Starting phenix.real_space_refine on Tue Jun 24 12:19:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yqz_34040/06_2025/7yqz_34040.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yqz_34040/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7yqz_34040/06_2025/7yqz_34040.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yqz_34040/06_2025/7yqz_34040.map" model { file = "/net/cci-nas-00/data/ceres_data/7yqz_34040/06_2025/7yqz_34040.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yqz_34040/06_2025/7yqz_34040.cif" } resolution = 3.84 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.051 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): 0.90s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 16.87, per 1000 atoms: 0.60 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: 6.23 Conformation dependent library (CDL) restraints added in 3.2 seconds 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: 3.47 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: 11.82 Time building geometry restraints manager: 7.65 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 1144 or resid 1301 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 1144 or resid 1301 through 1315)) selection = (chain 'C' and (resid 25 through 622 or resid 641 through 826 or resid 854 throu \ gh 1144 or resid 1301 through 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: 7.680 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: 0.980 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 62.320 Find NCS groups from input model: 2.050 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.220 ------------------------------------------------------------------------------- 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 : 6.53 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (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 TRP 0.032 0.002 TRP I 47 HIS 0.006 0.001 HIS A1048 PHE 0.045 0.002 PHE B 133 TYR 0.022 0.001 TYR B 265 ARG 0.007 0.000 ARG J 85 Details of bonding type rmsd link_NAG-ASN : bond 0.00785 ( 47) link_NAG-ASN : angle 2.83070 ( 141) link_BETA1-4 : bond 0.01118 ( 4) link_BETA1-4 : angle 3.28141 ( 12) hydrogen bonds : bond 0.25958 ( 773) hydrogen bonds : angle 8.92838 ( 2142) link_BETA1-6 : bond 0.00459 ( 2) link_BETA1-6 : angle 1.20440 ( 6) SS BOND : bond 0.00394 ( 43) SS BOND : angle 1.44500 ( 86) covalent geometry : bond 0.00473 (28912) covalent geometry : angle 0.80367 (39334) *********************** 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 : 4.325 Fit side-chains 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: 0.7606 (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 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: 0.4214 (mmm-85) REVERT: J 4 LEU cc_start: 0.8075 (mt) cc_final: 0.7862 (mt) REVERT: H 96 LEU cc_start: 0.8021 (tp) cc_final: 0.7768 (tp) outliers start: 2 outliers final: 0 residues processed: 252 average time/residue: 0.4836 time to fit residues: 198.1722 Evaluate side-chains 168 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 3.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 295 optimal weight: 3.9990 chunk 265 optimal weight: 6.9990 chunk 147 optimal weight: 9.9990 chunk 90 optimal weight: 0.6980 chunk 178 optimal weight: 3.9990 chunk 141 optimal weight: 10.0000 chunk 274 optimal weight: 0.9990 chunk 106 optimal weight: 8.9990 chunk 166 optimal weight: 2.9990 chunk 204 optimal weight: 10.0000 chunk 317 optimal weight: 0.0070 overall best weight: 1.7404 ------------------------------------------------------------------------------- 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 439 ASN A 955 ASN A1125 ASN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 116 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.107795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.082754 restraints weight = 95186.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.081517 restraints weight = 60659.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.082321 restraints weight = 67247.683| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 29008 Z= 0.157 Angle : 0.650 12.673 39579 Z= 0.323 Chirality : 0.045 0.254 4582 Planarity : 0.004 0.058 5021 Dihedral : 7.476 64.483 4901 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 0.43 % Allowed : 7.69 % Favored : 91.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.13), residues: 3481 helix: -0.75 (0.20), residues: 600 sheet: -0.68 (0.20), residues: 704 loop : -2.08 (0.12), residues: 2177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 47 HIS 0.005 0.001 HIS C 505 PHE 0.019 0.001 PHE C1089 TYR 0.026 0.001 TYR C 453 ARG 0.004 0.000 ARG C 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00413 ( 47) link_NAG-ASN : angle 2.46550 ( 141) link_BETA1-4 : bond 0.00305 ( 4) link_BETA1-4 : angle 2.97146 ( 12) hydrogen bonds : bond 0.05279 ( 773) hydrogen bonds : angle 6.20600 ( 2142) link_BETA1-6 : bond 0.00205 ( 2) link_BETA1-6 : angle 1.43992 ( 6) SS BOND : bond 0.00332 ( 43) SS BOND : angle 1.39848 ( 86) covalent geometry : bond 0.00354 (28912) covalent geometry : angle 0.62919 (39334) *********************** 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 211 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 198 time to evaluate : 3.464 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 979 ASP cc_start: 0.9050 (m-30) cc_final: 0.8848 (m-30) REVERT: B 133 PHE cc_start: 0.7013 (m-80) cc_final: 0.6263 (p90) REVERT: B 731 MET cc_start: 0.8806 (ptp) cc_final: 0.8599 (ptm) REVERT: B 867 ASP cc_start: 0.8148 (p0) cc_final: 0.7763 (p0) REVERT: I 48 MET cc_start: 0.6772 (mmm) cc_final: 0.6460 (mmm) outliers start: 13 outliers final: 12 residues processed: 204 average time/residue: 0.3706 time to fit residues: 126.6769 Evaluate side-chains 173 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 161 time to evaluate : 3.416 ------------------------------------------------------------------------------- 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 J residue 3 GLN 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 83 optimal weight: 0.8980 chunk 153 optimal weight: 6.9990 chunk 280 optimal weight: 3.9990 chunk 35 optimal weight: 0.3980 chunk 286 optimal weight: 4.9990 chunk 321 optimal weight: 9.9990 chunk 312 optimal weight: 7.9990 chunk 60 optimal weight: 7.9990 chunk 301 optimal weight: 8.9990 chunk 97 optimal weight: 3.9990 chunk 206 optimal weight: 6.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- 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 ** C1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 ASN A 493 GLN A 580 GLN A 913 GLN A 919 ASN A 965 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1125 ASN B 185 ASN B 487 ASN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN B1011 GLN I 3 GLN G 38 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.104878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.079504 restraints weight = 91955.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.078525 restraints weight = 63721.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.079248 restraints weight = 69311.854| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 29008 Z= 0.214 Angle : 0.670 12.707 39579 Z= 0.335 Chirality : 0.046 0.262 4582 Planarity : 0.004 0.054 5021 Dihedral : 6.819 58.541 4901 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 1.15 % Allowed : 12.27 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.14), residues: 3481 helix: -0.15 (0.21), residues: 598 sheet: -0.74 (0.20), residues: 709 loop : -2.08 (0.12), residues: 2174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP J 47 HIS 0.005 0.001 HIS A1048 PHE 0.035 0.002 PHE C 55 TYR 0.025 0.002 TYR C 453 ARG 0.006 0.000 ARG J 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00392 ( 47) link_NAG-ASN : angle 2.50031 ( 141) link_BETA1-4 : bond 0.00383 ( 4) link_BETA1-4 : angle 2.66567 ( 12) hydrogen bonds : bond 0.05189 ( 773) hydrogen bonds : angle 6.01142 ( 2142) link_BETA1-6 : bond 0.00247 ( 2) link_BETA1-6 : angle 1.32239 ( 6) SS BOND : bond 0.00367 ( 43) SS BOND : angle 1.53919 ( 86) covalent geometry : bond 0.00491 (28912) covalent geometry : angle 0.64961 (39334) *********************** 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 212 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 177 time to evaluate : 3.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 437 ASN cc_start: 0.8415 (m-40) cc_final: 0.8072 (t0) REVERT: A 979 ASP cc_start: 0.9034 (m-30) cc_final: 0.8667 (m-30) REVERT: B 133 PHE cc_start: 0.6859 (m-80) cc_final: 0.6294 (p90) REVERT: B 902 MET cc_start: 0.9225 (tpp) cc_final: 0.8914 (tpt) REVERT: I 48 MET cc_start: 0.6752 (mmm) cc_final: 0.6475 (mmm) REVERT: I 54 TYR cc_start: 0.7765 (t80) cc_final: 0.7550 (t80) REVERT: J 80 TYR cc_start: 0.6404 (m-80) cc_final: 0.6096 (m-10) REVERT: H 39 GLN cc_start: 0.6146 (mm110) cc_final: 0.4997 (mp10) outliers start: 35 outliers final: 24 residues processed: 200 average time/residue: 0.3703 time to fit residues: 124.0217 Evaluate side-chains 183 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 159 time to evaluate : 4.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 392 PHE Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain A residue 117 LEU 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 1034 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 697 MET 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 119 optimal weight: 3.9990 chunk 253 optimal weight: 0.9980 chunk 274 optimal weight: 0.3980 chunk 46 optimal weight: 2.9990 chunk 177 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 237 optimal weight: 7.9990 chunk 277 optimal weight: 4.9990 chunk 170 optimal weight: 2.9990 chunk 315 optimal weight: 30.0000 chunk 112 optimal weight: 2.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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** A 388 ASN A 774 GLN A1125 ASN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 957 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 = 0.3902 r_free = 0.3902 target = 0.107164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.076805 restraints weight = 94988.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.077887 restraints weight = 58207.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.078369 restraints weight = 39903.898| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1881 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= 0.122 Angle : 0.590 12.614 39579 Z= 0.292 Chirality : 0.044 0.247 4582 Planarity : 0.004 0.051 5021 Dihedral : 6.214 59.565 4901 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 1.51 % Allowed : 13.61 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.14), residues: 3481 helix: 0.27 (0.22), residues: 599 sheet: -0.62 (0.21), residues: 684 loop : -2.00 (0.12), residues: 2198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 47 HIS 0.008 0.001 HIS C 505 PHE 0.020 0.001 PHE C 92 TYR 0.022 0.001 TYR C 453 ARG 0.003 0.000 ARG J 84 Details of bonding type rmsd link_NAG-ASN : bond 0.00346 ( 47) link_NAG-ASN : angle 2.29172 ( 141) link_BETA1-4 : bond 0.00409 ( 4) link_BETA1-4 : angle 2.49585 ( 12) hydrogen bonds : bond 0.04198 ( 773) hydrogen bonds : angle 5.57917 ( 2142) link_BETA1-6 : bond 0.00310 ( 2) link_BETA1-6 : angle 1.33697 ( 6) SS BOND : bond 0.00363 ( 43) SS BOND : angle 1.31076 ( 86) covalent geometry : bond 0.00278 (28912) covalent geometry : angle 0.57097 (39334) *********************** 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 217 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 171 time to evaluate : 6.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 118 LEU cc_start: 0.8193 (tp) cc_final: 0.7483 (pp) REVERT: C 581 THR cc_start: 0.9088 (OUTLIER) cc_final: 0.8666 (p) REVERT: A 129 LYS cc_start: 0.8333 (tttt) cc_final: 0.8100 (tptm) REVERT: A 437 ASN cc_start: 0.8615 (m-40) cc_final: 0.8243 (t0) REVERT: A 1122 VAL cc_start: 0.7985 (OUTLIER) cc_final: 0.7757 (p) REVERT: B 133 PHE cc_start: 0.7317 (m-80) cc_final: 0.6754 (p90) REVERT: I 48 MET cc_start: 0.6778 (mmm) cc_final: 0.6530 (mmm) outliers start: 46 outliers final: 32 residues processed: 201 average time/residue: 0.4344 time to fit residues: 149.2260 Evaluate side-chains 196 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 162 time to evaluate : 3.020 ------------------------------------------------------------------------------- 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 391 CYS 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 581 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 375 PHE 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 931 ILE Chi-restraints excluded: chain A residue 1034 LEU 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 197 ILE 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 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 110 LEU Chi-restraints excluded: chain H residue 72 PHE Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain H residue 98 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 210 optimal weight: 0.0010 chunk 30 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 102 optimal weight: 10.0000 chunk 225 optimal weight: 7.9990 chunk 106 optimal weight: 0.0070 chunk 275 optimal weight: 0.7980 chunk 302 optimal weight: 4.9990 chunk 297 optimal weight: 0.3980 chunk 70 optimal weight: 1.9990 chunk 186 optimal weight: 1.9990 overall best weight: 0.6406 ------------------------------------------------------------------------------- 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** A1125 ASN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** 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 = 0.3906 r_free = 0.3906 target = 0.107547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.076380 restraints weight = 92568.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.077876 restraints weight = 57436.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.078612 restraints weight = 38268.238| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 29008 Z= 0.098 Angle : 0.561 12.577 39579 Z= 0.277 Chirality : 0.044 0.247 4582 Planarity : 0.004 0.049 5021 Dihedral : 5.689 59.425 4901 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 1.31 % Allowed : 14.79 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.14), residues: 3481 helix: 0.55 (0.22), residues: 605 sheet: -0.58 (0.21), residues: 688 loop : -1.91 (0.13), residues: 2188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 50 HIS 0.005 0.001 HIS A 49 PHE 0.019 0.001 PHE C 92 TYR 0.020 0.001 TYR C 453 ARG 0.003 0.000 ARG H 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00356 ( 47) link_NAG-ASN : angle 2.13768 ( 141) link_BETA1-4 : bond 0.00527 ( 4) link_BETA1-4 : angle 2.56816 ( 12) hydrogen bonds : bond 0.03745 ( 773) hydrogen bonds : angle 5.24835 ( 2142) link_BETA1-6 : bond 0.00343 ( 2) link_BETA1-6 : angle 1.28162 ( 6) SS BOND : bond 0.00364 ( 43) SS BOND : angle 1.25755 ( 86) covalent geometry : bond 0.00219 (28912) covalent geometry : angle 0.54265 (39334) *********************** 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 228 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 188 time to evaluate : 3.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 581 THR cc_start: 0.9033 (OUTLIER) cc_final: 0.8604 (p) REVERT: C 727 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8751 (mm) REVERT: A 175 PHE cc_start: 0.8042 (m-80) cc_final: 0.7833 (m-80) REVERT: A 1122 VAL cc_start: 0.7890 (OUTLIER) cc_final: 0.7681 (p) REVERT: B 303 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7849 (pp) REVERT: B 867 ASP cc_start: 0.8291 (p0) cc_final: 0.7896 (p0) REVERT: I 48 MET cc_start: 0.6833 (mmm) cc_final: 0.6593 (mmm) REVERT: I 54 TYR cc_start: 0.8244 (t80) cc_final: 0.7838 (t80) REVERT: I 114 PHE cc_start: 0.8431 (m-10) cc_final: 0.8188 (m-10) REVERT: J 29 PHE cc_start: 0.8461 (t80) cc_final: 0.8145 (t80) outliers start: 40 outliers final: 27 residues processed: 216 average time/residue: 0.3559 time to fit residues: 129.4027 Evaluate side-chains 197 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 166 time to evaluate : 2.914 ------------------------------------------------------------------------------- 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 493 GLN 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 117 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 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 A residue 1122 VAL Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 197 ILE 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 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 110 LEU Chi-restraints excluded: chain J residue 111 ILE 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 18 optimal weight: 8.9990 chunk 32 optimal weight: 0.9990 chunk 276 optimal weight: 6.9990 chunk 342 optimal weight: 20.0000 chunk 106 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 324 optimal weight: 40.0000 chunk 240 optimal weight: 9.9990 chunk 301 optimal weight: 9.9990 chunk 58 optimal weight: 3.9990 chunk 286 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 536 ASN A 954 HIS A1125 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.103252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.073687 restraints weight = 93957.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.073433 restraints weight = 59521.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.073806 restraints weight = 46546.712| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.116 29008 Z= 0.317 Angle : 0.751 13.182 39579 Z= 0.376 Chirality : 0.048 0.259 4582 Planarity : 0.005 0.051 5021 Dihedral : 6.395 59.371 4901 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 2.26 % Allowed : 16.52 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.14), residues: 3481 helix: 0.03 (0.21), residues: 603 sheet: -0.86 (0.20), residues: 732 loop : -2.14 (0.13), residues: 2146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP J 47 HIS 0.008 0.001 HIS B1064 PHE 0.034 0.002 PHE B1089 TYR 0.024 0.002 TYR A1067 ARG 0.005 0.001 ARG A 44 Details of bonding type rmsd link_NAG-ASN : bond 0.00470 ( 47) link_NAG-ASN : angle 2.53133 ( 141) link_BETA1-4 : bond 0.00467 ( 4) link_BETA1-4 : angle 2.75108 ( 12) hydrogen bonds : bond 0.05044 ( 773) hydrogen bonds : angle 5.96474 ( 2142) link_BETA1-6 : bond 0.00267 ( 2) link_BETA1-6 : angle 1.55621 ( 6) SS BOND : bond 0.00524 ( 43) SS BOND : angle 1.73947 ( 86) covalent geometry : bond 0.00727 (28912) covalent geometry : angle 0.73208 (39334) *********************** 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 236 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 167 time to evaluate : 3.583 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 118 LEU cc_start: 0.8281 (tp) cc_final: 0.7551 (pp) REVERT: C 546 LEU cc_start: 0.9327 (tt) cc_final: 0.8886 (tt) REVERT: A 449 TYR cc_start: 0.8372 (m-80) cc_final: 0.8071 (m-80) REVERT: A 1122 VAL cc_start: 0.7992 (OUTLIER) cc_final: 0.7756 (p) REVERT: A 1125 ASN cc_start: 0.8397 (OUTLIER) cc_final: 0.7914 (t0) REVERT: B 133 PHE cc_start: 0.7457 (m-80) cc_final: 0.6926 (p90) REVERT: B 1002 GLN cc_start: 0.8855 (tp40) cc_final: 0.8392 (tp40) REVERT: I 48 MET cc_start: 0.6814 (mmm) cc_final: 0.6561 (mmm) REVERT: I 70 MET cc_start: 0.6474 (mpp) cc_final: 0.6241 (mpp) REVERT: H 18 ARG cc_start: 0.7776 (tpp-160) cc_final: 0.7074 (mmm160) REVERT: H 27 GLN cc_start: 0.9143 (mm-40) cc_final: 0.8790 (mm-40) outliers start: 69 outliers final: 48 residues processed: 219 average time/residue: 0.4958 time to fit residues: 184.5305 Evaluate side-chains 206 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 156 time to evaluate : 3.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 302 THR 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 493 GLN 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 736 VAL Chi-restraints excluded: chain C residue 791 THR 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 212 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 375 PHE 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 976 VAL Chi-restraints excluded: chain A residue 979 ASP Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 197 ILE 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 697 MET Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 1060 VAL Chi-restraints excluded: chain B residue 1133 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 111 ILE Chi-restraints excluded: chain H residue 72 PHE Chi-restraints excluded: chain H residue 98 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 126 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 320 optimal weight: 30.0000 chunk 233 optimal weight: 8.9990 chunk 246 optimal weight: 8.9990 chunk 109 optimal weight: 6.9990 chunk 114 optimal weight: 10.0000 chunk 133 optimal weight: 0.4980 chunk 64 optimal weight: 0.9980 chunk 228 optimal weight: 3.9990 chunk 200 optimal weight: 0.7980 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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** A1088 HIS ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 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 = 0.3861 r_free = 0.3861 target = 0.105252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.072935 restraints weight = 92391.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.075368 restraints weight = 54144.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.075823 restraints weight = 35258.280| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29008 Z= 0.124 Angle : 0.610 12.566 39579 Z= 0.301 Chirality : 0.045 0.250 4582 Planarity : 0.004 0.045 5021 Dihedral : 5.905 59.720 4901 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 1.51 % Allowed : 17.67 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.14), residues: 3481 helix: 0.46 (0.22), residues: 602 sheet: -0.68 (0.21), residues: 694 loop : -2.02 (0.13), residues: 2185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP J 50 HIS 0.004 0.001 HIS A1048 PHE 0.051 0.001 PHE J 29 TYR 0.019 0.001 TYR C 453 ARG 0.007 0.000 ARG G 62 Details of bonding type rmsd link_NAG-ASN : bond 0.00329 ( 47) link_NAG-ASN : angle 2.22249 ( 141) link_BETA1-4 : bond 0.00504 ( 4) link_BETA1-4 : angle 2.51146 ( 12) hydrogen bonds : bond 0.04076 ( 773) hydrogen bonds : angle 5.40458 ( 2142) link_BETA1-6 : bond 0.00260 ( 2) link_BETA1-6 : angle 1.36955 ( 6) SS BOND : bond 0.00362 ( 43) SS BOND : angle 1.37880 ( 86) covalent geometry : bond 0.00282 (28912) covalent geometry : angle 0.59192 (39334) *********************** 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 219 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 173 time to evaluate : 2.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 546 LEU cc_start: 0.9260 (tt) cc_final: 0.8795 (tt) REVERT: A 175 PHE cc_start: 0.8159 (m-80) cc_final: 0.7910 (m-80) REVERT: A 957 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.8457 (pm20) REVERT: A 1050 MET cc_start: 0.7750 (mtp) cc_final: 0.7523 (mtp) REVERT: A 1122 VAL cc_start: 0.7872 (OUTLIER) cc_final: 0.7636 (p) REVERT: B 133 PHE cc_start: 0.7484 (m-80) cc_final: 0.7109 (p90) REVERT: B 1002 GLN cc_start: 0.8728 (tp40) cc_final: 0.8374 (tp-100) REVERT: I 48 MET cc_start: 0.6990 (mmm) cc_final: 0.6760 (mmm) REVERT: H 18 ARG cc_start: 0.7862 (tpp-160) cc_final: 0.7211 (mmm160) REVERT: H 27 GLN cc_start: 0.9138 (mm-40) cc_final: 0.8810 (mm-40) outliers start: 46 outliers final: 34 residues processed: 208 average time/residue: 0.3574 time to fit residues: 123.6994 Evaluate side-chains 198 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 162 time to evaluate : 2.878 ------------------------------------------------------------------------------- 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 493 GLN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 736 VAL 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 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 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 197 ILE 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 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 109 optimal weight: 1.9990 chunk 164 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 112 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 186 optimal weight: 2.9990 chunk 277 optimal weight: 4.9990 chunk 345 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 342 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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** J 3 GLN ** 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 = 0.3843 r_free = 0.3843 target = 0.104284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.071406 restraints weight = 93396.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.073267 restraints weight = 51758.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.074517 restraints weight = 35406.973| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 29008 Z= 0.184 Angle : 0.644 12.518 39579 Z= 0.318 Chirality : 0.045 0.252 4582 Planarity : 0.004 0.047 5021 Dihedral : 5.916 59.841 4901 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 1.80 % Allowed : 18.00 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.14), residues: 3481 helix: 0.42 (0.22), residues: 603 sheet: -0.84 (0.20), residues: 730 loop : -2.06 (0.13), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J 47 HIS 0.004 0.001 HIS A1048 PHE 0.044 0.002 PHE J 29 TYR 0.020 0.001 TYR C 453 ARG 0.007 0.000 ARG G 62 Details of bonding type rmsd link_NAG-ASN : bond 0.00344 ( 47) link_NAG-ASN : angle 2.28263 ( 141) link_BETA1-4 : bond 0.00471 ( 4) link_BETA1-4 : angle 2.64407 ( 12) hydrogen bonds : bond 0.04239 ( 773) hydrogen bonds : angle 5.48051 ( 2142) link_BETA1-6 : bond 0.00260 ( 2) link_BETA1-6 : angle 1.42312 ( 6) SS BOND : bond 0.00368 ( 43) SS BOND : angle 1.43517 ( 86) covalent geometry : bond 0.00428 (28912) covalent geometry : angle 0.62573 (39334) *********************** 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 216 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 161 time to evaluate : 2.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 236 THR cc_start: 0.9182 (OUTLIER) cc_final: 0.8963 (p) REVERT: C 546 LEU cc_start: 0.9277 (tt) cc_final: 0.8800 (tt) REVERT: A 117 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8531 (pp) REVERT: A 175 PHE cc_start: 0.8107 (m-80) cc_final: 0.7861 (m-80) REVERT: A 437 ASN cc_start: 0.8743 (m-40) cc_final: 0.8401 (t0) REVERT: A 1122 VAL cc_start: 0.7965 (OUTLIER) cc_final: 0.7708 (p) REVERT: B 1002 GLN cc_start: 0.8778 (tp40) cc_final: 0.8404 (tp-100) REVERT: I 48 MET cc_start: 0.6964 (mmm) cc_final: 0.6742 (mmm) REVERT: I 81 MET cc_start: 0.4048 (mmm) cc_final: 0.3597 (mmm) REVERT: G 55 ARG cc_start: 0.5585 (mmt180) cc_final: 0.4529 (mmm160) REVERT: J 25 SER cc_start: 0.8510 (p) cc_final: 0.8236 (m) REVERT: H 27 GLN cc_start: 0.9125 (mm-40) cc_final: 0.8779 (mm-40) outliers start: 55 outliers final: 46 residues processed: 204 average time/residue: 0.3466 time to fit residues: 119.1863 Evaluate side-chains 207 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 158 time to evaluate : 2.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 236 THR 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 493 GLN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 428 ASP Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 622 VAL 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 981 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1034 LEU 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 197 ILE Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 333 THR 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 1107 ARG 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 111 ILE 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 307 optimal weight: 0.0470 chunk 312 optimal weight: 0.7980 chunk 328 optimal weight: 9.9990 chunk 190 optimal weight: 0.9990 chunk 325 optimal weight: 6.9990 chunk 235 optimal weight: 1.9990 chunk 295 optimal weight: 4.9990 chunk 185 optimal weight: 4.9990 chunk 52 optimal weight: 0.6980 chunk 299 optimal weight: 5.9990 chunk 208 optimal weight: 0.0170 overall best weight: 0.5118 ------------------------------------------------------------------------------- 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** G 38 GLN ** 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 = 0.3883 r_free = 0.3883 target = 0.106396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.074364 restraints weight = 92850.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.077158 restraints weight = 52790.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.077498 restraints weight = 31887.698| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 29008 Z= 0.102 Angle : 0.587 12.561 39579 Z= 0.288 Chirality : 0.044 0.246 4582 Planarity : 0.004 0.046 5021 Dihedral : 5.502 59.747 4901 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 1.44 % Allowed : 18.52 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.14), residues: 3481 helix: 0.71 (0.22), residues: 606 sheet: -0.64 (0.20), residues: 711 loop : -1.94 (0.13), residues: 2164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP J 50 HIS 0.004 0.001 HIS A1048 PHE 0.021 0.001 PHE C 55 TYR 0.018 0.001 TYR C 453 ARG 0.005 0.000 ARG G 62 Details of bonding type rmsd link_NAG-ASN : bond 0.00355 ( 47) link_NAG-ASN : angle 2.09350 ( 141) link_BETA1-4 : bond 0.00595 ( 4) link_BETA1-4 : angle 2.50938 ( 12) hydrogen bonds : bond 0.03617 ( 773) hydrogen bonds : angle 5.10141 ( 2142) link_BETA1-6 : bond 0.00338 ( 2) link_BETA1-6 : angle 1.30145 ( 6) SS BOND : bond 0.00315 ( 43) SS BOND : angle 1.22983 ( 86) covalent geometry : bond 0.00228 (28912) covalent geometry : angle 0.57084 (39334) *********************** 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: 44 poor density : 175 time to evaluate : 4.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 118 LEU cc_start: 0.8180 (tp) cc_final: 0.7475 (pp) REVERT: C 236 THR cc_start: 0.9117 (OUTLIER) cc_final: 0.8903 (p) REVERT: C 546 LEU cc_start: 0.9252 (tt) cc_final: 0.8774 (tt) REVERT: A 117 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8627 (pp) REVERT: A 175 PHE cc_start: 0.8155 (m-80) cc_final: 0.7926 (m-80) REVERT: A 437 ASN cc_start: 0.8620 (m-40) cc_final: 0.8372 (t0) REVERT: A 957 GLN cc_start: 0.8644 (OUTLIER) cc_final: 0.8410 (pm20) REVERT: A 983 ARG cc_start: 0.8719 (ptp90) cc_final: 0.8517 (ptp90) REVERT: A 1122 VAL cc_start: 0.7887 (OUTLIER) cc_final: 0.7660 (p) REVERT: B 867 ASP cc_start: 0.8402 (p0) cc_final: 0.7974 (p0) REVERT: I 48 MET cc_start: 0.6827 (mmm) cc_final: 0.6596 (mmm) REVERT: G 55 ARG cc_start: 0.5254 (mmt180) cc_final: 0.4896 (mmt-90) REVERT: J 29 PHE cc_start: 0.8413 (t80) cc_final: 0.8096 (t80) REVERT: H 18 ARG cc_start: 0.7931 (tpp-160) cc_final: 0.7326 (mmm160) outliers start: 44 outliers final: 37 residues processed: 208 average time/residue: 0.5841 time to fit residues: 208.1045 Evaluate side-chains 203 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 162 time to evaluate : 4.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 236 THR 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 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 588 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 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 333 THR 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 1107 ARG 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 111 ILE 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 249 optimal weight: 4.9990 chunk 285 optimal weight: 0.9980 chunk 303 optimal weight: 6.9990 chunk 255 optimal weight: 0.7980 chunk 194 optimal weight: 0.0980 chunk 200 optimal weight: 4.9990 chunk 314 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 316 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 59 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.106523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.074038 restraints weight = 92481.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.076004 restraints weight = 50609.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.077307 restraints weight = 34140.336| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 29008 Z= 0.105 Angle : 0.587 12.543 39579 Z= 0.287 Chirality : 0.044 0.249 4582 Planarity : 0.004 0.062 5021 Dihedral : 5.311 59.731 4901 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 1.44 % Allowed : 18.72 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.14), residues: 3481 helix: 0.82 (0.22), residues: 605 sheet: -0.61 (0.20), residues: 715 loop : -1.88 (0.13), residues: 2161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP J 50 HIS 0.003 0.001 HIS A1048 PHE 0.020 0.001 PHE B 133 TYR 0.018 0.001 TYR C 453 ARG 0.008 0.000 ARG A 765 Details of bonding type rmsd link_NAG-ASN : bond 0.00333 ( 47) link_NAG-ASN : angle 2.07345 ( 141) link_BETA1-4 : bond 0.00547 ( 4) link_BETA1-4 : angle 2.57350 ( 12) hydrogen bonds : bond 0.03549 ( 773) hydrogen bonds : angle 5.01308 ( 2142) link_BETA1-6 : bond 0.00329 ( 2) link_BETA1-6 : angle 1.31326 ( 6) SS BOND : bond 0.00290 ( 43) SS BOND : angle 1.19256 ( 86) covalent geometry : bond 0.00241 (28912) covalent geometry : angle 0.57064 (39334) ********************** 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 215 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 171 time to evaluate : 3.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 118 LEU cc_start: 0.8278 (tp) cc_final: 0.7599 (pp) REVERT: C 191 GLU cc_start: 0.8538 (tp30) cc_final: 0.8143 (mm-30) REVERT: C 236 THR cc_start: 0.9177 (OUTLIER) cc_final: 0.8957 (p) REVERT: C 546 LEU cc_start: 0.9242 (tt) cc_final: 0.8752 (tt) REVERT: A 117 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8561 (pp) REVERT: A 175 PHE cc_start: 0.8140 (m-80) cc_final: 0.7931 (m-80) REVERT: A 437 ASN cc_start: 0.8529 (m-40) cc_final: 0.8297 (t0) REVERT: A 957 GLN cc_start: 0.8630 (OUTLIER) cc_final: 0.8406 (pm20) REVERT: A 1122 VAL cc_start: 0.7807 (OUTLIER) cc_final: 0.7591 (p) REVERT: B 303 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7778 (pp) REVERT: B 365 TYR cc_start: 0.7990 (m-80) cc_final: 0.7679 (m-80) REVERT: B 867 ASP cc_start: 0.8360 (p0) cc_final: 0.8003 (p0) REVERT: I 48 MET cc_start: 0.6852 (mmm) cc_final: 0.6518 (mmm) REVERT: I 54 TYR cc_start: 0.8319 (t80) cc_final: 0.8054 (t80) REVERT: I 81 MET cc_start: 0.3953 (mmm) cc_final: 0.3425 (mtt) REVERT: G 55 ARG cc_start: 0.5373 (mmt180) cc_final: 0.5039 (mmt-90) REVERT: J 29 PHE cc_start: 0.8375 (t80) cc_final: 0.8125 (t80) REVERT: H 18 ARG cc_start: 0.7792 (tpp-160) cc_final: 0.7298 (mmm160) outliers start: 44 outliers final: 36 residues processed: 204 average time/residue: 0.3857 time to fit residues: 131.5075 Evaluate side-chains 207 residues out of total 3066 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 166 time to evaluate : 2.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 277 LEU 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 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 588 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 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 333 THR 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 1107 ARG 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 111 ILE 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 311 optimal weight: 4.9990 chunk 175 optimal weight: 6.9990 chunk 299 optimal weight: 8.9990 chunk 261 optimal weight: 4.9990 chunk 219 optimal weight: 6.9990 chunk 283 optimal weight: 7.9990 chunk 109 optimal weight: 6.9990 chunk 336 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 300 optimal weight: 8.9990 chunk 22 optimal weight: 0.7980 overall best weight: 2.7586 ------------------------------------------------------------------------------- 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** A1125 ASN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN G 38 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 = 0.3849 r_free = 0.3849 target = 0.104426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.071616 restraints weight = 93566.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.073425 restraints weight = 53037.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.074660 restraints weight = 36697.601| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 29008 Z= 0.203 Angle : 0.650 13.119 39579 Z= 0.322 Chirality : 0.046 0.252 4582 Planarity : 0.004 0.046 5021 Dihedral : 5.643 59.758 4901 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 1.57 % Allowed : 18.95 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.14), residues: 3481 helix: 0.58 (0.22), residues: 603 sheet: -0.76 (0.20), residues: 725 loop : -1.98 (0.13), residues: 2153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP J 47 HIS 0.005 0.001 HIS B1064 PHE 0.022 0.002 PHE I 114 TYR 0.021 0.001 TYR C 904 ARG 0.006 0.000 ARG A 765 Details of bonding type rmsd link_NAG-ASN : bond 0.00359 ( 47) link_NAG-ASN : angle 2.24073 ( 141) link_BETA1-4 : bond 0.00460 ( 4) link_BETA1-4 : angle 2.66859 ( 12) hydrogen bonds : bond 0.04210 ( 773) hydrogen bonds : angle 5.36303 ( 2142) link_BETA1-6 : bond 0.00224 ( 2) link_BETA1-6 : angle 1.45720 ( 6) SS BOND : bond 0.00371 ( 43) SS BOND : angle 1.44275 ( 86) covalent geometry : bond 0.00468 (28912) covalent geometry : angle 0.63294 (39334) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9593.79 seconds wall clock time: 176 minutes 16.23 seconds (10576.23 seconds total)