Starting phenix.real_space_refine on Fri Jun 27 16:45:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7woa_32646/06_2025/7woa_32646.cif Found real_map, /net/cci-nas-00/data/ceres_data/7woa_32646/06_2025/7woa_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_32646/06_2025/7woa_32646.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7woa_32646/06_2025/7woa_32646.map" model { file = "/net/cci-nas-00/data/ceres_data/7woa_32646/06_2025/7woa_32646.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7woa_32646/06_2025/7woa_32646.cif" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 2} 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: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 2} 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: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 2} 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: 18.98, per 1000 atoms: 0.59 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: 8.21 Conformation dependent library (CDL) restraints added in 4.5 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: 5.19 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: 15.55 Time building geometry restraints manager: 9.90 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: 0.09 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: 4.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.540 Check model and map are aligned: 0.250 Set scattering table: 0.320 Process input model: 79.430 Find NCS groups from input model: 1.490 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.560 ------------------------------------------------------------------------------- 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 : 6.56 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.46 (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 TRP 0.005 0.000 TRP A 886 HIS 0.001 0.000 HIS B 190 PHE 0.010 0.001 PHE C 562 TYR 0.008 0.000 TYR E 265 ARG 0.002 0.000 ARG D 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00215 ( 39) link_NAG-ASN : angle 0.85185 ( 117) hydrogen bonds : bond 0.21983 ( 937) hydrogen bonds : angle 8.39696 ( 2598) SS BOND : bond 0.00121 ( 50) SS BOND : angle 0.54730 ( 100) covalent geometry : bond 0.00243 (32690) covalent geometry : angle 0.45109 (44513) *********************** 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 : 3.479 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: 0.5012 (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: 0.6894 (p0) REVERT: A 820 ASP cc_start: 0.7423 (OUTLIER) cc_final: 0.7002 (m-30) REVERT: A 947 LYS cc_start: 0.7507 (OUTLIER) cc_final: 0.7237 (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: 0.5919 (t80) REVERT: C 470 THR cc_start: 0.7525 (p) cc_final: 0.7317 (p) REVERT: C 855 PHE cc_start: 0.6406 (OUTLIER) cc_final: 0.5748 (t80) REVERT: C 878 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8538 (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: 0.7973 (m110) REVERT: E 396 TYR cc_start: 0.5683 (m-80) cc_final: 0.5242 (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: 0.8354 (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: 0.8591 (mt) REVERT: D 153 PHE cc_start: 0.4540 (OUTLIER) cc_final: 0.3723 (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: 0.7617 (pt) REVERT: B 76 ILE cc_start: 0.7957 (mt) cc_final: 0.7739 (mt) REVERT: B 104 LYS cc_start: 0.8272 (tptt) cc_final: 0.7643 (tttp) REVERT: B 124 GLU cc_start: 0.6711 (tm-30) cc_final: 0.6326 (mt-10) REVERT: B 136 LEU cc_start: 0.7534 (OUTLIER) cc_final: 0.7003 (pt) 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: 0.6849 (t80) REVERT: F 41 PRO cc_start: 0.7883 (Cg_exo) cc_final: 0.7496 (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: 0.6285 (m-10) REVERT: G 107 ILE cc_start: 0.6481 (OUTLIER) cc_final: 0.6150 (mp) REVERT: G 200 GLN cc_start: 0.5305 (OUTLIER) cc_final: 0.4532 (pp30) outliers start: 147 outliers final: 27 residues processed: 877 average time/residue: 0.4588 time to fit residues: 624.7020 Evaluate side-chains 418 residues out of total 3529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 378 time to evaluate : 3.712 ------------------------------------------------------------------------------- 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 424 LYS 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 340 optimal weight: 9.9990 chunk 305 optimal weight: 4.9990 chunk 169 optimal weight: 5.9990 chunk 104 optimal weight: 0.4980 chunk 206 optimal weight: 0.9980 chunk 163 optimal weight: 6.9990 chunk 315 optimal weight: 3.9990 chunk 122 optimal weight: 0.6980 chunk 192 optimal weight: 4.9990 chunk 235 optimal weight: 5.9990 chunk 365 optimal weight: 9.9990 overall best weight: 2.2384 ------------------------------------------------------------------------------- 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 762 GLN A 784 GLN A 872 GLN A 901 GLN A 926 GLN A 992 GLN A1005 GLN A1048 HIS ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 ASN C 14 GLN C 23 GLN C 173 GLN C 188 ASN C 211 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 ASN C 360 ASN C 414 GLN C 439 ASN C 498 GLN C 787 GLN C 901 GLN C 913 GLN C 954 GLN C 957 GLN C 965 GLN C1048 HIS E 14 GLN E 207 HIS E 218 GLN E 414 GLN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 437 ASN E 474 GLN E 493 GLN ** E 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 580 GLN E 641 ASN E 655 HIS E 675 GLN E 703 ASN E 710 ASN E 755 GLN E 762 GLN E 784 GLN E 949 GLN E 954 GLN E1002 GLN E1011 GLN E1048 HIS E1106 GLN 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 190 HIS B 200 GLN F 59 HIS F 112 GLN F 171 HIS F 206 ASN G 33 HIS G 39 GLN G 43 GLN G 148 GLN G 159 ASN G 167 GLN Total number of N/Q/H flips: 77 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.104640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.077207 restraints weight = 84922.306| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.50 r_work: 0.3169 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 32779 Z= 0.209 Angle : 0.670 12.594 44730 Z= 0.338 Chirality : 0.047 0.246 5156 Planarity : 0.005 0.055 5717 Dihedral : 7.375 58.952 5258 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 3.91 % Allowed : 11.16 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.12), residues: 4020 helix: 0.84 (0.20), residues: 701 sheet: -1.89 (0.16), residues: 889 loop : -2.90 (0.11), residues: 2430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 886 HIS 0.011 0.002 HIS C 146 PHE 0.021 0.002 PHE E 140 TYR 0.025 0.002 TYR B 50 ARG 0.010 0.001 ARG B 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00464 ( 39) link_NAG-ASN : angle 2.41850 ( 117) hydrogen bonds : bond 0.04454 ( 937) hydrogen bonds : angle 6.20156 ( 2598) SS BOND : bond 0.00635 ( 50) SS BOND : angle 2.22297 ( 100) covalent geometry : bond 0.00497 (32690) covalent geometry : angle 0.65209 (44513) *********************** 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 523 residues out of total 3529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 387 time to evaluate : 3.622 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: A 66 HIS cc_start: 0.6303 (m90) cc_final: 0.5963 (m90) REVERT: A 85 PRO cc_start: 0.7998 (Cg_exo) cc_final: 0.7728 (Cg_endo) REVERT: A 153 MET cc_start: 0.7188 (mtt) cc_final: 0.6121 (ppp) REVERT: A 233 ILE cc_start: 0.5522 (OUTLIER) cc_final: 0.5298 (pt) REVERT: A 619 GLU cc_start: 0.7528 (mt-10) cc_final: 0.7182 (tt0) REVERT: C 542 ASN cc_start: 0.8131 (t0) cc_final: 0.7885 (t0) REVERT: C 574 ASP cc_start: 0.8011 (t70) cc_final: 0.7646 (t0) REVERT: C 855 PHE cc_start: 0.6450 (OUTLIER) cc_final: 0.5298 (t80) REVERT: C 957 GLN cc_start: 0.8710 (tt0) cc_final: 0.8406 (tp-100) REVERT: E 351 TYR cc_start: 0.6351 (p90) cc_final: 0.6141 (p90) REVERT: E 377 PHE cc_start: 0.5275 (OUTLIER) cc_final: 0.4896 (m-80) REVERT: E 541 PHE cc_start: 0.8366 (p90) cc_final: 0.8159 (p90) REVERT: E 542 ASN cc_start: 0.7482 (t0) cc_final: 0.6687 (m-40) REVERT: E 804 GLN cc_start: 0.8437 (mm-40) cc_final: 0.7737 (mp10) REVERT: E 878 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8721 (mt) REVERT: D 153 PHE cc_start: 0.5434 (OUTLIER) cc_final: 0.5207 (t80) REVERT: D 155 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7506 (tp30) REVERT: B 124 GLU cc_start: 0.7240 (tm-30) cc_final: 0.6574 (mt-10) REVERT: B 136 LEU cc_start: 0.7218 (OUTLIER) cc_final: 0.6580 (pp) REVERT: B 166 GLU cc_start: 0.6894 (tp30) cc_final: 0.6545 (tp30) REVERT: B 184 LYS cc_start: 0.7339 (OUTLIER) cc_final: 0.6879 (ptpt) REVERT: B 212 ARG cc_start: 0.7506 (OUTLIER) cc_final: 0.6877 (mtm110) REVERT: F 27 ASP cc_start: 0.7545 (p0) cc_final: 0.6963 (p0) REVERT: F 39 GLN cc_start: 0.5602 (tp40) cc_final: 0.5303 (tp40) REVERT: F 112 GLN cc_start: 0.7992 (mt0) cc_final: 0.7763 (pt0) REVERT: G 24 ARG cc_start: 0.6866 (mtp-110) cc_final: 0.6588 (mtm-85) REVERT: G 40 LYS cc_start: 0.7138 (mttt) cc_final: 0.6430 (mtmm) REVERT: G 84 PHE cc_start: 0.6947 (m-10) cc_final: 0.6716 (m-10) REVERT: G 149 TRP cc_start: 0.3157 (m100) cc_final: 0.1954 (m100) REVERT: G 190 HIS cc_start: 0.5135 (m-70) cc_final: 0.4613 (m-70) REVERT: G 200 GLN cc_start: 0.6277 (OUTLIER) cc_final: 0.5312 (pp30) REVERT: G 212 ARG cc_start: 0.5841 (tmm160) cc_final: 0.5451 (ppt170) outliers start: 136 outliers final: 69 residues processed: 496 average time/residue: 0.4484 time to fit residues: 357.1119 Evaluate side-chains 389 residues out of total 3529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 310 time to evaluate : 3.776 ------------------------------------------------------------------------------- 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 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 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 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 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain C residue 24 LEU 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 358 ILE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 525 CYS 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 1050 MET 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 53 ASP 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 377 PHE 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 858 LEU Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 1122 VAL Chi-restraints excluded: chain E residue 1129 VAL Chi-restraints excluded: chain D residue 63 LYS Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 149 VAL Chi-restraints excluded: chain D residue 153 PHE 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 177 optimal weight: 6.9990 chunk 239 optimal weight: 4.9990 chunk 274 optimal weight: 7.9990 chunk 91 optimal weight: 4.9990 chunk 295 optimal weight: 3.9990 chunk 303 optimal weight: 2.9990 chunk 311 optimal weight: 0.7980 chunk 24 optimal weight: 30.0000 chunk 67 optimal weight: 0.6980 chunk 281 optimal weight: 3.9990 chunk 16 optimal weight: 9.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 ASN A 188 ASN A 245 HIS A 613 GLN ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN C 173 GLN C 354 ASN C 544 ASN C 613 GLN C 901 GLN C1083 HIS E 14 GLN E 245 HIS E 321 GLN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 641 ASN E 762 GLN E 901 GLN E 949 GLN E1002 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 ASN B 199 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.106651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.080362 restraints weight = 81894.080| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 3.04 r_work: 0.3075 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 32779 Z= 0.218 Angle : 0.644 13.269 44730 Z= 0.325 Chirality : 0.046 0.330 5156 Planarity : 0.004 0.057 5717 Dihedral : 7.216 59.856 5244 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 4.06 % Allowed : 12.08 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.12), residues: 4020 helix: 0.92 (0.20), residues: 690 sheet: -1.82 (0.16), residues: 943 loop : -2.68 (0.11), residues: 2387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 886 HIS 0.008 0.001 HIS A1048 PHE 0.023 0.002 PHE A 186 TYR 0.017 0.002 TYR C 380 ARG 0.005 0.001 ARG C 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00544 ( 39) link_NAG-ASN : angle 2.55212 ( 117) hydrogen bonds : bond 0.04587 ( 937) hydrogen bonds : angle 5.98099 ( 2598) SS BOND : bond 0.00516 ( 50) SS BOND : angle 2.22951 ( 100) covalent geometry : bond 0.00522 (32690) covalent geometry : angle 0.62296 (44513) *********************** 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 462 residues out of total 3529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 321 time to evaluate : 3.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 PRO cc_start: 0.7929 (Cg_exo) cc_final: 0.7533 (Cg_endo) REVERT: A 153 MET cc_start: 0.7382 (mtt) cc_final: 0.6031 (ppp) REVERT: A 237 ARG cc_start: 0.7537 (mtm-85) cc_final: 0.7288 (mtm-85) REVERT: A 505 TYR cc_start: 0.8559 (m-10) cc_final: 0.8310 (m-10) REVERT: C 574 ASP cc_start: 0.8308 (t70) cc_final: 0.7923 (t0) REVERT: C 616 ASN cc_start: 0.8765 (OUTLIER) cc_final: 0.8477 (t0) REVERT: C 855 PHE cc_start: 0.6487 (OUTLIER) cc_final: 0.5025 (t80) REVERT: C 957 GLN cc_start: 0.8861 (tt0) cc_final: 0.8603 (tp40) REVERT: E 177 MET cc_start: 0.6929 (mtp) cc_final: 0.6577 (mtp) REVERT: E 489 TYR cc_start: 0.2771 (OUTLIER) cc_final: 0.2187 (m-80) REVERT: E 541 PHE cc_start: 0.8351 (p90) cc_final: 0.8081 (p90) REVERT: E 759 PHE cc_start: 0.7494 (OUTLIER) cc_final: 0.7261 (p90) REVERT: E 804 GLN cc_start: 0.8488 (mm-40) cc_final: 0.7824 (mp10) REVERT: E 900 MET cc_start: 0.8770 (OUTLIER) cc_final: 0.8534 (mtt) REVERT: D 27 ASP cc_start: 0.8516 (p0) cc_final: 0.7426 (p0) REVERT: D 155 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7629 (tp30) REVERT: D 185 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7721 (pt) REVERT: B 117 PHE cc_start: 0.7481 (m-10) cc_final: 0.7165 (m-80) REVERT: B 124 GLU cc_start: 0.7340 (tm-30) cc_final: 0.6533 (mt-10) REVERT: B 136 LEU cc_start: 0.7070 (OUTLIER) cc_final: 0.6429 (pt) REVERT: B 184 LYS cc_start: 0.7387 (OUTLIER) cc_final: 0.6629 (ptpp) REVERT: B 212 ARG cc_start: 0.7477 (OUTLIER) cc_final: 0.6209 (mtm-85) REVERT: F 206 ASN cc_start: 0.7882 (OUTLIER) cc_final: 0.7491 (p0) REVERT: G 24 ARG cc_start: 0.6859 (mtp-110) cc_final: 0.6642 (mtm-85) REVERT: G 40 LYS cc_start: 0.7061 (mttt) cc_final: 0.6132 (tppt) REVERT: G 189 LYS cc_start: 0.6976 (pttt) cc_final: 0.6749 (pttt) REVERT: G 192 VAL cc_start: 0.7088 (OUTLIER) cc_final: 0.6199 (p) REVERT: G 200 GLN cc_start: 0.6186 (OUTLIER) cc_final: 0.5450 (pp30) outliers start: 141 outliers final: 89 residues processed: 433 average time/residue: 0.4556 time to fit residues: 318.0106 Evaluate side-chains 388 residues out of total 3529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 286 time to evaluate : 3.289 ------------------------------------------------------------------------------- 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 336 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 417 LYS 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 649 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 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 216 LEU 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 358 ILE Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 415 THR Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 525 CYS 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 1129 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 197 ILE Chi-restraints excluded: chain E residue 301 CYS Chi-restraints excluded: chain E residue 312 ILE Chi-restraints excluded: chain E residue 364 ASP 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 510 VAL 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 759 PHE Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 900 MET Chi-restraints excluded: chain E residue 1122 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 155 GLU Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 185 LEU 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 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 108 ASP 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 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 192 VAL Chi-restraints excluded: chain G residue 200 GLN Chi-restraints excluded: chain G residue 206 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 226 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 176 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 117 optimal weight: 4.9990 chunk 375 optimal weight: 20.0000 chunk 236 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 ASN ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN C 173 GLN C 354 ASN E 14 GLN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 949 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 206 ASN G 159 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.106345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.080476 restraints weight = 82027.484| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.84 r_work: 0.3084 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 32779 Z= 0.154 Angle : 0.585 11.659 44730 Z= 0.295 Chirality : 0.045 0.284 5156 Planarity : 0.004 0.058 5717 Dihedral : 6.942 59.917 5240 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 3.68 % Allowed : 13.23 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.12), residues: 4020 helix: 1.19 (0.20), residues: 689 sheet: -1.60 (0.16), residues: 932 loop : -2.55 (0.11), residues: 2399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 886 HIS 0.005 0.001 HIS E 519 PHE 0.027 0.001 PHE D 153 TYR 0.027 0.001 TYR F 32 ARG 0.005 0.000 ARG F 101 Details of bonding type rmsd link_NAG-ASN : bond 0.00375 ( 39) link_NAG-ASN : angle 2.28507 ( 117) hydrogen bonds : bond 0.04016 ( 937) hydrogen bonds : angle 5.72529 ( 2598) SS BOND : bond 0.00402 ( 50) SS BOND : angle 1.79109 ( 100) covalent geometry : bond 0.00366 (32690) covalent geometry : angle 0.56835 (44513) *********************** 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: 128 poor density : 311 time to evaluate : 3.568 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: 0.7788 (Cg_exo) cc_final: 0.7521 (Cg_endo) REVERT: A 153 MET cc_start: 0.7457 (mtt) cc_final: 0.6272 (ppp) REVERT: A 237 ARG cc_start: 0.7569 (mtm-85) cc_final: 0.7357 (mtm-85) REVERT: A 1129 VAL cc_start: 0.8617 (OUTLIER) cc_final: 0.8400 (t) REVERT: C 574 ASP cc_start: 0.8344 (t70) cc_final: 0.7959 (t0) REVERT: C 616 ASN cc_start: 0.8812 (OUTLIER) cc_final: 0.8563 (t0) REVERT: C 855 PHE cc_start: 0.6448 (OUTLIER) cc_final: 0.5076 (t80) REVERT: E 489 TYR cc_start: 0.2794 (OUTLIER) cc_final: 0.2194 (m-80) REVERT: E 541 PHE cc_start: 0.8332 (p90) cc_final: 0.8064 (p90) REVERT: E 804 GLN cc_start: 0.8441 (mm-40) cc_final: 0.7827 (mp10) REVERT: D 27 ASP cc_start: 0.8485 (p0) cc_final: 0.7684 (p0) REVERT: D 155 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7720 (tp30) REVERT: D 183 TYR cc_start: 0.7791 (m-80) cc_final: 0.7530 (m-80) REVERT: B 82 GLU cc_start: 0.8424 (pp20) cc_final: 0.8027 (pp20) REVERT: B 83 ASP cc_start: 0.7997 (m-30) cc_final: 0.7767 (m-30) REVERT: B 124 GLU cc_start: 0.7409 (tm-30) cc_final: 0.6618 (mt-10) REVERT: B 136 LEU cc_start: 0.7106 (OUTLIER) cc_final: 0.6418 (pp) REVERT: B 184 LYS cc_start: 0.7417 (OUTLIER) cc_final: 0.6652 (ptpp) REVERT: B 212 ARG cc_start: 0.7444 (OUTLIER) cc_final: 0.6161 (mtm-85) REVERT: F 98 ARG cc_start: 0.8030 (ttt-90) cc_final: 0.7667 (ttp-170) REVERT: F 183 TYR cc_start: 0.6339 (m-10) cc_final: 0.6016 (m-10) REVERT: G 40 LYS cc_start: 0.7062 (mttt) cc_final: 0.6171 (tppt) REVERT: G 189 LYS cc_start: 0.6890 (pttt) cc_final: 0.6615 (pttt) REVERT: G 190 HIS cc_start: 0.5184 (m170) cc_final: 0.4464 (m-70) REVERT: G 200 GLN cc_start: 0.6232 (OUTLIER) cc_final: 0.5560 (pp30) outliers start: 128 outliers final: 86 residues processed: 420 average time/residue: 0.4291 time to fit residues: 293.4969 Evaluate side-chains 379 residues out of total 3529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 284 time to evaluate : 3.270 ------------------------------------------------------------------------------- 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 66 HIS 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 417 LYS 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 512 VAL 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 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 1114 ILE Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 229 LEU 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 350 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 719 THR 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 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 83 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 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 731 MET Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 911 VAL Chi-restraints excluded: chain E residue 1122 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 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 79 LEU 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 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 165 THR Chi-restraints excluded: chain G residue 200 GLN Chi-restraints excluded: chain G residue 206 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 113 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 chunk 338 optimal weight: 7.9990 chunk 297 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 351 optimal weight: 7.9990 chunk 264 optimal weight: 0.4980 chunk 40 optimal weight: 2.9990 chunk 150 optimal weight: 0.0370 chunk 225 optimal weight: 10.0000 chunk 140 optimal weight: 10.0000 overall best weight: 1.7064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 GLN C 354 ASN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 474 GLN ** E 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 949 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.101201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.073881 restraints weight = 84748.872| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.64 r_work: 0.3083 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.4190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 32779 Z= 0.162 Angle : 0.590 11.859 44730 Z= 0.296 Chirality : 0.045 0.272 5156 Planarity : 0.004 0.060 5717 Dihedral : 6.777 59.699 5240 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 4.37 % Allowed : 13.46 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.12), residues: 4020 helix: 1.35 (0.21), residues: 677 sheet: -1.56 (0.16), residues: 950 loop : -2.44 (0.11), residues: 2393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 886 HIS 0.005 0.001 HIS C1064 PHE 0.024 0.001 PHE D 153 TYR 0.020 0.001 TYR A 170 ARG 0.004 0.000 ARG F 101 Details of bonding type rmsd link_NAG-ASN : bond 0.00417 ( 39) link_NAG-ASN : angle 2.33536 ( 117) hydrogen bonds : bond 0.04053 ( 937) hydrogen bonds : angle 5.62109 ( 2598) SS BOND : bond 0.00496 ( 50) SS BOND : angle 1.91212 ( 100) covalent geometry : bond 0.00384 (32690) covalent geometry : angle 0.57218 (44513) *********************** 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 460 residues out of total 3529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 308 time to evaluate : 3.245 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: 0.7787 (Cg_exo) cc_final: 0.7568 (Cg_endo) REVERT: A 153 MET cc_start: 0.7543 (mtt) cc_final: 0.6331 (ppp) REVERT: A 186 PHE cc_start: 0.5146 (m-10) cc_final: 0.4873 (m-80) REVERT: A 237 ARG cc_start: 0.7574 (mtm-85) cc_final: 0.7315 (mtm-85) REVERT: A 882 ILE cc_start: 0.9146 (OUTLIER) cc_final: 0.8881 (mp) REVERT: A 1129 VAL cc_start: 0.8637 (OUTLIER) cc_final: 0.8414 (t) REVERT: C 574 ASP cc_start: 0.8352 (t70) cc_final: 0.7943 (t0) REVERT: C 616 ASN cc_start: 0.8748 (OUTLIER) cc_final: 0.8459 (t0) REVERT: C 855 PHE cc_start: 0.6379 (OUTLIER) cc_final: 0.5048 (t80) REVERT: E 462 LYS cc_start: 0.7496 (OUTLIER) cc_final: 0.6990 (tmtt) REVERT: E 489 TYR cc_start: 0.2889 (OUTLIER) cc_final: 0.2193 (m-80) REVERT: E 541 PHE cc_start: 0.8333 (p90) cc_final: 0.8021 (p90) REVERT: E 710 ASN cc_start: 0.8034 (m-40) cc_final: 0.7811 (m-40) REVERT: E 804 GLN cc_start: 0.8382 (mm-40) cc_final: 0.7851 (mp10) REVERT: D 155 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7687 (tp30) REVERT: B 117 PHE cc_start: 0.7566 (m-10) cc_final: 0.7217 (m-80) REVERT: B 124 GLU cc_start: 0.7380 (tm-30) cc_final: 0.6588 (mt-10) REVERT: B 136 LEU cc_start: 0.7108 (OUTLIER) cc_final: 0.6468 (pt) REVERT: B 149 TRP cc_start: 0.5103 (m100) cc_final: 0.4885 (m100) REVERT: B 166 GLU cc_start: 0.7071 (tp30) cc_final: 0.6279 (tp30) REVERT: B 184 LYS cc_start: 0.7455 (OUTLIER) cc_final: 0.6741 (ptpp) REVERT: B 212 ARG cc_start: 0.7450 (OUTLIER) cc_final: 0.6135 (mtm-85) REVERT: F 27 ASP cc_start: 0.7763 (p0) cc_final: 0.7493 (p0) REVERT: F 32 TYR cc_start: 0.8326 (m-80) cc_final: 0.7991 (m-80) REVERT: F 98 ARG cc_start: 0.7871 (ttt-90) cc_final: 0.7638 (ttp80) REVERT: G 40 LYS cc_start: 0.7055 (mttt) cc_final: 0.5959 (tppt) REVERT: G 78 ARG cc_start: 0.6937 (mmp80) cc_final: 0.6438 (mmm160) REVERT: G 189 LYS cc_start: 0.6995 (pttt) cc_final: 0.6737 (pttt) REVERT: G 190 HIS cc_start: 0.5320 (m170) cc_final: 0.5062 (m170) REVERT: G 200 GLN cc_start: 0.6381 (OUTLIER) cc_final: 0.5598 (pp30) outliers start: 152 outliers final: 106 residues processed: 432 average time/residue: 0.4319 time to fit residues: 301.9192 Evaluate side-chains 399 residues out of total 3529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 282 time to evaluate : 3.301 ------------------------------------------------------------------------------- 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 66 HIS 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 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 417 LYS 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 512 VAL 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 882 ILE 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 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 277 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 415 THR Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 719 THR 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 1129 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 83 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 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 510 VAL Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 547 THR Chi-restraints excluded: chain E residue 552 LEU 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 858 LEU Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 911 VAL Chi-restraints excluded: chain E residue 1122 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 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 79 LEU 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 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 58 optimal weight: 2.9990 chunk 398 optimal weight: 7.9990 chunk 282 optimal weight: 2.9990 chunk 337 optimal weight: 3.9990 chunk 255 optimal weight: 10.0000 chunk 127 optimal weight: 0.7980 chunk 219 optimal weight: 0.9980 chunk 217 optimal weight: 4.9990 chunk 129 optimal weight: 8.9990 chunk 365 optimal weight: 8.9990 chunk 189 optimal weight: 0.8980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 GLN ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 14 GLN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 580 GLN E 949 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.111163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.084324 restraints weight = 77495.687| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.93 r_work: 0.3110 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.4369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 32779 Z= 0.162 Angle : 0.595 14.581 44730 Z= 0.298 Chirality : 0.045 0.261 5156 Planarity : 0.004 0.059 5717 Dihedral : 6.708 59.870 5240 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 4.17 % Allowed : 13.92 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.13), residues: 4020 helix: 1.41 (0.21), residues: 678 sheet: -1.50 (0.16), residues: 948 loop : -2.38 (0.11), residues: 2394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.004 0.001 HIS C1064 PHE 0.023 0.001 PHE C 157 TYR 0.016 0.001 TYR E 265 ARG 0.006 0.000 ARG G 41 Details of bonding type rmsd link_NAG-ASN : bond 0.00405 ( 39) link_NAG-ASN : angle 2.28932 ( 117) hydrogen bonds : bond 0.04052 ( 937) hydrogen bonds : angle 5.57414 ( 2598) SS BOND : bond 0.00462 ( 50) SS BOND : angle 1.84206 ( 100) covalent geometry : bond 0.00387 (32690) covalent geometry : angle 0.57808 (44513) *********************** 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 436 residues out of total 3529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 291 time to evaluate : 3.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 PRO cc_start: 0.7796 (Cg_exo) cc_final: 0.7550 (Cg_endo) REVERT: A 153 MET cc_start: 0.7574 (mtt) cc_final: 0.6433 (ppp) REVERT: A 170 TYR cc_start: 0.7162 (t80) cc_final: 0.6811 (t80) REVERT: A 186 PHE cc_start: 0.5325 (m-10) cc_final: 0.5070 (m-80) REVERT: A 237 ARG cc_start: 0.7658 (mtm-85) cc_final: 0.7424 (mtm-85) REVERT: A 660 TYR cc_start: 0.8721 (m-80) cc_final: 0.8264 (m-80) REVERT: A 882 ILE cc_start: 0.9142 (OUTLIER) cc_final: 0.8910 (mp) REVERT: A 1129 VAL cc_start: 0.8659 (OUTLIER) cc_final: 0.8425 (t) REVERT: C 574 ASP cc_start: 0.8332 (t70) cc_final: 0.7924 (t0) REVERT: C 616 ASN cc_start: 0.8751 (OUTLIER) cc_final: 0.8474 (t0) REVERT: C 855 PHE cc_start: 0.6484 (OUTLIER) cc_final: 0.5201 (t80) REVERT: E 462 LYS cc_start: 0.7463 (OUTLIER) cc_final: 0.6898 (ptpp) REVERT: E 489 TYR cc_start: 0.3272 (OUTLIER) cc_final: 0.2328 (m-80) REVERT: E 541 PHE cc_start: 0.8255 (p90) cc_final: 0.8046 (p90) REVERT: E 549 THR cc_start: 0.8627 (OUTLIER) cc_final: 0.8383 (m) REVERT: E 710 ASN cc_start: 0.8081 (m-40) cc_final: 0.7855 (m-40) REVERT: E 804 GLN cc_start: 0.8378 (mm-40) cc_final: 0.7848 (mp10) REVERT: D 155 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7732 (tp30) REVERT: D 178 GLN cc_start: 0.5837 (mm110) cc_final: 0.5623 (mp10) REVERT: B 117 PHE cc_start: 0.7517 (m-10) cc_final: 0.7181 (m-80) REVERT: B 136 LEU cc_start: 0.7147 (OUTLIER) cc_final: 0.6524 (pt) REVERT: B 149 TRP cc_start: 0.5227 (m100) cc_final: 0.5012 (m100) REVERT: B 184 LYS cc_start: 0.7468 (OUTLIER) cc_final: 0.6826 (ptpp) REVERT: B 212 ARG cc_start: 0.7380 (OUTLIER) cc_final: 0.6037 (mtm-85) REVERT: F 27 ASP cc_start: 0.7719 (p0) cc_final: 0.7391 (p0) REVERT: F 32 TYR cc_start: 0.8316 (m-80) cc_final: 0.7914 (m-80) REVERT: F 39 GLN cc_start: 0.5709 (tp40) cc_final: 0.5480 (tp40) REVERT: F 112 GLN cc_start: 0.7707 (mp10) cc_final: 0.7459 (pm20) REVERT: F 150 LYS cc_start: 0.4642 (mmmt) cc_final: 0.3913 (tppt) REVERT: G 40 LYS cc_start: 0.6823 (mttt) cc_final: 0.5972 (tppt) REVERT: G 78 ARG cc_start: 0.7019 (mmp80) cc_final: 0.6805 (tpp-160) REVERT: G 144 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7463 (pm20) REVERT: G 189 LYS cc_start: 0.7163 (pttt) cc_final: 0.6907 (pttt) REVERT: G 190 HIS cc_start: 0.5531 (m170) cc_final: 0.5305 (m170) REVERT: G 200 GLN cc_start: 0.6181 (OUTLIER) cc_final: 0.5580 (pp30) outliers start: 145 outliers final: 106 residues processed: 411 average time/residue: 0.4362 time to fit residues: 292.2861 Evaluate side-chains 395 residues out of total 3529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 276 time to evaluate : 3.401 ------------------------------------------------------------------------------- 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 66 HIS 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 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 417 LYS 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 512 VAL Chi-restraints excluded: chain A residue 531 THR 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 882 ILE 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 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 277 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 415 THR Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 719 THR 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 1129 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 53 ASP Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 83 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 197 ILE 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 336 CYS 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 510 VAL Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 549 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 1122 VAL Chi-restraints excluded: chain E residue 1129 VAL Chi-restraints excluded: chain D residue 117 THR 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 57 THR Chi-restraints excluded: chain B residue 78 ARG Chi-restraints excluded: chain B residue 79 LEU 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 190 HIS 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 261 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 chunk 212 optimal weight: 2.9990 chunk 211 optimal weight: 1.9990 chunk 377 optimal weight: 10.0000 chunk 178 optimal weight: 3.9990 chunk 30 optimal weight: 0.0010 chunk 41 optimal weight: 0.9990 chunk 374 optimal weight: 3.9990 chunk 246 optimal weight: 0.8980 chunk 249 optimal weight: 0.9990 overall best weight: 0.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN C 173 GLN ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 949 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.110607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.083990 restraints weight = 79041.301| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.96 r_work: 0.3107 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.4393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 32779 Z= 0.118 Angle : 0.562 12.038 44730 Z= 0.281 Chirality : 0.044 0.259 5156 Planarity : 0.004 0.059 5717 Dihedral : 6.486 58.580 5240 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 3.94 % Allowed : 14.33 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.13), residues: 4020 helix: 1.54 (0.21), residues: 682 sheet: -1.34 (0.16), residues: 969 loop : -2.31 (0.11), residues: 2369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 152 HIS 0.004 0.001 HIS E 519 PHE 0.019 0.001 PHE D 153 TYR 0.015 0.001 TYR E 265 ARG 0.005 0.000 ARG C 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00396 ( 39) link_NAG-ASN : angle 2.17812 ( 117) hydrogen bonds : bond 0.03720 ( 937) hydrogen bonds : angle 5.43758 ( 2598) SS BOND : bond 0.00399 ( 50) SS BOND : angle 1.87784 ( 100) covalent geometry : bond 0.00281 (32690) covalent geometry : angle 0.54541 (44513) *********************** 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 434 residues out of total 3529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 297 time to evaluate : 3.312 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 85 PRO cc_start: 0.7782 (Cg_exo) cc_final: 0.7537 (Cg_endo) REVERT: A 153 MET cc_start: 0.7490 (mtt) cc_final: 0.6395 (ppp) REVERT: A 170 TYR cc_start: 0.7125 (t80) cc_final: 0.6695 (t80) REVERT: A 186 PHE cc_start: 0.5296 (m-10) cc_final: 0.5042 (m-80) REVERT: A 237 ARG cc_start: 0.7535 (mtm-85) cc_final: 0.7308 (mtm-85) REVERT: A 660 TYR cc_start: 0.8705 (m-80) cc_final: 0.8240 (m-80) REVERT: A 882 ILE cc_start: 0.9086 (OUTLIER) cc_final: 0.8824 (mp) REVERT: A 1129 VAL cc_start: 0.8623 (OUTLIER) cc_final: 0.8418 (t) REVERT: C 474 GLN cc_start: 0.7083 (pt0) cc_final: 0.6248 (pm20) REVERT: C 574 ASP cc_start: 0.8268 (t70) cc_final: 0.7834 (t0) REVERT: C 616 ASN cc_start: 0.8668 (OUTLIER) cc_final: 0.8435 (t0) REVERT: C 855 PHE cc_start: 0.6442 (OUTLIER) cc_final: 0.5161 (t80) REVERT: E 462 LYS cc_start: 0.7419 (OUTLIER) cc_final: 0.6903 (ptpp) REVERT: E 489 TYR cc_start: 0.2881 (OUTLIER) cc_final: 0.2224 (m-80) REVERT: E 739 THR cc_start: 0.8908 (m) cc_final: 0.8680 (m) REVERT: E 751 ASN cc_start: 0.8726 (m-40) cc_final: 0.8328 (m110) REVERT: E 804 GLN cc_start: 0.8360 (mm-40) cc_final: 0.7847 (mp10) REVERT: D 155 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7818 (tp30) REVERT: B 104 LYS cc_start: 0.8304 (tptt) cc_final: 0.7848 (tttp) REVERT: B 117 PHE cc_start: 0.7541 (m-10) cc_final: 0.7129 (m-80) REVERT: B 136 LEU cc_start: 0.7166 (OUTLIER) cc_final: 0.6601 (pt) REVERT: B 184 LYS cc_start: 0.7502 (OUTLIER) cc_final: 0.6863 (ptpp) REVERT: B 208 LYS cc_start: 0.4524 (mtpt) cc_final: 0.3309 (ptmt) REVERT: B 212 ARG cc_start: 0.7404 (OUTLIER) cc_final: 0.6070 (mtm-85) REVERT: F 27 ASP cc_start: 0.7674 (p0) cc_final: 0.7152 (p0) REVERT: F 32 TYR cc_start: 0.8157 (m-80) cc_final: 0.7768 (m-80) REVERT: F 39 GLN cc_start: 0.5573 (tp40) cc_final: 0.5329 (tp40) REVERT: F 150 LYS cc_start: 0.4441 (mmmt) cc_final: 0.3941 (tppt) REVERT: G 40 LYS cc_start: 0.6887 (mttt) cc_final: 0.6013 (tppt) REVERT: G 49 ILE cc_start: 0.8160 (mt) cc_final: 0.7886 (mm) REVERT: G 144 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7372 (pm20) REVERT: G 189 LYS cc_start: 0.7037 (pttt) cc_final: 0.6823 (pttt) REVERT: G 200 GLN cc_start: 0.6455 (OUTLIER) cc_final: 0.5880 (pp30) outliers start: 137 outliers final: 102 residues processed: 407 average time/residue: 0.4185 time to fit residues: 279.3811 Evaluate side-chains 398 residues out of total 3529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 284 time to evaluate : 3.332 ------------------------------------------------------------------------------- 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 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 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 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 417 LYS 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 512 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 882 ILE 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 1114 ILE Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 229 LEU 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 350 VAL Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 390 LEU 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 518 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 719 THR 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 1122 VAL Chi-restraints excluded: chain C residue 1129 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 83 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 336 CYS 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 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 827 THR 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 1072 GLU Chi-restraints excluded: chain E residue 1122 VAL Chi-restraints excluded: chain E residue 1129 VAL Chi-restraints excluded: chain D residue 117 THR 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 79 LEU 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 190 HIS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 377 optimal weight: 20.0000 chunk 117 optimal weight: 6.9990 chunk 272 optimal weight: 0.6980 chunk 282 optimal weight: 3.9990 chunk 284 optimal weight: 0.6980 chunk 310 optimal weight: 0.0670 chunk 249 optimal weight: 10.0000 chunk 291 optimal weight: 3.9990 chunk 223 optimal weight: 4.9990 chunk 308 optimal weight: 1.9990 chunk 397 optimal weight: 20.0000 overall best weight: 1.4922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN C 173 GLN ** C 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 949 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 GLN G 190 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.106712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.080327 restraints weight = 81332.069| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.68 r_work: 0.3109 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.4529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 32779 Z= 0.146 Angle : 0.575 15.044 44730 Z= 0.289 Chirality : 0.044 0.252 5156 Planarity : 0.004 0.059 5717 Dihedral : 6.499 59.183 5240 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 3.83 % Allowed : 14.73 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.13), residues: 4020 helix: 1.55 (0.21), residues: 676 sheet: -1.30 (0.16), residues: 952 loop : -2.28 (0.11), residues: 2392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 152 HIS 0.004 0.001 HIS E 519 PHE 0.037 0.001 PHE C 157 TYR 0.015 0.001 TYR E 265 ARG 0.009 0.000 ARG C 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00399 ( 39) link_NAG-ASN : angle 2.20279 ( 117) hydrogen bonds : bond 0.03897 ( 937) hydrogen bonds : angle 5.42396 ( 2598) SS BOND : bond 0.00438 ( 50) SS BOND : angle 1.63997 ( 100) covalent geometry : bond 0.00348 (32690) covalent geometry : angle 0.55991 (44513) *********************** 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 431 residues out of total 3529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 298 time to evaluate : 3.831 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 85 PRO cc_start: 0.7770 (Cg_exo) cc_final: 0.7520 (Cg_endo) REVERT: A 153 MET cc_start: 0.7521 (mtt) cc_final: 0.6399 (ppp) REVERT: A 170 TYR cc_start: 0.7118 (t80) cc_final: 0.6717 (t80) REVERT: A 186 PHE cc_start: 0.5386 (m-10) cc_final: 0.5169 (m-80) REVERT: A 237 ARG cc_start: 0.7577 (mtm-85) cc_final: 0.7360 (mtm-85) REVERT: A 660 TYR cc_start: 0.8727 (m-80) cc_final: 0.8261 (m-80) REVERT: A 882 ILE cc_start: 0.9139 (OUTLIER) cc_final: 0.8870 (mp) REVERT: A 1129 VAL cc_start: 0.8666 (OUTLIER) cc_final: 0.8449 (t) REVERT: C 474 GLN cc_start: 0.7273 (pt0) cc_final: 0.6315 (pm20) REVERT: C 574 ASP cc_start: 0.8290 (t70) cc_final: 0.7872 (t0) REVERT: C 616 ASN cc_start: 0.8668 (OUTLIER) cc_final: 0.8445 (t0) REVERT: C 855 PHE cc_start: 0.6525 (OUTLIER) cc_final: 0.5238 (t80) REVERT: C 988 GLU cc_start: 0.8117 (tp30) cc_final: 0.7797 (mm-30) REVERT: E 326 ILE cc_start: 0.7996 (mm) cc_final: 0.7747 (mm) REVERT: E 462 LYS cc_start: 0.7403 (OUTLIER) cc_final: 0.6891 (ptpp) REVERT: E 489 TYR cc_start: 0.3146 (OUTLIER) cc_final: 0.2304 (m-80) REVERT: E 751 ASN cc_start: 0.8707 (m-40) cc_final: 0.8286 (m110) REVERT: E 804 GLN cc_start: 0.8398 (mm-40) cc_final: 0.7876 (mp10) REVERT: D 155 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7689 (tp30) REVERT: B 104 LYS cc_start: 0.8265 (tptt) cc_final: 0.7763 (tttp) REVERT: B 117 PHE cc_start: 0.7554 (m-10) cc_final: 0.7140 (m-80) REVERT: B 136 LEU cc_start: 0.7084 (OUTLIER) cc_final: 0.6530 (pt) REVERT: B 184 LYS cc_start: 0.7514 (OUTLIER) cc_final: 0.6865 (ptpp) REVERT: B 208 LYS cc_start: 0.4586 (mtpt) cc_final: 0.3429 (ptmt) REVERT: B 212 ARG cc_start: 0.7425 (OUTLIER) cc_final: 0.6040 (mtm-85) REVERT: F 27 ASP cc_start: 0.7705 (p0) cc_final: 0.7128 (p0) REVERT: F 32 TYR cc_start: 0.8197 (m-80) cc_final: 0.7727 (m-80) REVERT: F 39 GLN cc_start: 0.5655 (tp40) cc_final: 0.5417 (tp40) REVERT: F 150 LYS cc_start: 0.5025 (mmmt) cc_final: 0.4373 (tppt) REVERT: G 40 LYS cc_start: 0.6752 (mttt) cc_final: 0.5953 (tppt) REVERT: G 49 ILE cc_start: 0.8029 (mt) cc_final: 0.7711 (mm) REVERT: G 144 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7423 (pm20) REVERT: G 189 LYS cc_start: 0.7039 (pttt) cc_final: 0.6828 (pttt) REVERT: G 190 HIS cc_start: 0.5255 (m-70) cc_final: 0.5000 (m-70) REVERT: G 200 GLN cc_start: 0.6441 (OUTLIER) cc_final: 0.5841 (pp30) outliers start: 133 outliers final: 103 residues processed: 405 average time/residue: 0.4303 time to fit residues: 284.0457 Evaluate side-chains 404 residues out of total 3529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 289 time to evaluate : 3.335 ------------------------------------------------------------------------------- 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 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 318 PHE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 417 LYS 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 512 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 549 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 882 ILE 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 1129 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 277 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 415 THR Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 719 THR 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 1129 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 83 VAL Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 197 ILE 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 336 CYS 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 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 827 THR Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 911 VAL Chi-restraints excluded: chain E residue 1122 VAL Chi-restraints excluded: chain E residue 1129 VAL Chi-restraints excluded: chain D residue 117 THR 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 79 LEU 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 190 HIS Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 212 ARG Chi-restraints excluded: chain F residue 215 ASP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 140 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 343 optimal weight: 0.8980 chunk 339 optimal weight: 0.0000 chunk 165 optimal weight: 0.9980 chunk 387 optimal weight: 10.0000 chunk 312 optimal weight: 0.7980 chunk 297 optimal weight: 1.9990 chunk 183 optimal weight: 0.0050 chunk 69 optimal weight: 1.9990 chunk 191 optimal weight: 3.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 ASN A 394 ASN A 690 GLN A 856 ASN C 173 GLN ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 14 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 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 = 0.109906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.083536 restraints weight = 79283.877| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 3.11 r_work: 0.3121 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.4504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 32779 Z= 0.102 Angle : 0.546 13.617 44730 Z= 0.274 Chirality : 0.043 0.242 5156 Planarity : 0.004 0.059 5717 Dihedral : 6.220 58.704 5237 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 3.22 % Allowed : 15.59 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.13), residues: 4020 helix: 1.57 (0.21), residues: 701 sheet: -1.06 (0.16), residues: 953 loop : -2.19 (0.12), residues: 2366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 152 HIS 0.003 0.001 HIS E 519 PHE 0.029 0.001 PHE C 157 TYR 0.015 0.001 TYR E 265 ARG 0.007 0.000 ARG C 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00400 ( 39) link_NAG-ASN : angle 2.04730 ( 117) hydrogen bonds : bond 0.03434 ( 937) hydrogen bonds : angle 5.25893 ( 2598) SS BOND : bond 0.00366 ( 50) SS BOND : angle 1.60199 ( 100) covalent geometry : bond 0.00235 (32690) covalent geometry : angle 0.53199 (44513) *********************** 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 427 residues out of total 3529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 315 time to evaluate : 3.208 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 65 PHE cc_start: 0.7640 (m-80) cc_final: 0.7366 (m-80) REVERT: A 85 PRO cc_start: 0.7678 (Cg_exo) cc_final: 0.7437 (Cg_endo) REVERT: A 153 MET cc_start: 0.7540 (mtt) cc_final: 0.6379 (ppp) REVERT: A 186 PHE cc_start: 0.5318 (m-10) cc_final: 0.5062 (m-80) REVERT: A 237 ARG cc_start: 0.7505 (mtm-85) cc_final: 0.7297 (mtm-85) REVERT: A 660 TYR cc_start: 0.8732 (m-80) cc_final: 0.8245 (m-80) REVERT: A 882 ILE cc_start: 0.9020 (OUTLIER) cc_final: 0.8732 (mp) REVERT: C 133 PHE cc_start: 0.7234 (m-80) cc_final: 0.6644 (m-80) REVERT: C 474 GLN cc_start: 0.7033 (pt0) cc_final: 0.6168 (pm20) REVERT: C 574 ASP cc_start: 0.8247 (t70) cc_final: 0.7946 (t0) REVERT: C 616 ASN cc_start: 0.8540 (OUTLIER) cc_final: 0.8331 (t0) REVERT: C 815 ARG cc_start: 0.8421 (mtm-85) cc_final: 0.8127 (mtm180) REVERT: C 855 PHE cc_start: 0.6292 (OUTLIER) cc_final: 0.5034 (t80) REVERT: C 988 GLU cc_start: 0.8117 (tp30) cc_final: 0.7805 (mm-30) REVERT: E 326 ILE cc_start: 0.7935 (mm) cc_final: 0.7677 (mm) REVERT: E 489 TYR cc_start: 0.2837 (OUTLIER) cc_final: 0.2248 (m-80) REVERT: E 574 ASP cc_start: 0.8315 (t70) cc_final: 0.7887 (t0) REVERT: E 751 ASN cc_start: 0.8685 (m-40) cc_final: 0.8268 (m110) REVERT: E 804 GLN cc_start: 0.8383 (mm-40) cc_final: 0.7829 (mp10) REVERT: E 900 MET cc_start: 0.8337 (mmm) cc_final: 0.8117 (mtp) REVERT: D 155 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7838 (tp30) REVERT: D 183 TYR cc_start: 0.7608 (m-80) cc_final: 0.7373 (m-80) REVERT: B 104 LYS cc_start: 0.8286 (tptt) cc_final: 0.7833 (tttp) REVERT: B 117 PHE cc_start: 0.7535 (m-10) cc_final: 0.7146 (m-80) REVERT: B 136 LEU cc_start: 0.7109 (OUTLIER) cc_final: 0.6574 (pt) REVERT: B 184 LYS cc_start: 0.7546 (OUTLIER) cc_final: 0.6933 (ptpp) REVERT: B 208 LYS cc_start: 0.4538 (mtpt) cc_final: 0.3362 (ptmt) REVERT: B 212 ARG cc_start: 0.7418 (OUTLIER) cc_final: 0.6150 (mtm-85) REVERT: F 27 ASP cc_start: 0.7623 (p0) cc_final: 0.7036 (p0) REVERT: F 32 TYR cc_start: 0.8157 (m-80) cc_final: 0.7701 (m-80) REVERT: F 39 GLN cc_start: 0.5575 (tp40) cc_final: 0.5347 (tp40) REVERT: F 150 LYS cc_start: 0.5336 (mmmt) cc_final: 0.4706 (tppt) REVERT: F 183 TYR cc_start: 0.6826 (m-10) cc_final: 0.6077 (m-10) REVERT: F 215 ASP cc_start: 0.4726 (OUTLIER) cc_final: 0.4485 (t0) REVERT: G 40 LYS cc_start: 0.6864 (mttt) cc_final: 0.5991 (tppt) REVERT: G 49 ILE cc_start: 0.8178 (mt) cc_final: 0.7880 (mm) REVERT: G 124 GLU cc_start: 0.5354 (pp20) cc_final: 0.4508 (pm20) REVERT: G 144 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7349 (pm20) REVERT: G 190 HIS cc_start: 0.4612 (m-70) cc_final: 0.4351 (m-70) REVERT: G 200 GLN cc_start: 0.6506 (OUTLIER) cc_final: 0.5985 (pp30) outliers start: 112 outliers final: 84 residues processed: 401 average time/residue: 0.4148 time to fit residues: 270.3172 Evaluate side-chains 394 residues out of total 3529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 299 time to evaluate : 3.323 ------------------------------------------------------------------------------- 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 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 395 VAL Chi-restraints excluded: chain A residue 417 LYS 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 512 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 882 ILE 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 213 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 277 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 415 THR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 878 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 83 VAL 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 336 CYS 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 705 VAL Chi-restraints excluded: chain E residue 719 THR Chi-restraints excluded: chain E residue 731 MET Chi-restraints excluded: chain E residue 859 THR Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 911 VAL Chi-restraints excluded: chain E residue 1122 VAL Chi-restraints excluded: chain E residue 1129 VAL Chi-restraints excluded: chain D residue 117 THR 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 79 LEU 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 190 HIS 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 F residue 215 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 148 optimal weight: 0.9990 chunk 275 optimal weight: 0.8980 chunk 102 optimal weight: 4.9990 chunk 160 optimal weight: 2.9990 chunk 210 optimal weight: 0.9990 chunk 384 optimal weight: 10.0000 chunk 167 optimal weight: 0.5980 chunk 36 optimal weight: 0.0870 chunk 163 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 GLN ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 14 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.106709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.080600 restraints weight = 81748.507| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.80 r_work: 0.3119 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.4554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 32779 Z= 0.104 Angle : 0.548 13.028 44730 Z= 0.275 Chirality : 0.043 0.240 5156 Planarity : 0.004 0.059 5717 Dihedral : 6.155 58.982 5237 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 2.85 % Allowed : 15.91 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.13), residues: 4020 helix: 1.58 (0.20), residues: 707 sheet: -0.97 (0.16), residues: 960 loop : -2.12 (0.12), residues: 2353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 110 HIS 0.003 0.001 HIS E 519 PHE 0.027 0.001 PHE C 157 TYR 0.038 0.001 TYR A 170 ARG 0.005 0.000 ARG C 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00390 ( 39) link_NAG-ASN : angle 2.03664 ( 117) hydrogen bonds : bond 0.03444 ( 937) hydrogen bonds : angle 5.20751 ( 2598) SS BOND : bond 0.00384 ( 50) SS BOND : angle 1.35406 ( 100) covalent geometry : bond 0.00245 (32690) covalent geometry : angle 0.53555 (44513) ********************** 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 401 residues out of total 3529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 302 time to evaluate : 3.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.7641 (m-80) cc_final: 0.7398 (m-80) REVERT: A 85 PRO cc_start: 0.7629 (Cg_exo) cc_final: 0.7382 (Cg_endo) REVERT: A 153 MET cc_start: 0.7569 (mtt) cc_final: 0.6401 (ppp) REVERT: A 186 PHE cc_start: 0.5296 (m-10) cc_final: 0.5041 (m-80) REVERT: A 237 ARG cc_start: 0.7444 (mtm-85) cc_final: 0.7232 (mtm-85) REVERT: A 660 TYR cc_start: 0.8746 (m-80) cc_final: 0.8247 (m-80) REVERT: A 882 ILE cc_start: 0.9024 (OUTLIER) cc_final: 0.8708 (mp) REVERT: C 133 PHE cc_start: 0.7239 (m-80) cc_final: 0.6652 (m-80) REVERT: C 474 GLN cc_start: 0.7084 (pt0) cc_final: 0.6196 (pm20) REVERT: C 574 ASP cc_start: 0.8386 (t70) cc_final: 0.8000 (t0) REVERT: C 616 ASN cc_start: 0.8488 (OUTLIER) cc_final: 0.8256 (t0) REVERT: C 768 THR cc_start: 0.9045 (m) cc_final: 0.8810 (p) REVERT: C 855 PHE cc_start: 0.6364 (OUTLIER) cc_final: 0.5103 (t80) REVERT: C 988 GLU cc_start: 0.8171 (tp30) cc_final: 0.7864 (mm-30) REVERT: E 574 ASP cc_start: 0.8285 (t70) cc_final: 0.7852 (t0) REVERT: E 751 ASN cc_start: 0.8682 (m-40) cc_final: 0.8257 (m110) REVERT: E 804 GLN cc_start: 0.8408 (mm-40) cc_final: 0.7795 (mp10) REVERT: E 900 MET cc_start: 0.8362 (mmm) cc_final: 0.8123 (mtp) REVERT: D 155 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7797 (tp30) REVERT: D 183 TYR cc_start: 0.7587 (m-80) cc_final: 0.7377 (m-80) REVERT: B 104 LYS cc_start: 0.8254 (tptt) cc_final: 0.7784 (tttp) REVERT: B 117 PHE cc_start: 0.7570 (m-10) cc_final: 0.7192 (m-80) REVERT: B 136 LEU cc_start: 0.7126 (OUTLIER) cc_final: 0.6533 (pt) REVERT: B 184 LYS cc_start: 0.7490 (OUTLIER) cc_final: 0.6896 (ptpp) REVERT: B 208 LYS cc_start: 0.4526 (mtpt) cc_final: 0.3353 (ptmt) REVERT: B 212 ARG cc_start: 0.7456 (OUTLIER) cc_final: 0.6199 (mtm-85) REVERT: F 27 ASP cc_start: 0.7597 (p0) cc_final: 0.6911 (p0) REVERT: F 32 TYR cc_start: 0.8156 (m-80) cc_final: 0.7652 (m-80) REVERT: F 39 GLN cc_start: 0.5546 (tp40) cc_final: 0.5315 (tp40) REVERT: F 65 GLN cc_start: 0.7786 (tp-100) cc_final: 0.7568 (tp-100) REVERT: F 150 LYS cc_start: 0.5270 (mmmt) cc_final: 0.4679 (tppt) REVERT: F 183 TYR cc_start: 0.6774 (m-10) cc_final: 0.5983 (m-10) REVERT: G 40 LYS cc_start: 0.6828 (mttt) cc_final: 0.5975 (tppt) REVERT: G 49 ILE cc_start: 0.8196 (mt) cc_final: 0.7900 (mm) REVERT: G 78 ARG cc_start: 0.7064 (mmm160) cc_final: 0.6773 (mmp80) REVERT: G 124 GLU cc_start: 0.5338 (pp20) cc_final: 0.4483 (pm20) REVERT: G 144 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7395 (pm20) REVERT: G 190 HIS cc_start: 0.4762 (m-70) cc_final: 0.4480 (m-70) REVERT: G 200 GLN cc_start: 0.6449 (OUTLIER) cc_final: 0.5832 (tm-30) outliers start: 99 outliers final: 82 residues processed: 379 average time/residue: 0.4322 time to fit residues: 266.7308 Evaluate side-chains 388 residues out of total 3529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 297 time to evaluate : 3.241 ------------------------------------------------------------------------------- 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 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 395 VAL Chi-restraints excluded: chain A residue 417 LYS 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 512 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 882 ILE 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 A residue 1072 GLU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 277 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 415 THR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 804 GLN Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 878 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 83 VAL 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 336 CYS 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 705 VAL Chi-restraints excluded: chain E residue 719 THR Chi-restraints excluded: chain E residue 731 MET Chi-restraints excluded: chain E residue 859 THR Chi-restraints excluded: chain E residue 878 LEU Chi-restraints excluded: chain E residue 911 VAL Chi-restraints excluded: chain E residue 1122 VAL Chi-restraints excluded: chain E residue 1129 VAL Chi-restraints excluded: chain D residue 117 THR 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 79 LEU 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 190 HIS 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 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 200 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 403 random chunks: chunk 66 optimal weight: 0.7980 chunk 113 optimal weight: 9.9990 chunk 328 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 79 optimal weight: 0.0870 chunk 251 optimal weight: 7.9990 chunk 146 optimal weight: 6.9990 chunk 158 optimal weight: 0.0070 chunk 8 optimal weight: 6.9990 chunk 191 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 overall best weight: 1.1780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 14 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 ** 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 = 0.3844 r_free = 0.3844 target = 0.107124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.081266 restraints weight = 81243.413| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.89 r_work: 0.3121 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.4552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.275 32779 Z= 0.190 Angle : 0.753 59.144 44730 Z= 0.407 Chirality : 0.045 0.501 5156 Planarity : 0.004 0.125 5717 Dihedral : 6.167 58.965 5237 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.93 % Allowed : 15.85 % Favored : 81.21 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.13), residues: 4020 helix: 1.57 (0.20), residues: 707 sheet: -0.96 (0.16), residues: 960 loop : -2.13 (0.12), residues: 2353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 152 HIS 0.003 0.001 HIS E 519 PHE 0.021 0.001 PHE C 157 TYR 0.032 0.001 TYR A 170 ARG 0.005 0.000 ARG C 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00853 ( 39) link_NAG-ASN : angle 2.84146 ( 117) hydrogen bonds : bond 0.03467 ( 937) hydrogen bonds : angle 5.20718 ( 2598) SS BOND : bond 0.00547 ( 50) SS BOND : angle 2.07761 ( 100) covalent geometry : bond 0.00411 (32690) covalent geometry : angle 0.73391 (44513) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27139.20 seconds wall clock time: 467 minutes 38.17 seconds (28058.17 seconds total)