Starting phenix.real_space_refine on Mon Aug 25 13:43:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yqz_34040/08_2025/7yqz_34040.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yqz_34040/08_2025/7yqz_34040.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7yqz_34040/08_2025/7yqz_34040.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yqz_34040/08_2025/7yqz_34040.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yqz_34040/08_2025/7yqz_34040.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yqz_34040/08_2025/7yqz_34040.map" } resolution = 3.84 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.051 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 123 5.16 5 C 17981 2.51 5 N 4662 2.21 5 O 5500 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28266 Number of models: 1 Model: "" Number of chains: 12 Chain: "C" Number of atoms: 7986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 7986 Classifications: {'peptide': 1022} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 55, 'TRANS': 966} Chain breaks: 6 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 8013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 8013 Classifications: {'peptide': 1025} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 55, 'TRANS': 969} Chain breaks: 6 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "B" Number of atoms: 7991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 7991 Classifications: {'peptide': 1022} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 55, 'TRANS': 966} Chain breaks: 6 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "I" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 959 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "G" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 815 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "J" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 959 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "H" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 815 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "D" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "A" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "B" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Time building chain proxies: 5.97, per 1000 atoms: 0.21 Number of scatterers: 28266 At special positions: 0 Unit cell: (173.34, 157.29, 182.97, 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 123 16.00 O 5500 8.00 N 4662 7.00 C 17981 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, symmetry=0 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=2.04 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=2.05 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=2.04 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=2.04 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 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=2.04 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=2.04 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 B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 89 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 89 " distance=2.04 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 BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " BETA1-6 " NAG D 1 " - " FUC D 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG E 1 " - " FUC E 4 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A1074 " " NAG A1308 " - " ASN A 165 " " NAG A1309 " - " ASN A 616 " " NAG A1310 " - " ASN A 657 " " NAG A1311 " - " ASN A 709 " " NAG A1312 " - " ASN A 717 " " NAG A1313 " - " ASN A 801 " " NAG A1314 " - " ASN A1098 " " NAG A1315 " - " ASN A1134 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 603 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 657 " " NAG B1310 " - " ASN B 709 " " NAG B1311 " - " ASN B 717 " " NAG B1312 " - " ASN B 801 " " NAG B1313 " - " ASN B1074 " " NAG B1314 " - " ASN B1098 " " NAG B1315 " - " ASN B1134 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 603 " " NAG C1308 " - " ASN C 616 " " NAG C1309 " - " ASN C 657 " " NAG C1310 " - " ASN C 709 " " NAG C1311 " - " ASN C 717 " " NAG C1312 " - " ASN C 801 " " NAG C1313 " - " ASN C1074 " " NAG C1314 " - " ASN C1098 " " NAG C1315 " - " ASN C1134 " " NAG D 1 " - " ASN C 343 " " NAG E 1 " - " ASN A 343 " Time building additional restraints: 2.05 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 953.7 nanoseconds 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6566 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 55 sheets defined 18.3% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'C' and resid 294 through 303 removed outlier: 3.761A pdb=" N LEU C 303 " --> pdb=" O THR C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.903A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 388 removed outlier: 4.231A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.506A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.780A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 778 removed outlier: 3.797A pdb=" N LYS C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.518A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 868 through 881 removed outlier: 3.844A pdb=" N THR C 881 " --> pdb=" O LEU C 877 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 903 removed outlier: 4.250A pdb=" N ALA C 903 " --> pdb=" O PRO C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 918 No H-bonds generated for 'chain 'C' and resid 916 through 918' Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.577A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER C 939 " --> pdb=" O GLN C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.595A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.665A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.596A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 5.268A 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) removed outlier: 3.562A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLN C1002 " --> pdb=" O THR C 998 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TYR C1007 " --> pdb=" O SER C1003 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU C1024 " --> pdb=" O ALA C1020 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER C1030 " --> pdb=" O ALA C1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 342 removed outlier: 3.786A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 337 through 342' Processing helix chain 'A' and resid 365 through 370 removed outlier: 4.241A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 748 through 755 removed outlier: 3.886A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 781 removed outlier: 3.580A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 4.131A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 881 removed outlier: 3.695A pdb=" N THR A 881 " --> pdb=" O LEU A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.549A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 removed outlier: 4.347A pdb=" N MET A 902 " --> pdb=" O PRO A 899 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ALA A 903 " --> pdb=" O MET A 900 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N PHE A 906 " --> pdb=" O ALA A 903 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ASN A 907 " --> pdb=" O TYR A 904 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY A 908 " --> pdb=" O ARG A 905 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLY A 910 " --> pdb=" O ASN A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 4.489A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 913 through 918' Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.804A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER A 937 " --> pdb=" O LYS A 933 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A 938 " --> pdb=" O ILE A 934 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N SER A 939 " --> pdb=" O GLN A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.704A pdb=" N GLN A 957 " --> pdb=" O ASN A 953 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A 959 " --> pdb=" O ASN A 955 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.815A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER A 982 " --> pdb=" O ASN A 978 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG A 983 " --> pdb=" O ASP A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 3.666A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN A1002 " --> pdb=" O THR A 998 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER A1003 " --> pdb=" O GLY A 999 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 removed outlier: 3.777A pdb=" N LEU B 303 " --> pdb=" O THR B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.976A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 743 removed outlier: 3.727A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 759 through 783 removed outlier: 3.517A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR B 768 " --> pdb=" O LYS B 764 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.745A pdb=" N LEU B 821 " --> pdb=" O PRO B 817 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LEU B 822 " --> pdb=" O ILE B 818 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 851 through 855 Processing helix chain 'B' and resid 868 through 884 removed outlier: 4.020A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 4.045A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 903 Processing helix chain 'B' and resid 904 through 909 removed outlier: 4.508A pdb=" N ASN B 907 " --> pdb=" O TYR B 904 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY B 908 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 4.144A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.861A pdb=" N GLY B 932 " --> pdb=" O ASN B 928 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS B 933 " --> pdb=" O SER B 929 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.873A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.631A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.670A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN B1002 " --> pdb=" O THR B 998 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG B1019 " --> pdb=" O ALA B1015 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU B1024 " --> pdb=" O ALA B1020 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 91 removed outlier: 4.260A pdb=" N THR I 91 " --> pdb=" O SER I 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 65 removed outlier: 4.007A pdb=" N GLN J 65 " --> pdb=" O GLN J 62 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 26 through 30 removed outlier: 3.597A pdb=" N THR C 29 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL C 62 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU C 229 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'C' and resid 50 through 55 removed outlier: 4.158A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.589A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 116 through 118 Processing sheet with id=AA6, first strand: chain 'C' and resid 311 through 319 removed outlier: 3.503A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR C 315 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 324 through 326 removed outlier: 6.771A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE C 543 " --> pdb=" O LEU C 546 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP C 586 " --> pdb=" O THR C 553 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 354 through 355 removed outlier: 4.324A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR C 396 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR C 508 " --> pdb=" O ILE C 402 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'C' and resid 565 through 566 removed outlier: 6.881A pdb=" N PHE C 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.777A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 702 through 704 Processing sheet with id=AB4, first strand: chain 'C' and resid 717 through 719 removed outlier: 6.622A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR C1047 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 722 through 728 removed outlier: 3.558A pdb=" N HIS C1064 " --> pdb=" O THR C 723 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 1081 through 1082 Processing sheet with id=AB7, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AB8, first strand: chain 'A' and resid 28 through 30 removed outlier: 7.482A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LYS A 187 " --> pdb=" O VAL A 210 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N VAL A 210 " --> pdb=" O LYS A 187 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU A 229 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 51 through 55 removed outlier: 3.582A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 168 through 172 removed outlier: 3.887A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL A 127 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS A 129 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU A 118 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 312 through 319 removed outlier: 7.310A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL A 610 " --> pdb=" O ILE A 651 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 324 through 326 removed outlier: 3.695A pdb=" N ASN A 542 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N PHE A 543 " --> pdb=" O LEU A 546 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 356 through 357 removed outlier: 3.502A pdb=" N ALA A 397 " --> pdb=" O LYS A 356 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR A 396 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE A 402 " --> pdb=" O TYR A 508 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N TYR A 508 " --> pdb=" O ILE A 402 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TRP A 436 " --> pdb=" O ARG A 509 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N THR A 430 " --> pdb=" O PHE A 515 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'A' and resid 654 through 660 removed outlier: 3.739A pdb=" N GLU A 654 " --> pdb=" O ILE A 692 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA A 694 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ASN A 658 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 712 through 713 removed outlier: 3.566A pdb=" N ILE A 712 " --> pdb=" O PHE A1075 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 718 through 727 removed outlier: 3.656A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR A1047 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 718 through 727 removed outlier: 3.656A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 735 through 736 Processing sheet with id=AD2, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.564A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'A' and resid 1120 through 1122 removed outlier: 3.516A pdb=" N CYS A1082 " --> pdb=" O VAL A1133 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 29 through 30 removed outlier: 3.652A pdb=" N THR B 29 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER B 94 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG B 190 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.482A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 10.321A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 50 through 55 Processing sheet with id=AD6, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.834A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU B 117 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU B 118 " --> pdb=" O LYS B 129 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS B 129 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 311 through 316 removed outlier: 5.868A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 325 through 326 removed outlier: 3.642A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 379 through 380 removed outlier: 3.675A pdb=" N GLY B 431 " --> pdb=" O TYR B 380 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR B 508 " --> pdb=" O ILE B 402 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AE2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.033A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 717 through 728 removed outlier: 6.340A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR B1047 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 717 through 728 removed outlier: 6.340A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 735 through 736 Processing sheet with id=AE6, first strand: chain 'B' and resid 1120 through 1122 removed outlier: 3.565A pdb=" N PHE B1089 " --> pdb=" O PHE B1121 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 1094 through 1097 removed outlier: 3.682A pdb=" N VAL B1104 " --> pdb=" O GLN B1113 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AE9, first strand: chain 'I' and resid 49 through 51 removed outlier: 4.563A pdb=" N ASN I 116 " --> pdb=" O ARG I 98 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 49 through 51 Processing sheet with id=AF2, first strand: chain 'G' and resid 4 through 5 Processing sheet with id=AF3, first strand: chain 'G' and resid 19 through 22 removed outlier: 3.978A pdb=" N ASP G 71 " --> pdb=" O SER G 68 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 46 through 47 removed outlier: 3.602A pdb=" N ARG G 46 " --> pdb=" O GLN G 38 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AF6, first strand: chain 'J' and resid 49 through 51 removed outlier: 4.170A pdb=" N ASN J 116 " --> pdb=" O ARG J 98 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'J' and resid 49 through 51 Processing sheet with id=AF8, first strand: chain 'H' and resid 4 through 5 removed outlier: 3.935A pdb=" N CYS H 23 " --> pdb=" O PHE H 72 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N PHE H 72 " --> pdb=" O CYS H 23 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 10 through 11 Processing sheet with id=AG1, first strand: chain 'H' and resid 35 through 39 811 hydrogen bonds defined for protein. 2142 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: 4.72 Time building geometry restraints manager: 2.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.09 - 1.25: 4015 1.25 - 1.40: 7773 1.40 - 1.55: 16886 1.55 - 1.70: 82 1.70 - 1.85: 156 Bond restraints: 28912 Sorted by residual: bond pdb=" CG PRO C1079 " pdb=" CD PRO C1079 " ideal model delta sigma weight residual 1.503 1.095 0.408 3.40e-02 8.65e+02 1.44e+02 bond pdb=" N PRO C1079 " pdb=" CD PRO C1079 " ideal model delta sigma weight residual 1.473 1.546 -0.073 1.40e-02 5.10e+03 2.70e+01 bond pdb=" N ILE B 818 " pdb=" CA ILE B 818 " ideal model delta sigma weight residual 1.462 1.501 -0.039 1.06e-02 8.90e+03 1.37e+01 bond pdb=" N THR C 333 " pdb=" CA THR C 333 " ideal model delta sigma weight residual 1.457 1.498 -0.041 1.29e-02 6.01e+03 9.91e+00 bond pdb=" N CYS A 525 " pdb=" CA CYS A 525 " ideal model delta sigma weight residual 1.454 1.494 -0.040 1.31e-02 5.83e+03 9.41e+00 ... (remaining 28907 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.24: 39154 4.24 - 8.48: 163 8.48 - 12.72: 14 12.72 - 16.96: 2 16.96 - 21.20: 1 Bond angle restraints: 39334 Sorted by residual: angle pdb=" N PRO C1079 " pdb=" CD PRO C1079 " pdb=" CG PRO C1079 " ideal model delta sigma weight residual 103.20 82.00 21.20 1.50e+00 4.44e-01 2.00e+02 angle pdb=" CA PRO C1079 " pdb=" N PRO C1079 " pdb=" CD PRO C1079 " ideal model delta sigma weight residual 112.00 96.64 15.36 1.40e+00 5.10e-01 1.20e+02 angle pdb=" CA PRO C1079 " pdb=" CB PRO C1079 " pdb=" CG PRO C1079 " ideal model delta sigma weight residual 104.50 89.56 14.94 1.90e+00 2.77e-01 6.19e+01 angle pdb=" N GLU B 819 " pdb=" CA GLU B 819 " pdb=" C GLU B 819 " ideal model delta sigma weight residual 113.50 104.14 9.36 1.23e+00 6.61e-01 5.79e+01 angle pdb=" CA ARG I 85 " pdb=" CB ARG I 85 " pdb=" CG ARG I 85 " ideal model delta sigma weight residual 114.10 124.93 -10.83 2.00e+00 2.50e-01 2.93e+01 ... (remaining 39329 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.52: 16483 21.52 - 43.04: 1182 43.04 - 64.56: 139 64.56 - 86.08: 58 86.08 - 107.60: 15 Dihedral angle restraints: 17877 sinusoidal: 7641 harmonic: 10236 Sorted by residual: dihedral pdb=" CB CYS C 291 " pdb=" SG CYS C 291 " pdb=" SG CYS C 301 " pdb=" CB CYS C 301 " ideal model delta sinusoidal sigma weight residual 93.00 3.96 89.04 1 1.00e+01 1.00e-02 9.44e+01 dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual 93.00 6.30 86.70 1 1.00e+01 1.00e-02 9.05e+01 dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual -86.00 -0.31 -85.69 1 1.00e+01 1.00e-02 8.88e+01 ... (remaining 17874 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 3853 0.071 - 0.142: 668 0.142 - 0.213: 44 0.213 - 0.284: 13 0.284 - 0.355: 4 Chirality restraints: 4582 Sorted by residual: chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 343 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" C2 NAG E 2 " pdb=" C1 NAG E 2 " pdb=" C3 NAG E 2 " pdb=" N2 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.16 -0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" C2 NAG D 2 " pdb=" C1 NAG D 2 " pdb=" C3 NAG D 2 " pdb=" N2 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.17 -0.32 2.00e-01 2.50e+01 2.57e+00 ... (remaining 4579 not shown) Planarity restraints: 5068 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C1078 " 0.107 5.00e-02 4.00e+02 1.47e-01 3.44e+01 pdb=" N PRO C1079 " -0.253 5.00e-02 4.00e+02 pdb=" CA PRO C1079 " 0.073 5.00e-02 4.00e+02 pdb=" CD PRO C1079 " 0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TRP I 47 " 0.017 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" C TRP I 47 " -0.058 2.00e-02 2.50e+03 pdb=" O TRP I 47 " 0.022 2.00e-02 2.50e+03 pdb=" N MET I 48 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 817 " -0.016 2.00e-02 2.50e+03 3.13e-02 9.82e+00 pdb=" C PRO B 817 " 0.054 2.00e-02 2.50e+03 pdb=" O PRO B 817 " -0.020 2.00e-02 2.50e+03 pdb=" N ILE B 818 " -0.018 2.00e-02 2.50e+03 ... (remaining 5065 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.28: 14 2.28 - 2.94: 12341 2.94 - 3.59: 37469 3.59 - 4.25: 59949 4.25 - 4.90: 99603 Nonbonded interactions: 209376 Sorted by model distance: nonbonded pdb=" CG GLU B 96 " pdb=" CD1 ILE B 100 " model vdw 1.625 3.860 nonbonded pdb=" OE2 GLU B 96 " pdb=" CG1 ILE B 100 " model vdw 1.927 3.440 nonbonded pdb=" CD GLU B 96 " pdb=" CG1 ILE B 100 " model vdw 1.994 3.670 nonbonded pdb=" CG GLU B 96 " pdb=" CG1 ILE B 100 " model vdw 2.048 3.840 nonbonded pdb=" CG2 ILE A 100 " pdb=" CD2 LEU A 242 " model vdw 2.074 3.880 ... (remaining 209371 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 25 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 263 or resid 265 through 622 or \ resid 641 through 826 or resid 854 through 1315)) selection = (chain 'B' and (resid 25 through 99 or (resid 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 243 or resid 263 or resid 265 th \ rough 826 or resid 854 through 1315)) selection = (chain 'C' and (resid 25 through 622 or resid 641 through 826 or resid 854 throu \ gh 1315)) } ncs_group { reference = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 21.620 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 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 : 0.005 0.408 29008 Z= 0.220 Angle : 0.824 21.205 39579 Z= 0.421 Chirality : 0.053 0.355 4582 Planarity : 0.006 0.147 5021 Dihedral : 14.509 107.605 11182 Min Nonbonded Distance : 1.625 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.84 % Favored : 92.90 % Rotamer: Outliers : 0.07 % Allowed : 0.69 % Favored : 99.25 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.84 (0.13), residues: 3481 helix: -2.56 (0.15), residues: 576 sheet: -0.74 (0.20), residues: 731 loop : -2.19 (0.12), residues: 2174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 85 TYR 0.022 0.001 TYR B 265 PHE 0.045 0.002 PHE B 133 TRP 0.032 0.002 TRP I 47 HIS 0.006 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00473 (28912) covalent geometry : angle 0.80367 (39334) SS BOND : bond 0.00394 ( 43) SS BOND : angle 1.44500 ( 86) hydrogen bonds : bond 0.25958 ( 773) hydrogen bonds : angle 8.92838 ( 2142) link_BETA1-4 : bond 0.01118 ( 4) link_BETA1-4 : angle 3.28141 ( 12) link_BETA1-6 : bond 0.00459 ( 2) link_BETA1-6 : angle 1.20440 ( 6) link_NAG-ASN : bond 0.00785 ( 47) link_NAG-ASN : angle 2.83070 ( 141) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 250 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 ARG cc_start: 0.8274 (mtt180) cc_final: 0.7605 (mpp80) REVERT: A 983 ARG cc_start: 0.8746 (mtm180) cc_final: 0.8538 (ptp90) REVERT: A 1129 VAL cc_start: 0.9113 (m) cc_final: 0.8843 (p) REVERT: B 365 TYR cc_start: 0.8005 (m-80) cc_final: 0.7524 (m-80) REVERT: B 867 ASP cc_start: 0.8174 (p0) cc_final: 0.7778 (p0) REVERT: B 1002 GLN cc_start: 0.8687 (tp-100) cc_final: 0.8481 (tp-100) REVERT: G 55 ARG cc_start: 0.4435 (mmm160) cc_final: 0.4212 (mmm-85) REVERT: J 4 LEU cc_start: 0.8075 (mt) cc_final: 0.7860 (mt) REVERT: H 96 LEU cc_start: 0.8021 (tp) cc_final: 0.7770 (tp) outliers start: 2 outliers final: 0 residues processed: 252 average time/residue: 0.1515 time to fit residues: 61.4793 Evaluate side-chains 169 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 0.3980 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 3.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 GLN A 955 ASN A1011 GLN A1125 ASN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN I 3 GLN ** I 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 116 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.108438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.083479 restraints weight = 95139.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.082134 restraints weight = 59591.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.082993 restraints weight = 65786.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.083057 restraints weight = 47892.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.083895 restraints weight = 41751.287| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 29008 Z= 0.133 Angle : 0.633 12.734 39579 Z= 0.315 Chirality : 0.045 0.261 4582 Planarity : 0.004 0.058 5021 Dihedral : 7.534 68.422 4901 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 0.43 % Allowed : 7.33 % Favored : 92.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.21 (0.13), residues: 3481 helix: -0.70 (0.20), residues: 596 sheet: -0.63 (0.21), residues: 694 loop : -2.08 (0.12), residues: 2191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 158 TYR 0.024 0.001 TYR C 453 PHE 0.016 0.001 PHE A 392 TRP 0.012 0.001 TRP J 47 HIS 0.007 0.001 HIS C 505 Details of bonding type rmsd covalent geometry : bond 0.00294 (28912) covalent geometry : angle 0.61239 (39334) SS BOND : bond 0.00362 ( 43) SS BOND : angle 1.32132 ( 86) hydrogen bonds : bond 0.05429 ( 773) hydrogen bonds : angle 6.22284 ( 2142) link_BETA1-4 : bond 0.00436 ( 4) link_BETA1-4 : angle 2.83644 ( 12) link_BETA1-6 : bond 0.00473 ( 2) link_BETA1-6 : angle 1.34157 ( 6) link_NAG-ASN : bond 0.00441 ( 47) link_NAG-ASN : angle 2.44831 ( 141) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 202 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 979 ASP cc_start: 0.8996 (m-30) cc_final: 0.8611 (m-30) REVERT: A 984 LEU cc_start: 0.8516 (mp) cc_final: 0.8276 (tp) REVERT: B 133 PHE cc_start: 0.7079 (m-80) cc_final: 0.6274 (p90) REVERT: B 867 ASP cc_start: 0.8066 (p0) cc_final: 0.7659 (p0) REVERT: I 48 MET cc_start: 0.6762 (mmm) cc_final: 0.6445 (mmm) outliers start: 13 outliers final: 11 residues processed: 208 average time/residue: 0.1449 time to fit residues: 49.7094 Evaluate side-chains 182 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 171 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 72 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 212 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 chunk 317 optimal weight: 0.0570 chunk 96 optimal weight: 5.9990 chunk 26 optimal weight: 0.6980 chunk 191 optimal weight: 3.9990 chunk 147 optimal weight: 9.9990 chunk 169 optimal weight: 5.9990 chunk 233 optimal weight: 0.8980 chunk 303 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 overall best weight: 1.5302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 493 GLN ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1125 ASN B 185 ASN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B 957 GLN J 3 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.108030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.083203 restraints weight = 95443.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.081978 restraints weight = 60639.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.082636 restraints weight = 69112.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.082869 restraints weight = 48147.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.083423 restraints weight = 42145.022| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 29008 Z= 0.138 Angle : 0.603 12.688 39579 Z= 0.299 Chirality : 0.045 0.244 4582 Planarity : 0.004 0.053 5021 Dihedral : 6.660 58.174 4901 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 0.75 % Allowed : 10.70 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.93 (0.14), residues: 3481 helix: -0.01 (0.22), residues: 600 sheet: -0.58 (0.20), residues: 703 loop : -1.99 (0.12), residues: 2178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 67 TYR 0.027 0.001 TYR A 265 PHE 0.024 0.001 PHE B 375 TRP 0.010 0.001 TRP C 436 HIS 0.006 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00315 (28912) covalent geometry : angle 0.58299 (39334) SS BOND : bond 0.00333 ( 43) SS BOND : angle 1.31013 ( 86) hydrogen bonds : bond 0.04698 ( 773) hydrogen bonds : angle 5.76404 ( 2142) link_BETA1-4 : bond 0.00584 ( 4) link_BETA1-4 : angle 2.70388 ( 12) link_BETA1-6 : bond 0.00328 ( 2) link_BETA1-6 : angle 1.25240 ( 6) link_NAG-ASN : bond 0.00375 ( 47) link_NAG-ASN : angle 2.37009 ( 141) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 183 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 198 ASP cc_start: 0.8500 (t0) cc_final: 0.8247 (p0) REVERT: A 449 TYR cc_start: 0.8336 (m-80) cc_final: 0.8005 (m-80) REVERT: A 1125 ASN cc_start: 0.8025 (OUTLIER) cc_final: 0.7633 (t0) REVERT: B 133 PHE cc_start: 0.7040 (m-80) cc_final: 0.6498 (p90) REVERT: B 867 ASP cc_start: 0.8140 (p0) cc_final: 0.7719 (p0) REVERT: B 882 ILE cc_start: 0.8129 (pt) cc_final: 0.7659 (mt) REVERT: I 48 MET cc_start: 0.6723 (mmm) cc_final: 0.6451 (mmm) REVERT: I 54 TYR cc_start: 0.7894 (t80) cc_final: 0.7650 (t80) REVERT: I 70 MET cc_start: 0.6581 (mpp) cc_final: 0.6314 (mpp) REVERT: J 80 TYR cc_start: 0.6525 (m-80) cc_final: 0.6103 (m-10) outliers start: 23 outliers final: 19 residues processed: 196 average time/residue: 0.1683 time to fit residues: 54.0855 Evaluate side-chains 179 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 159 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 508 TYR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain I residue 20 VAL Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 110 LEU Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 72 PHE Chi-restraints excluded: chain H residue 93 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 261 optimal weight: 3.9990 chunk 219 optimal weight: 0.4980 chunk 133 optimal weight: 0.9980 chunk 167 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 chunk 115 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 142 optimal weight: 5.9990 chunk 346 optimal weight: 2.9990 chunk 290 optimal weight: 0.9980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1011 GLN B 334 ASN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.108064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.083167 restraints weight = 94905.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.081824 restraints weight = 62401.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.082468 restraints weight = 63573.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.083214 restraints weight = 46216.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.083267 restraints weight = 42288.740| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 29008 Z= 0.124 Angle : 0.583 12.593 39579 Z= 0.287 Chirality : 0.044 0.244 4582 Planarity : 0.004 0.050 5021 Dihedral : 6.134 58.782 4901 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 1.18 % Allowed : 11.94 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.81 (0.14), residues: 3481 helix: 0.30 (0.22), residues: 599 sheet: -0.55 (0.21), residues: 690 loop : -1.96 (0.12), residues: 2192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 983 TYR 0.019 0.001 TYR C 453 PHE 0.027 0.001 PHE C 92 TRP 0.013 0.001 TRP J 47 HIS 0.009 0.001 HIS C 505 Details of bonding type rmsd covalent geometry : bond 0.00281 (28912) covalent geometry : angle 0.56312 (39334) SS BOND : bond 0.00385 ( 43) SS BOND : angle 1.27564 ( 86) hydrogen bonds : bond 0.04206 ( 773) hydrogen bonds : angle 5.52520 ( 2142) link_BETA1-4 : bond 0.00449 ( 4) link_BETA1-4 : angle 2.54013 ( 12) link_BETA1-6 : bond 0.00316 ( 2) link_BETA1-6 : angle 1.30658 ( 6) link_NAG-ASN : bond 0.00354 ( 47) link_NAG-ASN : angle 2.27558 ( 141) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 170 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 983 ARG cc_start: 0.9067 (ptp-170) cc_final: 0.8807 (ptp90) REVERT: B 133 PHE cc_start: 0.6859 (m-80) cc_final: 0.6555 (p90) REVERT: B 867 ASP cc_start: 0.8097 (p0) cc_final: 0.7715 (p0) REVERT: I 48 MET cc_start: 0.6717 (mmm) cc_final: 0.6441 (mmm) outliers start: 36 outliers final: 21 residues processed: 193 average time/residue: 0.1761 time to fit residues: 57.0846 Evaluate side-chains 175 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 154 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain I residue 20 VAL Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 110 LEU Chi-restraints excluded: chain H residue 72 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 6 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 159 optimal weight: 2.9990 chunk 177 optimal weight: 0.7980 chunk 180 optimal weight: 0.9980 chunk 193 optimal weight: 0.5980 chunk 338 optimal weight: 5.9990 chunk 318 optimal weight: 9.9990 chunk 323 optimal weight: 30.0000 chunk 271 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN A 439 ASN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 43 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 = 0.3890 r_free = 0.3890 target = 0.106661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.074123 restraints weight = 93746.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.076047 restraints weight = 52490.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.077352 restraints weight = 36030.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.078176 restraints weight = 28248.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.078722 restraints weight = 24229.211| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29008 Z= 0.141 Angle : 0.588 12.577 39579 Z= 0.290 Chirality : 0.044 0.252 4582 Planarity : 0.004 0.057 5021 Dihedral : 5.836 59.149 4901 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 1.57 % Allowed : 12.96 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.74 (0.14), residues: 3481 helix: 0.48 (0.22), residues: 602 sheet: -0.55 (0.21), residues: 682 loop : -1.94 (0.13), residues: 2197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 765 TYR 0.021 0.001 TYR C 160 PHE 0.021 0.001 PHE C 92 TRP 0.013 0.001 TRP J 47 HIS 0.004 0.001 HIS C 505 Details of bonding type rmsd covalent geometry : bond 0.00324 (28912) covalent geometry : angle 0.56945 (39334) SS BOND : bond 0.00315 ( 43) SS BOND : angle 1.25355 ( 86) hydrogen bonds : bond 0.04082 ( 773) hydrogen bonds : angle 5.40444 ( 2142) link_BETA1-4 : bond 0.00475 ( 4) link_BETA1-4 : angle 2.59733 ( 12) link_BETA1-6 : bond 0.00276 ( 2) link_BETA1-6 : angle 1.34559 ( 6) link_NAG-ASN : bond 0.00334 ( 47) link_NAG-ASN : angle 2.21929 ( 141) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 174 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 118 LEU cc_start: 0.8303 (tp) cc_final: 0.7464 (pp) REVERT: C 581 THR cc_start: 0.9112 (OUTLIER) cc_final: 0.8680 (p) REVERT: C 727 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8686 (mt) REVERT: A 437 ASN cc_start: 0.8687 (m-40) cc_final: 0.8412 (t0) REVERT: A 1122 VAL cc_start: 0.7885 (OUTLIER) cc_final: 0.7666 (p) REVERT: B 133 PHE cc_start: 0.6938 (m-80) cc_final: 0.6701 (p90) REVERT: B 867 ASP cc_start: 0.8299 (p0) cc_final: 0.7903 (p0) REVERT: B 1002 GLN cc_start: 0.8772 (tp40) cc_final: 0.8229 (tp40) REVERT: I 48 MET cc_start: 0.6713 (mmm) cc_final: 0.6465 (mmm) REVERT: I 54 TYR cc_start: 0.8444 (t80) cc_final: 0.8061 (t80) REVERT: I 81 MET cc_start: 0.4391 (mmm) cc_final: 0.3970 (mmm) outliers start: 48 outliers final: 30 residues processed: 209 average time/residue: 0.1732 time to fit residues: 62.0587 Evaluate side-chains 191 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 158 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 508 TYR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain I residue 20 VAL Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 110 LEU Chi-restraints excluded: chain H residue 72 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 348 optimal weight: 10.0000 chunk 277 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 213 optimal weight: 9.9990 chunk 252 optimal weight: 5.9990 chunk 237 optimal weight: 3.9990 chunk 191 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 234 optimal weight: 9.9990 chunk 224 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 ASN A 954 HIS B 487 ASN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 59 ASN G 38 GLN G 92 HIS J 3 GLN ** J 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.104354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.072700 restraints weight = 92509.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.074121 restraints weight = 56326.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.074693 restraints weight = 39352.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.075347 restraints weight = 30997.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.075413 restraints weight = 28126.060| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 29008 Z= 0.222 Angle : 0.665 12.522 39579 Z= 0.331 Chirality : 0.046 0.251 4582 Planarity : 0.004 0.046 5021 Dihedral : 6.067 59.539 4901 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 1.80 % Allowed : 14.66 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.97 (0.14), residues: 3481 helix: 0.22 (0.22), residues: 603 sheet: -0.76 (0.20), residues: 716 loop : -2.06 (0.13), residues: 2162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 55 TYR 0.021 0.002 TYR C 453 PHE 0.025 0.002 PHE B1089 TRP 0.016 0.002 TRP J 47 HIS 0.006 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00510 (28912) covalent geometry : angle 0.64574 (39334) SS BOND : bond 0.00415 ( 43) SS BOND : angle 1.49919 ( 86) hydrogen bonds : bond 0.04582 ( 773) hydrogen bonds : angle 5.65899 ( 2142) link_BETA1-4 : bond 0.00484 ( 4) link_BETA1-4 : angle 2.65223 ( 12) link_BETA1-6 : bond 0.00255 ( 2) link_BETA1-6 : angle 1.47652 ( 6) link_NAG-ASN : bond 0.00378 ( 47) link_NAG-ASN : angle 2.36103 ( 141) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 168 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 118 LEU cc_start: 0.8225 (tp) cc_final: 0.7977 (tt) REVERT: C 546 LEU cc_start: 0.9290 (tt) cc_final: 0.8857 (tt) REVERT: C 581 THR cc_start: 0.9209 (OUTLIER) cc_final: 0.8687 (p) REVERT: C 727 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8930 (mm) REVERT: A 1122 VAL cc_start: 0.7882 (OUTLIER) cc_final: 0.7617 (p) REVERT: B 133 PHE cc_start: 0.7474 (m-80) cc_final: 0.6812 (p90) REVERT: B 902 MET cc_start: 0.9278 (tpp) cc_final: 0.9014 (tpt) REVERT: B 1002 GLN cc_start: 0.8894 (tp40) cc_final: 0.8348 (tp40) REVERT: I 48 MET cc_start: 0.6757 (mmm) cc_final: 0.6532 (mmm) REVERT: I 81 MET cc_start: 0.4344 (mmm) cc_final: 0.3975 (mmm) REVERT: H 27 GLN cc_start: 0.9149 (mm-40) cc_final: 0.8797 (mm-40) outliers start: 55 outliers final: 40 residues processed: 208 average time/residue: 0.1665 time to fit residues: 57.4559 Evaluate side-chains 200 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 157 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain I residue 20 VAL Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 37 TYR Chi-restraints excluded: chain G residue 73 THR Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 111 ILE Chi-restraints excluded: chain H residue 72 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 196 optimal weight: 0.7980 chunk 158 optimal weight: 4.9990 chunk 161 optimal weight: 8.9990 chunk 246 optimal weight: 40.0000 chunk 290 optimal weight: 2.9990 chunk 201 optimal weight: 0.9990 chunk 112 optimal weight: 4.9990 chunk 150 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 208 optimal weight: 0.5980 chunk 327 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.106421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.073956 restraints weight = 92936.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.075853 restraints weight = 52430.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.077128 restraints weight = 36100.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.077966 restraints weight = 28200.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 60)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.078512 restraints weight = 24170.540| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 29008 Z= 0.112 Angle : 0.590 12.596 39579 Z= 0.289 Chirality : 0.044 0.250 4582 Planarity : 0.004 0.048 5021 Dihedral : 5.623 59.883 4901 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 1.57 % Allowed : 15.87 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.73 (0.14), residues: 3481 helix: 0.57 (0.22), residues: 605 sheet: -0.65 (0.21), residues: 690 loop : -1.93 (0.13), residues: 2186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 62 TYR 0.018 0.001 TYR C 160 PHE 0.019 0.001 PHE C 92 TRP 0.015 0.001 TRP J 50 HIS 0.004 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00254 (28912) covalent geometry : angle 0.57106 (39334) SS BOND : bond 0.00316 ( 43) SS BOND : angle 1.48842 ( 86) hydrogen bonds : bond 0.03869 ( 773) hydrogen bonds : angle 5.23868 ( 2142) link_BETA1-4 : bond 0.00532 ( 4) link_BETA1-4 : angle 2.51928 ( 12) link_BETA1-6 : bond 0.00285 ( 2) link_BETA1-6 : angle 1.37326 ( 6) link_NAG-ASN : bond 0.00338 ( 47) link_NAG-ASN : angle 2.15392 ( 141) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 179 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 118 LEU cc_start: 0.8287 (tp) cc_final: 0.7610 (pp) REVERT: C 546 LEU cc_start: 0.9255 (tt) cc_final: 0.8803 (tt) REVERT: C 727 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8731 (mt) REVERT: A 1122 VAL cc_start: 0.7887 (OUTLIER) cc_final: 0.7658 (p) REVERT: B 133 PHE cc_start: 0.6955 (m-80) cc_final: 0.6724 (p90) REVERT: B 867 ASP cc_start: 0.8369 (p0) cc_final: 0.7939 (p0) REVERT: I 48 MET cc_start: 0.6883 (mmm) cc_final: 0.6662 (mmm) REVERT: I 81 MET cc_start: 0.4419 (mmm) cc_final: 0.4010 (mmm) REVERT: G 37 TYR cc_start: 0.7153 (OUTLIER) cc_final: 0.6928 (m-80) REVERT: H 18 ARG cc_start: 0.7043 (tpp-160) cc_final: 0.6597 (mmm160) REVERT: H 27 GLN cc_start: 0.9100 (mm-40) cc_final: 0.8773 (mm-40) outliers start: 48 outliers final: 35 residues processed: 213 average time/residue: 0.1627 time to fit residues: 57.6194 Evaluate side-chains 201 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 163 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 20 VAL Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 37 TYR Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 111 ILE Chi-restraints excluded: chain H residue 72 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 276 optimal weight: 6.9990 chunk 141 optimal weight: 8.9990 chunk 135 optimal weight: 0.9980 chunk 200 optimal weight: 0.0980 chunk 150 optimal weight: 0.3980 chunk 46 optimal weight: 0.8980 chunk 10 optimal weight: 10.0000 chunk 287 optimal weight: 1.9990 chunk 184 optimal weight: 0.9980 chunk 93 optimal weight: 0.5980 chunk 199 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 ASN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 GLN J 3 GLN ** J 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.107137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.074578 restraints weight = 92398.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.076546 restraints weight = 50714.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.077882 restraints weight = 34253.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 54)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.078738 restraints weight = 26426.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.079266 restraints weight = 22493.807| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 29008 Z= 0.099 Angle : 0.577 12.512 39579 Z= 0.282 Chirality : 0.044 0.252 4582 Planarity : 0.004 0.047 5021 Dihedral : 5.212 59.963 4901 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 1.54 % Allowed : 16.16 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.55 (0.14), residues: 3481 helix: 0.79 (0.23), residues: 613 sheet: -0.55 (0.21), residues: 694 loop : -1.83 (0.13), residues: 2174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 62 TYR 0.017 0.001 TYR C 160 PHE 0.020 0.001 PHE C 456 TRP 0.016 0.001 TRP J 50 HIS 0.003 0.001 HIS C 505 Details of bonding type rmsd covalent geometry : bond 0.00223 (28912) covalent geometry : angle 0.56076 (39334) SS BOND : bond 0.00301 ( 43) SS BOND : angle 1.18275 ( 86) hydrogen bonds : bond 0.03524 ( 773) hydrogen bonds : angle 4.98225 ( 2142) link_BETA1-4 : bond 0.00543 ( 4) link_BETA1-4 : angle 2.55147 ( 12) link_BETA1-6 : bond 0.00343 ( 2) link_BETA1-6 : angle 1.29920 ( 6) link_NAG-ASN : bond 0.00345 ( 47) link_NAG-ASN : angle 2.06063 ( 141) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 185 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 118 LEU cc_start: 0.8276 (tp) cc_final: 0.7604 (pp) REVERT: C 191 GLU cc_start: 0.8544 (tp30) cc_final: 0.8128 (mm-30) REVERT: C 581 THR cc_start: 0.9020 (OUTLIER) cc_final: 0.8590 (p) REVERT: C 727 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8703 (mt) REVERT: B 303 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7758 (pp) REVERT: B 867 ASP cc_start: 0.8328 (p0) cc_final: 0.7979 (p0) REVERT: I 48 MET cc_start: 0.6812 (mmm) cc_final: 0.6584 (mmm) REVERT: I 81 MET cc_start: 0.4427 (mmm) cc_final: 0.4074 (mmm) REVERT: I 114 PHE cc_start: 0.8582 (m-10) cc_final: 0.8293 (m-10) REVERT: J 29 PHE cc_start: 0.8539 (t80) cc_final: 0.8116 (t80) outliers start: 47 outliers final: 30 residues processed: 219 average time/residue: 0.1331 time to fit residues: 49.4585 Evaluate side-chains 200 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 167 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 3 GLN Chi-restraints excluded: chain H residue 72 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 296 optimal weight: 2.9990 chunk 144 optimal weight: 20.0000 chunk 18 optimal weight: 20.0000 chunk 253 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 106 optimal weight: 0.3980 chunk 290 optimal weight: 0.3980 chunk 72 optimal weight: 2.9990 chunk 204 optimal weight: 10.0000 chunk 317 optimal weight: 4.9990 chunk 220 optimal weight: 9.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 HIS ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.105942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.073419 restraints weight = 92596.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.075277 restraints weight = 52026.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.076505 restraints weight = 35748.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.077302 restraints weight = 28066.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.077830 restraints weight = 24051.001| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29008 Z= 0.145 Angle : 0.602 12.491 39579 Z= 0.296 Chirality : 0.044 0.245 4582 Planarity : 0.004 0.044 5021 Dihedral : 5.297 59.811 4901 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 1.37 % Allowed : 16.69 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.57 (0.14), residues: 3481 helix: 0.75 (0.22), residues: 610 sheet: -0.53 (0.21), residues: 698 loop : -1.85 (0.13), residues: 2173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 983 TYR 0.028 0.001 TYR C 501 PHE 0.017 0.001 PHE B1089 TRP 0.019 0.001 TRP G 36 HIS 0.004 0.001 HIS C 505 Details of bonding type rmsd covalent geometry : bond 0.00336 (28912) covalent geometry : angle 0.58496 (39334) SS BOND : bond 0.00320 ( 43) SS BOND : angle 1.31217 ( 86) hydrogen bonds : bond 0.03765 ( 773) hydrogen bonds : angle 5.10345 ( 2142) link_BETA1-4 : bond 0.00492 ( 4) link_BETA1-4 : angle 2.58099 ( 12) link_BETA1-6 : bond 0.00243 ( 2) link_BETA1-6 : angle 1.37886 ( 6) link_NAG-ASN : bond 0.00320 ( 47) link_NAG-ASN : angle 2.11092 ( 141) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 177 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 126 VAL cc_start: 0.7876 (OUTLIER) cc_final: 0.7562 (t) REVERT: C 191 GLU cc_start: 0.8549 (tp30) cc_final: 0.8144 (mm-30) REVERT: C 546 LEU cc_start: 0.9234 (tt) cc_final: 0.8746 (tt) REVERT: C 727 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8809 (mm) REVERT: A 437 ASN cc_start: 0.8568 (m-40) cc_final: 0.8297 (t0) REVERT: B 867 ASP cc_start: 0.8414 (p0) cc_final: 0.8052 (p0) REVERT: I 48 MET cc_start: 0.6887 (mmm) cc_final: 0.6664 (mmm) REVERT: I 54 TYR cc_start: 0.8432 (t80) cc_final: 0.8112 (t80) REVERT: I 81 MET cc_start: 0.4439 (mmm) cc_final: 0.4082 (mmm) REVERT: I 88 SER cc_start: 0.7921 (t) cc_final: 0.7710 (p) REVERT: I 114 PHE cc_start: 0.8409 (m-10) cc_final: 0.7893 (m-10) REVERT: G 37 TYR cc_start: 0.7097 (m-80) cc_final: 0.6531 (m-80) REVERT: G 55 ARG cc_start: 0.5544 (mmt180) cc_final: 0.4478 (mmm160) REVERT: J 29 PHE cc_start: 0.8586 (t80) cc_final: 0.8134 (t80) outliers start: 42 outliers final: 36 residues processed: 206 average time/residue: 0.1517 time to fit residues: 52.7635 Evaluate side-chains 206 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 168 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 72 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 54 optimal weight: 2.9990 chunk 7 optimal weight: 20.0000 chunk 324 optimal weight: 30.0000 chunk 52 optimal weight: 0.9980 chunk 318 optimal weight: 0.0370 chunk 246 optimal weight: 8.9990 chunk 134 optimal weight: 3.9990 chunk 327 optimal weight: 10.0000 chunk 342 optimal weight: 20.0000 chunk 32 optimal weight: 0.8980 chunk 216 optimal weight: 8.9990 overall best weight: 1.7862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 207 HIS ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 GLN ** J 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.105654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.073110 restraints weight = 92131.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.074948 restraints weight = 51993.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.076183 restraints weight = 35749.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.077003 restraints weight = 27940.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.077530 restraints weight = 23890.367| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29008 Z= 0.147 Angle : 0.609 12.506 39579 Z= 0.300 Chirality : 0.044 0.242 4582 Planarity : 0.004 0.044 5021 Dihedral : 5.365 59.998 4901 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 1.34 % Allowed : 16.98 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.60 (0.14), residues: 3481 helix: 0.72 (0.22), residues: 610 sheet: -0.59 (0.20), residues: 715 loop : -1.85 (0.13), residues: 2156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 62 TYR 0.021 0.001 TYR C 501 PHE 0.023 0.001 PHE B 133 TRP 0.016 0.001 TRP J 50 HIS 0.004 0.001 HIS C 505 Details of bonding type rmsd covalent geometry : bond 0.00341 (28912) covalent geometry : angle 0.59216 (39334) SS BOND : bond 0.00328 ( 43) SS BOND : angle 1.34295 ( 86) hydrogen bonds : bond 0.03873 ( 773) hydrogen bonds : angle 5.15705 ( 2142) link_BETA1-4 : bond 0.00588 ( 4) link_BETA1-4 : angle 2.54522 ( 12) link_BETA1-6 : bond 0.00246 ( 2) link_BETA1-6 : angle 1.40708 ( 6) link_NAG-ASN : bond 0.00324 ( 47) link_NAG-ASN : angle 2.12372 ( 141) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6962 Ramachandran restraints generated. 3481 Oldfield, 0 Emsley, 3481 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 170 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 118 LEU cc_start: 0.8246 (tp) cc_final: 0.7549 (pp) REVERT: C 126 VAL cc_start: 0.7749 (OUTLIER) cc_final: 0.7491 (t) REVERT: C 191 GLU cc_start: 0.8526 (tp30) cc_final: 0.8118 (mm-30) REVERT: C 546 LEU cc_start: 0.9244 (tt) cc_final: 0.8749 (tt) REVERT: C 727 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8775 (mm) REVERT: A 437 ASN cc_start: 0.8583 (m-40) cc_final: 0.8323 (t0) REVERT: B 867 ASP cc_start: 0.8366 (p0) cc_final: 0.7974 (p0) REVERT: I 48 MET cc_start: 0.6865 (mmm) cc_final: 0.6631 (mmm) REVERT: I 54 TYR cc_start: 0.8411 (t80) cc_final: 0.8196 (t80) REVERT: I 81 MET cc_start: 0.4431 (mmm) cc_final: 0.4082 (mmm) REVERT: I 114 PHE cc_start: 0.8371 (m-10) cc_final: 0.8027 (m-10) REVERT: G 37 TYR cc_start: 0.7100 (m-80) cc_final: 0.6338 (m-80) REVERT: J 29 PHE cc_start: 0.8641 (t80) cc_final: 0.8253 (t80) outliers start: 41 outliers final: 35 residues processed: 198 average time/residue: 0.1469 time to fit residues: 48.6611 Evaluate side-chains 204 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 167 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 904 TYR Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain H residue 72 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 112 optimal weight: 0.0470 chunk 61 optimal weight: 4.9990 chunk 205 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 chunk 115 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.3980 chunk 133 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 overall best weight: 0.8882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.106442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.074094 restraints weight = 92529.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.076023 restraints weight = 51489.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.077279 restraints weight = 34998.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.078064 restraints weight = 27297.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.078611 restraints weight = 23392.406| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29008 Z= 0.110 Angle : 0.593 12.489 39579 Z= 0.291 Chirality : 0.044 0.253 4582 Planarity : 0.004 0.045 5021 Dihedral : 5.236 59.885 4901 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 1.08 % Allowed : 17.47 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.54 (0.14), residues: 3481 helix: 0.82 (0.22), residues: 610 sheet: -0.56 (0.20), residues: 705 loop : -1.83 (0.13), residues: 2166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 24 TYR 0.020 0.001 TYR C 501 PHE 0.024 0.001 PHE C 55 TRP 0.017 0.001 TRP J 50 HIS 0.004 0.001 HIS C 505 Details of bonding type rmsd covalent geometry : bond 0.00250 (28912) covalent geometry : angle 0.57650 (39334) SS BOND : bond 0.00303 ( 43) SS BOND : angle 1.24089 ( 86) hydrogen bonds : bond 0.03684 ( 773) hydrogen bonds : angle 5.02331 ( 2142) link_BETA1-4 : bond 0.00522 ( 4) link_BETA1-4 : angle 2.50319 ( 12) link_BETA1-6 : bond 0.00291 ( 2) link_BETA1-6 : angle 1.35901 ( 6) link_NAG-ASN : bond 0.00324 ( 47) link_NAG-ASN : angle 2.07308 ( 141) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4418.92 seconds wall clock time: 77 minutes 22.57 seconds (4642.57 seconds total)