Starting phenix.real_space_refine on Mon Jun 23 20:58:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eyg_28686/06_2025/8eyg_28686.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eyg_28686/06_2025/8eyg_28686.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8eyg_28686/06_2025/8eyg_28686.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eyg_28686/06_2025/8eyg_28686.map" model { file = "/net/cci-nas-00/data/ceres_data/8eyg_28686/06_2025/8eyg_28686.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eyg_28686/06_2025/8eyg_28686.cif" } resolution = 3.73 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.020 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 124 5.16 5 C 17484 2.51 5 N 4544 2.21 5 O 5333 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 27485 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 8366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1069, 8366 Classifications: {'peptide': 1069} Link IDs: {'PTRANS': 56, 'TRANS': 1012} Chain breaks: 5 Chain: "B" Number of atoms: 8515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1088, 8515 Classifications: {'peptide': 1088} Link IDs: {'PTRANS': 59, 'TRANS': 1028} Chain breaks: 4 Chain: "C" Number of atoms: 8350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1067, 8350 Classifications: {'peptide': 1067} Link IDs: {'PTRANS': 56, 'TRANS': 1010} Chain breaks: 5 Chain: "E" Number of atoms: 868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 868 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "F" Number of atoms: 868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 868 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 16.53, per 1000 atoms: 0.60 Number of scatterers: 27485 At special positions: 0 Unit cell: (162.503, 162.503, 226.649, 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 124 16.00 O 5333 8.00 N 4544 7.00 C 17484 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=19, symmetry=0 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " NAG-ASN " NAG A1201 " - " ASN A 282 " " NAG A1202 " - " ASN A 331 " " NAG A1203 " - " ASN A 603 " " NAG A1204 " - " ASN A 616 " " NAG A1205 " - " ASN A 709 " " NAG A1206 " - " ASN A 717 " " NAG A1207 " - " ASN A1098 " " NAG A1208 " - " ASN A1134 " " NAG A1209 " - " ASN A 657 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 657 " " NAG B1303 " - " ASN B 616 " " NAG B1304 " - " ASN B 709 " " NAG B1305 " - " ASN B1074 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 331 " " NAG C1201 " - " ASN C 331 " " NAG C1202 " - " ASN C 603 " " NAG C1203 " - " ASN C 616 " " NAG C1204 " - " ASN C 657 " " NAG C1205 " - " ASN C 709 " " NAG C1206 " - " ASN C 717 " " NAG C1207 " - " ASN C1134 " " NAG C1208 " - " ASN C 343 " " NAG D 1 " - " ASN B1134 " " NAG G 1 " - " ASN B1098 " " NAG H 1 " - " ASN B 717 " " NAG I 1 " - " ASN B 801 " " NAG J 1 " - " ASN B 343 " " NAG K 1 " - " ASN A 343 " Time building additional restraints: 6.36 Conformation dependent library (CDL) restraints added in 3.4 seconds 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6442 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 54 sheets defined 20.8% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.41 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.862A pdb=" N GLU A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 407 Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 746 through 755 removed outlier: 4.042A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.729A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.201A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.679A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.563A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.659A pdb=" N GLN A 965 " --> pdb=" O THR A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.617A pdb=" N LEU A 984 " --> pdb=" O ILE A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 988 Processing helix chain 'A' and resid 989 through 1033 removed outlier: 4.733A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 removed outlier: 4.036A pdb=" N LEU A1145 " --> pdb=" O LEU A1141 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1141 through 1146' Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 364 through 370 removed outlier: 3.669A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 572 removed outlier: 3.539A pdb=" N THR B 572 " --> pdb=" O ILE B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 639 removed outlier: 3.833A pdb=" N VAL B 635 " --> pdb=" O PRO B 631 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TYR B 636 " --> pdb=" O THR B 632 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER B 637 " --> pdb=" O TRP B 633 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR B 638 " --> pdb=" O ARG B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.688A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.968A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU B 753 " --> pdb=" O CYS B 749 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.897A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 removed outlier: 3.513A pdb=" N ASN B 824 " --> pdb=" O ASP B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.912A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 907 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.749A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 938 Processing helix chain 'B' and resid 939 through 940 No H-bonds generated for 'chain 'B' and resid 939 through 940' Processing helix chain 'B' and resid 941 through 944 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.753A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.159A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1039 through 1043 removed outlier: 3.854A pdb=" N PHE B1042 " --> pdb=" O ARG B1039 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N CYS B1043 " --> pdb=" O VAL B1040 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1039 through 1043' Processing helix chain 'B' and resid 1141 through 1149 Processing helix chain 'C' and resid 294 through 303 removed outlier: 4.100A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N CYS C 301 " --> pdb=" O SER C 297 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N THR C 302 " --> pdb=" O GLU C 298 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU C 303 " --> pdb=" O THR C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 371 removed outlier: 4.773A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 366 through 371' Processing helix chain 'C' and resid 406 through 411 removed outlier: 3.603A pdb=" N ILE C 410 " --> pdb=" O GLU C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 4.086A pdb=" N TYR C 421 " --> pdb=" O ILE C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.693A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.556A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.502A pdb=" N LEU C 821 " --> pdb=" O PRO C 817 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 851 through 855 removed outlier: 4.076A pdb=" N LYS C 854 " --> pdb=" O CYS C 851 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE C 855 " --> pdb=" O ALA C 852 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 851 through 855' Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.656A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.737A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.245A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN C 919 " --> pdb=" O VAL C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 removed outlier: 4.183A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER C 940 " --> pdb=" O ASP C 936 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.021A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 977 through 981 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.102A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 removed outlier: 3.737A pdb=" N LEU C1145 " --> pdb=" O LEU C1141 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1141 through 1146' Processing helix chain 'E' and resid 26 through 30 removed outlier: 3.907A pdb=" N SER E 30 " --> pdb=" O GLY E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 65 removed outlier: 3.969A pdb=" N LYS E 65 " --> pdb=" O ASP E 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 62 through 65' Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'F' and resid 62 through 65 removed outlier: 3.729A pdb=" N LYS F 65 " --> pdb=" O ASP F 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 62 through 65' Processing helix chain 'F' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 4.342A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N TRP A 64 " --> pdb=" O ALA A 27 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER A 31 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA A 263 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE A 92 " --> pdb=" O PHE A 192 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 55 removed outlier: 3.806A pdb=" N HIS A 49 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE A 55 " --> pdb=" O GLN A 271 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLN A 271 " --> pdb=" O PHE A 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.743A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 115 through 121 removed outlier: 4.374A pdb=" N GLU A 132 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ASN A 164 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 115 through 121 removed outlier: 3.644A pdb=" N TYR A 170 " --> pdb=" O ILE A 128 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 151 through 156 removed outlier: 6.282A pdb=" N TRP A 152 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N HIS A 146 " --> pdb=" O TRP A 152 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLU A 156 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N HIS A 245 " --> pdb=" O THR A 259 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 195 through 197 removed outlier: 3.535A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 318 removed outlier: 5.912A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 357 through 358 Processing sheet with id=AB1, first strand: chain 'A' and resid 400 through 402 Processing sheet with id=AB2, first strand: chain 'A' and resid 565 through 566 removed outlier: 7.016A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 642 through 644 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.041A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE A 664 " --> pdb=" O ALA A 672 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 712 through 719 removed outlier: 7.310A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 722 through 727 Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1122 removed outlier: 3.524A pdb=" N HIS A1083 " --> pdb=" O LYS A1086 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.558A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N TYR B 91 " --> pdb=" O GLY B 268 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER B 205 " --> pdb=" O GLU B 224 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 50 through 53 Processing sheet with id=AC3, first strand: chain 'B' and resid 151 through 156 removed outlier: 3.741A pdb=" N SER B 151 " --> pdb=" O HIS B 146 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR B 144 " --> pdb=" O MET B 153 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N SER B 155 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N GLY B 142 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 9.558A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 278 through 279 removed outlier: 4.330A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.573A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY B 593 " --> pdb=" O PHE B 318 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 400 through 402 removed outlier: 3.588A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AC8, first strand: chain 'B' and resid 541 through 543 Processing sheet with id=AC9, first strand: chain 'B' and resid 551 through 553 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.955A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA B 672 " --> pdb=" O ILE B 664 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 3.610A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 734 through 736 removed outlier: 3.589A pdb=" N THR B 859 " --> pdb=" O SER B 735 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1081 through 1082 Processing sheet with id=AD6, first strand: chain 'B' and resid 1088 through 1090 Processing sheet with id=AD7, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD8, first strand: chain 'C' and resid 29 through 31 Processing sheet with id=AD9, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.099A pdb=" N PHE C 55 " --> pdb=" O GLN C 271 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLN C 271 " --> pdb=" O PHE C 55 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 91 through 94 removed outlier: 3.513A pdb=" N PHE C 192 " --> pdb=" O PHE C 92 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR C 204 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEU C 229 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 104 through 106 Processing sheet with id=AE3, first strand: chain 'C' and resid 118 through 121 removed outlier: 3.725A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 9.023A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 151 through 156 removed outlier: 3.738A pdb=" N SER C 151 " --> pdb=" O HIS C 146 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N SER C 155 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AE6, first strand: chain 'C' and resid 398 through 399 removed outlier: 3.524A pdb=" N ASP C 398 " --> pdb=" O VAL C 512 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N VAL C 512 " --> pdb=" O ASP C 398 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE8, first strand: chain 'C' and resid 664 through 667 removed outlier: 3.756A pdb=" N ILE C 664 " --> pdb=" O ALA C 672 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.471A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.471A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.606A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1122 removed outlier: 3.773A pdb=" N CYS C1082 " --> pdb=" O VAL C1133 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF5, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.772A pdb=" N THR E 78 " --> pdb=" O ASP E 73 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.789A pdb=" N THR E 111 " --> pdb=" O TYR E 94 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR E 94 " --> pdb=" O THR E 111 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL E 113 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL E 93 " --> pdb=" O GLN E 39 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ARG E 38 " --> pdb=" O PHE E 47 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N PHE E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 4 through 7 removed outlier: 4.065A pdb=" N VAL F 5 " --> pdb=" O ALA F 23 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA F 23 " --> pdb=" O VAL F 5 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER F 7 " --> pdb=" O SER F 21 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N SER F 21 " --> pdb=" O SER F 7 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU F 20 " --> pdb=" O LEU F 81 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU F 81 " --> pdb=" O LEU F 20 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR F 78 " --> pdb=" O ASP F 73 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR F 69 " --> pdb=" O GLN F 82 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.575A pdb=" N TYR F 94 " --> pdb=" O THR F 111 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL F 93 " --> pdb=" O GLN F 39 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLY F 35 " --> pdb=" O ALA F 97 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ARG F 38 " --> pdb=" O GLU F 46 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU F 46 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 49 through 51 762 hydrogen bonds defined for protein. 2055 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: 11.23 Time building geometry restraints manager: 7.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6679 1.33 - 1.45: 6016 1.45 - 1.58: 15264 1.58 - 1.70: 0 1.70 - 1.82: 158 Bond restraints: 28117 Sorted by residual: bond pdb=" C1 NAG A1201 " pdb=" O5 NAG A1201 " ideal model delta sigma weight residual 1.406 1.475 -0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" N LEU C 984 " pdb=" CA LEU C 984 " ideal model delta sigma weight residual 1.457 1.498 -0.040 1.29e-02 6.01e+03 9.76e+00 bond pdb=" N SER A 884 " pdb=" CA SER A 884 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.06e-02 8.90e+03 9.75e+00 bond pdb=" N ARG C 983 " pdb=" CA ARG C 983 " ideal model delta sigma weight residual 1.460 1.493 -0.033 1.14e-02 7.69e+03 8.29e+00 bond pdb=" C PRO C 986 " pdb=" O PRO C 986 " ideal model delta sigma weight residual 1.240 1.209 0.032 1.12e-02 7.97e+03 7.97e+00 ... (remaining 28112 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 37557 2.09 - 4.17: 633 4.17 - 6.26: 60 6.26 - 8.35: 5 8.35 - 10.43: 4 Bond angle restraints: 38259 Sorted by residual: angle pdb=" C ALA A 522 " pdb=" CA ALA A 522 " pdb=" CB ALA A 522 " ideal model delta sigma weight residual 116.54 110.30 6.24 1.15e+00 7.56e-01 2.94e+01 angle pdb=" N LEU C 335 " pdb=" CA LEU C 335 " pdb=" C LEU C 335 " ideal model delta sigma weight residual 110.91 116.28 -5.37 1.17e+00 7.31e-01 2.10e+01 angle pdb=" C ASN C 343 " pdb=" CA ASN C 343 " pdb=" CB ASN C 343 " ideal model delta sigma weight residual 115.79 110.60 5.19 1.19e+00 7.06e-01 1.90e+01 angle pdb=" N ASP C1041 " pdb=" CA ASP C1041 " pdb=" C ASP C1041 " ideal model delta sigma weight residual 110.44 105.39 5.05 1.20e+00 6.94e-01 1.77e+01 angle pdb=" N PHE A 338 " pdb=" CA PHE A 338 " pdb=" C PHE A 338 " ideal model delta sigma weight residual 114.75 109.52 5.23 1.26e+00 6.30e-01 1.72e+01 ... (remaining 38254 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.90: 16304 24.90 - 49.79: 659 49.79 - 74.68: 113 74.68 - 99.58: 54 99.58 - 124.47: 26 Dihedral angle restraints: 17156 sinusoidal: 7123 harmonic: 10033 Sorted by residual: dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual 93.00 31.99 61.01 1 1.00e+01 1.00e-02 4.95e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual 93.00 52.32 40.68 1 1.00e+01 1.00e-02 2.32e+01 dihedral pdb=" CA ASN C 334 " pdb=" C ASN C 334 " pdb=" N LEU C 335 " pdb=" CA LEU C 335 " ideal model delta harmonic sigma weight residual 180.00 158.40 21.60 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 17153 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 3557 0.054 - 0.107: 723 0.107 - 0.161: 117 0.161 - 0.215: 11 0.215 - 0.268: 4 Chirality restraints: 4412 Sorted by residual: chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN A 343 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" C1 NAG C1201 " pdb=" ND2 ASN C 331 " pdb=" C2 NAG C1201 " pdb=" O5 NAG C1201 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" C1 NAG B1304 " pdb=" ND2 ASN B 709 " pdb=" C2 NAG B1304 " pdb=" O5 NAG B1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 4409 not shown) Planarity restraints: 4952 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1209 " 0.294 2.00e-02 2.50e+03 2.48e-01 7.69e+02 pdb=" C7 NAG A1209 " -0.076 2.00e-02 2.50e+03 pdb=" C8 NAG A1209 " 0.184 2.00e-02 2.50e+03 pdb=" N2 NAG A1209 " -0.425 2.00e-02 2.50e+03 pdb=" O7 NAG A1209 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS C 336 " -0.042 5.00e-02 4.00e+02 6.42e-02 6.60e+00 pdb=" N PRO C 337 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO C 337 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 337 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 986 " -0.035 5.00e-02 4.00e+02 5.33e-02 4.54e+00 pdb=" N PRO B 987 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO B 987 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 987 " -0.030 5.00e-02 4.00e+02 ... (remaining 4949 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 555 2.67 - 3.23: 26610 3.23 - 3.78: 40648 3.78 - 4.34: 54193 4.34 - 4.90: 88988 Nonbonded interactions: 210994 Sorted by model distance: nonbonded pdb=" OD1 ASP B 53 " pdb=" N LEU B 54 " model vdw 2.112 3.120 nonbonded pdb=" O PRO B 384 " pdb=" OG1 THR B 385 " model vdw 2.190 3.040 nonbonded pdb=" O4 NAG C1201 " pdb=" O7 NAG C1201 " model vdw 2.210 3.040 nonbonded pdb=" O GLY B 880 " pdb=" OG SER B 884 " model vdw 2.216 3.040 nonbonded pdb=" OH TYR A 91 " pdb=" OE1 GLU A 191 " model vdw 2.223 3.040 ... (remaining 210989 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 14 through 675 or resid 690 through 827 or resid 852 throu \ gh 1146 or resid 1203 through 1209)) selection = (chain 'B' and (resid 14 through 617 or resid 641 through 827 or resid 852 throu \ gh 940 or resid 944 through 1146 or resid 1301 through 1307)) selection = (chain 'C' and (resid 14 through 675 or resid 690 through 827 or resid 852 throu \ gh 1146 or resid 1203 through 1209)) } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.770 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: 0.060 Extract box with map and model: 1.100 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 61.460 Find NCS groups from input model: 2.360 Set up NCS constraints: 0.290 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: 0.020 Load rotamer database and sin/cos tables:3.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 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 : 0.004 0.069 28172 Z= 0.185 Angle : 0.629 10.435 38405 Z= 0.334 Chirality : 0.045 0.268 4412 Planarity : 0.005 0.248 4922 Dihedral : 15.161 124.475 10657 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.56 % Allowed : 8.56 % Favored : 90.88 % Rotamer: Outliers : 0.63 % Allowed : 15.98 % Favored : 83.39 % 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: 3422 helix: 1.77 (0.22), residues: 573 sheet: -1.46 (0.20), residues: 638 loop : -2.15 (0.12), residues: 2211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 64 HIS 0.004 0.001 HIS B1048 PHE 0.028 0.001 PHE B 486 TYR 0.017 0.001 TYR B 904 ARG 0.003 0.000 ARG A1000 Details of bonding type rmsd link_NAG-ASN : bond 0.00447 ( 30) link_NAG-ASN : angle 2.06576 ( 90) link_BETA1-4 : bond 0.00628 ( 6) link_BETA1-4 : angle 2.51217 ( 18) hydrogen bonds : bond 0.23370 ( 751) hydrogen bonds : angle 8.56041 ( 2055) SS BOND : bond 0.00209 ( 19) SS BOND : angle 0.92276 ( 38) covalent geometry : bond 0.00356 (28117) covalent geometry : angle 0.61901 (38259) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 3004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 276 time to evaluate : 2.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 ARG cc_start: 0.6797 (mtt90) cc_final: 0.6595 (mtt90) REVERT: B 1135 ASN cc_start: 0.8276 (t0) cc_final: 0.7804 (t0) REVERT: C 725 GLU cc_start: 0.8330 (tt0) cc_final: 0.8094 (tt0) REVERT: F 19 ARG cc_start: 0.7349 (mmm-85) cc_final: 0.6900 (mmm-85) outliers start: 19 outliers final: 11 residues processed: 288 average time/residue: 0.3299 time to fit residues: 158.7028 Evaluate side-chains 276 residues out of total 3004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 265 time to evaluate : 2.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 105 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 288 optimal weight: 0.5980 chunk 259 optimal weight: 0.8980 chunk 143 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 174 optimal weight: 0.6980 chunk 138 optimal weight: 7.9990 chunk 268 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 162 optimal weight: 3.9990 chunk 199 optimal weight: 2.9990 chunk 310 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN A 901 GLN A1005 GLN B 563 GLN B 764 ASN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 HIS ** C 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 703 ASN C 787 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN C1088 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.258121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.186350 restraints weight = 34354.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.175408 restraints weight = 48542.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.170428 restraints weight = 33642.883| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.0879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 28172 Z= 0.172 Angle : 0.635 10.738 38405 Z= 0.317 Chirality : 0.046 0.241 4412 Planarity : 0.004 0.066 4922 Dihedral : 11.219 110.459 4501 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.38 % Allowed : 9.03 % Favored : 90.59 % Rotamer: Outliers : 2.93 % Allowed : 14.61 % Favored : 82.46 % 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: -1.83 (0.14), residues: 3422 helix: 1.82 (0.22), residues: 580 sheet: -1.53 (0.19), residues: 667 loop : -2.09 (0.12), residues: 2175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 436 HIS 0.005 0.001 HIS B1064 PHE 0.021 0.002 PHE B1042 TYR 0.017 0.001 TYR C1067 ARG 0.004 0.000 ARG A 34 Details of bonding type rmsd link_NAG-ASN : bond 0.00409 ( 30) link_NAG-ASN : angle 1.98647 ( 90) link_BETA1-4 : bond 0.00296 ( 6) link_BETA1-4 : angle 2.24486 ( 18) hydrogen bonds : bond 0.04965 ( 751) hydrogen bonds : angle 6.30013 ( 2055) SS BOND : bond 0.00301 ( 19) SS BOND : angle 1.17822 ( 38) covalent geometry : bond 0.00400 (28117) covalent geometry : angle 0.62557 (38259) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 3004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 292 time to evaluate : 3.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 LEU cc_start: 0.0133 (OUTLIER) cc_final: -0.0421 (mt) REVERT: A 614 ASP cc_start: 0.7215 (p0) cc_final: 0.6920 (p0) REVERT: A 753 LEU cc_start: 0.9185 (tp) cc_final: 0.8951 (tp) REVERT: A 983 ARG cc_start: 0.8156 (ptp-170) cc_final: 0.7792 (ptp90) REVERT: B 41 LYS cc_start: 0.7940 (mmmt) cc_final: 0.7711 (mmmt) REVERT: B 177 MET cc_start: 0.5236 (tpt) cc_final: 0.4528 (tpt) REVERT: B 954 GLN cc_start: 0.8043 (mt0) cc_final: 0.7787 (mt0) REVERT: B 1041 ASP cc_start: 0.6585 (t0) cc_final: 0.6291 (t0) REVERT: B 1094 VAL cc_start: 0.9118 (OUTLIER) cc_final: 0.8842 (m) REVERT: C 58 PHE cc_start: 0.7193 (OUTLIER) cc_final: 0.6312 (m-80) REVERT: C 315 THR cc_start: 0.7296 (p) cc_final: 0.6316 (t) REVERT: C 725 GLU cc_start: 0.8264 (tt0) cc_final: 0.7868 (tt0) REVERT: C 823 PHE cc_start: 0.7917 (t80) cc_final: 0.7663 (t80) REVERT: E 34 MET cc_start: 0.3543 (pmm) cc_final: 0.2625 (pmm) REVERT: F 19 ARG cc_start: 0.7382 (mmm-85) cc_final: 0.6846 (mmm-85) outliers start: 88 outliers final: 49 residues processed: 362 average time/residue: 0.3503 time to fit residues: 215.3974 Evaluate side-chains 319 residues out of total 3004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 267 time to evaluate : 2.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain F residue 45 ARG Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 105 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 46 optimal weight: 0.1980 chunk 143 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 256 optimal weight: 20.0000 chunk 314 optimal weight: 0.9990 chunk 291 optimal weight: 3.9990 chunk 158 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 309 optimal weight: 0.6980 chunk 12 optimal weight: 8.9990 chunk 179 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 317 ASN B 764 ASN B1005 GLN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 787 GLN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN C1088 HIS F 39 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.254007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.186698 restraints weight = 34233.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.180108 restraints weight = 53724.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.175102 restraints weight = 43873.067| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 28172 Z= 0.190 Angle : 0.628 9.884 38405 Z= 0.315 Chirality : 0.046 0.241 4412 Planarity : 0.004 0.068 4922 Dihedral : 9.139 106.983 4495 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.50 % Allowed : 8.50 % Favored : 91.00 % Rotamer: Outliers : 3.76 % Allowed : 14.98 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.14), residues: 3422 helix: 1.81 (0.22), residues: 579 sheet: -1.42 (0.19), residues: 672 loop : -2.09 (0.13), residues: 2171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 64 HIS 0.006 0.001 HIS B1088 PHE 0.020 0.002 PHE C 562 TYR 0.022 0.001 TYR B 453 ARG 0.006 0.000 ARG B 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00428 ( 30) link_NAG-ASN : angle 1.99053 ( 90) link_BETA1-4 : bond 0.00584 ( 6) link_BETA1-4 : angle 2.71878 ( 18) hydrogen bonds : bond 0.04771 ( 751) hydrogen bonds : angle 5.86607 ( 2055) SS BOND : bond 0.00323 ( 19) SS BOND : angle 1.39662 ( 38) covalent geometry : bond 0.00448 (28117) covalent geometry : angle 0.61731 (38259) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 3004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 295 time to evaluate : 2.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 296 LEU cc_start: 0.0903 (OUTLIER) cc_final: 0.0208 (mt) REVERT: A 586 ASP cc_start: 0.7906 (t0) cc_final: 0.7436 (t0) REVERT: A 614 ASP cc_start: 0.7292 (p0) cc_final: 0.7020 (p0) REVERT: A 966 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8754 (mp) REVERT: B 177 MET cc_start: 0.5317 (tpt) cc_final: 0.4501 (tpt) REVERT: B 281 GLU cc_start: 0.8214 (pp20) cc_final: 0.7713 (pp20) REVERT: B 364 ASP cc_start: 0.7240 (t0) cc_final: 0.6940 (t0) REVERT: B 654 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7314 (mm-30) REVERT: B 918 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7865 (mt-10) REVERT: B 954 GLN cc_start: 0.8017 (mt0) cc_final: 0.7703 (mt0) REVERT: B 1010 GLN cc_start: 0.8472 (tp40) cc_final: 0.8157 (tp40) REVERT: B 1083 HIS cc_start: 0.7263 (OUTLIER) cc_final: 0.6538 (m90) REVERT: B 1130 ILE cc_start: 0.8101 (pt) cc_final: 0.7865 (pt) REVERT: B 1135 ASN cc_start: 0.8209 (t0) cc_final: 0.7770 (t0) REVERT: C 58 PHE cc_start: 0.7495 (OUTLIER) cc_final: 0.6557 (m-80) REVERT: C 537 LYS cc_start: 0.8566 (tmtt) cc_final: 0.8206 (tttm) REVERT: C 725 GLU cc_start: 0.8391 (tt0) cc_final: 0.8007 (tt0) REVERT: C 731 MET cc_start: 0.9141 (ptt) cc_final: 0.8819 (ptt) REVERT: C 756 TYR cc_start: 0.8489 (OUTLIER) cc_final: 0.8206 (t80) REVERT: C 823 PHE cc_start: 0.7968 (t80) cc_final: 0.7678 (t80) REVERT: C 919 ASN cc_start: 0.8494 (OUTLIER) cc_final: 0.7413 (p0) REVERT: E 34 MET cc_start: 0.4300 (pmm) cc_final: 0.3187 (pmm) REVERT: F 19 ARG cc_start: 0.7315 (mmm-85) cc_final: 0.6837 (mmm-85) outliers start: 113 outliers final: 71 residues processed: 384 average time/residue: 0.3361 time to fit residues: 218.7242 Evaluate side-chains 357 residues out of total 3004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 280 time to evaluate : 3.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 919 ASN Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1083 HIS Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain F residue 45 ARG Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 105 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 199 optimal weight: 0.9980 chunk 301 optimal weight: 2.9990 chunk 279 optimal weight: 1.9990 chunk 166 optimal weight: 0.0050 chunk 85 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 33 optimal weight: 9.9990 chunk 227 optimal weight: 10.0000 chunk 260 optimal weight: 2.9990 chunk 241 optimal weight: 0.0570 chunk 37 optimal weight: 10.0000 overall best weight: 1.0116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN B 764 ASN B1005 GLN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 ASN ** C 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.258704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.197184 restraints weight = 34911.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.180588 restraints weight = 65782.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.177416 restraints weight = 40604.255| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 28172 Z= 0.193 Angle : 0.631 10.319 38405 Z= 0.316 Chirality : 0.047 0.327 4412 Planarity : 0.004 0.069 4922 Dihedral : 8.653 102.066 4493 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.44 % Allowed : 8.91 % Favored : 90.65 % Rotamer: Outliers : 3.96 % Allowed : 15.81 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.14), residues: 3422 helix: 1.63 (0.22), residues: 598 sheet: -1.40 (0.19), residues: 677 loop : -2.09 (0.13), residues: 2147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP F 36 HIS 0.005 0.001 HIS C1064 PHE 0.026 0.002 PHE A 559 TYR 0.020 0.001 TYR B 421 ARG 0.006 0.000 ARG A 34 Details of bonding type rmsd link_NAG-ASN : bond 0.00462 ( 30) link_NAG-ASN : angle 2.11055 ( 90) link_BETA1-4 : bond 0.00408 ( 6) link_BETA1-4 : angle 2.84715 ( 18) hydrogen bonds : bond 0.04449 ( 751) hydrogen bonds : angle 5.67448 ( 2055) SS BOND : bond 0.00647 ( 19) SS BOND : angle 1.56375 ( 38) covalent geometry : bond 0.00459 (28117) covalent geometry : angle 0.61913 (38259) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 3004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 296 time to evaluate : 2.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 GLU cc_start: 0.3398 (OUTLIER) cc_final: 0.1538 (pm20) REVERT: A 586 ASP cc_start: 0.7962 (t0) cc_final: 0.7558 (t0) REVERT: A 614 ASP cc_start: 0.7282 (p0) cc_final: 0.7007 (p0) REVERT: A 752 LEU cc_start: 0.8722 (tt) cc_final: 0.8520 (tt) REVERT: B 177 MET cc_start: 0.5265 (tpt) cc_final: 0.4615 (tpt) REVERT: B 281 GLU cc_start: 0.8297 (pp20) cc_final: 0.7870 (pp20) REVERT: B 364 ASP cc_start: 0.7800 (t0) cc_final: 0.7365 (t0) REVERT: B 654 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7323 (mm-30) REVERT: B 918 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7941 (mt-10) REVERT: B 954 GLN cc_start: 0.8101 (mt0) cc_final: 0.7725 (mt0) REVERT: B 990 GLU cc_start: 0.8101 (tt0) cc_final: 0.7851 (tt0) REVERT: B 1083 HIS cc_start: 0.7565 (OUTLIER) cc_final: 0.6662 (m90) REVERT: B 1135 ASN cc_start: 0.8208 (t0) cc_final: 0.7578 (t0) REVERT: C 56 LEU cc_start: 0.2851 (OUTLIER) cc_final: 0.2433 (tp) REVERT: C 58 PHE cc_start: 0.7463 (OUTLIER) cc_final: 0.6314 (m-80) REVERT: C 273 ARG cc_start: 0.5206 (ttp-170) cc_final: 0.4729 (ttp80) REVERT: C 537 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8162 (tttm) REVERT: C 725 GLU cc_start: 0.8762 (tt0) cc_final: 0.8488 (tt0) REVERT: C 731 MET cc_start: 0.9218 (ptt) cc_final: 0.9001 (ptt) REVERT: C 756 TYR cc_start: 0.8458 (OUTLIER) cc_final: 0.8141 (t80) REVERT: C 777 ASN cc_start: 0.8435 (t0) cc_final: 0.8141 (m-40) REVERT: C 804 GLN cc_start: 0.8606 (tp40) cc_final: 0.8226 (tp40) REVERT: C 805 ILE cc_start: 0.8616 (OUTLIER) cc_final: 0.8405 (tt) REVERT: E 34 MET cc_start: 0.3696 (pmm) cc_final: 0.2782 (pmm) REVERT: F 81 LEU cc_start: 0.3539 (pt) cc_final: 0.3316 (pp) outliers start: 119 outliers final: 79 residues processed: 388 average time/residue: 0.4332 time to fit residues: 287.6043 Evaluate side-chains 375 residues out of total 3004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 289 time to evaluate : 2.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 719 THR Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 537 LYS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1082 CYS Chi-restraints excluded: chain C residue 1083 HIS Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain F residue 45 ARG Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 105 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 226 optimal weight: 10.0000 chunk 137 optimal weight: 0.7980 chunk 321 optimal weight: 5.9990 chunk 74 optimal weight: 0.5980 chunk 291 optimal weight: 3.9990 chunk 181 optimal weight: 0.9980 chunk 307 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 269 optimal weight: 4.9990 chunk 185 optimal weight: 4.9990 chunk 101 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN B 764 ASN B1005 GLN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 556 ASN C 787 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.252762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.172700 restraints weight = 34243.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.167696 restraints weight = 33720.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.159088 restraints weight = 21083.105| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 28172 Z= 0.169 Angle : 0.618 10.761 38405 Z= 0.306 Chirality : 0.046 0.267 4412 Planarity : 0.004 0.069 4922 Dihedral : 8.157 95.861 4493 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.36 % Favored : 91.26 % Rotamer: Outliers : 4.13 % Allowed : 16.11 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.14), residues: 3422 helix: 1.80 (0.22), residues: 592 sheet: -1.38 (0.19), residues: 695 loop : -2.08 (0.13), residues: 2135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP F 36 HIS 0.004 0.001 HIS A 207 PHE 0.020 0.002 PHE B 192 TYR 0.019 0.001 TYR B 495 ARG 0.004 0.000 ARG A 34 Details of bonding type rmsd link_NAG-ASN : bond 0.00378 ( 30) link_NAG-ASN : angle 2.11146 ( 90) link_BETA1-4 : bond 0.00565 ( 6) link_BETA1-4 : angle 2.91373 ( 18) hydrogen bonds : bond 0.04247 ( 751) hydrogen bonds : angle 5.50043 ( 2055) SS BOND : bond 0.00363 ( 19) SS BOND : angle 1.37368 ( 38) covalent geometry : bond 0.00398 (28117) covalent geometry : angle 0.60582 (38259) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 3004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 294 time to evaluate : 3.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 TYR cc_start: -0.2079 (OUTLIER) cc_final: -0.4221 (t80) REVERT: A 556 ASN cc_start: 0.7689 (p0) cc_final: 0.7361 (p0) REVERT: A 586 ASP cc_start: 0.8018 (t0) cc_final: 0.7589 (t0) REVERT: A 614 ASP cc_start: 0.7269 (p0) cc_final: 0.6963 (p0) REVERT: A 752 LEU cc_start: 0.8821 (tt) cc_final: 0.8590 (tt) REVERT: A 756 TYR cc_start: 0.8482 (t80) cc_final: 0.7451 (t80) REVERT: B 41 LYS cc_start: 0.7935 (mmmt) cc_final: 0.6998 (mmtm) REVERT: B 53 ASP cc_start: 0.7765 (t0) cc_final: 0.7375 (t0) REVERT: B 177 MET cc_start: 0.5433 (tpt) cc_final: 0.5029 (tpt) REVERT: B 364 ASP cc_start: 0.7898 (t0) cc_final: 0.7502 (t0) REVERT: B 453 TYR cc_start: 0.8219 (p90) cc_final: 0.7976 (p90) REVERT: B 654 GLU cc_start: 0.7624 (mm-30) cc_final: 0.7231 (mm-30) REVERT: B 748 GLU cc_start: 0.7305 (pt0) cc_final: 0.6968 (pt0) REVERT: B 752 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8686 (mp) REVERT: B 918 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7736 (mt-10) REVERT: B 954 GLN cc_start: 0.7973 (mt0) cc_final: 0.7551 (mt0) REVERT: B 990 GLU cc_start: 0.8153 (tt0) cc_final: 0.7807 (tt0) REVERT: B 1083 HIS cc_start: 0.7543 (OUTLIER) cc_final: 0.6664 (m90) REVERT: B 1135 ASN cc_start: 0.8228 (t0) cc_final: 0.7542 (t0) REVERT: C 56 LEU cc_start: 0.2744 (OUTLIER) cc_final: 0.2379 (tp) REVERT: C 58 PHE cc_start: 0.7524 (OUTLIER) cc_final: 0.6342 (m-80) REVERT: C 537 LYS cc_start: 0.8558 (tmtt) cc_final: 0.8072 (tttm) REVERT: C 725 GLU cc_start: 0.8603 (tt0) cc_final: 0.8291 (tt0) REVERT: C 731 MET cc_start: 0.9167 (ptt) cc_final: 0.8861 (ptt) REVERT: C 756 TYR cc_start: 0.8537 (OUTLIER) cc_final: 0.8175 (t80) REVERT: C 777 ASN cc_start: 0.8394 (t0) cc_final: 0.8137 (m-40) REVERT: C 804 GLN cc_start: 0.8556 (tp40) cc_final: 0.7981 (tp40) REVERT: C 805 ILE cc_start: 0.8752 (OUTLIER) cc_final: 0.8537 (tt) REVERT: C 919 ASN cc_start: 0.8431 (OUTLIER) cc_final: 0.7301 (p0) REVERT: E 34 MET cc_start: 0.3508 (pmm) cc_final: 0.2624 (pmm) REVERT: F 81 LEU cc_start: 0.3844 (pt) cc_final: 0.3542 (pp) REVERT: F 87 LYS cc_start: 0.7659 (tmmt) cc_final: 0.7264 (tmmt) outliers start: 124 outliers final: 83 residues processed: 388 average time/residue: 0.3808 time to fit residues: 250.9358 Evaluate side-chains 371 residues out of total 3004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 280 time to evaluate : 2.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 826 VAL Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 919 ASN Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1083 HIS Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain F residue 45 ARG Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 105 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 165 optimal weight: 0.8980 chunk 59 optimal weight: 0.1980 chunk 135 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 144 optimal weight: 0.9980 chunk 164 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 223 optimal weight: 0.9980 chunk 200 optimal weight: 0.7980 chunk 207 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 GLN B 764 ASN B 774 GLN B1005 GLN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 949 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.253215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.188039 restraints weight = 34394.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.177374 restraints weight = 59299.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.167842 restraints weight = 45458.795| |-----------------------------------------------------------------------------| r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28172 Z= 0.146 Angle : 0.601 12.242 38405 Z= 0.297 Chirality : 0.045 0.241 4412 Planarity : 0.004 0.069 4922 Dihedral : 7.707 89.197 4493 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.45 % Favored : 91.23 % Rotamer: Outliers : 4.23 % Allowed : 16.94 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.14), residues: 3422 helix: 1.83 (0.22), residues: 593 sheet: -1.29 (0.19), residues: 696 loop : -2.05 (0.13), residues: 2133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 36 HIS 0.004 0.001 HIS B 519 PHE 0.017 0.001 PHE B 192 TYR 0.025 0.001 TYR B 495 ARG 0.004 0.000 ARG A 577 Details of bonding type rmsd link_NAG-ASN : bond 0.00384 ( 30) link_NAG-ASN : angle 2.05188 ( 90) link_BETA1-4 : bond 0.00523 ( 6) link_BETA1-4 : angle 3.02760 ( 18) hydrogen bonds : bond 0.03997 ( 751) hydrogen bonds : angle 5.30988 ( 2055) SS BOND : bond 0.00307 ( 19) SS BOND : angle 1.28017 ( 38) covalent geometry : bond 0.00340 (28117) covalent geometry : angle 0.58848 (38259) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 3004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 304 time to evaluate : 3.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 TYR cc_start: -0.1178 (OUTLIER) cc_final: -0.3753 (t80) REVERT: A 556 ASN cc_start: 0.7514 (p0) cc_final: 0.6977 (p0) REVERT: A 586 ASP cc_start: 0.7803 (t0) cc_final: 0.7458 (t0) REVERT: A 614 ASP cc_start: 0.7341 (p0) cc_final: 0.6988 (p0) REVERT: A 752 LEU cc_start: 0.8813 (tt) cc_final: 0.8535 (tt) REVERT: A 756 TYR cc_start: 0.8383 (t80) cc_final: 0.7499 (t80) REVERT: B 41 LYS cc_start: 0.7926 (mmmt) cc_final: 0.7056 (mmtm) REVERT: B 177 MET cc_start: 0.5316 (tpt) cc_final: 0.4894 (tpt) REVERT: B 281 GLU cc_start: 0.8189 (pp20) cc_final: 0.7985 (pp20) REVERT: B 353 TRP cc_start: 0.7034 (p90) cc_final: 0.6668 (p90) REVERT: B 654 GLU cc_start: 0.7558 (mm-30) cc_final: 0.7214 (mm-30) REVERT: B 748 GLU cc_start: 0.7034 (pt0) cc_final: 0.6817 (pt0) REVERT: B 954 GLN cc_start: 0.7993 (mt0) cc_final: 0.7559 (mt0) REVERT: B 977 LEU cc_start: 0.7455 (mp) cc_final: 0.7142 (mt) REVERT: B 990 GLU cc_start: 0.8112 (tt0) cc_final: 0.7813 (tt0) REVERT: B 1018 ILE cc_start: 0.9416 (OUTLIER) cc_final: 0.9204 (mm) REVERT: B 1041 ASP cc_start: 0.7020 (t0) cc_final: 0.6801 (t0) REVERT: B 1083 HIS cc_start: 0.7642 (OUTLIER) cc_final: 0.6830 (m90) REVERT: B 1086 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7856 (mtpt) REVERT: B 1135 ASN cc_start: 0.8275 (t0) cc_final: 0.7599 (t0) REVERT: C 56 LEU cc_start: 0.2908 (OUTLIER) cc_final: 0.2497 (tp) REVERT: C 58 PHE cc_start: 0.7672 (OUTLIER) cc_final: 0.6573 (m-80) REVERT: C 537 LYS cc_start: 0.8575 (tmtt) cc_final: 0.8306 (tttm) REVERT: C 725 GLU cc_start: 0.8435 (tt0) cc_final: 0.8087 (tt0) REVERT: C 731 MET cc_start: 0.9213 (ptt) cc_final: 0.8981 (ptt) REVERT: C 756 TYR cc_start: 0.8527 (OUTLIER) cc_final: 0.8251 (t80) REVERT: C 919 ASN cc_start: 0.8329 (OUTLIER) cc_final: 0.7217 (p0) REVERT: E 34 MET cc_start: 0.4021 (pmm) cc_final: 0.3099 (pmm) REVERT: F 81 LEU cc_start: 0.4388 (pt) cc_final: 0.3991 (pp) outliers start: 127 outliers final: 85 residues processed: 406 average time/residue: 0.4008 time to fit residues: 275.9706 Evaluate side-chains 380 residues out of total 3004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 287 time to evaluate : 2.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 919 ASN Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1083 HIS Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 105 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 120 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 chunk 283 optimal weight: 0.1980 chunk 116 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 43 optimal weight: 20.0000 chunk 211 optimal weight: 0.5980 chunk 315 optimal weight: 0.6980 chunk 199 optimal weight: 0.0570 chunk 220 optimal weight: 8.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 GLN B 764 ASN B 774 GLN B1005 GLN B1083 HIS ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.254414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.191848 restraints weight = 34430.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.184900 restraints weight = 56611.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.180511 restraints weight = 42882.619| |-----------------------------------------------------------------------------| r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6818 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 28172 Z= 0.127 Angle : 0.590 13.150 38405 Z= 0.292 Chirality : 0.045 0.223 4412 Planarity : 0.004 0.068 4922 Dihedral : 7.413 84.057 4493 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.98 % Favored : 91.67 % Rotamer: Outliers : 3.56 % Allowed : 17.58 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.14), residues: 3422 helix: 1.89 (0.22), residues: 593 sheet: -1.23 (0.19), residues: 696 loop : -2.01 (0.13), residues: 2133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 36 HIS 0.003 0.001 HIS B 519 PHE 0.024 0.001 PHE B 497 TYR 0.030 0.001 TYR B 495 ARG 0.004 0.000 ARG F 45 Details of bonding type rmsd link_NAG-ASN : bond 0.00387 ( 30) link_NAG-ASN : angle 2.04063 ( 90) link_BETA1-4 : bond 0.00518 ( 6) link_BETA1-4 : angle 3.05171 ( 18) hydrogen bonds : bond 0.03820 ( 751) hydrogen bonds : angle 5.18511 ( 2055) SS BOND : bond 0.00331 ( 19) SS BOND : angle 1.17967 ( 38) covalent geometry : bond 0.00290 (28117) covalent geometry : angle 0.57759 (38259) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 3004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 303 time to evaluate : 5.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 TYR cc_start: -0.0722 (OUTLIER) cc_final: -0.3530 (t80) REVERT: A 556 ASN cc_start: 0.7419 (p0) cc_final: 0.6923 (p0) REVERT: A 586 ASP cc_start: 0.7730 (t0) cc_final: 0.7419 (t0) REVERT: A 614 ASP cc_start: 0.7205 (p0) cc_final: 0.6830 (p0) REVERT: A 752 LEU cc_start: 0.8835 (tt) cc_final: 0.8552 (tt) REVERT: A 756 TYR cc_start: 0.8427 (t80) cc_final: 0.7603 (t80) REVERT: B 41 LYS cc_start: 0.7892 (mmmt) cc_final: 0.7030 (mmtm) REVERT: B 177 MET cc_start: 0.5349 (tpt) cc_final: 0.4923 (tpt) REVERT: B 281 GLU cc_start: 0.8095 (pp20) cc_final: 0.7886 (pp20) REVERT: B 353 TRP cc_start: 0.6984 (p90) cc_final: 0.6674 (p90) REVERT: B 654 GLU cc_start: 0.7625 (mm-30) cc_final: 0.7260 (mm-30) REVERT: B 918 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7695 (mt-10) REVERT: B 954 GLN cc_start: 0.7947 (mt0) cc_final: 0.7533 (mt0) REVERT: B 977 LEU cc_start: 0.7426 (mp) cc_final: 0.7141 (mt) REVERT: B 990 GLU cc_start: 0.8100 (tt0) cc_final: 0.7824 (tt0) REVERT: B 1083 HIS cc_start: 0.7759 (OUTLIER) cc_final: 0.7283 (m-70) REVERT: B 1086 LYS cc_start: 0.8088 (OUTLIER) cc_final: 0.7868 (mtpt) REVERT: B 1135 ASN cc_start: 0.8327 (t0) cc_final: 0.7884 (t0) REVERT: C 56 LEU cc_start: 0.2979 (OUTLIER) cc_final: 0.2569 (tp) REVERT: C 58 PHE cc_start: 0.7686 (OUTLIER) cc_final: 0.6606 (m-80) REVERT: C 378 LYS cc_start: -0.0019 (OUTLIER) cc_final: -0.0393 (mttp) REVERT: C 537 LYS cc_start: 0.8560 (tmtt) cc_final: 0.8326 (tttm) REVERT: C 725 GLU cc_start: 0.8311 (tt0) cc_final: 0.7953 (tt0) REVERT: C 731 MET cc_start: 0.9128 (ptt) cc_final: 0.8860 (ptt) REVERT: C 756 TYR cc_start: 0.8498 (OUTLIER) cc_final: 0.8170 (t80) REVERT: C 919 ASN cc_start: 0.8338 (OUTLIER) cc_final: 0.7163 (p0) REVERT: C 1029 MET cc_start: 0.8704 (tpp) cc_final: 0.7965 (ttt) REVERT: E 34 MET cc_start: 0.4158 (pmm) cc_final: 0.3285 (pmm) REVERT: F 81 LEU cc_start: 0.4486 (pt) cc_final: 0.4192 (pp) outliers start: 107 outliers final: 82 residues processed: 390 average time/residue: 0.5083 time to fit residues: 339.6051 Evaluate side-chains 386 residues out of total 3004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 296 time to evaluate : 3.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 727 LEU Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 919 ASN Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1013 ILE Chi-restraints excluded: chain C residue 1083 HIS Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain F residue 45 ARG Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 96 CYS Chi-restraints excluded: chain F residue 105 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 152 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 158 optimal weight: 0.5980 chunk 307 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 306 optimal weight: 0.9990 chunk 54 optimal weight: 0.4980 chunk 169 optimal weight: 2.9990 chunk 320 optimal weight: 9.9990 chunk 94 optimal weight: 1.9990 chunk 230 optimal weight: 7.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS A 564 GLN B 764 ASN B 774 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.252238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.181911 restraints weight = 34245.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.176081 restraints weight = 48777.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.176985 restraints weight = 48939.196| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 28172 Z= 0.157 Angle : 0.605 13.876 38405 Z= 0.300 Chirality : 0.046 0.225 4412 Planarity : 0.004 0.067 4922 Dihedral : 7.350 80.709 4493 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.65 % Favored : 91.03 % Rotamer: Outliers : 3.93 % Allowed : 17.28 % Favored : 78.79 % 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: -1.64 (0.14), residues: 3422 helix: 1.88 (0.22), residues: 593 sheet: -1.25 (0.19), residues: 693 loop : -2.02 (0.13), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 36 HIS 0.010 0.001 HIS B1083 PHE 0.026 0.001 PHE B 497 TYR 0.037 0.001 TYR B 495 ARG 0.008 0.000 ARG A 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00382 ( 30) link_NAG-ASN : angle 2.07819 ( 90) link_BETA1-4 : bond 0.00522 ( 6) link_BETA1-4 : angle 3.00734 ( 18) hydrogen bonds : bond 0.04006 ( 751) hydrogen bonds : angle 5.18313 ( 2055) SS BOND : bond 0.00268 ( 19) SS BOND : angle 1.20837 ( 38) covalent geometry : bond 0.00369 (28117) covalent geometry : angle 0.59333 (38259) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 3004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 291 time to evaluate : 3.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 TYR cc_start: -0.0478 (OUTLIER) cc_final: -0.3643 (t80) REVERT: A 556 ASN cc_start: 0.7524 (p0) cc_final: 0.6982 (p0) REVERT: A 559 PHE cc_start: 0.7075 (p90) cc_final: 0.6784 (p90) REVERT: A 586 ASP cc_start: 0.7832 (t0) cc_final: 0.7509 (t0) REVERT: A 614 ASP cc_start: 0.7237 (p0) cc_final: 0.6862 (p0) REVERT: A 752 LEU cc_start: 0.8861 (tt) cc_final: 0.8551 (tt) REVERT: A 756 TYR cc_start: 0.8532 (t80) cc_final: 0.7707 (t80) REVERT: B 41 LYS cc_start: 0.7913 (mmmt) cc_final: 0.7053 (mmtm) REVERT: B 177 MET cc_start: 0.5381 (tpt) cc_final: 0.4974 (tpt) REVERT: B 353 TRP cc_start: 0.7112 (p90) cc_final: 0.6761 (p90) REVERT: B 420 ASP cc_start: 0.7527 (m-30) cc_final: 0.7280 (p0) REVERT: B 654 GLU cc_start: 0.7607 (mm-30) cc_final: 0.7267 (mm-30) REVERT: B 954 GLN cc_start: 0.7997 (mt0) cc_final: 0.7572 (mt0) REVERT: B 977 LEU cc_start: 0.7458 (mp) cc_final: 0.7190 (mt) REVERT: B 1041 ASP cc_start: 0.7107 (t0) cc_final: 0.6827 (t0) REVERT: B 1083 HIS cc_start: 0.7313 (OUTLIER) cc_final: 0.6722 (m90) REVERT: B 1086 LYS cc_start: 0.8088 (OUTLIER) cc_final: 0.7843 (mtpt) REVERT: B 1135 ASN cc_start: 0.8068 (t0) cc_final: 0.7451 (t0) REVERT: C 56 LEU cc_start: 0.3189 (OUTLIER) cc_final: 0.2821 (tp) REVERT: C 58 PHE cc_start: 0.7800 (OUTLIER) cc_final: 0.6714 (m-80) REVERT: C 378 LYS cc_start: -0.0103 (OUTLIER) cc_final: -0.0447 (mttp) REVERT: C 725 GLU cc_start: 0.8511 (tt0) cc_final: 0.8126 (tt0) REVERT: C 731 MET cc_start: 0.9176 (ptt) cc_final: 0.8959 (ptt) REVERT: C 756 TYR cc_start: 0.8573 (OUTLIER) cc_final: 0.8292 (t80) REVERT: C 864 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8445 (tt) REVERT: C 919 ASN cc_start: 0.8304 (OUTLIER) cc_final: 0.7082 (p0) REVERT: C 1017 GLU cc_start: 0.7884 (tt0) cc_final: 0.7590 (tt0) REVERT: C 1029 MET cc_start: 0.8581 (tpp) cc_final: 0.7952 (ttt) REVERT: E 34 MET cc_start: 0.4115 (pmm) cc_final: 0.2938 (pmm) REVERT: F 81 LEU cc_start: 0.4525 (pt) cc_final: 0.4285 (pp) outliers start: 118 outliers final: 90 residues processed: 385 average time/residue: 0.3368 time to fit residues: 220.7720 Evaluate side-chains 383 residues out of total 3004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 284 time to evaluate : 2.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 774 GLN Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 919 ASN Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1083 HIS Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 105 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 227 optimal weight: 10.0000 chunk 101 optimal weight: 0.5980 chunk 105 optimal weight: 0.0170 chunk 3 optimal weight: 0.1980 chunk 207 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 chunk 261 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 47 optimal weight: 20.0000 chunk 66 optimal weight: 0.6980 chunk 49 optimal weight: 6.9990 overall best weight: 0.7020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 GLN B 764 ASN B1083 HIS ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.251744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.184801 restraints weight = 34265.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.176545 restraints weight = 55088.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.171776 restraints weight = 45772.056| |-----------------------------------------------------------------------------| r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 28172 Z= 0.150 Angle : 0.612 16.399 38405 Z= 0.302 Chirality : 0.046 0.295 4412 Planarity : 0.004 0.067 4922 Dihedral : 7.283 77.480 4493 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.45 % Favored : 91.23 % Rotamer: Outliers : 3.70 % Allowed : 17.61 % Favored : 78.70 % 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: -1.62 (0.14), residues: 3422 helix: 1.85 (0.22), residues: 599 sheet: -1.20 (0.19), residues: 689 loop : -2.02 (0.13), residues: 2134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 64 HIS 0.004 0.001 HIS A1088 PHE 0.030 0.001 PHE B 55 TYR 0.031 0.001 TYR B 495 ARG 0.007 0.000 ARG A 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00387 ( 30) link_NAG-ASN : angle 2.09347 ( 90) link_BETA1-4 : bond 0.00616 ( 6) link_BETA1-4 : angle 2.97635 ( 18) hydrogen bonds : bond 0.04010 ( 751) hydrogen bonds : angle 5.16533 ( 2055) SS BOND : bond 0.00256 ( 19) SS BOND : angle 1.26048 ( 38) covalent geometry : bond 0.00353 (28117) covalent geometry : angle 0.59986 (38259) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 3004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 297 time to evaluate : 2.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 TYR cc_start: -0.0807 (OUTLIER) cc_final: -0.4414 (t80) REVERT: A 556 ASN cc_start: 0.7549 (p0) cc_final: 0.7008 (p0) REVERT: A 559 PHE cc_start: 0.7069 (p90) cc_final: 0.6803 (p90) REVERT: A 586 ASP cc_start: 0.7863 (t0) cc_final: 0.7537 (t0) REVERT: A 614 ASP cc_start: 0.7306 (p0) cc_final: 0.6911 (p0) REVERT: A 752 LEU cc_start: 0.8881 (tt) cc_final: 0.8564 (tt) REVERT: A 756 TYR cc_start: 0.8514 (t80) cc_final: 0.7690 (t80) REVERT: B 41 LYS cc_start: 0.7919 (mmmt) cc_final: 0.7062 (mmtm) REVERT: B 177 MET cc_start: 0.5381 (tpt) cc_final: 0.4980 (tpt) REVERT: B 353 TRP cc_start: 0.7144 (p90) cc_final: 0.6791 (p90) REVERT: B 654 GLU cc_start: 0.7643 (mm-30) cc_final: 0.7277 (mm-30) REVERT: B 774 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.8232 (mp10) REVERT: B 954 GLN cc_start: 0.8039 (mt0) cc_final: 0.7615 (mt0) REVERT: B 1083 HIS cc_start: 0.7963 (OUTLIER) cc_final: 0.7640 (m-70) REVERT: B 1086 LYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7810 (mtpt) REVERT: B 1135 ASN cc_start: 0.8367 (t0) cc_final: 0.7935 (t0) REVERT: C 56 LEU cc_start: 0.3317 (OUTLIER) cc_final: 0.2959 (tp) REVERT: C 58 PHE cc_start: 0.7847 (OUTLIER) cc_final: 0.6760 (m-80) REVERT: C 725 GLU cc_start: 0.8352 (tt0) cc_final: 0.8012 (tt0) REVERT: C 756 TYR cc_start: 0.8559 (OUTLIER) cc_final: 0.8186 (t80) REVERT: C 919 ASN cc_start: 0.8415 (OUTLIER) cc_final: 0.7260 (p0) REVERT: C 1017 GLU cc_start: 0.7914 (tt0) cc_final: 0.7655 (tt0) REVERT: C 1029 MET cc_start: 0.8637 (tpp) cc_final: 0.7907 (ttm) REVERT: E 34 MET cc_start: 0.4095 (pmm) cc_final: 0.2907 (pmm) REVERT: F 81 LEU cc_start: 0.4813 (pt) cc_final: 0.4523 (pp) outliers start: 111 outliers final: 92 residues processed: 383 average time/residue: 0.3281 time to fit residues: 213.1371 Evaluate side-chains 386 residues out of total 3004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 286 time to evaluate : 2.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 774 GLN Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1083 HIS Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 919 ASN Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1083 HIS Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 96 CYS Chi-restraints excluded: chain F residue 105 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 286 optimal weight: 0.1980 chunk 211 optimal weight: 0.8980 chunk 178 optimal weight: 1.9990 chunk 176 optimal weight: 0.7980 chunk 117 optimal weight: 10.0000 chunk 50 optimal weight: 0.0980 chunk 218 optimal weight: 0.7980 chunk 36 optimal weight: 9.9990 chunk 42 optimal weight: 10.0000 chunk 166 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 GLN B 764 ASN B 774 GLN B1083 HIS ** C 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.252314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.182903 restraints weight = 34494.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.179259 restraints weight = 53364.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.178033 restraints weight = 51882.163| |-----------------------------------------------------------------------------| r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 28172 Z= 0.135 Angle : 0.606 14.728 38405 Z= 0.299 Chirality : 0.045 0.234 4412 Planarity : 0.004 0.066 4922 Dihedral : 7.173 72.925 4493 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.32 % Allowed : 8.65 % Favored : 91.03 % Rotamer: Outliers : 3.50 % Allowed : 17.91 % Favored : 78.60 % 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: -1.58 (0.14), residues: 3422 helix: 1.91 (0.22), residues: 598 sheet: -1.15 (0.19), residues: 689 loop : -2.01 (0.13), residues: 2135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 36 HIS 0.005 0.001 HIS B1083 PHE 0.027 0.001 PHE B 55 TYR 0.027 0.001 TYR B 495 ARG 0.007 0.000 ARG A 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00383 ( 30) link_NAG-ASN : angle 2.09523 ( 90) link_BETA1-4 : bond 0.00575 ( 6) link_BETA1-4 : angle 2.94531 ( 18) hydrogen bonds : bond 0.03892 ( 751) hydrogen bonds : angle 5.07336 ( 2055) SS BOND : bond 0.00283 ( 19) SS BOND : angle 1.34135 ( 38) covalent geometry : bond 0.00314 (28117) covalent geometry : angle 0.59339 (38259) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6844 Ramachandran restraints generated. 3422 Oldfield, 0 Emsley, 3422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 3004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 298 time to evaluate : 2.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 LEU cc_start: 0.1688 (OUTLIER) cc_final: 0.1457 (pp) REVERT: A 266 TYR cc_start: -0.0832 (OUTLIER) cc_final: -0.4444 (t80) REVERT: A 556 ASN cc_start: 0.7513 (p0) cc_final: 0.6949 (p0) REVERT: A 559 PHE cc_start: 0.7101 (p90) cc_final: 0.6877 (p90) REVERT: A 586 ASP cc_start: 0.7802 (t0) cc_final: 0.7592 (t0) REVERT: A 614 ASP cc_start: 0.7232 (p0) cc_final: 0.6844 (p0) REVERT: A 752 LEU cc_start: 0.8867 (tt) cc_final: 0.8552 (tt) REVERT: A 756 TYR cc_start: 0.8589 (t80) cc_final: 0.7771 (t80) REVERT: A 983 ARG cc_start: 0.8232 (ptp-110) cc_final: 0.7763 (mtm110) REVERT: B 41 LYS cc_start: 0.7896 (mmmt) cc_final: 0.7067 (mmtm) REVERT: B 177 MET cc_start: 0.5402 (tpt) cc_final: 0.5003 (tpt) REVERT: B 353 TRP cc_start: 0.7067 (p90) cc_final: 0.6718 (p90) REVERT: B 654 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7270 (mm-30) REVERT: B 954 GLN cc_start: 0.7993 (mt0) cc_final: 0.7560 (mt0) REVERT: B 1041 ASP cc_start: 0.6956 (t0) cc_final: 0.6694 (t0) REVERT: B 1086 LYS cc_start: 0.8028 (OUTLIER) cc_final: 0.7741 (mtpt) REVERT: B 1135 ASN cc_start: 0.8273 (t0) cc_final: 0.7833 (t0) REVERT: C 56 LEU cc_start: 0.3735 (OUTLIER) cc_final: 0.3442 (tp) REVERT: C 58 PHE cc_start: 0.7860 (OUTLIER) cc_final: 0.6808 (m-80) REVERT: C 725 GLU cc_start: 0.8353 (tt0) cc_final: 0.7993 (tt0) REVERT: C 756 TYR cc_start: 0.8572 (OUTLIER) cc_final: 0.8265 (t80) REVERT: C 919 ASN cc_start: 0.8336 (OUTLIER) cc_final: 0.7124 (p0) REVERT: C 1029 MET cc_start: 0.8333 (tpp) cc_final: 0.7685 (ttm) REVERT: E 34 MET cc_start: 0.4136 (pmm) cc_final: 0.2950 (pmm) REVERT: F 81 LEU cc_start: 0.4765 (pt) cc_final: 0.4547 (pp) outliers start: 105 outliers final: 85 residues processed: 380 average time/residue: 0.3330 time to fit residues: 215.7935 Evaluate side-chains 377 residues out of total 3004 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 285 time to evaluate : 2.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 266 TYR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1068 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 494 SER Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1086 LYS Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1130 ILE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 486 PHE Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 714 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 913 GLN Chi-restraints excluded: chain C residue 919 ASN Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1083 HIS Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 96 CYS Chi-restraints excluded: chain F residue 105 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 51 optimal weight: 6.9990 chunk 142 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 chunk 200 optimal weight: 0.9980 chunk 144 optimal weight: 6.9990 chunk 339 optimal weight: 0.7980 chunk 326 optimal weight: 30.0000 chunk 333 optimal weight: 8.9990 chunk 243 optimal weight: 1.9990 chunk 327 optimal weight: 8.9990 chunk 6 optimal weight: 4.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS A 564 GLN A 901 GLN A 926 GLN B 580 GLN B 764 ASN C 66 HIS C 115 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 978 ASN C1106 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.244626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.179527 restraints weight = 34328.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.172661 restraints weight = 58150.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.168867 restraints weight = 47216.902| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 28172 Z= 0.301 Angle : 0.761 15.503 38405 Z= 0.380 Chirality : 0.051 0.286 4412 Planarity : 0.005 0.067 4922 Dihedral : 7.699 71.135 4493 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.35 % Allowed : 10.55 % Favored : 89.10 % Rotamer: Outliers : 3.86 % Allowed : 17.78 % Favored : 78.36 % 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: -1.95 (0.14), residues: 3422 helix: 1.49 (0.21), residues: 592 sheet: -1.36 (0.19), residues: 678 loop : -2.21 (0.12), residues: 2152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 64 HIS 0.008 0.002 HIS C1058 PHE 0.032 0.002 PHE B 55 TYR 0.036 0.002 TYR B 904 ARG 0.009 0.001 ARG C 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00436 ( 30) link_NAG-ASN : angle 2.37749 ( 90) link_BETA1-4 : bond 0.00538 ( 6) link_BETA1-4 : angle 2.97945 ( 18) hydrogen bonds : bond 0.05242 ( 751) hydrogen bonds : angle 5.61319 ( 2055) SS BOND : bond 0.00375 ( 19) SS BOND : angle 1.91996 ( 38) covalent geometry : bond 0.00722 (28117) covalent geometry : angle 0.74810 (38259) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10280.84 seconds wall clock time: 183 minutes 1.85 seconds (10981.85 seconds total)