Starting phenix.real_space_refine on Fri May 30 08:34:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xo4_33336/05_2025/7xo4_33336.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xo4_33336/05_2025/7xo4_33336.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xo4_33336/05_2025/7xo4_33336.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xo4_33336/05_2025/7xo4_33336.map" model { file = "/net/cci-nas-00/data/ceres_data/7xo4_33336/05_2025/7xo4_33336.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xo4_33336/05_2025/7xo4_33336.cif" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 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: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 161 5.16 5 C 21346 2.51 5 N 5518 2.21 5 O 6383 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 231 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 33410 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 7763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7763 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 52, 'TRANS': 971} Chain breaks: 7 Unresolved non-hydrogen bonds: 267 Unresolved non-hydrogen angles: 325 Unresolved non-hydrogen dihedrals: 225 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 6, 'TYR:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 132 Chain: "B" Number of atoms: 7763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7763 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 52, 'TRANS': 971} Chain breaks: 7 Unresolved non-hydrogen bonds: 267 Unresolved non-hydrogen angles: 325 Unresolved non-hydrogen dihedrals: 225 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 6, 'TYR:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 132 Chain: "C" Number of atoms: 7700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1022, 7700 Classifications: {'peptide': 1022} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 52, 'TRANS': 969} Chain breaks: 7 Unresolved non-hydrogen bonds: 313 Unresolved non-hydrogen angles: 385 Unresolved non-hydrogen dihedrals: 251 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 10, 'TYR:plan': 2, 'ASN:plan1': 9, 'ASP:plan': 10, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 194 Chain: "D" Number of atoms: 4818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 591, 4818 Classifications: {'peptide': 591} Link IDs: {'PTRANS': 25, 'TRANS': 565} Chain breaks: 1 Chain: "E" Number of atoms: 4818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 591, 4818 Classifications: {'peptide': 591} Link IDs: {'PTRANS': 25, 'TRANS': 565} Chain breaks: 1 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' ZN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' ZN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 17.43, per 1000 atoms: 0.52 Number of scatterers: 33410 At special positions: 0 Unit cell: (165.624, 140.08, 245.552, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 161 16.00 O 6383 8.00 N 5518 7.00 C 21346 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " 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=2.19 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=1.23 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.31 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=1.47 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.18 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=1.78 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 D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=1.67 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 141 " distance=2.03 Simple disulfide: pdb=" SG CYS E 344 " - pdb=" SG CYS E 361 " distance=2.30 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A1074 " " NAG A1302 " - " ASN A 234 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A1098 " " NAG A1305 " - " ASN A 801 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A 657 " " NAG A1308 " - " ASN A 616 " " NAG A1309 " - " ASN A 603 " " NAG A1310 " - " ASN A 331 " " NAG A1311 " - " ASN A 165 " " NAG A1312 " - " ASN A 343 " " NAG B1301 " - " ASN B1074 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B1098 " " NAG B1305 " - " ASN B 801 " " NAG B1306 " - " ASN B 709 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 603 " " NAG B1310 " - " ASN B 331 " " NAG B1311 " - " ASN B 165 " " NAG B1312 " - " ASN B 370 " " NAG C1301 " - " ASN C 657 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 234 " " NAG C1304 " - " ASN C 603 " " NAG C1305 " - " ASN C1074 " " NAG C1306 " - " ASN C1134 " " NAG C1307 " - " ASN C1098 " " NAG C1308 " - " ASN C 165 " " NAG C1309 " - " ASN C 709 " " NAG C1310 " - " ASN C 801 " " NAG C1311 " - " ASN C 282 " " NAG D 902 " - " ASN D 546 " " NAG D 903 " - " ASN D 49 " " NAG E 902 " - " ASN E 546 " " NAG E 903 " - " ASN E 58 " Time building additional restraints: 7.98 Conformation dependent library (CDL) restraints added in 4.8 seconds 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8002 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 43 sheets defined 33.6% alpha, 18.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.41 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.765A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 368 Processing helix chain 'A' and resid 383 through 387 removed outlier: 4.003A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.811A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 removed outlier: 3.568A pdb=" N TYR A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.575A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.919A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 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: 3.691A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.858A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.949A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 913 through 918' Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.802A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 964 removed outlier: 4.556A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 968 Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.739A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.569A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 295 through 303 removed outlier: 3.584A pdb=" N THR B 299 " --> pdb=" O PRO B 295 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N CYS B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.563A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 removed outlier: 4.014A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 749 through 754 removed outlier: 3.582A pdb=" N LEU B 753 " --> pdb=" O CYS B 749 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 749 through 754' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.690A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.660A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.749A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 907 Processing helix chain 'B' and resid 908 through 910 No H-bonds generated for 'chain 'B' and resid 908 through 910' Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.739A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.786A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER B 937 " --> pdb=" O LYS B 933 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 964 removed outlier: 3.545A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 965 through 968 Processing helix chain 'B' and resid 977 through 984 removed outlier: 3.780A pdb=" N PHE B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.630A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASP B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY B 999 " --> pdb=" O ARG B 995 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.524A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 343 removed outlier: 4.094A pdb=" N ASN C 343 " --> pdb=" O ASP C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 388 removed outlier: 3.583A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 384 through 388' Processing helix chain 'C' and resid 404 through 410 removed outlier: 3.551A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.564A pdb=" N TYR C 421 " --> pdb=" O ASN C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 744 Processing helix chain 'C' and resid 753 through 757 removed outlier: 3.730A pdb=" N GLY C 757 " --> pdb=" O LEU C 754 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.512A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.650A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 removed outlier: 4.136A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 913 through 918' Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.514A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.804A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 977 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.827A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 53 removed outlier: 3.947A pdb=" N LEU D 29 " --> pdb=" O ALA D 25 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP D 38 " --> pdb=" O GLN D 34 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N TYR D 41 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLN D 42 " --> pdb=" O ASP D 38 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN D 53 " --> pdb=" O ASN D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 78 removed outlier: 3.633A pdb=" N LYS D 61 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU D 74 " --> pdb=" O SER D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 99 Processing helix chain 'D' and resid 109 through 129 removed outlier: 3.700A pdb=" N ASN D 113 " --> pdb=" O SER D 109 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR D 127 " --> pdb=" O MET D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 154 removed outlier: 3.817A pdb=" N MET D 152 " --> pdb=" O LEU D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 171 removed outlier: 3.672A pdb=" N ARG D 161 " --> pdb=" O ASP D 157 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA D 164 " --> pdb=" O SER D 160 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TRP D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU D 171 " --> pdb=" O GLY D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 194 removed outlier: 3.923A pdb=" N GLU D 181 " --> pdb=" O ARG D 177 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LYS D 187 " --> pdb=" O TYR D 183 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG D 192 " --> pdb=" O ASN D 188 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA D 193 " --> pdb=" O GLU D 189 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASN D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 204 removed outlier: 3.829A pdb=" N TRP D 203 " --> pdb=" O TYR D 199 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG D 204 " --> pdb=" O GLY D 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 199 through 204' Processing helix chain 'D' and resid 205 through 207 No H-bonds generated for 'chain 'D' and resid 205 through 207' Processing helix chain 'D' and resid 212 through 216 removed outlier: 3.980A pdb=" N ASN D 216 " --> pdb=" O ASP D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 248 removed outlier: 3.999A pdb=" N ASP D 225 " --> pdb=" O GLN D 221 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU D 227 " --> pdb=" O ILE D 223 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU D 232 " --> pdb=" O ARG D 228 " (cutoff:3.500A) Proline residue: D 235 - end of helix removed outlier: 3.532A pdb=" N ALA D 242 " --> pdb=" O GLU D 238 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR D 243 " --> pdb=" O HIS D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 298 removed outlier: 3.753A pdb=" N MET D 298 " --> pdb=" O ASP D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 317 removed outlier: 4.255A pdb=" N PHE D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN D 309 " --> pdb=" O GLU D 305 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU D 310 " --> pdb=" O ARG D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 330 Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.848A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 402 through 412 removed outlier: 3.800A pdb=" N GLU D 406 " --> pdb=" O GLU D 402 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ILE D 407 " --> pdb=" O ALA D 403 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 422 removed outlier: 3.554A pdb=" N LYS D 419 " --> pdb=" O PRO D 415 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY D 422 " --> pdb=" O LEU D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 447 removed outlier: 3.565A pdb=" N GLN D 442 " --> pdb=" O PHE D 438 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 466 removed outlier: 3.576A pdb=" N MET D 462 " --> pdb=" O LYS D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 485 removed outlier: 3.786A pdb=" N LYS D 476 " --> pdb=" O GLN D 472 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 502 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 532 removed outlier: 4.064A pdb=" N THR D 517 " --> pdb=" O ILE D 513 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN D 522 " --> pdb=" O ARG D 518 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN D 526 " --> pdb=" O GLN D 522 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N CYS D 530 " --> pdb=" O GLN D 526 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 559 removed outlier: 4.038A pdb=" N GLY D 551 " --> pdb=" O SER D 547 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN D 552 " --> pdb=" O THR D 548 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER D 559 " --> pdb=" O LEU D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 574 Processing helix chain 'D' and resid 581 through 588 removed outlier: 3.719A pdb=" N TYR D 587 " --> pdb=" O PRO D 583 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE D 588 " --> pdb=" O LEU D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 596 removed outlier: 3.889A pdb=" N LYS D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 53 removed outlier: 3.729A pdb=" N PHE E 28 " --> pdb=" O ASN E 24 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN E 30 " --> pdb=" O LYS E 26 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU E 35 " --> pdb=" O ASN E 31 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASP E 38 " --> pdb=" O GLN E 34 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA E 46 " --> pdb=" O GLN E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 78 removed outlier: 3.706A pdb=" N GLU E 64 " --> pdb=" O GLN E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 83 removed outlier: 3.668A pdb=" N SER E 82 " --> pdb=" O THR E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 101 removed outlier: 4.055A pdb=" N GLN E 96 " --> pdb=" O ILE E 92 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA E 99 " --> pdb=" O ARG E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 129 removed outlier: 3.830A pdb=" N ASN E 113 " --> pdb=" O SER E 109 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE E 119 " --> pdb=" O GLN E 115 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR E 122 " --> pdb=" O THR E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 153 removed outlier: 3.710A pdb=" N MET E 152 " --> pdb=" O LEU E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 174 removed outlier: 3.660A pdb=" N ARG E 161 " --> pdb=" O ASP E 157 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N TRP E 163 " --> pdb=" O ASN E 159 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA E 164 " --> pdb=" O SER E 160 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TRP E 168 " --> pdb=" O ALA E 164 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL E 172 " --> pdb=" O TRP E 168 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LYS E 174 " --> pdb=" O ALA E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 194 removed outlier: 3.929A pdb=" N GLU E 182 " --> pdb=" O PRO E 178 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA E 191 " --> pdb=" O LYS E 187 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ARG E 192 " --> pdb=" O ASN E 188 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA E 193 " --> pdb=" O GLU E 189 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASN E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 205 removed outlier: 3.742A pdb=" N TRP E 203 " --> pdb=" O TYR E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 248 removed outlier: 3.683A pdb=" N GLU E 232 " --> pdb=" O ARG E 228 " (cutoff:3.500A) Proline residue: E 235 - end of helix removed outlier: 4.447A pdb=" N HIS E 239 " --> pdb=" O PRO E 235 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU E 240 " --> pdb=" O LEU E 236 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL E 244 " --> pdb=" O LEU E 240 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ARG E 245 " --> pdb=" O HIS E 241 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG E 246 " --> pdb=" O ALA E 242 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LYS E 247 " --> pdb=" O TYR E 243 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU E 248 " --> pdb=" O VAL E 244 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 251 No H-bonds generated for 'chain 'E' and resid 249 through 251' Processing helix chain 'E' and resid 295 through 300 removed outlier: 3.880A pdb=" N ASN E 299 " --> pdb=" O ASP E 295 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLN E 300 " --> pdb=" O ALA E 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 295 through 300' Processing helix chain 'E' and resid 303 through 317 removed outlier: 3.836A pdb=" N ILE E 307 " --> pdb=" O ASP E 303 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N PHE E 308 " --> pdb=" O ALA E 304 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 329 removed outlier: 3.651A pdb=" N TRP E 328 " --> pdb=" O GLN E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 385 removed outlier: 3.712A pdb=" N GLY E 377 " --> pdb=" O HIS E 373 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N HIS E 378 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR E 385 " --> pdb=" O TYR E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 393 Processing helix chain 'E' and resid 403 through 413 removed outlier: 4.101A pdb=" N ILE E 407 " --> pdb=" O ALA E 403 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER E 409 " --> pdb=" O GLY E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 422 removed outlier: 3.657A pdb=" N GLY E 422 " --> pdb=" O LEU E 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 445 removed outlier: 3.571A pdb=" N GLU E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS E 441 " --> pdb=" O ASN E 437 " (cutoff:3.500A) Processing helix chain 'E' and resid 446 through 448 No H-bonds generated for 'chain 'E' and resid 446 through 448' Processing helix chain 'E' and resid 449 through 465 removed outlier: 4.095A pdb=" N ARG E 465 " --> pdb=" O TRP E 461 " (cutoff:3.500A) Processing helix chain 'E' and resid 469 through 471 No H-bonds generated for 'chain 'E' and resid 469 through 471' Processing helix chain 'E' and resid 472 through 484 Processing helix chain 'E' and resid 498 through 502 Processing helix chain 'E' and resid 503 through 508 removed outlier: 4.003A pdb=" N ASN E 508 " --> pdb=" O PHE E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 512 through 533 removed outlier: 4.094A pdb=" N TYR E 516 " --> pdb=" O PHE E 512 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR E 519 " --> pdb=" O TYR E 515 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ILE E 520 " --> pdb=" O TYR E 516 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N PHE E 523 " --> pdb=" O THR E 519 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA E 533 " --> pdb=" O LEU E 529 " (cutoff:3.500A) Processing helix chain 'E' and resid 547 through 559 removed outlier: 3.787A pdb=" N GLY E 551 " --> pdb=" O SER E 547 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLN E 552 " --> pdb=" O THR E 548 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS E 556 " --> pdb=" O GLN E 552 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N MET E 557 " --> pdb=" O LYS E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 572 removed outlier: 3.980A pdb=" N ASN E 572 " --> pdb=" O LYS E 568 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 588 removed outlier: 3.620A pdb=" N LEU E 585 " --> pdb=" O VAL E 581 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N PHE E 588 " --> pdb=" O LEU E 584 " (cutoff:3.500A) Processing helix chain 'E' and resid 588 through 599 removed outlier: 3.674A pdb=" N ASP E 593 " --> pdb=" O GLN E 589 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TRP E 594 " --> pdb=" O PRO E 590 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.747A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA A 264 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 55 removed outlier: 3.656A pdb=" N HIS A 49 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.977A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 310 through 319 removed outlier: 7.093A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.553A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY A 548 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR A 572 " --> pdb=" O ASP A 568 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.949A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR A 396 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY A 431 " --> pdb=" O TYR A 380 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'A' and resid 473 through 474 removed outlier: 4.109A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.006A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.457A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.457A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR A1105 " --> pdb=" O VAL A1094 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.150A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB5, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.780A pdb=" N THR B 29 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA B 264 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LYS B 202 " --> pdb=" O LYS B 195 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.306A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.420A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.554A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.633A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR B 170 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 310 through 319 removed outlier: 5.295A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY B 593 " --> pdb=" O PHE B 318 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.621A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE B 541 " --> pdb=" O GLY B 548 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR B 588 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU B 585 " --> pdb=" O VAL B 576 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N PHE C 43 " --> pdb=" O PHE B 565 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 376 through 380 removed outlier: 3.768A pdb=" N THR B 376 " --> pdb=" O ALA B 435 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY B 431 " --> pdb=" O TYR B 380 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE B 434 " --> pdb=" O VAL B 511 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER B 514 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC3, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.521A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AC5, first strand: chain 'B' and resid 711 through 713 removed outlier: 3.756A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 717 through 719 Processing sheet with id=AC7, first strand: chain 'B' and resid 717 through 719 removed outlier: 3.546A pdb=" N VAL B1061 " --> pdb=" O GLN B1054 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.047A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD1, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.733A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.579A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA C 264 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL C 90 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE C 194 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 48 through 55 removed outlier: 7.345A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.833A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL C 130 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.291A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.742A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASP C 586 " --> pdb=" O THR C 553 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR C 572 " --> pdb=" O ASP C 568 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.019A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG C 509 " --> pdb=" O TRP C 436 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TRP C 436 " --> pdb=" O ARG C 509 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 361 through 362 removed outlier: 4.242A pdb=" N CYS C 525 " --> pdb=" O CYS C 361 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N VAL C 524 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 453 through 454 Processing sheet with id=AD9, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.848A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.891A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA C1070 " --> pdb=" O ASN C 717 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.891A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA C1070 " --> pdb=" O ASN C 717 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR C1105 " --> pdb=" O VAL C1094 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.427A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE5, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.733A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'D' and resid 347 through 350 removed outlier: 4.046A pdb=" N THR D 347 " --> pdb=" O LYS D 359 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS D 359 " --> pdb=" O THR D 347 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TRP D 349 " --> pdb=" O ARG D 357 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG D 357 " --> pdb=" O TRP D 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'E' and resid 350 through 352 removed outlier: 4.413A pdb=" N GLY E 352 " --> pdb=" O ASP E 355 " (cutoff:3.500A) 1234 hydrogen bonds defined for protein. 3483 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 15.44 Time building geometry restraints manager: 9.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10666 1.34 - 1.46: 6608 1.46 - 1.58: 16721 1.58 - 1.70: 0 1.70 - 1.82: 225 Bond restraints: 34220 Sorted by residual: bond pdb=" C1 NAG D 903 " pdb=" O5 NAG D 903 " ideal model delta sigma weight residual 1.406 1.486 -0.080 2.00e-02 2.50e+03 1.59e+01 bond pdb=" N GLU E 145 " pdb=" CA GLU E 145 " ideal model delta sigma weight residual 1.461 1.490 -0.029 9.20e-03 1.18e+04 9.67e+00 bond pdb=" C1 NAG E 902 " pdb=" O5 NAG E 902 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 6.06e+00 bond pdb=" N LEU E 144 " pdb=" CA LEU E 144 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.29e-02 6.01e+03 5.64e+00 bond pdb=" C GLU E 145 " pdb=" N PRO E 146 " ideal model delta sigma weight residual 1.330 1.358 -0.028 1.19e-02 7.06e+03 5.64e+00 ... (remaining 34215 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 45306 1.33 - 2.65: 1111 2.65 - 3.98: 179 3.98 - 5.31: 33 5.31 - 6.64: 7 Bond angle restraints: 46636 Sorted by residual: angle pdb=" N VAL A 503 " pdb=" CA VAL A 503 " pdb=" C VAL A 503 " ideal model delta sigma weight residual 113.71 108.98 4.73 9.50e-01 1.11e+00 2.48e+01 angle pdb=" C ASP E 149 " pdb=" N GLU E 150 " pdb=" CA GLU E 150 " ideal model delta sigma weight residual 120.60 113.96 6.64 1.60e+00 3.91e-01 1.72e+01 angle pdb=" N VAL E 574 " pdb=" CA VAL E 574 " pdb=" C VAL E 574 " ideal model delta sigma weight residual 113.53 109.84 3.69 9.80e-01 1.04e+00 1.42e+01 angle pdb=" N PRO A 373 " pdb=" CA PRO A 373 " pdb=" C PRO A 373 " ideal model delta sigma weight residual 114.68 110.18 4.50 1.28e+00 6.10e-01 1.24e+01 angle pdb=" N PHE A 375 " pdb=" CA PHE A 375 " pdb=" C PHE A 375 " ideal model delta sigma weight residual 113.18 109.03 4.15 1.21e+00 6.83e-01 1.18e+01 ... (remaining 46631 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.13: 20116 23.13 - 46.25: 447 46.25 - 69.38: 72 69.38 - 92.50: 32 92.50 - 115.63: 46 Dihedral angle restraints: 20713 sinusoidal: 8298 harmonic: 12415 Sorted by residual: dihedral pdb=" CB CYS C 291 " pdb=" SG CYS C 291 " pdb=" SG CYS C 301 " pdb=" CB CYS C 301 " ideal model delta sinusoidal sigma weight residual 93.00 160.48 -67.48 1 1.00e+01 1.00e-02 5.92e+01 dihedral pdb=" CB CYS D 530 " pdb=" SG CYS D 530 " pdb=" SG CYS D 542 " pdb=" CB CYS D 542 " ideal model delta sinusoidal sigma weight residual -86.00 -150.90 64.90 1 1.00e+01 1.00e-02 5.53e+01 dihedral pdb=" CB CYS C 391 " pdb=" SG CYS C 391 " pdb=" SG CYS C 525 " pdb=" CB CYS C 525 " ideal model delta sinusoidal sigma weight residual -86.00 -141.35 55.35 1 1.00e+01 1.00e-02 4.14e+01 ... (remaining 20710 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 4804 0.069 - 0.137: 515 0.137 - 0.206: 7 0.206 - 0.275: 4 0.275 - 0.343: 5 Chirality restraints: 5335 Sorted by residual: chirality pdb=" C1 NAG B1304 " pdb=" ND2 ASN B1098 " pdb=" C2 NAG B1304 " pdb=" O5 NAG B1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.95e+00 chirality pdb=" C1 NAG A1304 " pdb=" ND2 ASN A1098 " pdb=" C2 NAG A1304 " pdb=" O5 NAG A1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" C1 NAG C1309 " pdb=" ND2 ASN C 709 " pdb=" C2 NAG C1309 " pdb=" O5 NAG C1309 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.59e+00 ... (remaining 5332 not shown) Planarity restraints: 6036 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 985 " -0.024 5.00e-02 4.00e+02 3.63e-02 2.11e+00 pdb=" N PRO B 986 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO B 986 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 986 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 986 " 0.024 5.00e-02 4.00e+02 3.57e-02 2.04e+00 pdb=" N PRO A 987 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 987 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 987 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 234 " 0.024 5.00e-02 4.00e+02 3.55e-02 2.02e+00 pdb=" N PRO D 235 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO D 235 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 235 " 0.020 5.00e-02 4.00e+02 ... (remaining 6033 not shown) Histogram of nonbonded interaction distances: 1.18 - 1.93: 4 1.93 - 2.67: 468 2.67 - 3.41: 44450 3.41 - 4.16: 75159 4.16 - 4.90: 135515 Nonbonded interactions: 255596 Sorted by model distance: nonbonded pdb=" NE2 GLN E 388 " pdb=" O LEU E 392 " model vdw 1.184 3.120 nonbonded pdb=" CG1 VAL A1094 " pdb=" OH TYR B 904 " model vdw 1.688 3.460 nonbonded pdb=" OE1 GLU C 406 " pdb=" OE1 GLN C 409 " model vdw 1.877 3.040 nonbonded pdb=" OE1 GLU C 406 " pdb=" CD GLN C 409 " model vdw 1.925 3.270 nonbonded pdb=" OE1 GLU C 406 " pdb=" NE2 GLN C 409 " model vdw 1.947 3.120 ... (remaining 255591 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 27 through 39 or (resid 40 through 41 and (name N or name \ CA or name C or name O or name CB )) or resid 42 through 45 or (resid 46 and (na \ me N or name CA or name C or name O or name CB )) or resid 47 through 51 or (res \ id 52 through 53 and (name N or name CA or name C or name O or name CB )) or res \ id 54 through 68 or (resid 80 and (name N or name CA or name C or name O or name \ CB )) or resid 81 through 86 or (resid 87 and (name N or name CA or name C or n \ ame O or name CB )) or resid 88 through 96 or (resid 97 through 98 and (name N o \ r name CA or name C or name O or name CB )) or resid 99 through 114 or (resid 11 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 116 through \ 133 or (resid 134 and (name N or name CA or name C or name O or name CB )) or re \ sid 135 through 136 or (resid 137 and (name N or name CA or name C or name O or \ name CB )) or resid 138 through 160 or (resid 161 through 164 and (name N or nam \ e CA or name C or name O or name CB )) or resid 165 through 209 or (resid 210 an \ d (name N or name CA or name C or name O or name CB )) or resid 215 through 253 \ or (resid 254 and (name N or name CA or name C or name O or name CB )) or resid \ 255 through 318 or (resid 319 and (name N or name CA or name C or name O or name \ CB )) or resid 320 through 355 or (resid 356 through 357 and (name N or name CA \ or name C or name O or name CB )) or resid 358 through 387 or (resid 388 and (n \ ame N or name CA or name C or name O or name CB )) or resid 389 through 404 or ( \ resid 405 and (name N or name CA or name C or name O or name CB )) or resid 406 \ through 414 or (resid 415 and (name N or name CA or name C or name O or name CB \ )) or resid 416 through 426 or (resid 427 and (name N or name CA or name C or na \ me O or name CB )) or resid 428 through 447 or (resid 448 and (name N or name CA \ or name C or name O or name CB )) or resid 449 through 453 or (resid 454 and (n \ ame N or name CA or name C or name O or name CB )) or resid 455 through 457 or ( \ resid 458 through 459 and (name N or name CA or name C or name O or name CB )) o \ r resid 460 through 464 or (resid 465 and (name N or name CA or name C or name O \ or name CB )) or resid 466 through 473 or (resid 474 through 475 and (name N or \ name CA or name C or name O or name CB )) or resid 476 through 486 or (resid 48 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 488 through \ 499 or (resid 500 and (name N or name CA or name C or name O or name CB )) or re \ sid 501 through 515 or (resid 516 and (name N or name CA or name C or name O or \ name CB )) or resid 517 through 522 or (resid 523 and (name N or name CA or name \ C or name O or name CB )) or resid 524 through 527 or (resid 528 through 529 an \ d (name N or name CA or name C or name O or name CB )) or resid 530 through 553 \ or (resid 554 and (name N or name CA or name C or name O or name CB )) or resid \ 555 or (resid 556 through 558 and (name N or name CA or name C or name O or name \ CB )) or resid 559 through 563 or (resid 564 and (name N or name CA or name C o \ r name O or name CB )) or resid 565 through 570 or (resid 571 through 572 and (n \ ame N or name CA or name C or name O or name CB )) or resid 573 through 620 or r \ esid 641 through 676 or (resid 690 and (name N or name CA or name C or name O or \ name CB )) or resid 691 through 747 or (resid 748 and (name N or name CA or nam \ e C or name O or name CB )) or resid 749 through 827 or (resid 828 and (name N o \ r name CA or name C or name O or name CB )) or resid 855 through 984 or (resid 9 \ 85 and (name N or name CA or name C or name O or name CB )) or resid 986 through \ 987 or (resid 988 through 989 and (name N or name CA or name C or name O or nam \ e CB )) or resid 990 through 1037 or (resid 1038 and (name N or name CA or name \ C or name O or name CB )) or resid 1039 through 1050 or (resid 1051 and (name N \ or name CA or name C or name O or name CB )) or resid 1052 through 1110 or (resi \ d 1111 and (name N or name CA or name C or name O or name CB )) or resid 1112 th \ rough 1143 or (resid 1144 through 1146 and (name N or name CA or name C or name \ O or name CB )) or resid 1301 through 1311)) selection = (chain 'B' and (resid 27 through 39 or (resid 40 through 41 and (name N or name \ CA or name C or name O or name CB )) or resid 42 through 45 or (resid 46 and (na \ me N or name CA or name C or name O or name CB )) or resid 47 through 51 or (res \ id 52 through 53 and (name N or name CA or name C or name O or name CB )) or res \ id 54 through 68 or (resid 80 and (name N or name CA or name C or name O or name \ CB )) or resid 81 through 86 or (resid 87 and (name N or name CA or name C or n \ ame O or name CB )) or resid 88 through 96 or (resid 97 through 98 and (name N o \ r name CA or name C or name O or name CB )) or resid 99 through 114 or (resid 11 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 116 through \ 133 or (resid 134 and (name N or name CA or name C or name O or name CB )) or re \ sid 135 through 136 or (resid 137 and (name N or name CA or name C or name O or \ name CB )) or resid 138 through 160 or (resid 161 through 164 and (name N or nam \ e CA or name C or name O or name CB )) or resid 165 through 209 or (resid 210 an \ d (name N or name CA or name C or name O or name CB )) or resid 215 through 253 \ or (resid 254 and (name N or name CA or name C or name O or name CB )) or resid \ 255 through 318 or (resid 319 and (name N or name CA or name C or name O or name \ CB )) or resid 320 through 355 or (resid 356 through 357 and (name N or name CA \ or name C or name O or name CB )) or resid 358 through 387 or (resid 388 and (n \ ame N or name CA or name C or name O or name CB )) or resid 389 through 404 or ( \ resid 405 and (name N or name CA or name C or name O or name CB )) or resid 406 \ through 414 or (resid 415 and (name N or name CA or name C or name O or name CB \ )) or resid 416 through 426 or (resid 427 and (name N or name CA or name C or na \ me O or name CB )) or resid 428 through 447 or (resid 448 and (name N or name CA \ or name C or name O or name CB )) or resid 449 through 453 or (resid 454 and (n \ ame N or name CA or name C or name O or name CB )) or resid 455 through 457 or ( \ resid 458 through 459 and (name N or name CA or name C or name O or name CB )) o \ r resid 460 through 464 or (resid 465 and (name N or name CA or name C or name O \ or name CB )) or resid 466 through 473 or (resid 474 through 475 and (name N or \ name CA or name C or name O or name CB )) or resid 476 through 486 or (resid 48 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 488 through \ 499 or (resid 500 and (name N or name CA or name C or name O or name CB )) or re \ sid 501 through 515 or (resid 516 and (name N or name CA or name C or name O or \ name CB )) or resid 517 through 522 or (resid 523 and (name N or name CA or name \ C or name O or name CB )) or resid 524 through 527 or (resid 528 through 529 an \ d (name N or name CA or name C or name O or name CB )) or resid 530 through 553 \ or (resid 554 and (name N or name CA or name C or name O or name CB )) or resid \ 555 or (resid 556 through 558 and (name N or name CA or name C or name O or name \ CB )) or resid 559 through 563 or (resid 564 and (name N or name CA or name C o \ r name O or name CB )) or resid 565 through 570 or (resid 571 through 572 and (n \ ame N or name CA or name C or name O or name CB )) or resid 573 through 620 or r \ esid 641 through 676 or (resid 690 and (name N or name CA or name C or name O or \ name CB )) or resid 691 through 747 or (resid 748 and (name N or name CA or nam \ e C or name O or name CB )) or resid 749 through 827 or (resid 828 and (name N o \ r name CA or name C or name O or name CB )) or resid 855 through 984 or (resid 9 \ 85 and (name N or name CA or name C or name O or name CB )) or resid 986 through \ 987 or (resid 988 through 989 and (name N or name CA or name C or name O or nam \ e CB )) or resid 990 through 1037 or (resid 1038 and (name N or name CA or name \ C or name O or name CB )) or resid 1039 through 1050 or (resid 1051 and (name N \ or name CA or name C or name O or name CB )) or resid 1052 through 1110 or (resi \ d 1111 and (name N or name CA or name C or name O or name CB )) or resid 1112 th \ rough 1143 or (resid 1144 through 1146 and (name N or name CA or name C or name \ O or name CB )) or resid 1301 through 1311)) selection = (chain 'C' and (resid 27 through 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB )) or resid 42 through 67 or (resid 68 through 80 and (na \ me N or name CA or name C or name O or name CB )) or resid 81 through 107 or (re \ sid 108 through 113 and (name N or name CA or name C or name O or name CB )) or \ resid 114 through 175 or (resid 176 through 187 and (name N or name CA or name C \ or name O or name CB )) or resid 188 through 199 or (resid 200 and (name N or n \ ame CA or name C or name O or name CB )) or resid 201 through 217 or (resid 218 \ and (name N or name CA or name C or name O or name CB )) or resid 219 through 22 \ 3 or (resid 224 and (name N or name CA or name C or name O or name CB )) or resi \ d 225 through 248 or (resid 249 through 250 and (name N or name CA or name C or \ name O or name CB )) or resid 251 through 303 or (resid 304 and (name N or name \ CA or name C or name O or name CB )) or resid 305 through 320 or (resid 321 and \ (name N or name CA or name C or name O or name CB )) or resid 322 through 556 or \ (resid 557 through 558 and (name N or name CA or name C or name O or name CB )) \ or resid 559 through 568 or (resid 569 through 572 and (name N or name CA or na \ me C or name O or name CB )) or resid 573 through 662 or (resid 663 and (name N \ or name CA or name C or name O or name CB )) or resid 664 through 701 or (resid \ 702 and (name N or name CA or name C or name O or name CB )) or resid 703 throug \ h 739 or (resid 740 and (name N or name CA or name C or name O or name CB )) or \ resid 741 through 794 or (resid 795 and (name N or name CA or name C or name O o \ r name CB )) or resid 796 through 807 or (resid 808 and (name N or name CA or na \ me C or name O or name CB )) or resid 809 through 818 or (resid 819 and (name N \ or name CA or name C or name O or name CB )) or resid 820 through 824 or (resid \ 825 and (name N or name CA or name C or name O or name CB )) or resid 826 throug \ h 917 or (resid 918 and (name N or name CA or name C or name O or name CB )) or \ resid 919 through 946 or (resid 947 and (name N or name CA or name C or name O o \ r name CB )) or resid 948 through 963 or (resid 964 and (name N or name CA or na \ me C or name O or name CB )) or resid 965 through 1072 or (resid 1073 and (name \ N or name CA or name C or name O or name CB )) or resid 1074 through 1137 or (re \ sid 1138 and (name N or name CA or name C or name O or name CB )) or resid 1139 \ through 1140 or (resid 1141 through 1142 and (name N or name CA or name C or nam \ e O or name CB )) or resid 1143 through 1145 or (resid 1146 and (name N or name \ CA or name C or name O or name CB )) or resid 1301 through 1311)) } ncs_group { reference = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.350 Check model and map are aligned: 0.230 Set scattering table: 0.290 Process input model: 76.100 Find NCS groups from input model: 2.180 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3835 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 : 0.007 0.798 34296 Z= 0.341 Angle : 0.658 37.155 46827 Z= 0.350 Chirality : 0.042 0.343 5335 Planarity : 0.003 0.036 5997 Dihedral : 11.874 115.631 12600 Min Nonbonded Distance : 1.184 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % 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: -2.83 (0.11), residues: 4196 helix: -1.35 (0.13), residues: 1207 sheet: -1.06 (0.18), residues: 699 loop : -2.51 (0.11), residues: 2290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 594 HIS 0.003 0.000 HIS E 265 PHE 0.009 0.001 PHE A 168 TYR 0.009 0.001 TYR A 495 ARG 0.002 0.000 ARG E 246 Details of bonding type rmsd link_NAG-ASN : bond 0.00570 ( 39) link_NAG-ASN : angle 2.39565 ( 117) hydrogen bonds : bond 0.23692 ( 1210) hydrogen bonds : angle 8.14929 ( 3483) SS BOND : bond 0.19058 ( 37) SS BOND : angle 10.20817 ( 74) covalent geometry : bond 0.00246 (34220) covalent geometry : angle 0.50445 (46636) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 3713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 605 time to evaluate : 3.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.6621 (t0) cc_final: 0.6379 (t0) REVERT: A 238 PHE cc_start: 0.6843 (p90) cc_final: 0.6358 (p90) REVERT: A 266 TYR cc_start: 0.7058 (m-80) cc_final: 0.6852 (m-80) REVERT: A 743 CYS cc_start: 0.5933 (m) cc_final: 0.5686 (m) REVERT: A 776 LYS cc_start: 0.7908 (ttpt) cc_final: 0.7607 (ttpt) REVERT: A 779 GLN cc_start: 0.8121 (tt0) cc_final: 0.7862 (tt0) REVERT: A 881 THR cc_start: 0.7957 (m) cc_final: 0.7411 (p) REVERT: A 1038 LYS cc_start: 0.7317 (mtpp) cc_final: 0.7116 (mtpp) REVERT: A 1116 THR cc_start: 0.7295 (p) cc_final: 0.7077 (m) REVERT: B 309 GLU cc_start: 0.6919 (mt-10) cc_final: 0.6598 (mt-10) REVERT: B 605 SER cc_start: 0.7595 (t) cc_final: 0.7289 (t) REVERT: B 730 SER cc_start: 0.7953 (p) cc_final: 0.7663 (t) REVERT: B 1127 ASP cc_start: 0.7276 (t70) cc_final: 0.6982 (t0) REVERT: C 543 PHE cc_start: 0.7175 (m-10) cc_final: 0.6945 (m-80) REVERT: C 902 MET cc_start: 0.8232 (mmt) cc_final: 0.8027 (mmt) REVERT: C 964 LYS cc_start: 0.7534 (tttp) cc_final: 0.7322 (ttmm) REVERT: D 270 MET cc_start: -0.0438 (mtt) cc_final: -0.3977 (ttt) REVERT: D 332 MET cc_start: -0.0530 (ttm) cc_final: -0.0937 (ttm) REVERT: D 366 MET cc_start: 0.0929 (ttt) cc_final: 0.0671 (ttt) REVERT: E 360 MET cc_start: -0.0386 (ttt) cc_final: -0.0593 (tpt) outliers start: 0 outliers final: 0 residues processed: 605 average time/residue: 0.4189 time to fit residues: 422.2190 Evaluate side-chains 481 residues out of total 3713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 481 time to evaluate : 3.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 358 optimal weight: 40.0000 chunk 321 optimal weight: 9.9990 chunk 178 optimal weight: 0.9980 chunk 109 optimal weight: 7.9990 chunk 216 optimal weight: 5.9990 chunk 171 optimal weight: 2.9990 chunk 332 optimal weight: 40.0000 chunk 128 optimal weight: 1.9990 chunk 202 optimal weight: 1.9990 chunk 247 optimal weight: 3.9990 chunk 385 optimal weight: 50.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 115 GLN ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS A 271 GLN A 422 ASN ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 762 GLN A 774 GLN A 920 GLN A 926 GLN A 955 ASN A 965 GLN A1071 GLN A1088 HIS A1134 ASN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 314 GLN B 394 ASN B 409 GLN B 448 ASN B 474 GLN B 613 GLN B 690 GLN B 901 GLN B 914 ASN B 925 ASN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 953 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 978 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 710 ASN C 777 ASN C 784 GLN C 804 GLN C 895 GLN C 901 GLN C 920 GLN C 955 ASN C1083 HIS C1101 HIS D 81 GLN D 89 GLN D 98 GLN D 101 GLN D 115 GLN D 397 ASN D 524 GLN D 540 HIS E 98 GLN E 101 GLN E 102 GLN E 221 GLN E 290 ASN E 309 GLN E 368 ASN E 417 HIS E 437 ASN E 524 GLN E 531 GLN Total number of N/Q/H flips: 58 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.241059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.168420 restraints weight = 51301.671| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 2.49 r_work: 0.3590 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3423 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.169 34296 Z= 0.460 Angle : 0.848 14.214 46827 Z= 0.433 Chirality : 0.058 0.582 5335 Planarity : 0.006 0.104 5997 Dihedral : 8.854 108.020 5368 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.10 % Favored : 95.85 % Rotamer: Outliers : 2.90 % Allowed : 9.48 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.12), residues: 4196 helix: -0.60 (0.14), residues: 1234 sheet: -0.89 (0.17), residues: 830 loop : -2.24 (0.11), residues: 2132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 886 HIS 0.021 0.002 HIS A1064 PHE 0.041 0.004 PHE C 543 TYR 0.048 0.003 TYR C 265 ARG 0.008 0.001 ARG C 273 Details of bonding type rmsd link_NAG-ASN : bond 0.00835 ( 39) link_NAG-ASN : angle 3.28149 ( 117) hydrogen bonds : bond 0.05995 ( 1210) hydrogen bonds : angle 5.55793 ( 3483) SS BOND : bond 0.01454 ( 37) SS BOND : angle 3.15674 ( 74) covalent geometry : bond 0.01072 (34220) covalent geometry : angle 0.82453 (46636) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 695 residues out of total 3713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 594 time to evaluate : 3.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 PHE cc_start: 0.8065 (t80) cc_final: 0.7734 (t80) REVERT: A 543 PHE cc_start: 0.7908 (m-10) cc_final: 0.7589 (m-10) REVERT: A 571 ASP cc_start: 0.6801 (t0) cc_final: 0.6394 (t0) REVERT: A 643 PHE cc_start: 0.8335 (t80) cc_final: 0.8043 (t80) REVERT: A 743 CYS cc_start: 0.7536 (m) cc_final: 0.7101 (m) REVERT: A 748 GLU cc_start: 0.7929 (mp0) cc_final: 0.7428 (mp0) REVERT: A 776 LYS cc_start: 0.8663 (ttpt) cc_final: 0.8416 (ttmm) REVERT: A 870 ILE cc_start: 0.8340 (pt) cc_final: 0.7928 (mt) REVERT: A 1019 ARG cc_start: 0.8257 (ttp-110) cc_final: 0.8038 (ttp80) REVERT: A 1031 GLU cc_start: 0.8432 (mt-10) cc_final: 0.8175 (mt-10) REVERT: A 1038 LYS cc_start: 0.8690 (mtpp) cc_final: 0.8451 (mttm) REVERT: A 1097 SER cc_start: 0.8813 (t) cc_final: 0.8608 (p) REVERT: A 1120 THR cc_start: 0.8630 (m) cc_final: 0.8360 (p) REVERT: A 1139 ASP cc_start: 0.8051 (t70) cc_final: 0.7771 (t0) REVERT: B 318 PHE cc_start: 0.8673 (OUTLIER) cc_final: 0.8284 (p90) REVERT: B 329 PHE cc_start: 0.7573 (m-80) cc_final: 0.7237 (m-80) REVERT: B 532 ASN cc_start: 0.7155 (t0) cc_final: 0.6794 (p0) REVERT: B 554 GLU cc_start: 0.7172 (tm-30) cc_final: 0.6911 (tm-30) REVERT: B 586 ASP cc_start: 0.7873 (t70) cc_final: 0.7626 (t0) REVERT: B 659 SER cc_start: 0.8375 (m) cc_final: 0.7954 (p) REVERT: B 743 CYS cc_start: 0.8251 (m) cc_final: 0.7263 (m) REVERT: B 749 CYS cc_start: 0.7780 (OUTLIER) cc_final: 0.6999 (t) REVERT: B 860 VAL cc_start: 0.8870 (OUTLIER) cc_final: 0.8611 (p) REVERT: B 949 GLN cc_start: 0.8375 (tp40) cc_final: 0.8084 (tp40) REVERT: B 957 GLN cc_start: 0.7956 (tm-30) cc_final: 0.7743 (tm-30) REVERT: B 969 LYS cc_start: 0.8839 (mtmt) cc_final: 0.8474 (mtmm) REVERT: B 1074 ASN cc_start: 0.7668 (m110) cc_final: 0.7414 (m110) REVERT: B 1118 ASP cc_start: 0.8121 (p0) cc_final: 0.7904 (p0) REVERT: C 59 PHE cc_start: 0.8376 (m-10) cc_final: 0.8105 (m-80) REVERT: C 90 VAL cc_start: 0.8486 (t) cc_final: 0.8198 (p) REVERT: C 99 ASN cc_start: 0.7642 (t0) cc_final: 0.7367 (t0) REVERT: C 190 ARG cc_start: 0.8095 (mtm-85) cc_final: 0.7753 (mtm-85) REVERT: C 365 TYR cc_start: 0.7888 (m-80) cc_final: 0.7648 (m-80) REVERT: C 396 TYR cc_start: 0.7442 (m-80) cc_final: 0.6935 (m-80) REVERT: C 436 TRP cc_start: 0.7671 (p90) cc_final: 0.7365 (p90) REVERT: C 543 PHE cc_start: 0.8402 (m-10) cc_final: 0.8005 (m-10) REVERT: C 581 THR cc_start: 0.8536 (t) cc_final: 0.8210 (t) REVERT: C 603 ASN cc_start: 0.7900 (t0) cc_final: 0.7510 (t0) REVERT: C 608 VAL cc_start: 0.8806 (OUTLIER) cc_final: 0.8519 (p) REVERT: C 644 GLN cc_start: 0.8490 (tp40) cc_final: 0.8208 (tp40) REVERT: C 670 ILE cc_start: 0.8507 (OUTLIER) cc_final: 0.8196 (pt) REVERT: C 722 VAL cc_start: 0.8970 (m) cc_final: 0.8707 (t) REVERT: C 776 LYS cc_start: 0.8430 (ttmt) cc_final: 0.8193 (ttpp) REVERT: C 784 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.8136 (mt0) REVERT: C 804 GLN cc_start: 0.8572 (mm-40) cc_final: 0.8024 (mm-40) REVERT: C 950 ASP cc_start: 0.8221 (t70) cc_final: 0.8016 (t70) REVERT: C 961 THR cc_start: 0.8722 (OUTLIER) cc_final: 0.8495 (p) REVERT: C 969 LYS cc_start: 0.8953 (mtpt) cc_final: 0.8675 (mtpp) REVERT: C 970 PHE cc_start: 0.8182 (m-10) cc_final: 0.7838 (m-10) REVERT: C 994 ASP cc_start: 0.7874 (m-30) cc_final: 0.7474 (t70) REVERT: C 995 ARG cc_start: 0.8089 (mtp-110) cc_final: 0.7863 (ttm110) REVERT: C 1019 ARG cc_start: 0.8161 (tpt170) cc_final: 0.7890 (tpt170) REVERT: C 1066 THR cc_start: 0.8803 (OUTLIER) cc_final: 0.8571 (p) REVERT: E 37 GLU cc_start: 0.6307 (tt0) cc_final: 0.5842 (tm-30) REVERT: E 150 GLU cc_start: 0.2663 (tp30) cc_final: 0.2196 (tp30) REVERT: E 474 MET cc_start: -0.0740 (tpp) cc_final: -0.1543 (tpp) outliers start: 101 outliers final: 40 residues processed: 664 average time/residue: 0.4487 time to fit residues: 494.6122 Evaluate side-chains 561 residues out of total 3713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 513 time to evaluate : 3.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 784 GLN Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1098 ASN Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain E residue 221 GLN Chi-restraints excluded: chain E residue 437 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 318 optimal weight: 30.0000 chunk 26 optimal weight: 0.8980 chunk 350 optimal weight: 20.0000 chunk 219 optimal weight: 0.4980 chunk 137 optimal weight: 0.0040 chunk 4 optimal weight: 2.9990 chunk 197 optimal weight: 0.4980 chunk 70 optimal weight: 0.9980 chunk 347 optimal weight: 50.0000 chunk 178 optimal weight: 0.7980 chunk 420 optimal weight: 0.0980 overall best weight: 0.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN B 762 GLN B 784 GLN B 901 GLN B 935 GLN B 955 ASN B1002 GLN C 125 ASN C 239 GLN C 271 GLN C1002 GLN C1054 GLN D 42 GLN D 277 ASN D 353 HIS D 373 HIS ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 221 GLN E 345 HIS E 388 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4656 r_free = 0.4656 target = 0.242218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.174625 restraints weight = 52850.899| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 3.41 r_work: 0.3583 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 34296 Z= 0.124 Angle : 0.581 13.435 46827 Z= 0.284 Chirality : 0.045 0.431 5335 Planarity : 0.004 0.055 5997 Dihedral : 7.109 96.772 5368 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.13 % Allowed : 12.76 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.55 (0.12), residues: 4196 helix: 0.24 (0.15), residues: 1221 sheet: -0.73 (0.17), residues: 847 loop : -1.95 (0.12), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 477 HIS 0.004 0.001 HIS C1064 PHE 0.024 0.001 PHE C 168 TYR 0.020 0.001 TYR A 170 ARG 0.008 0.000 ARG C 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00564 ( 39) link_NAG-ASN : angle 2.68945 ( 117) hydrogen bonds : bond 0.03946 ( 1210) hydrogen bonds : angle 4.88313 ( 3483) SS BOND : bond 0.00424 ( 37) SS BOND : angle 2.52304 ( 74) covalent geometry : bond 0.00276 (34220) covalent geometry : angle 0.55791 (46636) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 3713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 527 time to evaluate : 3.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.6943 (p) cc_final: 0.5863 (t) REVERT: A 168 PHE cc_start: 0.5505 (OUTLIER) cc_final: 0.5086 (p90) REVERT: A 237 ARG cc_start: 0.7317 (mtp-110) cc_final: 0.6959 (ttm110) REVERT: A 571 ASP cc_start: 0.6577 (t0) cc_final: 0.6212 (t0) REVERT: A 643 PHE cc_start: 0.8146 (t80) cc_final: 0.7849 (t80) REVERT: A 773 GLU cc_start: 0.7571 (tt0) cc_final: 0.7315 (tt0) REVERT: A 776 LYS cc_start: 0.8555 (ttpt) cc_final: 0.8263 (ttmm) REVERT: A 823 PHE cc_start: 0.7879 (t80) cc_final: 0.7644 (t80) REVERT: A 870 ILE cc_start: 0.7983 (pt) cc_final: 0.7665 (mt) REVERT: A 1019 ARG cc_start: 0.8074 (ttp-110) cc_final: 0.7641 (ttp80) REVERT: A 1031 GLU cc_start: 0.8306 (mt-10) cc_final: 0.8020 (mt-10) REVERT: A 1120 THR cc_start: 0.8416 (m) cc_final: 0.8163 (p) REVERT: A 1139 ASP cc_start: 0.7966 (t70) cc_final: 0.7629 (t0) REVERT: B 42 VAL cc_start: 0.8215 (t) cc_final: 0.7899 (t) REVERT: B 318 PHE cc_start: 0.8652 (OUTLIER) cc_final: 0.8276 (p90) REVERT: B 552 LEU cc_start: 0.8045 (mp) cc_final: 0.7835 (mt) REVERT: B 578 ASP cc_start: 0.7047 (t0) cc_final: 0.6760 (t70) REVERT: B 591 SER cc_start: 0.8151 (t) cc_final: 0.7772 (m) REVERT: B 703 ASN cc_start: 0.8403 (t0) cc_final: 0.7908 (t0) REVERT: B 730 SER cc_start: 0.8748 (p) cc_final: 0.8480 (m) REVERT: B 860 VAL cc_start: 0.8754 (OUTLIER) cc_final: 0.8472 (m) REVERT: B 949 GLN cc_start: 0.8198 (tp40) cc_final: 0.7862 (tp40) REVERT: B 1074 ASN cc_start: 0.7295 (m110) cc_final: 0.7048 (m110) REVERT: B 1118 ASP cc_start: 0.7919 (p0) cc_final: 0.7662 (p0) REVERT: C 48 LEU cc_start: 0.8351 (mt) cc_final: 0.8140 (mp) REVERT: C 51 THR cc_start: 0.8541 (OUTLIER) cc_final: 0.8199 (p) REVERT: C 59 PHE cc_start: 0.8219 (m-10) cc_final: 0.8007 (m-80) REVERT: C 99 ASN cc_start: 0.7534 (t0) cc_final: 0.7324 (t0) REVERT: C 138 ASP cc_start: 0.5804 (t0) cc_final: 0.5569 (t0) REVERT: C 190 ARG cc_start: 0.7810 (mtm-85) cc_final: 0.7579 (mtm-85) REVERT: C 281 GLU cc_start: 0.7330 (pp20) cc_final: 0.6968 (pp20) REVERT: C 365 TYR cc_start: 0.7886 (m-80) cc_final: 0.7607 (m-80) REVERT: C 396 TYR cc_start: 0.7120 (m-80) cc_final: 0.6761 (m-10) REVERT: C 436 TRP cc_start: 0.7562 (p90) cc_final: 0.7350 (p90) REVERT: C 543 PHE cc_start: 0.8131 (m-10) cc_final: 0.7889 (m-10) REVERT: C 581 THR cc_start: 0.8253 (t) cc_final: 0.7881 (t) REVERT: C 603 ASN cc_start: 0.7685 (t0) cc_final: 0.7197 (t0) REVERT: C 644 GLN cc_start: 0.8184 (tp40) cc_final: 0.7921 (tp-100) REVERT: C 670 ILE cc_start: 0.8431 (OUTLIER) cc_final: 0.8127 (pt) REVERT: C 671 CYS cc_start: 0.6995 (OUTLIER) cc_final: 0.6756 (p) REVERT: C 884 SER cc_start: 0.8815 (m) cc_final: 0.8568 (m) REVERT: C 949 GLN cc_start: 0.8156 (tp40) cc_final: 0.7786 (tp-100) REVERT: C 969 LYS cc_start: 0.8802 (mtpt) cc_final: 0.8495 (mtpp) REVERT: C 984 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.8012 (tp) REVERT: C 997 ILE cc_start: 0.8538 (mm) cc_final: 0.8292 (mt) REVERT: C 1019 ARG cc_start: 0.7998 (tpt170) cc_final: 0.7776 (tpt170) REVERT: C 1066 THR cc_start: 0.8620 (OUTLIER) cc_final: 0.8416 (p) REVERT: D 527 GLU cc_start: 0.4620 (tt0) cc_final: 0.4405 (tt0) REVERT: E 74 GLU cc_start: 0.5281 (OUTLIER) cc_final: 0.4969 (tp30) REVERT: E 360 MET cc_start: -0.2298 (tpt) cc_final: -0.2664 (tpt) REVERT: E 474 MET cc_start: -0.1067 (tpp) cc_final: -0.1610 (tpp) outliers start: 74 outliers final: 38 residues processed: 575 average time/residue: 0.4185 time to fit residues: 401.1720 Evaluate side-chains 538 residues out of total 3713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 491 time to evaluate : 3.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 955 ASN Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain E residue 221 GLN Chi-restraints excluded: chain E residue 579 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 47 optimal weight: 0.9980 chunk 70 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 234 optimal weight: 0.0270 chunk 413 optimal weight: 50.0000 chunk 74 optimal weight: 0.6980 chunk 192 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 158 optimal weight: 0.5980 chunk 212 optimal weight: 7.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN A1135 ASN B 66 HIS ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 532 ASN B 784 GLN C1002 GLN ** E 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 221 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.241473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.172663 restraints weight = 52629.195| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 3.01 r_work: 0.3573 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3393 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 34296 Z= 0.142 Angle : 0.576 16.561 46827 Z= 0.279 Chirality : 0.045 0.447 5335 Planarity : 0.004 0.045 5997 Dihedral : 6.685 98.492 5368 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.84 % Allowed : 13.62 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.27 (0.12), residues: 4196 helix: 0.51 (0.15), residues: 1253 sheet: -0.52 (0.17), residues: 830 loop : -1.86 (0.12), residues: 2113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 477 HIS 0.006 0.001 HIS A1064 PHE 0.029 0.001 PHE C 168 TYR 0.018 0.001 TYR C 170 ARG 0.009 0.000 ARG C 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00594 ( 39) link_NAG-ASN : angle 2.91469 ( 117) hydrogen bonds : bond 0.03738 ( 1210) hydrogen bonds : angle 4.69789 ( 3483) SS BOND : bond 0.00483 ( 37) SS BOND : angle 2.49458 ( 74) covalent geometry : bond 0.00328 (34220) covalent geometry : angle 0.54946 (46636) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 3713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 516 time to evaluate : 3.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.7365 (p) cc_final: 0.6115 (t) REVERT: A 168 PHE cc_start: 0.6275 (OUTLIER) cc_final: 0.5700 (p90) REVERT: A 204 TYR cc_start: 0.8677 (m-80) cc_final: 0.8213 (m-80) REVERT: A 229 LEU cc_start: 0.7623 (mt) cc_final: 0.7385 (mm) REVERT: A 237 ARG cc_start: 0.7715 (mtp-110) cc_final: 0.7347 (ttm110) REVERT: A 571 ASP cc_start: 0.6913 (t0) cc_final: 0.6508 (t0) REVERT: A 643 PHE cc_start: 0.8198 (t80) cc_final: 0.7808 (t80) REVERT: A 776 LYS cc_start: 0.8748 (ttpt) cc_final: 0.8498 (ttmm) REVERT: A 1019 ARG cc_start: 0.8290 (ttp-110) cc_final: 0.8064 (ttp80) REVERT: A 1139 ASP cc_start: 0.8178 (t70) cc_final: 0.7903 (t0) REVERT: B 318 PHE cc_start: 0.8708 (OUTLIER) cc_final: 0.8449 (p90) REVERT: B 730 SER cc_start: 0.8806 (p) cc_final: 0.8534 (m) REVERT: B 860 VAL cc_start: 0.8834 (OUTLIER) cc_final: 0.8594 (p) REVERT: B 949 GLN cc_start: 0.8425 (tp40) cc_final: 0.8152 (tp40) REVERT: B 957 GLN cc_start: 0.7849 (tm-30) cc_final: 0.7396 (tm-30) REVERT: B 977 LEU cc_start: 0.8175 (mt) cc_final: 0.7925 (mt) REVERT: B 1074 ASN cc_start: 0.7683 (m110) cc_final: 0.7430 (m110) REVERT: B 1118 ASP cc_start: 0.8180 (p0) cc_final: 0.7913 (p0) REVERT: C 51 THR cc_start: 0.8631 (OUTLIER) cc_final: 0.8278 (p) REVERT: C 99 ASN cc_start: 0.7717 (t0) cc_final: 0.7441 (t0) REVERT: C 190 ARG cc_start: 0.8171 (mtm-85) cc_final: 0.7855 (mtm-85) REVERT: C 281 GLU cc_start: 0.7572 (pp20) cc_final: 0.7243 (pp20) REVERT: C 351 TYR cc_start: 0.7928 (p90) cc_final: 0.7610 (p90) REVERT: C 365 TYR cc_start: 0.7897 (m-80) cc_final: 0.7617 (m-80) REVERT: C 396 TYR cc_start: 0.7601 (m-80) cc_final: 0.7328 (m-10) REVERT: C 400 PHE cc_start: 0.7992 (p90) cc_final: 0.7550 (p90) REVERT: C 436 TRP cc_start: 0.7813 (p90) cc_final: 0.7566 (p90) REVERT: C 543 PHE cc_start: 0.8405 (m-10) cc_final: 0.8111 (m-10) REVERT: C 603 ASN cc_start: 0.7876 (t0) cc_final: 0.7418 (t0) REVERT: C 608 VAL cc_start: 0.8836 (OUTLIER) cc_final: 0.8515 (p) REVERT: C 644 GLN cc_start: 0.8336 (tp40) cc_final: 0.8071 (tp-100) REVERT: C 670 ILE cc_start: 0.8527 (OUTLIER) cc_final: 0.8260 (pt) REVERT: C 671 CYS cc_start: 0.7558 (OUTLIER) cc_final: 0.7300 (p) REVERT: C 722 VAL cc_start: 0.8955 (m) cc_final: 0.8670 (t) REVERT: C 742 ILE cc_start: 0.8110 (OUTLIER) cc_final: 0.7841 (mt) REVERT: C 765 ARG cc_start: 0.8340 (ttm-80) cc_final: 0.7927 (ttm-80) REVERT: C 825 LYS cc_start: 0.8654 (ttpp) cc_final: 0.8398 (ttpp) REVERT: C 884 SER cc_start: 0.8882 (m) cc_final: 0.8636 (m) REVERT: C 969 LYS cc_start: 0.8856 (mtpt) cc_final: 0.8560 (mtpp) REVERT: C 984 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8127 (tp) REVERT: C 997 ILE cc_start: 0.8684 (mm) cc_final: 0.8453 (mt) REVERT: C 1066 THR cc_start: 0.8699 (OUTLIER) cc_final: 0.8480 (p) REVERT: E 74 GLU cc_start: 0.5290 (OUTLIER) cc_final: 0.5078 (mm-30) REVERT: E 360 MET cc_start: -0.1739 (tpt) cc_final: -0.2650 (tpt) REVERT: E 474 MET cc_start: -0.1074 (tpp) cc_final: -0.1613 (tpp) outliers start: 99 outliers final: 54 residues processed: 576 average time/residue: 0.4235 time to fit residues: 405.2285 Evaluate side-chains 560 residues out of total 3713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 495 time to evaluate : 3.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1135 ASN Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 474 MET Chi-restraints excluded: chain E residue 74 GLU Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 221 GLN Chi-restraints excluded: chain E residue 513 ILE Chi-restraints excluded: chain E residue 557 MET Chi-restraints excluded: chain E residue 579 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 294 optimal weight: 0.5980 chunk 325 optimal weight: 20.0000 chunk 37 optimal weight: 20.0000 chunk 343 optimal weight: 20.0000 chunk 173 optimal weight: 0.9990 chunk 385 optimal weight: 0.0470 chunk 110 optimal weight: 0.0670 chunk 375 optimal weight: 40.0000 chunk 68 optimal weight: 0.9990 chunk 279 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 overall best weight: 0.5420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A 955 ASN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 532 ASN B 784 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 978 ASN C 613 GLN C 949 GLN C1002 GLN C1010 GLN E 96 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4646 r_free = 0.4646 target = 0.241413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.173431 restraints weight = 52595.434| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 3.32 r_work: 0.3560 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 34296 Z= 0.133 Angle : 0.568 15.939 46827 Z= 0.275 Chirality : 0.045 0.469 5335 Planarity : 0.004 0.041 5997 Dihedral : 6.360 97.074 5368 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.59 % Allowed : 14.43 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.05 (0.12), residues: 4196 helix: 0.73 (0.15), residues: 1257 sheet: -0.45 (0.17), residues: 828 loop : -1.72 (0.12), residues: 2111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 477 HIS 0.005 0.001 HIS A1064 PHE 0.028 0.001 PHE A 92 TYR 0.015 0.001 TYR C 170 ARG 0.008 0.000 ARG C 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00592 ( 39) link_NAG-ASN : angle 2.89393 ( 117) hydrogen bonds : bond 0.03586 ( 1210) hydrogen bonds : angle 4.58518 ( 3483) SS BOND : bond 0.00480 ( 37) SS BOND : angle 2.33532 ( 74) covalent geometry : bond 0.00306 (34220) covalent geometry : angle 0.54295 (46636) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 3713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 515 time to evaluate : 3.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.7153 (p) cc_final: 0.6018 (t) REVERT: A 168 PHE cc_start: 0.5833 (OUTLIER) cc_final: 0.5311 (p90) REVERT: A 204 TYR cc_start: 0.8607 (m-80) cc_final: 0.8106 (m-80) REVERT: A 571 ASP cc_start: 0.6670 (t0) cc_final: 0.6284 (t0) REVERT: A 643 PHE cc_start: 0.8053 (t80) cc_final: 0.7727 (t80) REVERT: A 722 VAL cc_start: 0.8660 (m) cc_final: 0.8454 (t) REVERT: A 776 LYS cc_start: 0.8618 (ttpt) cc_final: 0.8344 (ttmm) REVERT: A 811 LYS cc_start: 0.8346 (mmtp) cc_final: 0.7928 (mttm) REVERT: A 1019 ARG cc_start: 0.8004 (ttp-110) cc_final: 0.7733 (ttp80) REVERT: A 1139 ASP cc_start: 0.7936 (t70) cc_final: 0.7632 (t0) REVERT: B 194 PHE cc_start: 0.6165 (m-80) cc_final: 0.5916 (m-80) REVERT: B 615 VAL cc_start: 0.8943 (t) cc_final: 0.8704 (m) REVERT: B 703 ASN cc_start: 0.8360 (t0) cc_final: 0.7993 (t0) REVERT: B 708 SER cc_start: 0.7976 (t) cc_final: 0.7639 (m) REVERT: B 821 LEU cc_start: 0.8430 (tp) cc_final: 0.8183 (tt) REVERT: B 860 VAL cc_start: 0.8755 (OUTLIER) cc_final: 0.8532 (p) REVERT: B 949 GLN cc_start: 0.8238 (tp40) cc_final: 0.7926 (tp40) REVERT: B 1074 ASN cc_start: 0.7307 (m110) cc_final: 0.7072 (m110) REVERT: B 1105 THR cc_start: 0.8428 (p) cc_final: 0.8209 (p) REVERT: B 1118 ASP cc_start: 0.7912 (p0) cc_final: 0.7646 (p0) REVERT: C 51 THR cc_start: 0.8502 (OUTLIER) cc_final: 0.8127 (p) REVERT: C 99 ASN cc_start: 0.7553 (t0) cc_final: 0.7296 (t0) REVERT: C 190 ARG cc_start: 0.7901 (mtm-85) cc_final: 0.7645 (mtm-85) REVERT: C 351 TYR cc_start: 0.7733 (p90) cc_final: 0.7474 (p90) REVERT: C 355 ARG cc_start: 0.7910 (mtt180) cc_final: 0.7541 (mmm160) REVERT: C 365 TYR cc_start: 0.7815 (m-80) cc_final: 0.7582 (m-80) REVERT: C 396 TYR cc_start: 0.7436 (m-80) cc_final: 0.7121 (m-10) REVERT: C 400 PHE cc_start: 0.7732 (p90) cc_final: 0.7385 (p90) REVERT: C 436 TRP cc_start: 0.7622 (p90) cc_final: 0.7384 (p90) REVERT: C 543 PHE cc_start: 0.8225 (m-10) cc_final: 0.7625 (m-10) REVERT: C 603 ASN cc_start: 0.7645 (t0) cc_final: 0.7176 (t0) REVERT: C 608 VAL cc_start: 0.8806 (OUTLIER) cc_final: 0.8492 (p) REVERT: C 670 ILE cc_start: 0.8461 (OUTLIER) cc_final: 0.8165 (pt) REVERT: C 671 CYS cc_start: 0.6921 (OUTLIER) cc_final: 0.6656 (p) REVERT: C 742 ILE cc_start: 0.8011 (OUTLIER) cc_final: 0.7741 (mt) REVERT: C 804 GLN cc_start: 0.8358 (mm-40) cc_final: 0.7721 (mm-40) REVERT: C 825 LYS cc_start: 0.8550 (ttpp) cc_final: 0.8283 (ttpp) REVERT: C 884 SER cc_start: 0.8803 (m) cc_final: 0.8524 (m) REVERT: C 969 LYS cc_start: 0.8740 (mtpt) cc_final: 0.8443 (mtpp) REVERT: C 984 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.8061 (tp) REVERT: C 997 ILE cc_start: 0.8512 (mm) cc_final: 0.8293 (mt) REVERT: C 1066 THR cc_start: 0.8586 (OUTLIER) cc_final: 0.8371 (p) REVERT: D 240 LEU cc_start: 0.2205 (tp) cc_final: 0.1966 (mp) REVERT: D 297 MET cc_start: -0.1995 (mtt) cc_final: -0.2350 (mtt) REVERT: D 298 MET cc_start: 0.3121 (mpp) cc_final: 0.2459 (mmt) REVERT: D 332 MET cc_start: -0.5508 (ttm) cc_final: -0.5947 (ttt) REVERT: E 474 MET cc_start: -0.1128 (tpp) cc_final: -0.1676 (tpp) outliers start: 90 outliers final: 59 residues processed: 570 average time/residue: 0.4154 time to fit residues: 391.4834 Evaluate side-chains 564 residues out of total 3713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 496 time to evaluate : 3.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 950 ASP Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1098 ASN Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 460 ARG Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 513 ILE Chi-restraints excluded: chain E residue 557 MET Chi-restraints excluded: chain E residue 560 LEU Chi-restraints excluded: chain E residue 579 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 58 optimal weight: 0.6980 chunk 205 optimal weight: 0.9990 chunk 128 optimal weight: 0.7980 chunk 404 optimal weight: 2.9990 chunk 262 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 64 optimal weight: 0.4980 chunk 373 optimal weight: 50.0000 chunk 120 optimal weight: 0.4980 chunk 11 optimal weight: 1.9990 chunk 115 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 784 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN B1058 HIS C 613 GLN C 949 GLN C1002 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4643 r_free = 0.4643 target = 0.244564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.175271 restraints weight = 51210.252| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 3.55 r_work: 0.3527 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 34296 Z= 0.146 Angle : 0.570 14.784 46827 Z= 0.277 Chirality : 0.045 0.479 5335 Planarity : 0.004 0.049 5997 Dihedral : 6.139 94.131 5368 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.96 % Allowed : 14.63 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.93 (0.13), residues: 4196 helix: 0.85 (0.15), residues: 1257 sheet: -0.35 (0.17), residues: 802 loop : -1.67 (0.12), residues: 2137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 477 HIS 0.006 0.001 HIS A1064 PHE 0.039 0.001 PHE B 643 TYR 0.019 0.001 TYR A 170 ARG 0.010 0.000 ARG C 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00538 ( 39) link_NAG-ASN : angle 2.90671 ( 117) hydrogen bonds : bond 0.03642 ( 1210) hydrogen bonds : angle 4.53672 ( 3483) SS BOND : bond 0.00403 ( 37) SS BOND : angle 2.34269 ( 74) covalent geometry : bond 0.00338 (34220) covalent geometry : angle 0.54463 (46636) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8392 Ramachandran restraints generated. 4196 Oldfield, 0 Emsley, 4196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 3713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 520 time to evaluate : 3.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.7241 (p) cc_final: 0.6103 (t) REVERT: A 168 PHE cc_start: 0.6126 (OUTLIER) cc_final: 0.5530 (p90) REVERT: A 204 TYR cc_start: 0.8602 (m-80) cc_final: 0.8087 (m-80) REVERT: A 239 GLN cc_start: 0.6812 (OUTLIER) cc_final: 0.6194 (tt0) REVERT: A 571 ASP cc_start: 0.6808 (t0) cc_final: 0.6391 (t0) REVERT: A 643 PHE cc_start: 0.8043 (t80) cc_final: 0.7689 (t80) REVERT: A 776 LYS cc_start: 0.8670 (ttpt) cc_final: 0.8401 (ttmm) REVERT: A 1019 ARG cc_start: 0.8003 (ttp-110) cc_final: 0.7781 (ttp80) REVERT: A 1139 ASP cc_start: 0.7990 (t70) cc_final: 0.7744 (t0) REVERT: B 194 PHE cc_start: 0.6439 (m-80) cc_final: 0.6148 (m-80) REVERT: B 615 VAL cc_start: 0.8978 (t) cc_final: 0.8723 (m) REVERT: B 703 ASN cc_start: 0.8418 (t0) cc_final: 0.7934 (t0) REVERT: B 708 SER cc_start: 0.7987 (t) cc_final: 0.7656 (m) REVERT: B 821 LEU cc_start: 0.8478 (tp) cc_final: 0.8228 (tt) REVERT: B 860 VAL cc_start: 0.8790 (OUTLIER) cc_final: 0.8549 (p) REVERT: B 949 GLN cc_start: 0.8320 (tp40) cc_final: 0.7999 (tp40) REVERT: B 957 GLN cc_start: 0.7739 (tm-30) cc_final: 0.7341 (tm-30) REVERT: B 977 LEU cc_start: 0.8208 (mp) cc_final: 0.7756 (mt) REVERT: B 1074 ASN cc_start: 0.7365 (m110) cc_final: 0.7121 (m110) REVERT: B 1105 THR cc_start: 0.8393 (p) cc_final: 0.8189 (p) REVERT: B 1118 ASP cc_start: 0.7925 (p0) cc_final: 0.7670 (p0) REVERT: C 51 THR cc_start: 0.8509 (OUTLIER) cc_final: 0.8132 (p) REVERT: C 99 ASN cc_start: 0.7605 (t0) cc_final: 0.7293 (t0) REVERT: C 190 ARG cc_start: 0.7965 (mtm-85) cc_final: 0.7676 (mtm-85) REVERT: C 342 PHE cc_start: 0.8425 (t80) cc_final: 0.7979 (t80) REVERT: C 351 TYR cc_start: 0.8063 (p90) cc_final: 0.7619 (p90) REVERT: C 355 ARG cc_start: 0.8066 (mtt180) cc_final: 0.7587 (mmm160) REVERT: C 365 TYR cc_start: 0.7780 (m-80) cc_final: 0.7509 (m-80) REVERT: C 396 TYR cc_start: 0.7624 (m-80) cc_final: 0.7230 (m-10) REVERT: C 400 PHE cc_start: 0.7892 (p90) cc_final: 0.7382 (p90) REVERT: C 436 TRP cc_start: 0.7707 (p90) cc_final: 0.7359 (p90) REVERT: C 543 PHE cc_start: 0.8259 (m-10) cc_final: 0.7565 (m-10) REVERT: C 603 ASN cc_start: 0.7538 (t0) cc_final: 0.7079 (t0) REVERT: C 608 VAL cc_start: 0.8800 (OUTLIER) cc_final: 0.8482 (p) REVERT: C 670 ILE cc_start: 0.8477 (OUTLIER) cc_final: 0.8191 (pt) REVERT: C 671 CYS cc_start: 0.7077 (OUTLIER) cc_final: 0.6814 (p) REVERT: C 765 ARG cc_start: 0.8012 (ttm-80) cc_final: 0.7761 (ttm-80) REVERT: C 804 GLN cc_start: 0.8395 (mm-40) cc_final: 0.7688 (mm-40) REVERT: C 825 LYS cc_start: 0.8555 (ttpp) cc_final: 0.8277 (ttpp) REVERT: C 884 SER cc_start: 0.8797 (m) cc_final: 0.8526 (m) REVERT: C 969 LYS cc_start: 0.8752 (mtpt) cc_final: 0.8383 (mtpp) REVERT: C 984 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8093 (tp) REVERT: C 997 ILE cc_start: 0.8539 (mm) cc_final: 0.8310 (mt) REVERT: C 1066 THR cc_start: 0.8631 (OUTLIER) cc_final: 0.8395 (p) REVERT: D 298 MET cc_start: 0.3186 (mpp) cc_final: 0.2407 (mmt) REVERT: D 332 MET cc_start: -0.4838 (ttm) cc_final: -0.5871 (ttt) REVERT: E 37 GLU cc_start: 0.6161 (tt0) cc_final: 0.5599 (tm-30) REVERT: E 150 GLU cc_start: 0.2588 (tp30) cc_final: 0.2264 (tp30) REVERT: E 474 MET cc_start: -0.0961 (tpp) cc_final: -0.1534 (tpp) REVERT: E 544 ILE cc_start: 0.1170 (OUTLIER) cc_final: 0.0661 (mm) outliers start: 103 outliers final: 72 residues processed: 585 average time/residue: 0.4253 time to fit residues: 411.7172 Evaluate side-chains 591 residues out of total 3713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 509 time to evaluate : 3.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 693 ILE Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 317 ASN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 742 ILE Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 596 SER Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 671 CYS Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1098 ASN Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 580 ASP Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 361 CYS Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 557 MET Chi-restraints excluded: chain E residue 560 LEU Chi-restraints excluded: chain E residue 579 MET Chi-restraints excluded: chain E residue 581 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.7869 > 50: distance: 10 - 19: 11.415 distance: 19 - 20: 8.086 distance: 20 - 21: 11.727 distance: 20 - 23: 25.245 distance: 21 - 22: 14.566 distance: 21 - 29: 15.723 distance: 23 - 24: 19.628 distance: 24 - 25: 25.375 distance: 24 - 26: 21.037 distance: 25 - 27: 16.018 distance: 26 - 28: 14.806 distance: 27 - 28: 33.686 distance: 29 - 30: 16.200 distance: 30 - 31: 9.722 distance: 30 - 33: 9.488 distance: 31 - 32: 5.886 distance: 31 - 36: 12.502 distance: 33 - 34: 3.440 distance: 33 - 35: 4.556 distance: 36 - 37: 3.752 distance: 37 - 38: 5.462 distance: 37 - 40: 6.521 distance: 38 - 39: 5.208 distance: 41 - 42: 22.959 distance: 42 - 43: 13.698 distance: 42 - 45: 22.489 distance: 43 - 44: 14.505 distance: 43 - 49: 8.583 distance: 45 - 46: 8.224 distance: 46 - 47: 15.006 distance: 46 - 48: 6.000 distance: 49 - 50: 6.420 distance: 50 - 51: 22.450 distance: 50 - 53: 18.207 distance: 51 - 52: 23.058 distance: 51 - 57: 16.449 distance: 53 - 54: 21.556 distance: 54 - 55: 11.819 distance: 54 - 56: 13.136 distance: 57 - 58: 21.286 distance: 57 - 63: 32.374 distance: 58 - 59: 24.146 distance: 58 - 61: 10.734 distance: 59 - 60: 25.233 distance: 59 - 64: 4.738 distance: 61 - 62: 12.959 distance: 62 - 63: 20.123 distance: 64 - 65: 19.910 distance: 65 - 66: 41.029 distance: 65 - 68: 33.387 distance: 66 - 67: 69.362 distance: 68 - 69: 4.380 distance: 68 - 70: 43.369 distance: 71 - 72: 33.796 distance: 71 - 148: 36.412 distance: 72 - 73: 42.641 distance: 72 - 75: 28.592 distance: 73 - 74: 16.080 distance: 73 - 79: 25.446 distance: 74 - 145: 26.720 distance: 76 - 77: 55.362 distance: 76 - 78: 24.877 distance: 79 - 80: 24.138 distance: 79 - 85: 16.742 distance: 80 - 81: 3.492 distance: 80 - 83: 17.877 distance: 81 - 82: 15.506 distance: 81 - 86: 35.021 distance: 83 - 84: 43.256 distance: 84 - 85: 11.571 distance: 86 - 87: 23.192 distance: 87 - 88: 13.896 distance: 87 - 90: 10.173 distance: 88 - 89: 6.411 distance: 88 - 97: 25.286 distance: 90 - 91: 15.224 distance: 91 - 92: 8.769 distance: 92 - 94: 25.920 distance: 93 - 95: 12.097 distance: 94 - 96: 21.717 distance: 95 - 96: 17.520