --> pdb=" O LEU E 244 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ARG E 246 " --> pdb=" O LEU E 141 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL E 143 " --> pdb=" O ARG E 246 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 311 through 319 removed outlier: 7.173A pdb=" N VAL E 595 " --> pdb=" O THR E 315 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ASN E 317 " --> pdb=" O GLY E 593 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLY E 593 " --> pdb=" O ASN E 317 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLY E 594 " --> pdb=" O GLN E 613 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 325 through 326 Processing sheet with id=AE6, first strand: chain 'E' and resid 356 through 358 removed outlier: 3.844A pdb=" N ILE E 358 " --> pdb=" O VAL E 395 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N VAL E 395 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR E 396 " --> pdb=" O SER E 514 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL E 512 " --> pdb=" O ASP E 398 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N PHE E 400 " --> pdb=" O VAL E 510 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL E 510 " --> pdb=" O PHE E 400 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE E 402 " --> pdb=" O TYR E 508 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 452 through 453 Processing sheet with id=AE8, first strand: chain 'E' and resid 565 through 566 removed outlier: 3.613A pdb=" N GLY E 566 " --> pdb=" O ALA E 575 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ALA E 575 " --> pdb=" O GLY E 566 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'E' and resid 654 through 655 removed outlier: 6.039A pdb=" N GLU E 654 " --> pdb=" O ALA E 694 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N THR E 696 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN E 675 " --> pdb=" O SER E 691 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER E 673 " --> pdb=" O ILE E 693 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE E 670 " --> pdb=" O ILE E 666 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 711 through 722 removed outlier: 7.052A pdb=" N GLN E1071 " --> pdb=" O THR E 716 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N PHE E 718 " --> pdb=" O PRO E1069 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N ILE E 720 " --> pdb=" O TYR E1067 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N TYR E1067 " --> pdb=" O ILE E 720 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL E 722 " --> pdb=" O VAL E1065 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL E1065 " --> pdb=" O VAL E 722 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N TYR E1067 " --> pdb=" O HIS E1048 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N HIS E1048 " --> pdb=" O TYR E1067 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 725 through 728 Processing sheet with id=AF3, first strand: chain 'E' and resid 733 through 736 removed outlier: 4.207A pdb=" N LYS E 733 " --> pdb=" O LEU E 861 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 1120 through 1125 removed outlier: 3.689A pdb=" N SER E1123 " --> pdb=" O ALA E1087 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N ALA E1087 " --> pdb=" O SER E1123 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 4 through 6 Processing sheet with id=AF6, first strand: chain 'D' and resid 57 through 58 removed outlier: 3.623A pdb=" N ILE D 57 " --> pdb=" O ILE D 52 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TRP D 36 " --> pdb=" O GLY D 49 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA D 92 " --> pdb=" O VAL D 116 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL D 116 " --> pdb=" O ALA D 92 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 127 through 129 removed outlier: 4.036A pdb=" N LYS D 150 " --> pdb=" O SER D 127 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU D 148 " --> pdb=" O PHE D 129 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL D 149 " --> pdb=" O LEU D 185 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N TYR D 183 " --> pdb=" O ASP D 151 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 145 through 146 removed outlier: 3.667A pdb=" N LEU D 145 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N VAL D 188 " --> pdb=" O HIS D 171 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N HIS D 171 " --> pdb=" O VAL D 188 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 158 through 161 removed outlier: 3.573A pdb=" N LYS D 216 " --> pdb=" O CYS D 203 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'B' and resid 5 through 6 removed outlier: 4.112A pdb=" N THR B 5 " --> pdb=" O ARG B 24 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG B 24 " --> pdb=" O THR B 5 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE B 76 " --> pdb=" O ALA B 19 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'B' and resid 5 through 6 removed outlier: 4.112A pdb=" N THR B 5 " --> pdb=" O ARG B 24 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG B 24 " --> pdb=" O THR B 5 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'B' and resid 10 through 13 removed outlier: 3.503A pdb=" N LEU B 13 " --> pdb=" O GLU B 106 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'B' and resid 54 through 55 removed outlier: 6.747A pdb=" N TRP B 36 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N TYR B 50 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LEU B 34 " --> pdb=" O TYR B 50 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'B' and resid 117 through 119 removed outlier: 3.604A pdb=" N PHE B 117 " --> pdb=" O LEU B 136 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL B 134 " --> pdb=" O PHE B 119 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N TYR B 174 " --> pdb=" O ASN B 139 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'B' and resid 147 through 150 Processing sheet with id=AG7, first strand: chain 'F' and resid 18 through 23 removed outlier: 4.051A pdb=" N VAL F 18 " --> pdb=" O LEU F 83 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'F' and resid 45 through 51 removed outlier: 3.507A pdb=" N ARG F 38 " --> pdb=" O GLU F 46 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N TRP F 36 " --> pdb=" O MET F 48 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N ARG F 50 " --> pdb=" O PHE F 34 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N PHE F 34 " --> pdb=" O ARG F 50 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA F 97 " --> pdb=" O SER F 35 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL F 37 " --> pdb=" O PHE F 95 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'F' and resid 127 through 129 removed outlier: 3.916A pdb=" N LEU F 148 " --> pdb=" O PHE F 129 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N CYS F 147 " --> pdb=" O SER F 187 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER F 187 " --> pdb=" O CYS F 147 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL F 149 " --> pdb=" O LEU F 185 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N VAL F 188 " --> pdb=" O HIS F 171 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N HIS F 171 " --> pdb=" O VAL F 188 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'G' and resid 54 through 55 removed outlier: 3.526A pdb=" N SER G 54 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR G 50 " --> pdb=" O SER G 54 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN G 91 " --> pdb=" O THR G 98 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N THR G 98 " --> pdb=" O GLN G 91 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'G' and resid 64 through 66 Processing sheet with id=AH3, first strand: chain 'G' and resid 136 through 140 removed outlier: 3.996A pdb=" N LEU G 176 " --> pdb=" O LEU G 137 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N TYR G 174 " --> pdb=" O ASN G 139 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'G' and resid 146 through 149 957 hydrogen bonds defined for protein. 2598 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.27 Time building geometry restraints manager: 3.59 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: 10243 1.34 - 1.46: 7593 1.46 - 1.58: 14686 1.58 - 1.70: 0 1.70 - 1.82: 168 Bond restraints: 32690 Sorted by residual: bond pdb=" C GLU D 155 " pdb=" N PRO D 156 " ideal model delta sigma weight residual 1.333 1.350 -0.017 7.80e-03 1.64e+04 4.68e+00 bond pdb=" C TYR G 141 " pdb=" N PRO G 142 " ideal model delta sigma weight residual 1.333 1.353 -0.020 1.01e-02 9.80e+03 3.75e+00 bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.44e+00 bond pdb=" C1 NAG C1311 " pdb=" O5 NAG C1311 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.26e+00 bond pdb=" C1 NAG E1307 " pdb=" O5 NAG E1307 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.21e+00 ... (remaining 32685 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.23: 43356 1.23 - 2.46: 882 2.46 - 3.69: 235 3.69 - 4.92: 28 4.92 - 6.15: 12 Bond angle restraints: 44513 Sorted by residual: angle pdb=" N PRO D 156 " pdb=" CA PRO D 156 " pdb=" C PRO D 156 " ideal model delta sigma weight residual 114.68 110.65 4.03 1.28e+00 6.10e-01 9.92e+00 angle pdb=" CA PRO D 156 " pdb=" C PRO D 156 " pdb=" O PRO D 156 " ideal model delta sigma weight residual 118.29 121.11 -2.82 9.60e-01 1.09e+00 8.64e+00 angle pdb=" C PRO F 154 " pdb=" N GLU F 155 " pdb=" CA GLU F 155 " ideal model delta sigma weight residual 120.97 124.89 -3.92 1.48e+00 4.57e-01 7.01e+00 angle pdb=" C VAL G 151 " pdb=" N ASP G 152 " pdb=" CA ASP G 152 " ideal model delta sigma weight residual 121.54 126.32 -4.78 1.91e+00 2.74e-01 6.26e+00 angle pdb=" C ASP A 290 " pdb=" N CYS A 291 " pdb=" CA CYS A 291 " ideal model delta sigma weight residual 121.54 126.28 -4.74 1.91e+00 2.74e-01 6.17e+00 ... (remaining 44508 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 19075 17.69 - 35.38: 699 35.38 - 53.07: 134 53.07 - 70.76: 53 70.76 - 88.45: 8 Dihedral angle restraints: 19969 sinusoidal: 8176 harmonic: 11793 Sorted by residual: dihedral pdb=" CA VAL G 151 " pdb=" C VAL G 151 " pdb=" N ASP G 152 " pdb=" CA ASP G 152 " ideal model delta harmonic sigma weight residual 180.00 158.69 21.31 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA GLU D 155 " pdb=" C GLU D 155 " pdb=" N PRO D 156 " pdb=" CA PRO D 156 " ideal model delta harmonic sigma weight residual 180.00 159.15 20.85 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA CYS A 379 " pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " pdb=" SG CYS A 432 " ideal model delta sinusoidal sigma weight residual 79.00 5.67 73.33 1 2.00e+01 2.50e-03 1.71e+01 ... (remaining 19966 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 3420 0.031 - 0.063: 1097 0.063 - 0.094: 356 0.094 - 0.126: 272 0.126 - 0.157: 11 Chirality restraints: 5156 Sorted by residual: chirality pdb=" C1 NAG E1302 " pdb=" ND2 ASN E 165 " pdb=" C2 NAG E1302 " pdb=" O5 NAG E1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-01 2.50e+01 6.17e-01 chirality pdb=" C1 NAG E1301 " pdb=" ND2 ASN E 61 " pdb=" C2 NAG E1301 " pdb=" O5 NAG E1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-01 2.50e+01 5.38e-01 chirality pdb=" C1 NAG E1313 " pdb=" ND2 ASN E1134 " pdb=" C2 NAG E1313 " pdb=" O5 NAG E1313 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 5.10e-01 ... (remaining 5153 not shown) Planarity restraints: 5756 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU G 80 " 0.034 5.00e-02 4.00e+02 5.23e-02 4.38e+00 pdb=" N PRO G 81 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO G 81 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO G 81 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 119 " -0.034 5.00e-02 4.00e+02 5.17e-02 4.27e+00 pdb=" N PRO B 120 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 120 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 120 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 155 " 0.034 5.00e-02 4.00e+02 5.12e-02 4.19e+00 pdb=" N PRO D 156 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO D 156 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO D 156 " 0.029 5.00e-02 4.00e+02 ... (remaining 5753 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 4650 2.76 - 3.30: 29897 3.30 - 3.83: 52760 3.83 - 4.37: 60605 4.37 - 4.90: 107117 Nonbonded interactions: 255029 Sorted by model distance: nonbonded pdb=" OE1 GLU G 106 " pdb=" OH TYR G 174 " model vdw 2.229 3.040 nonbonded pdb=" OH TYR G 37 " pdb=" OE1 GLN G 90 " model vdw 2.243 3.040 nonbonded pdb=" OE1 GLU E 406 " pdb=" OH TYR E 495 " model vdw 2.244 3.040 nonbonded pdb=" OD1 ASN E 122 " pdb=" OG1 THR E 124 " model vdw 2.255 3.040 nonbonded pdb=" OG SER A 735 " pdb=" OG1 THR A 859 " model vdw 2.269 3.040 ... (remaining 255024 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'F' } 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: 3.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.630 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 30.760 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 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 : 0.002 0.052 32779 Z= 0.124 Angle : 0.453 6.149 44730 Z= 0.240 Chirality : 0.041 0.157 5156 Planarity : 0.004 0.052 5717 Dihedral : 9.461 88.449 12241 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 4.23 % Allowed : 5.58 % Favored : 90.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.46 (0.12), residues: 4020 helix: 0.65 (0.20), residues: 681 sheet: -2.47 (0.16), residues: 866 loop : -3.30 (0.10), residues: 2473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 98 TYR 0.008 0.000 TYR E 265 PHE 0.010 0.001 PHE C 562 TRP 0.005 0.000 TRP A 886 HIS 0.001 0.000 HIS B 190 Details of bonding type rmsd covalent geometry : bond 0.00243 (32690) covalent geometry : angle 0.45109 (44513) SS BOND : bond 0.00121 ( 50) SS BOND : angle 0.54730 ( 100) hydrogen bonds : bond 0.21983 ( 937) hydrogen bonds : angle 8.39696 ( 2598) link_NAG-ASN : bond 0.00215 ( 39) link_NAG-ASN : angle 0.85185 ( 117) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 929 residues out of total 3529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 782 time to evaluate : 1.152 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: A 233 ILE cc_start: 0.5507 (OUTLIER) cc_final: 0.5009 (pt) REVERT: A 281 GLU cc_start: 0.7213 (mp0) cc_final: 0.6998 (mp0) REVERT: A 384 PRO cc_start: 0.7336 (Cg_exo) cc_final: 0.7131 (Cg_endo) REVERT: A 556 ASN cc_start: 0.7099 (p0) cc_final: 0.6893 (p0) REVERT: A 820 ASP cc_start: 0.7423 (OUTLIER) cc_final: 0.7001 (m-30) REVERT: A 947 LYS cc_start: 0.7507 (OUTLIER) cc_final: 0.7234 (mttp) REVERT: C 137 ASN cc_start: 0.3759 (p0) cc_final: 0.3484 (p0) REVERT: C 369 TYR cc_start: 0.6273 (t80) cc_final: 0.5918 (t80) REVERT: C 470 THR cc_start: 0.7525 (p) cc_final: 0.7315 (p) REVERT: C 855 PHE cc_start: 0.6406 (OUTLIER) cc_final: 0.5750 (t80) REVERT: C 878 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8539 (mm) REVERT: E 177 MET cc_start: 0.7021 (mtp) cc_final: 0.6655 (mtt) REVERT: E 317 ASN cc_start: 0.8228 (m-40) cc_final: 0.7974 (m110) REVERT: E 396 TYR cc_start: 0.5683 (m-80) cc_final: 0.5241 (m-80) REVERT: E 542 ASN cc_start: 0.6595 (t0) cc_final: 0.6051 (m-40) REVERT: E 581 THR cc_start: 0.8629 (OUTLIER) cc_final: 0.8355 (p) REVERT: E 751 ASN cc_start: 0.8325 (m-40) cc_final: 0.7989 (m110) REVERT: E 878 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8592 (mt) REVERT: D 153 PHE cc_start: 0.4540 (OUTLIER) cc_final: 0.3724 (t80) REVERT: D 155 GLU cc_start: 0.7495 (tm-30) cc_final: 0.7222 (mm-30) REVERT: D 185 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7618 (pt) REVERT: B 76 ILE cc_start: 0.7957 (mt) cc_final: 0.7744 (mt) REVERT: B 104 LYS cc_start: 0.8272 (tptt) cc_final: 0.7645 (tttp) REVERT: B 124 GLU cc_start: 0.6711 (tm-30) cc_final: 0.6416 (mt-10) REVERT: B 136 LEU cc_start: 0.7534 (OUTLIER) cc_final: 0.6872 (pp) REVERT: B 150 LYS cc_start: 0.7456 (ttmm) cc_final: 0.7245 (tmtt) REVERT: B 184 LYS cc_start: 0.7433 (OUTLIER) cc_final: 0.7005 (ptpt) REVERT: F 29 PHE cc_start: 0.7296 (t80) cc_final: 0.6848 (t80) REVERT: F 41 PRO cc_start: 0.7883 (Cg_exo) cc_final: 0.7499 (Cg_endo) REVERT: F 203 CYS cc_start: 0.2717 (p) cc_final: 0.2393 (t) REVERT: G 84 PHE cc_start: 0.6564 (m-10) cc_final: 0.6284 (m-10) REVERT: G 107 ILE cc_start: 0.6481 (OUTLIER) cc_final: 0.6149 (mp) REVERT: G 200 GLN cc_start: 0.5305 (OUTLIER) cc_final: 0.4532 (pp30) outliers start: 147 outliers final: 26 residues processed: 877 average time/residue: 0.2104 time to fit residues: 288.1834 Evaluate side-chains 413 residues out of total 3529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 374 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 301 CYS Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 581 THR Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 1129 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 146 LYS Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 18 ARG Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 200 GLN Chi-restraints excluded: chain G residue 206 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 20.0000 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 0.0470 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 0.3980 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 0.9990 chunk 401 optimal weight: 20.0000 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 0.0270 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 GLN A 137 ASN A 149 ASN A 173 GLN ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 ASN A 218 GLN A 439 ASN A 493 GLN A 498 GLN A 607 GLN A 658 ASN A 784 GLN A 872 GLN A 901 GLN ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN A 954 GLN A 969 ASN A 992 GLN A1005 GLN A1048 HIS A1088 HIS A1119 ASN C 23 GLN C 66 HIS C 173 GLN C 188 ASN C 211 ASN C 239 GLN C 354 ASN C 360 ASN C 414 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 ASN C 498 GLN C 641 ASN C 787 GLN C 913 GLN C 954 GLN C 957 GLN C1054 GLN E 49 HIS E 207 HIS E 218 GLN E 321 GLN E 414 GLN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 437 ASN E 474 GLN E 493 GLN E 580 GLN E 641 ASN E 675 GLN E 690 GLN E 710 ASN E 755 GLN E 762 GLN E 784 GLN E 949 GLN E 954 GLN E1002 GLN E1011 GLN E1054 GLN E1083 HIS D 1 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 ASN D 39 GLN D 65 GLN B 27 GLN B 31 ASN B 190 HIS B 200 GLN F 59 HIS F 112 GLN F 206 ASN G 39 GLN G 43 GLN G 148 GLN G 159 ASN G 161 GLN G 167 GLN ** G 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 79 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.109394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.083452 restraints weight = 86765.621| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.58 r_work: 0.3304 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 32779 Z= 0.113 Angle : 0.577 15.205 44730 Z= 0.290 Chirality : 0.044 0.315 5156 Planarity : 0.004 0.070 5717 Dihedral : 6.961 59.788 5254 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.28 % Allowed : 11.39 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.68 (0.12), residues: 4020 helix: 1.37 (0.21), residues: 684 sheet: -1.79 (0.16), residues: 869 loop : -2.88 (0.11), residues: 2467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 18 TYR 0.026 0.001 TYR B 187 PHE 0.019 0.001 PHE B 140 TRP 0.011 0.001 TRP A 64 HIS 0.010 0.001 HIS E 519 Details of bonding type rmsd covalent geometry : bond 0.00261 (32690) covalent geometry : angle 0.55819 (44513) SS BOND : bond 0.00413 ( 50) SS BOND : angle 1.88318 ( 100) hydrogen bonds : bond 0.03842 ( 937) hydrogen bonds : angle 6.19124 ( 2598) link_NAG-ASN : bond 0.00403 ( 39) link_NAG-ASN : angle 2.42218 ( 117) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 3529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 427 time to evaluate : 1.018 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 66 HIS cc_start: 0.6269 (m90) cc_final: 0.5890 (m90) REVERT: A 85 PRO cc_start: 0.8011 (Cg_exo) cc_final: 0.7598 (Cg_endo) REVERT: A 153 MET cc_start: 0.7115 (mtt) cc_final: 0.5935 (ppp) REVERT: A 233 ILE cc_start: 0.5280 (OUTLIER) cc_final: 0.4958 (pt) REVERT: A 244 LEU cc_start: 0.4765 (pp) cc_final: 0.3618 (mt) REVERT: A 556 ASN cc_start: 0.7765 (p0) cc_final: 0.7409 (p0) REVERT: A 819 GLU cc_start: 0.8288 (mt-10) cc_final: 0.8030 (mt-10) REVERT: A 820 ASP cc_start: 0.8273 (OUTLIER) cc_final: 0.7817 (m-30) REVERT: A 904 TYR cc_start: 0.8335 (m-10) cc_final: 0.7534 (m-80) REVERT: A 990 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7598 (tt0) REVERT: C 470 THR cc_start: 0.7815 (p) cc_final: 0.7607 (p) REVERT: C 574 ASP cc_start: 0.7616 (t70) cc_final: 0.7265 (t0) REVERT: C 615 VAL cc_start: 0.8685 (t) cc_final: 0.8468 (m) REVERT: C 855 PHE cc_start: 0.6440 (OUTLIER) cc_final: 0.5698 (t80) REVERT: C 878 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8603 (mm) REVERT: C 957 GLN cc_start: 0.8599 (tt0) cc_final: 0.8326 (tp40) REVERT: E 177 MET cc_start: 0.7147 (mtp) cc_final: 0.6655 (mtt) REVERT: E 317 ASN cc_start: 0.8673 (m-40) cc_final: 0.8434 (m-40) REVERT: E 377 PHE cc_start: 0.5196 (OUTLIER) cc_final: 0.4829 (m-80) REVERT: E 542 ASN cc_start: 0.7328 (t0) cc_final: 0.6615 (m-40) REVERT: E 751 ASN cc_start: 0.8710 (m-40) cc_final: 0.8334 (m110) REVERT: E 878 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8646 (mt) REVERT: D 27 ASP cc_start: 0.8384 (p0) cc_final: 0.7463 (p0) REVERT: D 155 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7285 (mm-30) REVERT: D 185 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.7500 (pt) REVERT: B 124 GLU cc_start: 0.7266 (tm-30) cc_final: 0.6541 (mt-10) REVERT: B 136 LEU cc_start: 0.7325 (OUTLIER) cc_final: 0.6808 (pp) REVERT: B 184 LYS cc_start: 0.7404 (OUTLIER) cc_final: 0.6901 (ptpt) REVERT: B 212 ARG cc_start: 0.7442 (OUTLIER) cc_final: 0.6422 (mtm-85) REVERT: F 216 LYS cc_start: 0.6745 (mmtm) cc_final: 0.6516 (tppt) REVERT: G 84 PHE cc_start: 0.6816 (m-10) cc_final: 0.6559 (m-10) REVERT: G 149 TRP cc_start: 0.3176 (m100) cc_final: 0.1975 (m100) REVERT: G 171 ASP cc_start: 0.5708 (OUTLIER) cc_final: 0.5492 (p0) REVERT: G 188 GLU cc_start: 0.6127 (mp0) cc_final: 0.5677 (mp0) REVERT: G 190 HIS cc_start: 0.5309 (m-70) cc_final: 0.4842 (m-70) REVERT: G 200 GLN cc_start: 0.6165 (OUTLIER) cc_final: 0.5202 (pp30) REVERT: G 212 ARG cc_start: 0.5769 (tmm160) cc_final: 0.5365 (ppt170) outliers start: 114 outliers final: 58 residues processed: 516 average time/residue: 0.1927 time to fit residues: 160.1756 Evaluate side-chains 420 residues out of total 3529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 349 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 301 CYS Chi-restraints excluded: chain E residue 377 PHE Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 489 TYR Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 588 THR Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 1129 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 146 LYS Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain F residue 206 ASN Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 18 ARG Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 171 ASP Chi-restraints excluded: chain G residue 200 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 382 optimal weight: 6.9990 chunk 273 optimal weight: 6.9990 chunk 350 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 175 optimal weight: 4.9990 chunk 182 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 176 optimal weight: 6.9990 chunk 378 optimal weight: 0.9990 chunk 56 optimal weight: 7.9990 chunk 299 optimal weight: 4.9990 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 69 HIS A 185 ASN A 188 ASN A 245 HIS A 613 GLN A 762 GLN C 164 ASN C 173 GLN C 354 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN C 641 ASN C 901 GLN C 965 GLN C1048 HIS E 14 GLN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 448 ASN ** E 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 580 GLN E 644 GLN E 655 HIS E 762 GLN E 949 GLN E1002 GLN E1048 HIS E1054 GLN E1106 GLN B 138 ASN B 199 HIS F 171 HIS G 33 HIS Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.109695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.082775 restraints weight = 79868.737| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 3.24 r_work: 0.3097 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 32779 Z= 0.221 Angle : 0.675 13.071 44730 Z= 0.343 Chirality : 0.047 0.302 5156 Planarity : 0.005 0.062 5717 Dihedral : 7.013 59.288 5244 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 4.29 % Allowed : 11.22 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.55 (0.12), residues: 4020 helix: 0.95 (0.20), residues: 691 sheet: -1.66 (0.16), residues: 911 loop : -2.65 (0.11), residues: 2418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 905 TYR 0.023 0.002 TYR B 193 PHE 0.026 0.002 PHE A 186 TRP 0.027 0.002 TRP A 886 HIS 0.011 0.002 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00528 (32690) covalent geometry : angle 0.65669 (44513) SS BOND : bond 0.00641 ( 50) SS BOND : angle 2.25472 ( 100) hydrogen bonds : bond 0.04761 ( 937) hydrogen bonds : angle 5.97605 ( 2598) link_NAG-ASN : bond 0.00564 ( 39) link_NAG-ASN : angle 2.39683 ( 117) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 3529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 330 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 PRO cc_start: 0.7833 (Cg_exo) cc_final: 0.7613 (Cg_endo) REVERT: A 153 MET cc_start: 0.7449 (mtt) cc_final: 0.6304 (ppp) REVERT: A 237 ARG cc_start: 0.7633 (mtm-85) cc_final: 0.7430 (mtm110) REVERT: A 574 ASP cc_start: 0.7989 (m-30) cc_final: 0.7754 (t0) REVERT: A 918 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8088 (mp0) REVERT: C 574 ASP cc_start: 0.8304 (t70) cc_final: 0.7918 (t0) REVERT: C 779 GLN cc_start: 0.8699 (tm-30) cc_final: 0.8479 (tt0) REVERT: C 855 PHE cc_start: 0.6357 (OUTLIER) cc_final: 0.4998 (t80) REVERT: C 947 LYS cc_start: 0.8753 (mptt) cc_final: 0.8522 (mtmm) REVERT: C 957 GLN cc_start: 0.8843 (tt0) cc_final: 0.8605 (tp40) REVERT: E 177 MET cc_start: 0.7245 (mtp) cc_final: 0.6649 (mtp) REVERT: E 448 ASN cc_start: 0.5072 (OUTLIER) cc_final: 0.4729 (m110) REVERT: E 489 TYR cc_start: 0.2699 (OUTLIER) cc_final: 0.2220 (m-80) REVERT: E 542 ASN cc_start: 0.7383 (t0) cc_final: 0.6294 (m-40) REVERT: E 747 THR cc_start: 0.8601 (p) cc_final: 0.8171 (m) REVERT: E 751 ASN cc_start: 0.8747 (m-40) cc_final: 0.8279 (m110) REVERT: E 768 THR cc_start: 0.9016 (m) cc_final: 0.8802 (m) REVERT: E 804 GLN cc_start: 0.8455 (mm-40) cc_final: 0.7761 (mp10) REVERT: E 878 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8727 (mt) REVERT: D 155 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7819 (tm-30) REVERT: D 183 TYR cc_start: 0.7737 (m-80) cc_final: 0.7375 (m-80) REVERT: B 82 GLU cc_start: 0.8304 (pp20) cc_final: 0.7895 (pp20) REVERT: B 117 PHE cc_start: 0.7468 (m-10) cc_final: 0.7092 (m-80) REVERT: B 124 GLU cc_start: 0.7392 (tm-30) cc_final: 0.6531 (mt-10) REVERT: B 136 LEU cc_start: 0.6993 (OUTLIER) cc_final: 0.6345 (pt) REVERT: B 184 LYS cc_start: 0.7338 (OUTLIER) cc_final: 0.6843 (ptpt) REVERT: B 212 ARG cc_start: 0.7462 (OUTLIER) cc_final: 0.6871 (mtm110) REVERT: F 27 ASP cc_start: 0.7675 (p0) cc_final: 0.6938 (p0) REVERT: F 39 GLN cc_start: 0.5493 (tp40) cc_final: 0.5233 (tp40) REVERT: F 206 ASN cc_start: 0.8000 (OUTLIER) cc_final: 0.6814 (p0) REVERT: G 40 LYS cc_start: 0.6782 (mtmm) cc_final: 0.6346 (mttt) REVERT: G 63 PHE cc_start: 0.6592 (m-80) cc_final: 0.6375 (m-80) REVERT: G 189 LYS cc_start: 0.6942 (pttt) cc_final: 0.6738 (pttt) REVERT: G 192 VAL cc_start: 0.7102 (OUTLIER) cc_final: 0.6256 (p) REVERT: G 200 GLN cc_start: 0.6183 (OUTLIER) cc_final: 0.5353 (pp30) REVERT: G 212 ARG cc_start: 0.6039 (tmm160) cc_final: 0.5708 (ppt170) outliers start: 149 outliers final: 81 residues processed: 452 average time/residue: 0.1881 time to fit residues: 138.9145 Evaluate side-chains 383 residues out of total 3529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 290 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 284 THR Chi-restraints excluded: chain E residue 301 CYS Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 489 TYR Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 547 THR Chi-restraints excluded: chain E residue 588 THR Chi-restraints excluded: chain E residue 719 THR Chi-restraints excluded: chain E residue 731 MET Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 1114 ILE Chi-restraints excluded: chain E residue 1129 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 146 LYS Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain F residue 206 ASN Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 18 ARG Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 163 SER Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain G residue 200 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 119 optimal weight: 7.9990 chunk 195 optimal weight: 4.9990 chunk 118 optimal weight: 0.9990 chunk 283 optimal weight: 0.5980 chunk 151 optimal weight: 0.0980 chunk 96 optimal weight: 3.9990 chunk 292 optimal weight: 2.9990 chunk 330 optimal weight: 4.9990 chunk 398 optimal weight: 30.0000 chunk 267 optimal weight: 4.9990 chunk 275 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 394 ASN C 115 GLN C 173 GLN C 354 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 14 GLN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 448 ASN ** E 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 901 GLN B 153 ASN B 190 HIS G 39 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.108545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.081593 restraints weight = 81118.711| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.65 r_work: 0.3137 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 32779 Z= 0.128 Angle : 0.571 11.936 44730 Z= 0.287 Chirality : 0.044 0.272 5156 Planarity : 0.004 0.060 5717 Dihedral : 6.561 59.505 5238 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.54 % Allowed : 12.51 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.25 (0.12), residues: 4020 helix: 1.28 (0.20), residues: 702 sheet: -1.48 (0.16), residues: 931 loop : -2.50 (0.11), residues: 2387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 41 TYR 0.020 0.001 TYR F 32 PHE 0.018 0.001 PHE D 153 TRP 0.011 0.001 TRP A 886 HIS 0.005 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00298 (32690) covalent geometry : angle 0.55146 (44513) SS BOND : bond 0.00415 ( 50) SS BOND : angle 2.06779 ( 100) hydrogen bonds : bond 0.03826 ( 937) hydrogen bonds : angle 5.64791 ( 2598) link_NAG-ASN : bond 0.00371 ( 39) link_NAG-ASN : angle 2.27783 ( 117) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 3529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 316 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 SER cc_start: 0.7978 (m) cc_final: 0.7629 (p) REVERT: A 85 PRO cc_start: 0.7729 (Cg_exo) cc_final: 0.7496 (Cg_endo) REVERT: A 153 MET cc_start: 0.7480 (mtt) cc_final: 0.6452 (ppp) REVERT: A 186 PHE cc_start: 0.5066 (m-10) cc_final: 0.4764 (m-80) REVERT: A 505 TYR cc_start: 0.8455 (m-10) cc_final: 0.8212 (m-10) REVERT: A 725 GLU cc_start: 0.8566 (tt0) cc_final: 0.8302 (tt0) REVERT: C 574 ASP cc_start: 0.8185 (t70) cc_final: 0.7752 (t0) REVERT: C 616 ASN cc_start: 0.8784 (OUTLIER) cc_final: 0.8495 (t0) REVERT: C 855 PHE cc_start: 0.6447 (OUTLIER) cc_final: 0.5129 (t80) REVERT: E 351 TYR cc_start: 0.6627 (p90) cc_final: 0.5989 (p90) REVERT: E 448 ASN cc_start: 0.5292 (OUTLIER) cc_final: 0.4973 (m110) REVERT: E 489 TYR cc_start: 0.2944 (OUTLIER) cc_final: 0.2315 (m-80) REVERT: E 542 ASN cc_start: 0.7378 (t0) cc_final: 0.6271 (m-40) REVERT: E 720 ILE cc_start: 0.8893 (OUTLIER) cc_final: 0.8503 (mp) REVERT: E 747 THR cc_start: 0.8538 (p) cc_final: 0.8152 (m) REVERT: E 751 ASN cc_start: 0.8695 (m-40) cc_final: 0.8244 (m110) REVERT: E 768 THR cc_start: 0.8968 (m) cc_final: 0.8766 (m) REVERT: E 795 LYS cc_start: 0.8196 (mmtp) cc_final: 0.7889 (mptt) REVERT: E 804 GLN cc_start: 0.8402 (mm-40) cc_final: 0.7752 (mp10) REVERT: E 988 GLU cc_start: 0.8329 (mm-30) cc_final: 0.7900 (mp0) REVERT: D 155 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7777 (tm-30) REVERT: B 82 GLU cc_start: 0.8181 (pp20) cc_final: 0.7752 (pp20) REVERT: B 117 PHE cc_start: 0.7447 (m-10) cc_final: 0.7144 (m-80) REVERT: B 124 GLU cc_start: 0.7337 (tm-30) cc_final: 0.6576 (mt-10) REVERT: B 136 LEU cc_start: 0.7065 (OUTLIER) cc_final: 0.6449 (pt) REVERT: B 184 LYS cc_start: 0.7430 (OUTLIER) cc_final: 0.6815 (ptpp) REVERT: B 208 LYS cc_start: 0.4050 (mtpt) cc_final: 0.3203 (ptmt) REVERT: B 212 ARG cc_start: 0.7367 (OUTLIER) cc_final: 0.6716 (mtm110) REVERT: F 39 GLN cc_start: 0.5543 (tp40) cc_final: 0.5245 (tp40) REVERT: F 82 GLU cc_start: 0.6339 (tm-30) cc_final: 0.5690 (tm-30) REVERT: F 206 ASN cc_start: 0.7967 (OUTLIER) cc_final: 0.6866 (p0) REVERT: G 63 PHE cc_start: 0.6567 (m-80) cc_final: 0.6310 (m-80) REVERT: G 124 GLU cc_start: 0.5688 (tm-30) cc_final: 0.5155 (mt-10) REVERT: G 189 LYS cc_start: 0.6919 (pttt) cc_final: 0.6637 (pttt) REVERT: G 190 HIS cc_start: 0.5229 (m170) cc_final: 0.4486 (m-70) REVERT: G 200 GLN cc_start: 0.6072 (OUTLIER) cc_final: 0.5334 (pp30) outliers start: 123 outliers final: 78 residues processed: 419 average time/residue: 0.1918 time to fit residues: 130.5468 Evaluate side-chains 391 residues out of total 3529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 302 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 284 THR Chi-restraints excluded: chain E residue 301 CYS Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 448 ASN Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 489 TYR Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 588 THR Chi-restraints excluded: chain E residue 719 THR Chi-restraints excluded: chain E residue 720 ILE Chi-restraints excluded: chain E residue 731 MET Chi-restraints excluded: chain E residue 858 LEU Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain E residue 1129 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 146 LYS Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain F residue 206 ASN Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 18 ARG Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 163 SER Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 200 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 24 optimal weight: 0.0870 chunk 105 optimal weight: 2.9990 chunk 181 optimal weight: 3.9990 chunk 223 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 126 optimal weight: 0.8980 chunk 142 optimal weight: 2.9990 chunk 235 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 345 optimal weight: 0.0040 chunk 357 optimal weight: 9.9990 overall best weight: 0.9974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 173 GLN C 354 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 14 GLN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 448 ASN ** E 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 159 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.113487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.087120 restraints weight = 77288.032| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 3.42 r_work: 0.3109 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 32779 Z= 0.119 Angle : 0.557 11.933 44730 Z= 0.280 Chirality : 0.044 0.276 5156 Planarity : 0.004 0.060 5717 Dihedral : 6.329 59.892 5238 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 3.83 % Allowed : 13.03 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.13), residues: 4020 helix: 1.42 (0.20), residues: 708 sheet: -1.32 (0.16), residues: 949 loop : -2.44 (0.11), residues: 2363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 355 TYR 0.027 0.001 TYR F 32 PHE 0.020 0.001 PHE E 759 TRP 0.008 0.001 TRP A 886 HIS 0.004 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00282 (32690) covalent geometry : angle 0.53809 (44513) SS BOND : bond 0.00379 ( 50) SS BOND : angle 2.00332 ( 100) hydrogen bonds : bond 0.03679 ( 937) hydrogen bonds : angle 5.50250 ( 2598) link_NAG-ASN : bond 0.00400 ( 39) link_NAG-ASN : angle 2.23056 ( 117) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 3529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 316 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 SER cc_start: 0.7943 (m) cc_final: 0.7710 (p) REVERT: A 85 PRO cc_start: 0.7659 (Cg_exo) cc_final: 0.7226 (Cg_endo) REVERT: A 153 MET cc_start: 0.7464 (mtt) cc_final: 0.6442 (ppp) REVERT: A 170 TYR cc_start: 0.7126 (t80) cc_final: 0.6632 (t80) REVERT: A 186 PHE cc_start: 0.5069 (m-10) cc_final: 0.4842 (m-80) REVERT: A 505 TYR cc_start: 0.8344 (m-10) cc_final: 0.8136 (m-10) REVERT: A 725 GLU cc_start: 0.8357 (tt0) cc_final: 0.8085 (tt0) REVERT: A 776 LYS cc_start: 0.8923 (ttpp) cc_final: 0.8668 (tttm) REVERT: A 918 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7973 (mp0) REVERT: C 153 MET cc_start: 0.6543 (ptp) cc_final: 0.6295 (ptp) REVERT: C 574 ASP cc_start: 0.7942 (t70) cc_final: 0.7469 (t0) REVERT: C 616 ASN cc_start: 0.8655 (OUTLIER) cc_final: 0.8416 (t0) REVERT: C 855 PHE cc_start: 0.6417 (OUTLIER) cc_final: 0.5068 (t80) REVERT: E 351 TYR cc_start: 0.6619 (p90) cc_final: 0.6114 (p90) REVERT: E 489 TYR cc_start: 0.2819 (OUTLIER) cc_final: 0.2278 (m-80) REVERT: E 720 ILE cc_start: 0.8773 (OUTLIER) cc_final: 0.8439 (mp) REVERT: E 747 THR cc_start: 0.8418 (p) cc_final: 0.8057 (m) REVERT: E 751 ASN cc_start: 0.8588 (m-40) cc_final: 0.8128 (m110) REVERT: E 768 THR cc_start: 0.8810 (m) cc_final: 0.8581 (m) REVERT: E 795 LYS cc_start: 0.8097 (mmtp) cc_final: 0.7747 (mptt) REVERT: E 804 GLN cc_start: 0.8250 (mm-40) cc_final: 0.7667 (mp10) REVERT: E 988 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7767 (mp0) REVERT: D 155 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7775 (tp30) REVERT: B 82 GLU cc_start: 0.8231 (pp20) cc_final: 0.7726 (pp20) REVERT: B 124 GLU cc_start: 0.7304 (tm-30) cc_final: 0.6685 (pt0) REVERT: B 136 LEU cc_start: 0.7011 (OUTLIER) cc_final: 0.6357 (pp) REVERT: B 149 TRP cc_start: 0.5050 (m100) cc_final: 0.4814 (m100) REVERT: B 184 LYS cc_start: 0.7437 (OUTLIER) cc_final: 0.6758 (ptpp) REVERT: B 212 ARG cc_start: 0.7378 (OUTLIER) cc_final: 0.6181 (mtm-85) REVERT: F 82 GLU cc_start: 0.6247 (tm-30) cc_final: 0.5595 (tm-30) REVERT: F 206 ASN cc_start: 0.7921 (OUTLIER) cc_final: 0.7158 (p0) REVERT: G 40 LYS cc_start: 0.6627 (mtmm) cc_final: 0.6269 (mttt) REVERT: G 63 PHE cc_start: 0.6561 (m-80) cc_final: 0.6321 (m-80) REVERT: G 124 GLU cc_start: 0.5679 (tm-30) cc_final: 0.5177 (mt-10) REVERT: G 189 LYS cc_start: 0.7060 (pttt) cc_final: 0.6821 (pttt) REVERT: G 190 HIS cc_start: 0.5146 (m170) cc_final: 0.4878 (m170) REVERT: G 200 GLN cc_start: 0.6228 (OUTLIER) cc_final: 0.5554 (pp30) outliers start: 133 outliers final: 87 residues processed: 428 average time/residue: 0.1891 time to fit residues: 132.5965 Evaluate side-chains 392 residues out of total 3529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 294 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 284 THR Chi-restraints excluded: chain E residue 301 CYS Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 489 TYR Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 588 THR Chi-restraints excluded: chain E residue 719 THR Chi-restraints excluded: chain E residue 720 ILE Chi-restraints excluded: chain E residue 731 MET Chi-restraints excluded: chain E residue 858 LEU Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 911 VAL Chi-restraints excluded: chain E residue 1129 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 171 HIS Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 146 LYS Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain F residue 206 ASN Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 18 ARG Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 163 SER Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 200 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 0 optimal weight: 30.0000 chunk 368 optimal weight: 10.0000 chunk 345 optimal weight: 0.0010 chunk 169 optimal weight: 9.9990 chunk 209 optimal weight: 1.9990 chunk 28 optimal weight: 0.0020 chunk 114 optimal weight: 4.9990 chunk 23 optimal weight: 9.9990 chunk 96 optimal weight: 4.9990 chunk 267 optimal weight: 10.0000 chunk 16 optimal weight: 8.9990 overall best weight: 2.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 334 ASN A 856 ASN C 173 GLN C 354 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C1083 HIS ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 1 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 GLN ** G 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.108311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.081724 restraints weight = 79461.089| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 3.20 r_work: 0.3063 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.4354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 32779 Z= 0.212 Angle : 0.639 14.701 44730 Z= 0.322 Chirality : 0.046 0.262 5156 Planarity : 0.004 0.093 5717 Dihedral : 6.605 59.982 5238 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 4.11 % Allowed : 13.43 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.19 (0.12), residues: 4020 helix: 1.23 (0.20), residues: 687 sheet: -1.46 (0.16), residues: 936 loop : -2.38 (0.11), residues: 2397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.001 ARG F 98 TYR 0.036 0.002 TYR E 396 PHE 0.027 0.002 PHE C 157 TRP 0.013 0.001 TRP E 886 HIS 0.007 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00506 (32690) covalent geometry : angle 0.62119 (44513) SS BOND : bond 0.00552 ( 50) SS BOND : angle 2.01445 ( 100) hydrogen bonds : bond 0.04429 ( 937) hydrogen bonds : angle 5.64145 ( 2598) link_NAG-ASN : bond 0.00452 ( 39) link_NAG-ASN : angle 2.42281 ( 117) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 3529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 318 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 SER cc_start: 0.8049 (m) cc_final: 0.7770 (p) REVERT: A 153 MET cc_start: 0.7547 (mtt) cc_final: 0.6401 (ppp) REVERT: A 170 TYR cc_start: 0.7189 (t80) cc_final: 0.6729 (t80) REVERT: A 186 PHE cc_start: 0.5316 (m-10) cc_final: 0.5066 (m-80) REVERT: A 918 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8033 (mp0) REVERT: C 574 ASP cc_start: 0.8444 (t70) cc_final: 0.8032 (t0) REVERT: C 616 ASN cc_start: 0.8759 (OUTLIER) cc_final: 0.8470 (t0) REVERT: C 815 ARG cc_start: 0.8436 (mtm-85) cc_final: 0.8121 (mtm110) REVERT: C 855 PHE cc_start: 0.6464 (OUTLIER) cc_final: 0.5064 (t80) REVERT: E 244 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7943 (pp) REVERT: E 351 TYR cc_start: 0.6628 (p90) cc_final: 0.6178 (p90) REVERT: E 462 LYS cc_start: 0.7641 (OUTLIER) cc_final: 0.7054 (ptpp) REVERT: E 489 TYR cc_start: 0.2853 (OUTLIER) cc_final: 0.2225 (m-80) REVERT: E 549 THR cc_start: 0.8434 (OUTLIER) cc_final: 0.8210 (m) REVERT: E 710 ASN cc_start: 0.8094 (m-40) cc_final: 0.7882 (m-40) REVERT: E 747 THR cc_start: 0.8629 (p) cc_final: 0.8251 (m) REVERT: E 751 ASN cc_start: 0.8662 (m-40) cc_final: 0.8203 (m110) REVERT: E 804 GLN cc_start: 0.8373 (mm-40) cc_final: 0.7799 (mp10) REVERT: D 13 ARG cc_start: 0.7741 (mmt180) cc_final: 0.7537 (mmt180) REVERT: D 155 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7900 (tp30) REVERT: B 82 GLU cc_start: 0.8265 (pp20) cc_final: 0.7813 (pp20) REVERT: B 117 PHE cc_start: 0.7563 (m-80) cc_final: 0.7224 (m-80) REVERT: B 124 GLU cc_start: 0.7491 (tm-30) cc_final: 0.7046 (pt0) REVERT: B 136 LEU cc_start: 0.7006 (OUTLIER) cc_final: 0.6398 (pt) REVERT: B 184 LYS cc_start: 0.7452 (OUTLIER) cc_final: 0.6767 (ptpp) REVERT: B 212 ARG cc_start: 0.7319 (OUTLIER) cc_final: 0.6551 (mtm110) REVERT: F 31 ASN cc_start: 0.8589 (t0) cc_final: 0.8148 (t0) REVERT: F 82 GLU cc_start: 0.6169 (tm-30) cc_final: 0.5552 (tm-30) REVERT: G 63 PHE cc_start: 0.6687 (m-80) cc_final: 0.6436 (m-80) REVERT: G 78 ARG cc_start: 0.7182 (mmp80) cc_final: 0.6913 (tpp-160) REVERT: G 106 GLU cc_start: 0.7288 (tt0) cc_final: 0.6967 (mp0) REVERT: G 124 GLU cc_start: 0.6020 (tm-30) cc_final: 0.5530 (mt-10) REVERT: G 144 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7497 (pm20) REVERT: G 166 GLU cc_start: 0.4147 (pt0) cc_final: 0.3608 (pm20) REVERT: G 189 LYS cc_start: 0.7026 (pttt) cc_final: 0.6808 (pttt) REVERT: G 190 HIS cc_start: 0.5093 (m170) cc_final: 0.4854 (m170) REVERT: G 200 GLN cc_start: 0.6451 (OUTLIER) cc_final: 0.5636 (tm-30) outliers start: 143 outliers final: 98 residues processed: 435 average time/residue: 0.1870 time to fit residues: 133.3005 Evaluate side-chains 402 residues out of total 3529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 291 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 284 THR Chi-restraints excluded: chain E residue 301 CYS Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 462 LYS Chi-restraints excluded: chain E residue 489 TYR Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 547 THR Chi-restraints excluded: chain E residue 549 THR Chi-restraints excluded: chain E residue 588 THR Chi-restraints excluded: chain E residue 705 VAL Chi-restraints excluded: chain E residue 719 THR Chi-restraints excluded: chain E residue 731 MET Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 911 VAL Chi-restraints excluded: chain E residue 1129 VAL Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 146 LYS Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 18 ARG Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain G residue 163 SER Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 200 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 37 optimal weight: 0.4980 chunk 359 optimal weight: 7.9990 chunk 289 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 298 optimal weight: 2.9990 chunk 390 optimal weight: 6.9990 chunk 243 optimal weight: 0.6980 chunk 192 optimal weight: 0.6980 chunk 275 optimal weight: 0.7980 chunk 381 optimal weight: 9.9990 chunk 342 optimal weight: 9.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 ASN C 173 GLN C 354 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 474 GLN ** E 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 GLN G 148 GLN ** G 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.108826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.083415 restraints weight = 80424.142| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 3.24 r_work: 0.3104 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.4341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 32779 Z= 0.107 Angle : 0.560 12.933 44730 Z= 0.281 Chirality : 0.044 0.257 5156 Planarity : 0.004 0.059 5717 Dihedral : 6.229 59.084 5235 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.31 % Allowed : 14.44 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.92 (0.13), residues: 4020 helix: 1.53 (0.20), residues: 689 sheet: -1.23 (0.16), residues: 951 loop : -2.27 (0.11), residues: 2380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 357 TYR 0.030 0.001 TYR E 396 PHE 0.024 0.001 PHE E 400 TRP 0.007 0.001 TRP F 36 HIS 0.004 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00250 (32690) covalent geometry : angle 0.54331 (44513) SS BOND : bond 0.00353 ( 50) SS BOND : angle 1.83378 ( 100) hydrogen bonds : bond 0.03661 ( 937) hydrogen bonds : angle 5.41955 ( 2598) link_NAG-ASN : bond 0.00397 ( 39) link_NAG-ASN : angle 2.14120 ( 117) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 3529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 303 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 SER cc_start: 0.7977 (m) cc_final: 0.7748 (p) REVERT: A 85 PRO cc_start: 0.7692 (Cg_exo) cc_final: 0.7263 (Cg_endo) REVERT: A 153 MET cc_start: 0.7510 (mtt) cc_final: 0.6395 (ppp) REVERT: A 574 ASP cc_start: 0.8400 (t0) cc_final: 0.8054 (t0) REVERT: A 725 GLU cc_start: 0.8447 (tt0) cc_final: 0.8222 (tt0) REVERT: A 918 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7922 (mp0) REVERT: C 474 GLN cc_start: 0.6958 (pt0) cc_final: 0.6123 (pm20) REVERT: C 574 ASP cc_start: 0.8026 (t70) cc_final: 0.7543 (t0) REVERT: C 616 ASN cc_start: 0.8557 (OUTLIER) cc_final: 0.8281 (t0) REVERT: C 815 ARG cc_start: 0.8347 (mtm-85) cc_final: 0.8032 (mtm110) REVERT: C 855 PHE cc_start: 0.6291 (OUTLIER) cc_final: 0.4954 (t80) REVERT: E 351 TYR cc_start: 0.6745 (p90) cc_final: 0.6240 (p90) REVERT: E 489 TYR cc_start: 0.2957 (OUTLIER) cc_final: 0.2292 (m-80) REVERT: E 537 LYS cc_start: 0.8236 (tttm) cc_final: 0.8011 (tttt) REVERT: E 720 ILE cc_start: 0.8772 (OUTLIER) cc_final: 0.8483 (mp) REVERT: E 747 THR cc_start: 0.8466 (p) cc_final: 0.8156 (m) REVERT: E 751 ASN cc_start: 0.8541 (m-40) cc_final: 0.8104 (m110) REVERT: E 804 GLN cc_start: 0.8174 (mm-40) cc_final: 0.7607 (mp10) REVERT: D 73 ASP cc_start: 0.8114 (t0) cc_final: 0.7885 (t0) REVERT: D 155 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7811 (tp30) REVERT: B 82 GLU cc_start: 0.8209 (pp20) cc_final: 0.7809 (pp20) REVERT: B 117 PHE cc_start: 0.7592 (m-10) cc_final: 0.7248 (m-80) REVERT: B 124 GLU cc_start: 0.7484 (tm-30) cc_final: 0.6807 (pt0) REVERT: B 136 LEU cc_start: 0.7047 (OUTLIER) cc_final: 0.6426 (pt) REVERT: B 184 LYS cc_start: 0.7542 (OUTLIER) cc_final: 0.6874 (ptpp) REVERT: B 212 ARG cc_start: 0.7279 (OUTLIER) cc_final: 0.6019 (mtm-85) REVERT: F 82 GLU cc_start: 0.6037 (tm-30) cc_final: 0.5469 (tm-30) REVERT: G 40 LYS cc_start: 0.6585 (mtmm) cc_final: 0.6227 (mttt) REVERT: G 63 PHE cc_start: 0.6687 (m-80) cc_final: 0.6470 (m-80) REVERT: G 78 ARG cc_start: 0.7147 (mmp80) cc_final: 0.6923 (tpp-160) REVERT: G 106 GLU cc_start: 0.7194 (tt0) cc_final: 0.6905 (mp0) REVERT: G 124 GLU cc_start: 0.5800 (tm-30) cc_final: 0.5471 (mt-10) REVERT: G 144 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7403 (pm20) REVERT: G 166 GLU cc_start: 0.3974 (pt0) cc_final: 0.3373 (pm20) REVERT: G 190 HIS cc_start: 0.4806 (m170) cc_final: 0.4539 (m170) REVERT: G 200 GLN cc_start: 0.6358 (OUTLIER) cc_final: 0.5631 (tm-30) outliers start: 115 outliers final: 87 residues processed: 395 average time/residue: 0.1870 time to fit residues: 121.3466 Evaluate side-chains 384 residues out of total 3529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 286 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 215 ASP Chi-restraints excluded: chain E residue 284 THR Chi-restraints excluded: chain E residue 301 CYS Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 349 SER Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 489 TYR Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 547 THR Chi-restraints excluded: chain E residue 588 THR Chi-restraints excluded: chain E residue 720 ILE Chi-restraints excluded: chain E residue 731 MET Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 1129 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 146 LYS Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain F residue 112 GLN Chi-restraints excluded: chain F residue 206 ASN Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 18 ARG Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain G residue 163 SER Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 200 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 380 optimal weight: 20.0000 chunk 162 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 144 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 299 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 149 optimal weight: 6.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 173 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 GLN ** G 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 190 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.106018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.080034 restraints weight = 81941.623| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.81 r_work: 0.3090 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.4466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 32779 Z= 0.153 Angle : 0.585 12.028 44730 Z= 0.293 Chirality : 0.044 0.255 5156 Planarity : 0.004 0.061 5717 Dihedral : 6.285 59.322 5235 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 3.57 % Allowed : 14.30 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.92 (0.13), residues: 4020 helix: 1.42 (0.20), residues: 689 sheet: -1.21 (0.16), residues: 943 loop : -2.24 (0.11), residues: 2388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 214 TYR 0.037 0.001 TYR A 170 PHE 0.025 0.001 PHE E 400 TRP 0.009 0.001 TRP C 152 HIS 0.005 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00367 (32690) covalent geometry : angle 0.56936 (44513) SS BOND : bond 0.00413 ( 50) SS BOND : angle 1.78256 ( 100) hydrogen bonds : bond 0.03936 ( 937) hydrogen bonds : angle 5.42061 ( 2598) link_NAG-ASN : bond 0.00402 ( 39) link_NAG-ASN : angle 2.21760 ( 117) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 3529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 300 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 SER cc_start: 0.8037 (m) cc_final: 0.7744 (p) REVERT: A 85 PRO cc_start: 0.7687 (Cg_exo) cc_final: 0.7308 (Cg_endo) REVERT: A 97 LYS cc_start: 0.5737 (pptt) cc_final: 0.5252 (ptmm) REVERT: A 153 MET cc_start: 0.7518 (mtt) cc_final: 0.6401 (ppp) REVERT: A 574 ASP cc_start: 0.8683 (t0) cc_final: 0.8388 (t0) REVERT: A 660 TYR cc_start: 0.8694 (m-80) cc_final: 0.8242 (m-80) REVERT: A 918 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8098 (mp0) REVERT: C 474 GLN cc_start: 0.7163 (pt0) cc_final: 0.6247 (pm20) REVERT: C 574 ASP cc_start: 0.8379 (t70) cc_final: 0.7943 (t0) REVERT: C 616 ASN cc_start: 0.8609 (OUTLIER) cc_final: 0.8315 (t0) REVERT: C 815 ARG cc_start: 0.8419 (mtm-85) cc_final: 0.8136 (mtm110) REVERT: C 855 PHE cc_start: 0.6373 (OUTLIER) cc_final: 0.5093 (t80) REVERT: E 351 TYR cc_start: 0.6687 (p90) cc_final: 0.6176 (p90) REVERT: E 489 TYR cc_start: 0.2912 (OUTLIER) cc_final: 0.2243 (m-80) REVERT: E 747 THR cc_start: 0.8607 (p) cc_final: 0.8292 (m) REVERT: E 751 ASN cc_start: 0.8637 (m-40) cc_final: 0.8218 (m110) REVERT: E 804 GLN cc_start: 0.8376 (mm-40) cc_final: 0.7777 (mp10) REVERT: E 902 MET cc_start: 0.8752 (mmm) cc_final: 0.8424 (tpt) REVERT: D 73 ASP cc_start: 0.8276 (t0) cc_final: 0.8001 (t0) REVERT: D 155 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7916 (tp30) REVERT: B 82 GLU cc_start: 0.8287 (pp20) cc_final: 0.7922 (pp20) REVERT: B 117 PHE cc_start: 0.7589 (m-10) cc_final: 0.7259 (m-80) REVERT: B 124 GLU cc_start: 0.7510 (tm-30) cc_final: 0.7137 (pt0) REVERT: B 136 LEU cc_start: 0.7048 (OUTLIER) cc_final: 0.6432 (pt) REVERT: B 184 LYS cc_start: 0.7496 (OUTLIER) cc_final: 0.6817 (ptpp) REVERT: B 212 ARG cc_start: 0.7325 (OUTLIER) cc_final: 0.6037 (mtm-85) REVERT: F 82 GLU cc_start: 0.6080 (tm-30) cc_final: 0.5542 (tm-30) REVERT: F 101 ARG cc_start: 0.8228 (mtm110) cc_final: 0.7530 (mtm110) REVERT: G 40 LYS cc_start: 0.6588 (mtmm) cc_final: 0.6131 (mttt) REVERT: G 78 ARG cc_start: 0.7184 (mmp80) cc_final: 0.6974 (tpp-160) REVERT: G 106 GLU cc_start: 0.7209 (tt0) cc_final: 0.6649 (mp0) REVERT: G 124 GLU cc_start: 0.6016 (tm-30) cc_final: 0.5604 (mt-10) REVERT: G 144 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7430 (pm20) REVERT: G 166 GLU cc_start: 0.4116 (pt0) cc_final: 0.3471 (pm20) REVERT: G 189 LYS cc_start: 0.6537 (pttt) cc_final: 0.6274 (pttt) REVERT: G 200 GLN cc_start: 0.6427 (OUTLIER) cc_final: 0.5719 (tm-30) outliers start: 124 outliers final: 96 residues processed: 399 average time/residue: 0.1915 time to fit residues: 125.2391 Evaluate side-chains 393 residues out of total 3529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 287 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1137 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 215 ASP Chi-restraints excluded: chain E residue 284 THR Chi-restraints excluded: chain E residue 301 CYS Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 349 SER Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 489 TYR Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 547 THR Chi-restraints excluded: chain E residue 588 THR Chi-restraints excluded: chain E residue 719 THR Chi-restraints excluded: chain E residue 731 MET Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 911 VAL Chi-restraints excluded: chain E residue 977 LEU Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain E residue 1129 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 146 LYS Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 18 ARG Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain G residue 163 SER Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 200 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 20 optimal weight: 10.0000 chunk 230 optimal weight: 9.9990 chunk 48 optimal weight: 0.4980 chunk 127 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 287 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 377 optimal weight: 9.9990 chunk 194 optimal weight: 4.9990 chunk 352 optimal weight: 6.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 173 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN F 112 GLN ** G 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.107084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.080950 restraints weight = 80891.024| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.91 r_work: 0.3108 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.4506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 32779 Z= 0.120 Angle : 0.564 14.421 44730 Z= 0.282 Chirality : 0.044 0.246 5156 Planarity : 0.004 0.060 5717 Dihedral : 6.174 58.673 5235 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 3.31 % Allowed : 14.56 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.13), residues: 4020 helix: 1.48 (0.20), residues: 695 sheet: -1.12 (0.16), residues: 936 loop : -2.17 (0.12), residues: 2389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 214 TYR 0.035 0.001 TYR A 170 PHE 0.020 0.001 PHE D 153 TRP 0.008 0.001 TRP C 152 HIS 0.005 0.001 HIS G 190 Details of bonding type rmsd covalent geometry : bond 0.00287 (32690) covalent geometry : angle 0.54837 (44513) SS BOND : bond 0.00383 ( 50) SS BOND : angle 1.73865 ( 100) hydrogen bonds : bond 0.03689 ( 937) hydrogen bonds : angle 5.32881 ( 2598) link_NAG-ASN : bond 0.00390 ( 39) link_NAG-ASN : angle 2.12860 ( 117) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 3529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 299 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 SER cc_start: 0.8009 (m) cc_final: 0.7762 (p) REVERT: A 85 PRO cc_start: 0.7688 (Cg_exo) cc_final: 0.7346 (Cg_endo) REVERT: A 153 MET cc_start: 0.7499 (mtt) cc_final: 0.6401 (ppp) REVERT: A 574 ASP cc_start: 0.8658 (t0) cc_final: 0.8373 (t0) REVERT: A 660 TYR cc_start: 0.8678 (m-80) cc_final: 0.8216 (m-80) REVERT: A 918 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.8122 (mp0) REVERT: C 133 PHE cc_start: 0.7303 (m-80) cc_final: 0.6778 (m-80) REVERT: C 474 GLN cc_start: 0.7097 (pt0) cc_final: 0.6205 (pm20) REVERT: C 574 ASP cc_start: 0.8332 (t70) cc_final: 0.7867 (t0) REVERT: C 616 ASN cc_start: 0.8560 (OUTLIER) cc_final: 0.8298 (t0) REVERT: C 815 ARG cc_start: 0.8402 (mtm-85) cc_final: 0.8074 (mtm180) REVERT: C 855 PHE cc_start: 0.6300 (OUTLIER) cc_final: 0.5008 (t80) REVERT: E 326 ILE cc_start: 0.8032 (mm) cc_final: 0.7783 (mm) REVERT: E 351 TYR cc_start: 0.6675 (p90) cc_final: 0.5960 (p90) REVERT: E 489 TYR cc_start: 0.2944 (OUTLIER) cc_final: 0.2281 (m-80) REVERT: E 747 THR cc_start: 0.8586 (p) cc_final: 0.8250 (m) REVERT: E 751 ASN cc_start: 0.8630 (m-40) cc_final: 0.8201 (m110) REVERT: E 804 GLN cc_start: 0.8365 (mm-40) cc_final: 0.7748 (mp10) REVERT: E 902 MET cc_start: 0.8718 (mmm) cc_final: 0.8382 (tpt) REVERT: D 73 ASP cc_start: 0.8285 (t0) cc_final: 0.8017 (t0) REVERT: D 145 LEU cc_start: 0.3992 (OUTLIER) cc_final: 0.3741 (pt) REVERT: D 155 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7931 (tp30) REVERT: B 117 PHE cc_start: 0.7580 (m-10) cc_final: 0.7255 (m-80) REVERT: B 136 LEU cc_start: 0.7057 (OUTLIER) cc_final: 0.6441 (pt) REVERT: B 184 LYS cc_start: 0.7541 (OUTLIER) cc_final: 0.6918 (ptpp) REVERT: B 212 ARG cc_start: 0.7311 (OUTLIER) cc_final: 0.6030 (mtm-85) REVERT: F 82 GLU cc_start: 0.6065 (tm-30) cc_final: 0.5496 (tm-30) REVERT: F 101 ARG cc_start: 0.8239 (mtm110) cc_final: 0.7596 (mtm110) REVERT: G 124 GLU cc_start: 0.6006 (tm-30) cc_final: 0.5593 (mt-10) REVERT: G 144 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7419 (pm20) REVERT: G 166 GLU cc_start: 0.4072 (pt0) cc_final: 0.3435 (pm20) REVERT: G 200 GLN cc_start: 0.6381 (OUTLIER) cc_final: 0.5731 (tm-30) outliers start: 115 outliers final: 94 residues processed: 388 average time/residue: 0.1929 time to fit residues: 122.8217 Evaluate side-chains 391 residues out of total 3529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 286 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 215 ASP Chi-restraints excluded: chain E residue 284 THR Chi-restraints excluded: chain E residue 301 CYS Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 489 TYR Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 547 THR Chi-restraints excluded: chain E residue 588 THR Chi-restraints excluded: chain E residue 719 THR Chi-restraints excluded: chain E residue 731 MET Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 911 VAL Chi-restraints excluded: chain E residue 977 LEU Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain E residue 1129 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 146 LYS Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain F residue 112 GLN Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 18 ARG Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain G residue 163 SER Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 200 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 95 optimal weight: 1.9990 chunk 173 optimal weight: 4.9990 chunk 354 optimal weight: 10.0000 chunk 353 optimal weight: 6.9990 chunk 296 optimal weight: 3.9990 chunk 400 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 147 optimal weight: 8.9990 chunk 127 optimal weight: 0.6980 chunk 398 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 173 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 GLN ** G 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.106536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.080574 restraints weight = 82126.665| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.78 r_work: 0.3103 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.4562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 32779 Z= 0.127 Angle : 0.570 13.748 44730 Z= 0.285 Chirality : 0.044 0.243 5156 Planarity : 0.004 0.090 5717 Dihedral : 6.152 58.522 5235 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 3.22 % Allowed : 14.79 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.13), residues: 4020 helix: 1.50 (0.20), residues: 695 sheet: -1.10 (0.16), residues: 930 loop : -2.14 (0.12), residues: 2395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 98 TYR 0.039 0.001 TYR A 170 PHE 0.020 0.001 PHE D 153 TRP 0.008 0.001 TRP F 36 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00302 (32690) covalent geometry : angle 0.55537 (44513) SS BOND : bond 0.00385 ( 50) SS BOND : angle 1.65658 ( 100) hydrogen bonds : bond 0.03704 ( 937) hydrogen bonds : angle 5.30517 ( 2598) link_NAG-ASN : bond 0.00389 ( 39) link_NAG-ASN : angle 2.12543 ( 117) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8040 Ramachandran restraints generated. 4020 Oldfield, 0 Emsley, 4020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 3529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 288 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 PRO cc_start: 0.7665 (Cg_exo) cc_final: 0.7445 (Cg_endo) REVERT: A 97 LYS cc_start: 0.5699 (pptt) cc_final: 0.5241 (ptmm) REVERT: A 153 MET cc_start: 0.7507 (mtt) cc_final: 0.6398 (ppp) REVERT: A 574 ASP cc_start: 0.8678 (t0) cc_final: 0.8394 (t0) REVERT: A 660 TYR cc_start: 0.8681 (m-80) cc_final: 0.8217 (m-80) REVERT: A 918 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8169 (mp0) REVERT: C 133 PHE cc_start: 0.7275 (m-80) cc_final: 0.6695 (m-80) REVERT: C 346 ARG cc_start: 0.7021 (tpt170) cc_final: 0.6733 (tmt170) REVERT: C 474 GLN cc_start: 0.7116 (pt0) cc_final: 0.6216 (pm20) REVERT: C 574 ASP cc_start: 0.8351 (t70) cc_final: 0.7899 (t0) REVERT: C 616 ASN cc_start: 0.8549 (OUTLIER) cc_final: 0.8296 (t0) REVERT: C 815 ARG cc_start: 0.8398 (mtm-85) cc_final: 0.8133 (mtm110) REVERT: C 855 PHE cc_start: 0.6331 (OUTLIER) cc_final: 0.5040 (t80) REVERT: E 198 ASP cc_start: 0.8156 (t0) cc_final: 0.7914 (p0) REVERT: E 326 ILE cc_start: 0.8042 (mm) cc_final: 0.7787 (mm) REVERT: E 351 TYR cc_start: 0.6665 (p90) cc_final: 0.5962 (p90) REVERT: E 489 TYR cc_start: 0.2877 (OUTLIER) cc_final: 0.2274 (m-80) REVERT: E 747 THR cc_start: 0.8586 (p) cc_final: 0.8247 (m) REVERT: E 751 ASN cc_start: 0.8639 (m-40) cc_final: 0.8210 (m110) REVERT: E 804 GLN cc_start: 0.8371 (mm-40) cc_final: 0.7776 (mp10) REVERT: E 902 MET cc_start: 0.8726 (mmm) cc_final: 0.8387 (tpt) REVERT: D 73 ASP cc_start: 0.8298 (t0) cc_final: 0.8027 (t0) REVERT: D 145 LEU cc_start: 0.4179 (OUTLIER) cc_final: 0.3931 (pt) REVERT: D 155 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7951 (tp30) REVERT: B 117 PHE cc_start: 0.7553 (m-10) cc_final: 0.7262 (m-80) REVERT: B 136 LEU cc_start: 0.7041 (OUTLIER) cc_final: 0.6436 (pt) REVERT: B 184 LYS cc_start: 0.7555 (OUTLIER) cc_final: 0.6910 (ptpp) REVERT: B 212 ARG cc_start: 0.7308 (OUTLIER) cc_final: 0.6032 (mtm-85) REVERT: F 65 GLN cc_start: 0.7811 (tp-100) cc_final: 0.7569 (tp-100) REVERT: F 82 GLU cc_start: 0.6064 (tm-30) cc_final: 0.5545 (tm-30) REVERT: F 101 ARG cc_start: 0.8233 (mtm110) cc_final: 0.7588 (mtm110) REVERT: G 124 GLU cc_start: 0.6017 (tm-30) cc_final: 0.5581 (mt-10) REVERT: G 144 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7435 (pm20) REVERT: G 166 GLU cc_start: 0.4053 (pt0) cc_final: 0.3422 (pm20) REVERT: G 200 GLN cc_start: 0.6474 (OUTLIER) cc_final: 0.5660 (tm-30) outliers start: 112 outliers final: 97 residues processed: 375 average time/residue: 0.1871 time to fit residues: 115.7021 Evaluate side-chains 392 residues out of total 3529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 284 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 440 ASN Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 918 GLU Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 215 ASP Chi-restraints excluded: chain E residue 284 THR Chi-restraints excluded: chain E residue 301 CYS Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 430 THR Chi-restraints excluded: chain E residue 461 LEU Chi-restraints excluded: chain E residue 489 TYR Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 546 LEU Chi-restraints excluded: chain E residue 588 THR Chi-restraints excluded: chain E residue 719 THR Chi-restraints excluded: chain E residue 731 MET Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 911 VAL Chi-restraints excluded: chain E residue 977 LEU Chi-restraints excluded: chain E residue 1128 VAL Chi-restraints excluded: chain E residue 1129 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 155 GLU Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 146 LYS Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 184 LYS Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain F residue 112 GLN Chi-restraints excluded: chain G residue 13 LEU Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 18 ARG Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain G residue 163 SER Chi-restraints excluded: chain G residue 165 THR Chi-restraints excluded: chain G residue 200 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 35 optimal weight: 7.9990 chunk 350 optimal weight: 0.9980 chunk 174 optimal weight: 1.9990 chunk 311 optimal weight: 3.9990 chunk 139 optimal weight: 0.9980 chunk 384 optimal weight: 9.9990 chunk 226 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 178 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 147 optimal weight: 9.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 173 GLN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 GLN ** G 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.106045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.079814 restraints weight = 81549.725| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.87 r_work: 0.3092 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.4653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 32779 Z= 0.153 Angle : 0.588 13.811 44730 Z= 0.295 Chirality : 0.045 0.243 5156 Planarity : 0.004 0.060 5717 Dihedral : 6.210 59.147 5233 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % Rotamer: Outliers : 3.39 % Allowed : 14.87 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.13), residues: 4020 helix: 1.55 (0.20), residues: 683 sheet: -1.12 (0.16), residues: 939 loop : -2.14 (0.12), residues: 2398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 98 TYR 0.037 0.001 TYR A 170 PHE 0.020 0.001 PHE D 153 TRP 0.009 0.001 TRP E 886 HIS 0.005 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00368 (32690) covalent geometry : angle 0.57237 (44513) SS BOND : bond 0.00427 ( 50) SS BOND : angle 1.82182 ( 100) hydrogen bonds : bond 0.03883 ( 937) hydrogen bonds : angle 5.35134 ( 2598) link_NAG-ASN : bond 0.00395 ( 39) link_NAG-ASN : angle 2.17530 ( 117) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11070.10 seconds wall clock time: 188 minutes 55.49 seconds (11335.49 seconds total)