Starting phenix.real_space_refine on Tue Aug 26 06:31:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xo7_33339/08_2025/7xo7_33339.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xo7_33339/08_2025/7xo7_33339.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xo7_33339/08_2025/7xo7_33339.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xo7_33339/08_2025/7xo7_33339.map" model { file = "/net/cci-nas-00/data/ceres_data/7xo7_33339/08_2025/7xo7_33339.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xo7_33339/08_2025/7xo7_33339.cif" } resolution = 3.38 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.021 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 S 163 5.16 5 Cl 2 4.86 5 C 21870 2.51 5 N 5627 2.21 5 O 6545 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 99 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34209 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 8001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 8001 Classifications: {'peptide': 1026} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 56, 'TRANS': 969} Chain breaks: 7 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 7943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 7943 Classifications: {'peptide': 1025} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 55, 'TRANS': 969} Chain breaks: 8 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 4, 'GLU:plan': 2, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 53 Chain: "C" Number of atoms: 8001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 8001 Classifications: {'peptide': 1026} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 56, 'TRANS': 969} Chain breaks: 7 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "E" Number of atoms: 4857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4857 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 27, 'TRANS': 567} Chain: "F" Number of atoms: 4857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4857 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 27, 'TRANS': 567} Chain: "A" 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: "B" 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: "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: "E" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 44 Unusual residues: {' CL': 1, ' ZN': 1, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 44 Unusual residues: {' CL': 1, ' ZN': 1, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 8.14, per 1000 atoms: 0.24 Number of scatterers: 34209 At special positions: 0 Unit cell: (161.504, 138.432, 241.432, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 Cl 2 17.00 S 163 16.00 O 6545 8.00 N 5627 7.00 C 21870 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=32, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 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 B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 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 A1098 " " NAG A1303 " - " ASN A 801 " " NAG A1304 " - " ASN A 709 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 603 " " NAG A1308 " - " ASN A1134 " " NAG A1309 " - " ASN A 61 " " NAG A1310 " - " ASN A 122 " " NAG A1311 " - " ASN A 331 " " NAG B1301 " - " ASN B1074 " " NAG B1302 " - " ASN B1098 " " NAG B1303 " - " ASN B 801 " " NAG B1304 " - " ASN B 709 " " NAG B1305 " - " ASN B 657 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 603 " " NAG B1308 " - " ASN B1134 " " NAG B1309 " - " ASN B 61 " " NAG B1310 " - " ASN B 122 " " NAG B1311 " - " ASN B 331 " " NAG C1301 " - " ASN C1074 " " NAG C1302 " - " ASN C1098 " " NAG C1303 " - " ASN C 801 " " NAG C1304 " - " ASN C 709 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 603 " " NAG C1308 " - " ASN C1134 " " NAG C1309 " - " ASN C 61 " " NAG C1310 " - " ASN C 122 " " NAG C1311 " - " ASN C 331 " " NAG E 903 " - " ASN E 322 " " NAG E 904 " - " ASN E 546 " " NAG E 905 " - " ASN E 90 " " NAG F 903 " - " ASN F 322 " " NAG F 904 " - " ASN F 546 " " NAG F 905 " - " ASN F 90 " Time building additional restraints: 3.07 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E 902 " pdb="ZN ZN E 902 " - pdb=" NE2 HIS E 374 " pdb=" ZN F 902 " pdb="ZN ZN F 902 " - pdb=" NE2 HIS F 374 " 8426 Ramachandran restraints generated. 4213 Oldfield, 0 Emsley, 4213 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8016 Finding SS restraints... Secondary structure from input PDB file: 125 helices and 51 sheets defined 35.9% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.672A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 370 removed outlier: 3.677A pdb=" N TYR A 369 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 390 removed outlier: 3.708A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.515A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 778 removed outlier: 3.861A pdb=" N LYS A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ARG A 765 " --> pdb=" O THR A 761 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 868 through 884 Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.507A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.785A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.531A pdb=" N ILE A 923 " --> pdb=" O ASN A 919 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (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 965 removed outlier: 4.137A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU A 962 " --> pdb=" O ALA A 958 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N VAL A 963 " --> pdb=" O LEU A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.780A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER A 982 " --> pdb=" O ASN A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 988 Processing helix chain 'A' and resid 989 through 1033 removed outlier: 3.514A pdb=" N THR A1006 " --> pdb=" O GLN A1002 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 364 through 368 removed outlier: 3.933A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.661A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 746 through 757 removed outlier: 3.591A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TYR B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLY B 757 " --> pdb=" O LEU B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 778 removed outlier: 4.011A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 868 through 884 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.537A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.772A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.565A pdb=" N ILE B 923 " --> pdb=" O ASN B 919 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 965 removed outlier: 4.194A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.735A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 988 Processing helix chain 'B' and resid 989 through 1033 removed outlier: 3.538A pdb=" N ILE B 993 " --> pdb=" O ALA B 989 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR B1007 " --> pdb=" O SER B1003 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.982A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 370 removed outlier: 3.703A pdb=" N TYR C 369 " --> pdb=" O SER C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 390 removed outlier: 3.568A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.513A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.598A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 759 through 778 removed outlier: 3.758A pdb=" N LYS C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ARG C 765 " --> pdb=" O THR C 761 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.612A pdb=" N ALA C 871 " --> pdb=" O ASP C 867 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.762A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 940 removed outlier: 3.924A pdb=" N ILE C 923 " --> pdb=" O ASN C 919 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER C 940 " --> pdb=" O ASP C 936 " (cutoff:3.500A) Processing helix chain 'C' and resid 941 through 947 removed outlier: 3.684A pdb=" N LEU C 945 " --> pdb=" O PRO C 942 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY C 946 " --> pdb=" O SER C 943 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LYS C 947 " --> pdb=" O ALA C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 949 through 957 Processing helix chain 'C' and resid 960 through 965 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 976 through 984 removed outlier: 3.771A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER C 982 " --> pdb=" O ASN C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 5.235A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing helix chain 'E' and resid 20 through 53 removed outlier: 3.565A pdb=" N GLN E 24 " --> pdb=" O THR E 20 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP E 38 " --> pdb=" O HIS E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 81 removed outlier: 3.547A pdb=" N ALA E 65 " --> pdb=" O ASN E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 101 Processing helix chain 'E' and resid 103 through 108 removed outlier: 3.918A pdb=" N SER E 106 " --> pdb=" O ASN E 103 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL E 107 " --> pdb=" O GLY E 104 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU E 108 " --> pdb=" O SER E 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 103 through 108' Processing helix chain 'E' and resid 109 through 129 removed outlier: 3.668A pdb=" N SER E 124 " --> pdb=" O LEU E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 155 Processing helix chain 'E' and resid 157 through 194 removed outlier: 3.525A pdb=" N TRP E 168 " --> pdb=" O ALA E 164 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG E 169 " --> pdb=" O TRP E 165 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LYS E 174 " --> pdb=" O SER E 170 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLN E 175 " --> pdb=" O GLU E 171 " (cutoff:3.500A) Proline residue: E 178 - end of helix removed outlier: 3.794A pdb=" N GLU E 182 " --> pdb=" O PRO E 178 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL E 185 " --> pdb=" O GLU E 181 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 204 removed outlier: 3.532A pdb=" N TRP E 203 " --> pdb=" O TYR E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 218 through 252 removed outlier: 3.860A pdb=" N LEU E 222 " --> pdb=" O SER E 218 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ILE E 223 " --> pdb=" O ARG E 219 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU E 224 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLU E 232 " --> pdb=" O HIS E 228 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE E 233 " --> pdb=" O THR E 229 " (cutoff:3.500A) Proline residue: E 235 - end of helix removed outlier: 3.547A pdb=" N HIS E 239 " --> pdb=" O PRO E 235 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N ASN E 250 " --> pdb=" O ALA E 246 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA E 251 " --> pdb=" O LYS E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 267 No H-bonds generated for 'chain 'E' and resid 265 through 267' Processing helix chain 'E' and resid 275 through 279 Processing helix chain 'E' and resid 293 through 300 removed outlier: 3.699A pdb=" N VAL E 298 " --> pdb=" O THR E 294 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP E 299 " --> pdb=" O ASP E 295 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLN E 300 " --> pdb=" O ALA E 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 319 removed outlier: 3.531A pdb=" N VAL E 318 " --> pdb=" O PHE E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 331 removed outlier: 4.198A pdb=" N TRP E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU E 329 " --> pdb=" O GLN E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 385 removed outlier: 3.523A pdb=" N HIS E 373 " --> pdb=" O PHE E 369 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR E 385 " --> pdb=" O TYR E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 386 through 388 No H-bonds generated for 'chain 'E' and resid 386 through 388' Processing helix chain 'E' and resid 389 through 393 Processing helix chain 'E' and resid 399 through 413 removed outlier: 3.585A pdb=" N VAL E 404 " --> pdb=" O PHE E 400 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N SER E 409 " --> pdb=" O GLY E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 421 Processing helix chain 'E' and resid 431 through 444 Processing helix chain 'E' and resid 449 through 466 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 499 through 502 Processing helix chain 'E' and resid 503 through 508 Processing helix chain 'E' and resid 513 through 533 removed outlier: 3.790A pdb=" N THR E 519 " --> pdb=" O TYR E 515 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N PHE E 523 " --> pdb=" O THR E 519 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN E 531 " --> pdb=" O GLU E 527 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA E 532 " --> pdb=" O ALA E 528 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 542 Processing helix chain 'E' and resid 547 through 561 removed outlier: 3.893A pdb=" N MET E 557 " --> pdb=" O LYS E 553 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU E 560 " --> pdb=" O ASN E 556 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY E 561 " --> pdb=" O MET E 557 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 574 removed outlier: 3.508A pdb=" N ASN E 572 " --> pdb=" O LEU E 568 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL E 573 " --> pdb=" O ALA E 569 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 588 removed outlier: 3.670A pdb=" N PHE E 588 " --> pdb=" O LEU E 584 " (cutoff:3.500A) Processing helix chain 'E' and resid 588 through 599 Processing helix chain 'F' and resid 20 through 53 removed outlier: 3.562A pdb=" N GLN F 24 " --> pdb=" O THR F 20 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP F 38 " --> pdb=" O HIS F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 81 removed outlier: 3.553A pdb=" N ALA F 65 " --> pdb=" O ASN F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 99 Processing helix chain 'F' and resid 103 through 108 removed outlier: 3.919A pdb=" N SER F 106 " --> pdb=" O ASN F 103 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL F 107 " --> pdb=" O GLY F 104 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU F 108 " --> pdb=" O SER F 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 103 through 108' Processing helix chain 'F' and resid 109 through 129 removed outlier: 3.665A pdb=" N SER F 124 " --> pdb=" O LEU F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 155 Processing helix chain 'F' and resid 157 through 194 removed outlier: 3.521A pdb=" N TRP F 168 " --> pdb=" O ALA F 164 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG F 169 " --> pdb=" O TRP F 165 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LYS F 174 " --> pdb=" O SER F 170 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLN F 175 " --> pdb=" O GLU F 171 " (cutoff:3.500A) Proline residue: F 178 - end of helix removed outlier: 3.802A pdb=" N GLU F 182 " --> pdb=" O PRO F 178 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL F 185 " --> pdb=" O GLU F 181 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN F 194 " --> pdb=" O MET F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 204 removed outlier: 3.538A pdb=" N TRP F 203 " --> pdb=" O TYR F 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 218 through 252 removed outlier: 3.863A pdb=" N LEU F 222 " --> pdb=" O SER F 218 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ILE F 223 " --> pdb=" O ARG F 219 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU F 224 " --> pdb=" O GLY F 220 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLU F 232 " --> pdb=" O HIS F 228 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE F 233 " --> pdb=" O THR F 229 " (cutoff:3.500A) Proline residue: F 235 - end of helix removed outlier: 3.566A pdb=" N HIS F 239 " --> pdb=" O PRO F 235 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET F 249 " --> pdb=" O ARG F 245 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ASN F 250 " --> pdb=" O ALA F 246 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ALA F 251 " --> pdb=" O LYS F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 267 No H-bonds generated for 'chain 'F' and resid 265 through 267' Processing helix chain 'F' and resid 275 through 279 Processing helix chain 'F' and resid 293 through 300 removed outlier: 3.721A pdb=" N VAL F 298 " --> pdb=" O THR F 294 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP F 299 " --> pdb=" O ASP F 295 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLN F 300 " --> pdb=" O ALA F 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 319 removed outlier: 3.520A pdb=" N VAL F 318 " --> pdb=" O PHE F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 331 removed outlier: 4.175A pdb=" N TRP F 328 " --> pdb=" O THR F 324 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU F 329 " --> pdb=" O GLN F 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 385 removed outlier: 3.509A pdb=" N HIS F 373 " --> pdb=" O PHE F 369 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR F 385 " --> pdb=" O TYR F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 386 through 388 No H-bonds generated for 'chain 'F' and resid 386 through 388' Processing helix chain 'F' and resid 389 through 393 Processing helix chain 'F' and resid 399 through 413 removed outlier: 3.596A pdb=" N VAL F 404 " --> pdb=" O PHE F 400 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY F 405 " --> pdb=" O HIS F 401 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N MET F 408 " --> pdb=" O VAL F 404 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N SER F 409 " --> pdb=" O GLY F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 421 Processing helix chain 'F' and resid 431 through 444 Processing helix chain 'F' and resid 449 through 466 Processing helix chain 'F' and resid 469 through 471 No H-bonds generated for 'chain 'F' and resid 469 through 471' Processing helix chain 'F' and resid 472 through 484 Processing helix chain 'F' and resid 499 through 502 Processing helix chain 'F' and resid 503 through 508 Processing helix chain 'F' and resid 513 through 533 removed outlier: 3.793A pdb=" N THR F 519 " --> pdb=" O TYR F 515 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N PHE F 523 " --> pdb=" O THR F 519 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLN F 531 " --> pdb=" O GLU F 527 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA F 532 " --> pdb=" O ALA F 528 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 542 Processing helix chain 'F' and resid 547 through 561 removed outlier: 3.883A pdb=" N MET F 557 " --> pdb=" O LYS F 553 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU F 560 " --> pdb=" O ASN F 556 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY F 561 " --> pdb=" O MET F 557 " (cutoff:3.500A) Processing helix chain 'F' and resid 565 through 574 removed outlier: 3.523A pdb=" N ASN F 572 " --> pdb=" O LEU F 568 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL F 573 " --> pdb=" O ALA F 569 " (cutoff:3.500A) Processing helix chain 'F' and resid 581 through 588 removed outlier: 3.511A pdb=" N LEU F 585 " --> pdb=" O VAL F 581 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE F 588 " --> pdb=" O LEU F 584 " (cutoff:3.500A) Processing helix chain 'F' and resid 588 through 599 Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.990A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 63 through 65 Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 94 removed outlier: 3.786A pdb=" N LEU A 229 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 126 through 132 removed outlier: 4.063A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU A 241 " --> pdb=" O GLY A 103 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLN A 239 " --> pdb=" O ILE A 105 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 3.666A pdb=" N THR A 315 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 326 removed outlier: 3.702A pdb=" N LEU A 585 " --> pdb=" O VAL A 576 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 356 removed outlier: 3.932A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA A 376 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.543A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.065A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER A 673 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.175A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 714 removed outlier: 3.842A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 717 through 728 removed outlier: 3.836A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 29 Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.980A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 90 through 94 removed outlier: 4.141A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 126 through 132 removed outlier: 4.102A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU B 241 " --> pdb=" O GLY B 103 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 316 removed outlier: 3.520A pdb=" N THR B 315 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY B 648 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.156A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TRP B 436 " --> pdb=" O ARG B 509 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 361 through 362 removed outlier: 4.058A pdb=" N CYS B 525 " --> pdb=" O CYS B 361 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 453 through 454 removed outlier: 3.518A pdb=" N ARG B 493 " --> pdb=" O TYR B 453 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 539 through 543 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 656 removed outlier: 3.607A pdb=" N GLU B 654 " --> pdb=" O ILE B 692 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE B 664 " --> pdb=" O ALA B 672 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 712 through 714 removed outlier: 3.800A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 717 through 728 removed outlier: 3.854A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 3.958A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.505A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.994A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 90 through 94 removed outlier: 3.765A pdb=" N LEU C 229 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 171 through 172 removed outlier: 4.387A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 316 removed outlier: 3.516A pdb=" N THR C 315 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE C 643 " --> pdb=" O LEU C 650 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 325 through 326 Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 356 removed outlier: 3.786A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA C 397 " --> pdb=" O LYS C 356 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.541A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 656 removed outlier: 3.598A pdb=" N GLU C 654 " --> pdb=" O ILE C 692 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 712 through 714 removed outlier: 3.826A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 717 through 728 removed outlier: 3.875A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.028A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF1, first strand: chain 'E' and resid 131 through 134 removed outlier: 3.656A pdb=" N VAL E 132 " --> pdb=" O LEU E 142 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU E 142 " --> pdb=" O VAL E 132 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ASN E 134 " --> pdb=" O GLU E 140 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N GLU E 140 " --> pdb=" O ASN E 134 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'E' and resid 262 through 263 removed outlier: 5.818A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'E' and resid 347 through 352 removed outlier: 6.304A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 131 through 134 removed outlier: 3.663A pdb=" N VAL F 132 " --> pdb=" O LEU F 142 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU F 142 " --> pdb=" O VAL F 132 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ASN F 134 " --> pdb=" O GLU F 140 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N GLU F 140 " --> pdb=" O ASN F 134 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'F' and resid 262 through 263 removed outlier: 5.836A pdb=" N LEU F 262 " --> pdb=" O VAL F 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'F' and resid 347 through 352 removed outlier: 6.340A pdb=" N ASP F 355 " --> pdb=" O LEU F 351 " (cutoff:3.500A) 1343 hydrogen bonds defined for protein. 3702 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: 8.23 Time building geometry restraints manager: 4.05 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: 10768 1.34 - 1.46: 6241 1.46 - 1.58: 17812 1.58 - 1.70: 0 1.70 - 1.82: 229 Bond restraints: 35050 Sorted by residual: bond pdb=" C THR B 208 " pdb=" N PRO B 209 " ideal model delta sigma weight residual 1.330 1.373 -0.043 1.22e-02 6.72e+03 1.25e+01 bond pdb=" C LEU C 216 " pdb=" N PRO C 217 " ideal model delta sigma weight residual 1.326 1.369 -0.043 1.44e-02 4.82e+03 8.96e+00 bond pdb=" N THR A 208 " pdb=" CA THR A 208 " ideal model delta sigma weight residual 1.453 1.476 -0.023 8.30e-03 1.45e+04 7.89e+00 bond pdb=" N HIS A 207 " pdb=" CA HIS A 207 " ideal model delta sigma weight residual 1.460 1.486 -0.026 1.20e-02 6.94e+03 4.73e+00 bond pdb=" N PRO B 209 " pdb=" CD PRO B 209 " ideal model delta sigma weight residual 1.473 1.502 -0.029 1.40e-02 5.10e+03 4.29e+00 ... (remaining 35045 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 46541 1.26 - 2.52: 893 2.52 - 3.79: 217 3.79 - 5.05: 34 5.05 - 6.31: 10 Bond angle restraints: 47695 Sorted by residual: angle pdb=" N ILE A 100 " pdb=" CA ILE A 100 " pdb=" C ILE A 100 " ideal model delta sigma weight residual 111.90 108.76 3.14 8.10e-01 1.52e+00 1.51e+01 angle pdb=" CA LEU C 216 " pdb=" C LEU C 216 " pdb=" N PRO C 217 " ideal model delta sigma weight residual 118.44 123.83 -5.39 1.59e+00 3.96e-01 1.15e+01 angle pdb=" CA LEU C 216 " pdb=" C LEU C 216 " pdb=" O LEU C 216 " ideal model delta sigma weight residual 120.16 115.93 4.23 1.37e+00 5.33e-01 9.52e+00 angle pdb=" C THR A 208 " pdb=" CA THR A 208 " pdb=" CB THR A 208 " ideal model delta sigma weight residual 109.22 104.57 4.65 1.52e+00 4.33e-01 9.37e+00 angle pdb=" CA PRO B 209 " pdb=" N PRO B 209 " pdb=" CD PRO B 209 " ideal model delta sigma weight residual 112.00 107.84 4.16 1.40e+00 5.10e-01 8.83e+00 ... (remaining 47690 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.26: 20563 17.26 - 34.51: 589 34.51 - 51.77: 110 51.77 - 69.02: 12 69.02 - 86.28: 5 Dihedral angle restraints: 21279 sinusoidal: 8826 harmonic: 12453 Sorted by residual: dihedral pdb=" CB GLU A 169 " pdb=" CG GLU A 169 " pdb=" CD GLU A 169 " pdb=" OE1 GLU A 169 " ideal model delta sinusoidal sigma weight residual 0.00 86.28 -86.28 1 3.00e+01 1.11e-03 9.97e+00 dihedral pdb=" N THR A 208 " pdb=" CA THR A 208 " pdb=" CB THR A 208 " pdb=" OG1 THR A 208 " ideal model delta sinusoidal sigma weight residual 60.00 115.94 -55.94 3 1.50e+01 4.44e-03 9.37e+00 dihedral pdb=" CB GLU E 110 " pdb=" CG GLU E 110 " pdb=" CD GLU E 110 " pdb=" OE1 GLU E 110 " ideal model delta sinusoidal sigma weight residual 0.00 -80.66 80.66 1 3.00e+01 1.11e-03 8.94e+00 ... (remaining 21276 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 5222 0.099 - 0.199: 175 0.199 - 0.298: 7 0.298 - 0.398: 0 0.398 - 0.497: 1 Chirality restraints: 5405 Sorted by residual: chirality pdb=" C1 NAG B1310 " pdb=" ND2 ASN B 122 " pdb=" C2 NAG B1310 " pdb=" O5 NAG B1310 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-01 2.50e+01 6.19e+00 chirality pdb=" C1 NAG F 903 " pdb=" ND2 ASN F 322 " pdb=" C2 NAG F 903 " pdb=" O5 NAG F 903 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" C1 NAG C1310 " pdb=" ND2 ASN C 122 " pdb=" C2 NAG C1310 " pdb=" O5 NAG C1310 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 5402 not shown) Planarity restraints: 6154 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 122 " -0.051 2.00e-02 2.50e+03 2.65e-01 8.75e+02 pdb=" CG ASN B 122 " -0.068 2.00e-02 2.50e+03 pdb=" OD1 ASN B 122 " 0.236 2.00e-02 2.50e+03 pdb=" ND2 ASN B 122 " -0.433 2.00e-02 2.50e+03 pdb=" C1 NAG B1310 " 0.316 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO C 209 " 0.010 2.00e-02 2.50e+03 2.01e-02 4.05e+00 pdb=" C PRO C 209 " -0.035 2.00e-02 2.50e+03 pdb=" O PRO C 209 " 0.013 2.00e-02 2.50e+03 pdb=" N ILE C 210 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 520 " -0.023 5.00e-02 4.00e+02 3.45e-02 1.90e+00 pdb=" N PRO A 521 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO A 521 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 521 " -0.019 5.00e-02 4.00e+02 ... (remaining 6151 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 318 2.60 - 3.17: 28097 3.17 - 3.75: 51237 3.75 - 4.32: 70910 4.32 - 4.90: 117474 Nonbonded interactions: 268036 Sorted by model distance: nonbonded pdb=" CE1 PHE B 168 " pdb=" CD ARG C 357 " model vdw 2.025 3.740 nonbonded pdb=" ND2 ASN B 121 " pdb=" CD1 LEU B 176 " model vdw 2.127 3.540 nonbonded pdb=" O VAL B 130 " pdb=" OG1 THR B 167 " model vdw 2.147 3.040 nonbonded pdb=" OE1 GLU E 402 " pdb="ZN ZN E 902 " model vdw 2.185 2.230 nonbonded pdb=" OG1 THR B 124 " pdb=" O6 NAG B1310 " model vdw 2.199 3.040 ... (remaining 268031 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 355 or (resid 356 through 357 and (name N or na \ me CA or name C or name O or name CB )) or resid 358 through 387 or (resid 388 a \ nd (name N or name CA or name C or name O or name CB )) or resid 389 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 name O or nam \ e 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 (name N or na \ me CA or name C or name O or name CB )) or resid 455 through 457 or (resid 458 t \ hrough 459 and (name N or name CA or name C or name O or name CB )) or 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 487 and (name \ N or name CA or name C or name O or name CB )) or resid 488 through 499 or (res \ id 500 and (name N or name CA or name C or name O or name CB )) or resid 501 thr \ ough 515 or (resid 516 and (name N or name CA or name C or name O or name CB )) \ or resid 517 through 520 or (resid 522 through 523 and (name N or name CA or nam \ e C or name O or name CB )) or resid 524 through 1311)) selection = chain 'B' selection = (chain 'C' and (resid 27 through 355 or (resid 356 through 357 and (name N or na \ me CA or name C or name O or name CB )) or resid 358 through 387 or (resid 388 a \ nd (name N or name CA or name C or name O or name CB )) or resid 389 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 name O or nam \ e 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 (name N or na \ me CA or name C or name O or name CB )) or resid 455 through 457 or (resid 458 t \ hrough 459 and (name N or name CA or name C or name O or name CB )) or 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 487 and (name \ N or name CA or name C or name O or name CB )) or resid 488 through 499 or (res \ id 500 and (name N or name CA or name C or name O or name CB )) or resid 501 thr \ ough 515 or (resid 516 and (name N or name CA or name C or name O or name CB )) \ or resid 517 through 520 or (resid 522 through 523 and (name N or name CA or nam \ e C or name O or name CB )) or resid 524 through 1311)) } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 7.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.620 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 37.140 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.080 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: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5287 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 : 0.003 0.182 35123 Z= 0.130 Angle : 0.462 12.186 47876 Z= 0.242 Chirality : 0.042 0.497 5405 Planarity : 0.003 0.034 6115 Dihedral : 8.030 86.275 13167 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.08 % Allowed : 4.70 % Favored : 95.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.21 (0.11), residues: 4213 helix: -1.66 (0.12), residues: 1331 sheet: -1.23 (0.19), residues: 627 loop : -2.77 (0.10), residues: 2255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 765 TYR 0.011 0.001 TYR A 369 PHE 0.009 0.001 PHE A 371 TRP 0.005 0.000 TRP E 302 HIS 0.002 0.000 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00232 (35050) covalent geometry : angle 0.44938 (47695) SS BOND : bond 0.00067 ( 32) SS BOND : angle 0.52883 ( 64) hydrogen bonds : bond 0.21599 ( 1343) hydrogen bonds : angle 7.23171 ( 3702) metal coordination : bond 0.13723 ( 2) link_NAG-ASN : bond 0.00738 ( 39) link_NAG-ASN : angle 2.20804 ( 117) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8426 Ramachandran restraints generated. 4213 Oldfield, 0 Emsley, 4213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8426 Ramachandran restraints generated. 4213 Oldfield, 0 Emsley, 4213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 862 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 859 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.6361 (mtt180) cc_final: 0.5829 (mtt180) REVERT: A 194 PHE cc_start: 0.8098 (m-10) cc_final: 0.7856 (m-10) REVERT: A 317 ASN cc_start: 0.7744 (m-40) cc_final: 0.7199 (m-40) REVERT: A 586 ASP cc_start: 0.6430 (m-30) cc_final: 0.6111 (m-30) REVERT: A 670 ILE cc_start: 0.8548 (mp) cc_final: 0.8332 (mt) REVERT: A 747 THR cc_start: 0.7548 (p) cc_final: 0.7345 (m) REVERT: A 759 PHE cc_start: 0.6096 (m-10) cc_final: 0.5862 (m-10) REVERT: A 772 VAL cc_start: 0.8416 (p) cc_final: 0.8190 (p) REVERT: A 774 GLN cc_start: 0.7370 (mm-40) cc_final: 0.7023 (mm-40) REVERT: A 909 ILE cc_start: 0.5638 (pt) cc_final: 0.3347 (mt) REVERT: A 974 SER cc_start: 0.8346 (t) cc_final: 0.7970 (m) REVERT: A 1019 ARG cc_start: 0.6615 (ttm110) cc_final: 0.6217 (ttm170) REVERT: A 1110 TYR cc_start: 0.7923 (t80) cc_final: 0.7703 (t80) REVERT: B 88 ASP cc_start: 0.6779 (m-30) cc_final: 0.6552 (m-30) REVERT: B 276 LEU cc_start: 0.7806 (tp) cc_final: 0.7530 (tt) REVERT: B 317 ASN cc_start: 0.7250 (m110) cc_final: 0.6851 (m110) REVERT: B 599 THR cc_start: 0.8188 (t) cc_final: 0.7856 (p) REVERT: B 755 GLN cc_start: 0.6933 (tm-30) cc_final: 0.6650 (tm-30) REVERT: B 928 ASN cc_start: 0.7854 (m-40) cc_final: 0.7468 (m-40) REVERT: B 947 LYS cc_start: 0.8165 (mttt) cc_final: 0.7957 (mtpp) REVERT: B 969 LYS cc_start: 0.7851 (ptpt) cc_final: 0.7618 (ptpp) REVERT: B 1017 GLU cc_start: 0.6776 (tp30) cc_final: 0.6450 (tp30) REVERT: B 1019 ARG cc_start: 0.6688 (ttm110) cc_final: 0.6288 (ttp80) REVERT: B 1072 GLU cc_start: 0.7664 (pm20) cc_final: 0.7203 (pm20) REVERT: B 1084 ASP cc_start: 0.7020 (t0) cc_final: 0.6609 (t0) REVERT: B 1123 SER cc_start: 0.7828 (t) cc_final: 0.7549 (t) REVERT: C 195 LYS cc_start: 0.6701 (mtmt) cc_final: 0.6483 (mtmt) REVERT: C 210 ILE cc_start: 0.4422 (OUTLIER) cc_final: 0.4168 (pt) REVERT: C 276 LEU cc_start: 0.7859 (tp) cc_final: 0.7610 (tp) REVERT: C 304 LYS cc_start: 0.8252 (ttmt) cc_final: 0.8017 (ttmm) REVERT: C 542 ASN cc_start: 0.7752 (t0) cc_final: 0.7531 (t0) REVERT: C 670 ILE cc_start: 0.8795 (mp) cc_final: 0.8556 (mt) REVERT: C 737 ASP cc_start: 0.6206 (t0) cc_final: 0.5883 (t0) REVERT: C 774 GLN cc_start: 0.7509 (mm-40) cc_final: 0.7143 (mm110) REVERT: C 790 LYS cc_start: 0.7854 (mtmm) cc_final: 0.7649 (mtmm) REVERT: C 881 THR cc_start: 0.8067 (t) cc_final: 0.7808 (t) REVERT: C 931 ILE cc_start: 0.7595 (mm) cc_final: 0.7232 (mm) REVERT: C 981 LEU cc_start: 0.7624 (mt) cc_final: 0.7370 (mt) REVERT: C 1017 GLU cc_start: 0.7342 (tp30) cc_final: 0.6553 (tp30) REVERT: C 1018 ILE cc_start: 0.7683 (mm) cc_final: 0.7361 (mm) REVERT: C 1072 GLU cc_start: 0.7645 (pm20) cc_final: 0.7307 (pm20) REVERT: C 1123 SER cc_start: 0.7853 (m) cc_final: 0.7529 (t) REVERT: E 39 LEU cc_start: 0.6080 (mt) cc_final: 0.5767 (mt) REVERT: E 72 PHE cc_start: 0.5324 (t80) cc_final: 0.4813 (t80) REVERT: E 117 ASN cc_start: 0.6732 (m-40) cc_final: 0.6343 (m-40) REVERT: E 521 TYR cc_start: 0.6044 (m-10) cc_final: 0.5485 (m-80) REVERT: F 323 MET cc_start: -0.2235 (mmt) cc_final: -0.3441 (mmt) outliers start: 3 outliers final: 2 residues processed: 861 average time/residue: 0.2292 time to fit residues: 321.6979 Evaluate side-chains 719 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 716 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 216 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 0.0060 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.0270 chunk 401 optimal weight: 5.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 10.0000 overall best weight: 0.5054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN A 439 ASN A 474 GLN A 580 GLN A 607 GLN A 613 GLN A 755 GLN A 907 ASN A 935 GLN A 965 GLN A1010 GLN A1106 GLN B 81 ASN B 173 GLN B 394 ASN B 519 HIS B 606 ASN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B 955 ASN B1010 GLN B1106 GLN B1119 ASN B1125 ASN C 66 HIS C 439 ASN C 474 GLN C 607 GLN C 907 ASN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN C 960 ASN C 965 GLN C1106 GLN C1125 ASN E 33 ASN E 51 ASN E 60 GLN E 81 GLN E 121 ASN E 239 HIS E 300 GLN E 325 GLN E 330 ASN E 340 GLN E 429 GLN F 60 GLN F 81 GLN ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 239 HIS F 300 GLN F 325 GLN F 340 GLN F 429 GLN F 493 HIS F 524 GLN F 526 GLN F 552 GLN F 556 ASN F 586 ASN ** F 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 57 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.230461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.169693 restraints weight = 55588.931| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 3.12 r_work: 0.3658 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 35123 Z= 0.139 Angle : 0.553 9.995 47876 Z= 0.278 Chirality : 0.045 0.330 5405 Planarity : 0.004 0.039 6115 Dihedral : 4.972 58.944 5397 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.78 % Allowed : 8.96 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.73 (0.12), residues: 4213 helix: 0.18 (0.14), residues: 1354 sheet: -0.82 (0.19), residues: 634 loop : -2.17 (0.11), residues: 2225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 328 TYR 0.021 0.001 TYR B1138 PHE 0.028 0.002 PHE B 55 TRP 0.028 0.001 TRP C 436 HIS 0.006 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00302 (35050) covalent geometry : angle 0.53911 (47695) SS BOND : bond 0.00268 ( 32) SS BOND : angle 1.05608 ( 64) hydrogen bonds : bond 0.03953 ( 1343) hydrogen bonds : angle 4.73845 ( 3702) metal coordination : bond 0.01052 ( 2) link_NAG-ASN : bond 0.00589 ( 39) link_NAG-ASN : angle 2.42331 ( 117) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8426 Ramachandran restraints generated. 4213 Oldfield, 0 Emsley, 4213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8426 Ramachandran restraints generated. 4213 Oldfield, 0 Emsley, 4213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 811 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 745 time to evaluate : 1.401 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 40 ASP cc_start: 0.6941 (t0) cc_final: 0.6640 (t0) REVERT: A 206 LYS cc_start: 0.8262 (tppt) cc_final: 0.7768 (tppt) REVERT: A 273 ARG cc_start: 0.7318 (mtp85) cc_final: 0.7051 (mtp85) REVERT: A 289 VAL cc_start: 0.8772 (t) cc_final: 0.8493 (p) REVERT: A 574 ASP cc_start: 0.7216 (p0) cc_final: 0.6929 (p0) REVERT: A 588 THR cc_start: 0.7481 (m) cc_final: 0.7214 (t) REVERT: A 737 ASP cc_start: 0.7343 (t0) cc_final: 0.6858 (t0) REVERT: A 774 GLN cc_start: 0.8089 (mm-40) cc_final: 0.7772 (mp10) REVERT: A 964 LYS cc_start: 0.8334 (ttmm) cc_final: 0.8082 (tppp) REVERT: A 970 PHE cc_start: 0.8320 (m-80) cc_final: 0.8012 (m-10) REVERT: A 979 ASP cc_start: 0.6875 (t0) cc_final: 0.6395 (t0) REVERT: A 988 GLU cc_start: 0.7717 (mp0) cc_final: 0.7448 (mp0) REVERT: A 1014 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7939 (ttm170) REVERT: A 1019 ARG cc_start: 0.7351 (ttm110) cc_final: 0.7132 (ttp80) REVERT: A 1075 PHE cc_start: 0.8227 (m-80) cc_final: 0.7896 (m-80) REVERT: A 1088 HIS cc_start: 0.8496 (m170) cc_final: 0.8205 (m170) REVERT: A 1110 TYR cc_start: 0.8403 (t80) cc_final: 0.8130 (t80) REVERT: B 81 ASN cc_start: 0.8044 (OUTLIER) cc_final: 0.7243 (m-40) REVERT: B 88 ASP cc_start: 0.7250 (m-30) cc_final: 0.7019 (m-30) REVERT: B 198 ASP cc_start: 0.6220 (t0) cc_final: 0.5903 (t0) REVERT: B 203 ILE cc_start: 0.8841 (pt) cc_final: 0.8536 (mt) REVERT: B 233 ILE cc_start: 0.6788 (OUTLIER) cc_final: 0.6551 (mt) REVERT: B 276 LEU cc_start: 0.8216 (tp) cc_final: 0.7919 (tt) REVERT: B 289 VAL cc_start: 0.8750 (t) cc_final: 0.8539 (m) REVERT: B 488 CYS cc_start: 0.1587 (OUTLIER) cc_final: 0.1228 (t) REVERT: B 599 THR cc_start: 0.8467 (t) cc_final: 0.8123 (p) REVERT: B 659 SER cc_start: 0.8443 (m) cc_final: 0.8230 (p) REVERT: B 704 SER cc_start: 0.8329 (m) cc_final: 0.7900 (p) REVERT: B 755 GLN cc_start: 0.8009 (tm-30) cc_final: 0.7610 (tm-30) REVERT: B 774 GLN cc_start: 0.8310 (mp10) cc_final: 0.8032 (mm110) REVERT: B 917 TYR cc_start: 0.7417 (m-10) cc_final: 0.7199 (m-10) REVERT: B 947 LYS cc_start: 0.8586 (mttt) cc_final: 0.8231 (mtpp) REVERT: B 965 GLN cc_start: 0.6788 (tt0) cc_final: 0.6357 (tt0) REVERT: B 969 LYS cc_start: 0.8414 (ptpt) cc_final: 0.8016 (ptpp) REVERT: B 970 PHE cc_start: 0.7977 (m-80) cc_final: 0.7572 (m-80) REVERT: B 1019 ARG cc_start: 0.7595 (ttm110) cc_final: 0.7378 (tmm-80) REVERT: B 1029 MET cc_start: 0.8414 (tpp) cc_final: 0.8169 (ttm) REVERT: B 1075 PHE cc_start: 0.8016 (m-80) cc_final: 0.7777 (m-10) REVERT: B 1084 ASP cc_start: 0.7718 (t0) cc_final: 0.7276 (t0) REVERT: B 1123 SER cc_start: 0.8301 (t) cc_final: 0.8050 (t) REVERT: C 53 ASP cc_start: 0.7407 (t0) cc_final: 0.7152 (t0) REVERT: C 235 ILE cc_start: 0.7754 (mm) cc_final: 0.7506 (mm) REVERT: C 271 GLN cc_start: 0.8177 (mm-40) cc_final: 0.7873 (mt0) REVERT: C 293 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7452 (pp) REVERT: C 304 LYS cc_start: 0.8743 (ttmt) cc_final: 0.8486 (ttmm) REVERT: C 383 SER cc_start: 0.9056 (m) cc_final: 0.8771 (p) REVERT: C 584 ILE cc_start: 0.7694 (mt) cc_final: 0.7436 (mm) REVERT: C 587 ILE cc_start: 0.8736 (mp) cc_final: 0.8509 (mp) REVERT: C 642 VAL cc_start: 0.8664 (t) cc_final: 0.8353 (p) REVERT: C 644 GLN cc_start: 0.7324 (tp40) cc_final: 0.7005 (tp40) REVERT: C 658 ASN cc_start: 0.8093 (OUTLIER) cc_final: 0.7581 (p0) REVERT: C 663 ASP cc_start: 0.7867 (m-30) cc_final: 0.7629 (m-30) REVERT: C 722 VAL cc_start: 0.8127 (m) cc_final: 0.7531 (p) REVERT: C 774 GLN cc_start: 0.7989 (mm-40) cc_final: 0.7736 (mm110) REVERT: C 776 LYS cc_start: 0.8660 (tttm) cc_final: 0.8355 (tttm) REVERT: C 784 GLN cc_start: 0.8498 (mt0) cc_final: 0.8295 (mt0) REVERT: C 825 LYS cc_start: 0.8307 (mtpt) cc_final: 0.7984 (mtpt) REVERT: C 931 ILE cc_start: 0.8139 (mm) cc_final: 0.7919 (mm) REVERT: C 1038 LYS cc_start: 0.8247 (mmmt) cc_final: 0.7959 (mmmm) REVERT: E 22 GLU cc_start: 0.6835 (tt0) cc_final: 0.6549 (tt0) REVERT: E 23 GLU cc_start: 0.7271 (mm-30) cc_final: 0.7059 (mm-30) REVERT: E 31 LYS cc_start: 0.7370 (tptp) cc_final: 0.7149 (tptp) REVERT: E 39 LEU cc_start: 0.7899 (mt) cc_final: 0.7658 (mt) REVERT: E 76 GLN cc_start: 0.7752 (mm-40) cc_final: 0.7060 (mm-40) REVERT: E 82 MET cc_start: 0.6759 (mtt) cc_final: 0.6294 (mpp) REVERT: E 243 TYR cc_start: 0.6134 (t80) cc_final: 0.5903 (t80) REVERT: E 355 ASP cc_start: 0.6608 (t0) cc_final: 0.6263 (t0) REVERT: E 358 ILE cc_start: 0.7134 (mt) cc_final: 0.6888 (mt) REVERT: E 388 GLN cc_start: 0.6824 (mm-40) cc_final: 0.6605 (mm-40) REVERT: E 400 PHE cc_start: 0.7347 (m-80) cc_final: 0.6553 (m-80) REVERT: E 408 MET cc_start: 0.7427 (mmt) cc_final: 0.7096 (mmm) REVERT: E 452 PHE cc_start: 0.5730 (t80) cc_final: 0.5257 (t80) REVERT: E 455 MET cc_start: 0.8774 (ppp) cc_final: 0.8429 (ppp) REVERT: E 474 MET cc_start: 0.6169 (OUTLIER) cc_final: 0.5847 (mtp) REVERT: E 522 GLN cc_start: 0.7761 (tt0) cc_final: 0.7527 (pt0) REVERT: E 557 MET cc_start: 0.4877 (tmm) cc_final: 0.4668 (tmm) REVERT: E 571 GLU cc_start: 0.7117 (tt0) cc_final: 0.6912 (pt0) outliers start: 66 outliers final: 26 residues processed: 785 average time/residue: 0.2219 time to fit residues: 285.7225 Evaluate side-chains 725 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 692 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 1014 ARG Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 695 TYR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain E residue 64 ASN Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 474 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 353 optimal weight: 0.0670 chunk 96 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 264 optimal weight: 2.9990 chunk 186 optimal weight: 1.9990 chunk 382 optimal weight: 40.0000 chunk 101 optimal weight: 0.5980 chunk 414 optimal weight: 50.0000 chunk 386 optimal weight: 8.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.5324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A 935 GLN A1106 GLN A1135 ASN B 30 ASN B 606 ASN B 613 GLN ** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1135 ASN C 658 ASN C 755 GLN C 804 GLN C 907 ASN C 935 GLN C 955 ASN C1119 ASN E 34 HIS E 81 GLN ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 522 GLN F 526 GLN ** F 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.220129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.154479 restraints weight = 53270.025| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 2.97 r_work: 0.3483 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.093 35123 Z= 0.289 Angle : 0.703 20.899 47876 Z= 0.354 Chirality : 0.049 0.345 5405 Planarity : 0.005 0.069 6115 Dihedral : 5.252 53.775 5393 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.54 % Allowed : 11.23 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.42 (0.12), residues: 4213 helix: 0.43 (0.14), residues: 1371 sheet: -0.67 (0.19), residues: 619 loop : -1.98 (0.12), residues: 2223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 328 TYR 0.035 0.002 TYR A 279 PHE 0.028 0.002 PHE C1052 TRP 0.024 0.001 TRP E 566 HIS 0.018 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00651 (35050) covalent geometry : angle 0.67534 (47695) SS BOND : bond 0.00542 ( 32) SS BOND : angle 1.82252 ( 64) hydrogen bonds : bond 0.04988 ( 1343) hydrogen bonds : angle 4.85924 ( 3702) metal coordination : bond 0.00131 ( 2) link_NAG-ASN : bond 0.00681 ( 39) link_NAG-ASN : angle 3.79382 ( 117) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8426 Ramachandran restraints generated. 4213 Oldfield, 0 Emsley, 4213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8426 Ramachandran restraints generated. 4213 Oldfield, 0 Emsley, 4213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 847 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 753 time to evaluate : 1.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.7615 (t0) cc_final: 0.7332 (t0) REVERT: A 206 LYS cc_start: 0.8444 (tppt) cc_final: 0.8033 (tppt) REVERT: A 289 VAL cc_start: 0.8784 (t) cc_final: 0.8460 (p) REVERT: A 299 THR cc_start: 0.8523 (m) cc_final: 0.8116 (p) REVERT: A 533 LEU cc_start: 0.8624 (tt) cc_final: 0.8364 (tp) REVERT: A 537 LYS cc_start: 0.8387 (ttmt) cc_final: 0.8109 (mtpt) REVERT: A 542 ASN cc_start: 0.8681 (t0) cc_final: 0.8372 (t0) REVERT: A 543 PHE cc_start: 0.8380 (m-10) cc_final: 0.8039 (m-80) REVERT: A 574 ASP cc_start: 0.7380 (p0) cc_final: 0.7088 (p0) REVERT: A 577 ARG cc_start: 0.8347 (ttm-80) cc_final: 0.8135 (ttm-80) REVERT: A 588 THR cc_start: 0.7817 (m) cc_final: 0.7558 (t) REVERT: A 606 ASN cc_start: 0.8229 (m-40) cc_final: 0.8010 (m-40) REVERT: A 615 VAL cc_start: 0.8512 (p) cc_final: 0.8242 (m) REVERT: A 646 ARG cc_start: 0.7369 (mmt180) cc_final: 0.7088 (tmt170) REVERT: A 661 GLU cc_start: 0.7712 (tp30) cc_final: 0.7494 (tp30) REVERT: A 710 ASN cc_start: 0.8075 (p0) cc_final: 0.7701 (p0) REVERT: A 737 ASP cc_start: 0.7722 (t0) cc_final: 0.7373 (t0) REVERT: A 774 GLN cc_start: 0.8072 (mm-40) cc_final: 0.7865 (mp10) REVERT: A 781 VAL cc_start: 0.8681 (OUTLIER) cc_final: 0.8398 (t) REVERT: A 884 SER cc_start: 0.8837 (OUTLIER) cc_final: 0.8590 (p) REVERT: A 950 ASP cc_start: 0.7505 (t0) cc_final: 0.7129 (t0) REVERT: A 957 GLN cc_start: 0.8162 (tt0) cc_final: 0.7844 (tt0) REVERT: A 1029 MET cc_start: 0.8343 (tpp) cc_final: 0.8079 (ttm) REVERT: A 1030 SER cc_start: 0.8725 (t) cc_final: 0.8415 (m) REVERT: A 1102 TRP cc_start: 0.8545 (m100) cc_final: 0.8035 (m100) REVERT: A 1105 THR cc_start: 0.8419 (t) cc_final: 0.8011 (p) REVERT: B 30 ASN cc_start: 0.8210 (OUTLIER) cc_final: 0.7934 (p0) REVERT: B 58 PHE cc_start: 0.8531 (m-10) cc_final: 0.8282 (m-10) REVERT: B 198 ASP cc_start: 0.7449 (t0) cc_final: 0.6945 (t0) REVERT: B 233 ILE cc_start: 0.7744 (OUTLIER) cc_final: 0.7231 (mp) REVERT: B 269 TYR cc_start: 0.7880 (m-80) cc_final: 0.7571 (m-80) REVERT: B 289 VAL cc_start: 0.8822 (t) cc_final: 0.8550 (m) REVERT: B 305 SER cc_start: 0.8774 (m) cc_final: 0.8536 (t) REVERT: B 353 TRP cc_start: 0.7005 (p-90) cc_final: 0.6311 (p-90) REVERT: B 488 CYS cc_start: 0.1387 (OUTLIER) cc_final: 0.1094 (t) REVERT: B 599 THR cc_start: 0.8445 (t) cc_final: 0.8101 (p) REVERT: B 603 ASN cc_start: 0.8035 (t0) cc_final: 0.7553 (t0) REVERT: B 615 VAL cc_start: 0.8401 (p) cc_final: 0.8159 (m) REVERT: B 656 VAL cc_start: 0.8520 (t) cc_final: 0.8259 (t) REVERT: B 658 ASN cc_start: 0.8500 (OUTLIER) cc_final: 0.7937 (p0) REVERT: B 698 SER cc_start: 0.8678 (t) cc_final: 0.8270 (p) REVERT: B 704 SER cc_start: 0.8518 (m) cc_final: 0.8112 (p) REVERT: B 710 ASN cc_start: 0.8133 (p0) cc_final: 0.7784 (p0) REVERT: B 737 ASP cc_start: 0.7565 (t70) cc_final: 0.7296 (m-30) REVERT: B 755 GLN cc_start: 0.8014 (tm-30) cc_final: 0.7677 (tm-30) REVERT: B 814 LYS cc_start: 0.8052 (mmmt) cc_final: 0.7710 (mmmt) REVERT: B 907 ASN cc_start: 0.8341 (t0) cc_final: 0.7975 (t0) REVERT: B 947 LYS cc_start: 0.8608 (mttt) cc_final: 0.8228 (mtpp) REVERT: B 963 VAL cc_start: 0.8958 (m) cc_final: 0.8657 (t) REVERT: B 969 LYS cc_start: 0.8465 (ptpt) cc_final: 0.8142 (ptpp) REVERT: B 1014 ARG cc_start: 0.8396 (tpp80) cc_final: 0.8054 (ttm170) REVERT: B 1017 GLU cc_start: 0.7786 (tp30) cc_final: 0.7438 (tp30) REVERT: B 1019 ARG cc_start: 0.7750 (ttm110) cc_final: 0.7467 (ttp80) REVERT: B 1027 THR cc_start: 0.8377 (m) cc_final: 0.8032 (t) REVERT: B 1031 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7755 (mt-10) REVERT: B 1084 ASP cc_start: 0.7805 (t0) cc_final: 0.7303 (t0) REVERT: B 1116 THR cc_start: 0.8261 (m) cc_final: 0.7905 (t) REVERT: B 1123 SER cc_start: 0.8178 (t) cc_final: 0.7880 (t) REVERT: B 1134 ASN cc_start: 0.7669 (m-40) cc_final: 0.7184 (m-40) REVERT: C 58 PHE cc_start: 0.8142 (m-10) cc_final: 0.7838 (m-10) REVERT: C 104 TRP cc_start: 0.7942 (m-90) cc_final: 0.7656 (m-90) REVERT: C 281 GLU cc_start: 0.8045 (pp20) cc_final: 0.7761 (pp20) REVERT: C 304 LYS cc_start: 0.8810 (ttmt) cc_final: 0.8578 (ttmm) REVERT: C 316 SER cc_start: 0.8468 (t) cc_final: 0.8265 (p) REVERT: C 383 SER cc_start: 0.9109 (m) cc_final: 0.8873 (p) REVERT: C 511 VAL cc_start: 0.7406 (OUTLIER) cc_final: 0.6994 (m) REVERT: C 541 PHE cc_start: 0.8478 (p90) cc_final: 0.8265 (p90) REVERT: C 559 PHE cc_start: 0.8045 (m-10) cc_final: 0.7416 (m-80) REVERT: C 581 THR cc_start: 0.8249 (m) cc_final: 0.8045 (t) REVERT: C 583 GLU cc_start: 0.7280 (tp30) cc_final: 0.7007 (tp30) REVERT: C 584 ILE cc_start: 0.7642 (mt) cc_final: 0.7296 (mm) REVERT: C 642 VAL cc_start: 0.8879 (OUTLIER) cc_final: 0.8596 (p) REVERT: C 658 ASN cc_start: 0.8135 (OUTLIER) cc_final: 0.7757 (p0) REVERT: C 663 ASP cc_start: 0.7968 (m-30) cc_final: 0.7667 (m-30) REVERT: C 698 SER cc_start: 0.8767 (t) cc_final: 0.8480 (t) REVERT: C 710 ASN cc_start: 0.8060 (p0) cc_final: 0.7615 (p0) REVERT: C 770 ILE cc_start: 0.8819 (OUTLIER) cc_final: 0.8601 (tt) REVERT: C 921 LYS cc_start: 0.8406 (mmtm) cc_final: 0.8105 (mmmm) REVERT: C 983 ARG cc_start: 0.7941 (ttt180) cc_final: 0.7600 (mtp85) REVERT: C 984 LEU cc_start: 0.7865 (tp) cc_final: 0.7587 (tp) REVERT: C 995 ARG cc_start: 0.8566 (ttm170) cc_final: 0.8227 (ttm170) REVERT: C 1001 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8477 (tt) REVERT: C 1051 SER cc_start: 0.8294 (t) cc_final: 0.8052 (m) REVERT: C 1127 ASP cc_start: 0.7285 (m-30) cc_final: 0.7060 (m-30) REVERT: E 22 GLU cc_start: 0.6864 (tt0) cc_final: 0.6589 (tt0) REVERT: E 23 GLU cc_start: 0.7291 (mm-30) cc_final: 0.7016 (mm-30) REVERT: E 32 PHE cc_start: 0.7992 (t80) cc_final: 0.7500 (t80) REVERT: E 39 LEU cc_start: 0.7944 (mt) cc_final: 0.7662 (mt) REVERT: E 73 LEU cc_start: 0.7992 (tp) cc_final: 0.7717 (tp) REVERT: E 76 GLN cc_start: 0.7668 (mm-40) cc_final: 0.7219 (mm-40) REVERT: E 82 MET cc_start: 0.7090 (mtt) cc_final: 0.6496 (mpp) REVERT: E 91 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7820 (pp) REVERT: E 97 LEU cc_start: 0.7563 (mt) cc_final: 0.7171 (tp) REVERT: E 119 ILE cc_start: 0.7303 (mm) cc_final: 0.7065 (tt) REVERT: E 123 MET cc_start: 0.8555 (mtt) cc_final: 0.8251 (mpp) REVERT: E 208 GLU cc_start: 0.6802 (tm-30) cc_final: 0.6446 (tm-30) REVERT: E 243 TYR cc_start: 0.6099 (t80) cc_final: 0.5724 (t80) REVERT: E 355 ASP cc_start: 0.6885 (t0) cc_final: 0.6441 (t0) REVERT: E 388 GLN cc_start: 0.7035 (mm-40) cc_final: 0.6787 (mm-40) REVERT: E 397 ASN cc_start: 0.7611 (p0) cc_final: 0.7138 (p0) REVERT: E 400 PHE cc_start: 0.7820 (m-80) cc_final: 0.7345 (m-80) REVERT: E 406 GLU cc_start: 0.7306 (mt-10) cc_final: 0.7046 (mm-30) REVERT: E 454 TYR cc_start: 0.7298 (t80) cc_final: 0.7031 (t80) REVERT: E 455 MET cc_start: 0.8614 (ppp) cc_final: 0.8181 (ppp) REVERT: E 456 LEU cc_start: 0.8232 (tt) cc_final: 0.7966 (mt) REVERT: E 457 GLU cc_start: 0.8351 (mm-30) cc_final: 0.7728 (mm-30) REVERT: E 461 TRP cc_start: 0.6619 (m-10) cc_final: 0.6058 (m-10) REVERT: E 474 MET cc_start: 0.6409 (mtp) cc_final: 0.5849 (mtp) REVERT: E 480 MET cc_start: 0.6026 (mtp) cc_final: 0.5660 (mtp) REVERT: E 520 LEU cc_start: 0.8389 (mp) cc_final: 0.8041 (mp) REVERT: E 557 MET cc_start: 0.4940 (tmm) cc_final: 0.4662 (tmm) REVERT: E 571 GLU cc_start: 0.7192 (tt0) cc_final: 0.6843 (pt0) REVERT: F 323 MET cc_start: -0.0509 (mmt) cc_final: -0.1248 (mmp) REVERT: F 557 MET cc_start: 0.5591 (tmm) cc_final: 0.5332 (tmm) outliers start: 94 outliers final: 45 residues processed: 807 average time/residue: 0.2266 time to fit residues: 297.9438 Evaluate side-chains 756 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 698 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 695 TYR Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 884 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 997 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 695 TYR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 959 LEU Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 658 ASN Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 861 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1091 ARG Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain E residue 64 ASN Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 283 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 24 optimal weight: 0.7980 chunk 177 optimal weight: 0.5980 chunk 241 optimal weight: 0.9980 chunk 193 optimal weight: 0.5980 chunk 176 optimal weight: 0.0770 chunk 93 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 180 optimal weight: 0.0980 chunk 68 optimal weight: 0.0870 chunk 423 optimal weight: 0.9980 chunk 289 optimal weight: 0.9980 overall best weight: 0.2916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A 787 GLN A 856 ASN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 703 ASN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 755 GLN C 774 GLN C 949 GLN C 955 ASN ** E 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 34 HIS ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 330 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.223636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.158610 restraints weight = 53469.693| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 3.14 r_work: 0.3510 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 35123 Z= 0.109 Angle : 0.561 21.955 47876 Z= 0.276 Chirality : 0.044 0.338 5405 Planarity : 0.004 0.051 6115 Dihedral : 4.481 51.093 5392 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.13 % Allowed : 13.17 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.98 (0.12), residues: 4213 helix: 0.92 (0.14), residues: 1356 sheet: -0.55 (0.19), residues: 628 loop : -1.75 (0.12), residues: 2229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 577 TYR 0.018 0.001 TYR B1138 PHE 0.035 0.001 PHE A 643 TRP 0.022 0.001 TRP E 302 HIS 0.004 0.000 HIS B1101 Details of bonding type rmsd covalent geometry : bond 0.00237 (35050) covalent geometry : angle 0.52556 (47695) SS BOND : bond 0.00288 ( 32) SS BOND : angle 1.40157 ( 64) hydrogen bonds : bond 0.03590 ( 1343) hydrogen bonds : angle 4.55339 ( 3702) metal coordination : bond 0.00010 ( 2) link_NAG-ASN : bond 0.00701 ( 39) link_NAG-ASN : angle 3.91221 ( 117) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8426 Ramachandran restraints generated. 4213 Oldfield, 0 Emsley, 4213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8426 Ramachandran restraints generated. 4213 Oldfield, 0 Emsley, 4213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 800 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 721 time to evaluate : 1.344 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: A 40 ASP cc_start: 0.7576 (t0) cc_final: 0.7302 (t0) REVERT: A 190 ARG cc_start: 0.7429 (mtt180) cc_final: 0.6946 (mtt180) REVERT: A 206 LYS cc_start: 0.8342 (tppt) cc_final: 0.7937 (tppt) REVERT: A 227 VAL cc_start: 0.7525 (p) cc_final: 0.7244 (t) REVERT: A 289 VAL cc_start: 0.8833 (t) cc_final: 0.8443 (p) REVERT: A 291 CYS cc_start: 0.6478 (m) cc_final: 0.5996 (m) REVERT: A 299 THR cc_start: 0.8445 (m) cc_final: 0.8100 (p) REVERT: A 537 LYS cc_start: 0.8253 (ttmt) cc_final: 0.7899 (mtpt) REVERT: A 542 ASN cc_start: 0.8686 (t0) cc_final: 0.8375 (t0) REVERT: A 574 ASP cc_start: 0.7270 (p0) cc_final: 0.7034 (p0) REVERT: A 606 ASN cc_start: 0.8294 (m-40) cc_final: 0.8079 (m-40) REVERT: A 646 ARG cc_start: 0.7505 (mmt180) cc_final: 0.7195 (tmt170) REVERT: A 655 TYR cc_start: 0.8277 (t80) cc_final: 0.7787 (t80) REVERT: A 710 ASN cc_start: 0.8009 (p0) cc_final: 0.7598 (p0) REVERT: A 737 ASP cc_start: 0.6752 (t0) cc_final: 0.6535 (t0) REVERT: A 774 GLN cc_start: 0.8106 (mm-40) cc_final: 0.7874 (mm-40) REVERT: A 884 SER cc_start: 0.8827 (m) cc_final: 0.8569 (p) REVERT: A 950 ASP cc_start: 0.7407 (t0) cc_final: 0.7117 (t0) REVERT: A 957 GLN cc_start: 0.8104 (tt0) cc_final: 0.7716 (tt0) REVERT: A 1019 ARG cc_start: 0.7584 (ttp80) cc_final: 0.7376 (ttp80) REVERT: A 1029 MET cc_start: 0.8271 (tpp) cc_final: 0.7962 (ttm) REVERT: A 1030 SER cc_start: 0.8728 (t) cc_final: 0.8455 (m) REVERT: A 1083 HIS cc_start: 0.7979 (t-170) cc_final: 0.7626 (t-170) REVERT: A 1110 TYR cc_start: 0.8615 (t80) cc_final: 0.8263 (t80) REVERT: A 1120 THR cc_start: 0.8695 (OUTLIER) cc_final: 0.8353 (p) REVERT: A 1123 SER cc_start: 0.8672 (t) cc_final: 0.8435 (t) REVERT: B 58 PHE cc_start: 0.8518 (m-10) cc_final: 0.8267 (m-10) REVERT: B 198 ASP cc_start: 0.7350 (t0) cc_final: 0.6823 (t0) REVERT: B 233 ILE cc_start: 0.7728 (OUTLIER) cc_final: 0.7306 (mp) REVERT: B 269 TYR cc_start: 0.7841 (m-80) cc_final: 0.7488 (m-80) REVERT: B 305 SER cc_start: 0.8809 (m) cc_final: 0.8543 (t) REVERT: B 353 TRP cc_start: 0.6917 (p-90) cc_final: 0.6276 (p-90) REVERT: B 488 CYS cc_start: 0.1465 (OUTLIER) cc_final: 0.1180 (t) REVERT: B 599 THR cc_start: 0.8415 (t) cc_final: 0.8072 (p) REVERT: B 603 ASN cc_start: 0.7900 (t0) cc_final: 0.7433 (t0) REVERT: B 703 ASN cc_start: 0.8325 (t0) cc_final: 0.7910 (t0) REVERT: B 704 SER cc_start: 0.8452 (m) cc_final: 0.8064 (p) REVERT: B 710 ASN cc_start: 0.8120 (p0) cc_final: 0.7735 (p0) REVERT: B 736 VAL cc_start: 0.8699 (m) cc_final: 0.8469 (p) REVERT: B 737 ASP cc_start: 0.7356 (t70) cc_final: 0.7095 (m-30) REVERT: B 755 GLN cc_start: 0.8091 (tm-30) cc_final: 0.7801 (tm-30) REVERT: B 790 LYS cc_start: 0.8487 (mttt) cc_final: 0.8262 (mttp) REVERT: B 808 ASP cc_start: 0.7667 (t0) cc_final: 0.7382 (t0) REVERT: B 814 LYS cc_start: 0.7901 (mmmt) cc_final: 0.7573 (mmmt) REVERT: B 858 LEU cc_start: 0.8724 (mm) cc_final: 0.8517 (mt) REVERT: B 907 ASN cc_start: 0.8294 (t0) cc_final: 0.7929 (t0) REVERT: B 947 LYS cc_start: 0.8542 (mttt) cc_final: 0.8196 (mtpp) REVERT: B 955 ASN cc_start: 0.7769 (m-40) cc_final: 0.7539 (m-40) REVERT: B 969 LYS cc_start: 0.8466 (ptpt) cc_final: 0.8106 (ptpp) REVERT: B 996 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8284 (mp) REVERT: B 1019 ARG cc_start: 0.7709 (ttm110) cc_final: 0.7415 (ttp80) REVERT: B 1027 THR cc_start: 0.8342 (m) cc_final: 0.8081 (t) REVERT: B 1029 MET cc_start: 0.8399 (tpp) cc_final: 0.8097 (ttm) REVERT: B 1031 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7885 (mt-10) REVERT: B 1084 ASP cc_start: 0.7721 (t0) cc_final: 0.7233 (t0) REVERT: B 1123 SER cc_start: 0.8237 (t) cc_final: 0.7937 (t) REVERT: C 58 PHE cc_start: 0.8161 (m-10) cc_final: 0.7889 (m-80) REVERT: C 158 ARG cc_start: 0.6623 (mmm-85) cc_final: 0.6361 (mmt90) REVERT: C 281 GLU cc_start: 0.7974 (pp20) cc_final: 0.7685 (pp20) REVERT: C 304 LYS cc_start: 0.8819 (ttmt) cc_final: 0.8573 (ttmm) REVERT: C 316 SER cc_start: 0.8527 (t) cc_final: 0.8209 (p) REVERT: C 317 ASN cc_start: 0.7757 (m-40) cc_final: 0.7550 (m-40) REVERT: C 383 SER cc_start: 0.9064 (m) cc_final: 0.8761 (p) REVERT: C 429 PHE cc_start: 0.6567 (t80) cc_final: 0.6206 (t80) REVERT: C 642 VAL cc_start: 0.8898 (t) cc_final: 0.8639 (p) REVERT: C 663 ASP cc_start: 0.7951 (m-30) cc_final: 0.7596 (m-30) REVERT: C 698 SER cc_start: 0.8534 (t) cc_final: 0.8296 (t) REVERT: C 710 ASN cc_start: 0.8049 (p0) cc_final: 0.7810 (p0) REVERT: C 773 GLU cc_start: 0.8004 (tt0) cc_final: 0.7777 (tt0) REVERT: C 921 LYS cc_start: 0.8285 (mmtm) cc_final: 0.7933 (mmtm) REVERT: C 984 LEU cc_start: 0.7701 (tp) cc_final: 0.7451 (tp) REVERT: C 995 ARG cc_start: 0.8486 (ttm170) cc_final: 0.8114 (ttm170) REVERT: C 1051 SER cc_start: 0.8340 (t) cc_final: 0.8129 (m) REVERT: C 1094 VAL cc_start: 0.8135 (OUTLIER) cc_final: 0.7277 (t) REVERT: C 1127 ASP cc_start: 0.7274 (m-30) cc_final: 0.7020 (m-30) REVERT: E 32 PHE cc_start: 0.7940 (t80) cc_final: 0.7427 (t80) REVERT: E 33 ASN cc_start: 0.7475 (t160) cc_final: 0.7203 (t0) REVERT: E 39 LEU cc_start: 0.7776 (mt) cc_final: 0.7511 (mt) REVERT: E 60 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7730 (mp10) REVERT: E 73 LEU cc_start: 0.8049 (tp) cc_final: 0.7767 (tp) REVERT: E 76 GLN cc_start: 0.7737 (mm-40) cc_final: 0.7321 (mm-40) REVERT: E 82 MET cc_start: 0.6944 (mtt) cc_final: 0.6425 (mpp) REVERT: E 91 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7760 (pp) REVERT: E 119 ILE cc_start: 0.7351 (mm) cc_final: 0.7143 (tt) REVERT: E 123 MET cc_start: 0.8553 (mtt) cc_final: 0.8260 (mpp) REVERT: E 208 GLU cc_start: 0.6744 (tm-30) cc_final: 0.6443 (tm-30) REVERT: E 243 TYR cc_start: 0.5931 (t80) cc_final: 0.5575 (t80) REVERT: E 306 ARG cc_start: 0.7342 (tpp80) cc_final: 0.7004 (tpp80) REVERT: E 355 ASP cc_start: 0.6653 (t0) cc_final: 0.6210 (t0) REVERT: E 382 ASP cc_start: 0.7158 (m-30) cc_final: 0.6928 (m-30) REVERT: E 388 GLN cc_start: 0.6995 (mm-40) cc_final: 0.6749 (mm-40) REVERT: E 394 ASN cc_start: 0.6760 (p0) cc_final: 0.6084 (p0) REVERT: E 400 PHE cc_start: 0.7558 (m-80) cc_final: 0.7104 (m-80) REVERT: E 406 GLU cc_start: 0.7314 (mt-10) cc_final: 0.7008 (mm-30) REVERT: E 444 LEU cc_start: 0.7819 (mt) cc_final: 0.7325 (pp) REVERT: E 452 PHE cc_start: 0.6090 (t80) cc_final: 0.5545 (t80) REVERT: E 454 TYR cc_start: 0.7134 (t80) cc_final: 0.6876 (t80) REVERT: E 455 MET cc_start: 0.8558 (ppp) cc_final: 0.8153 (ppp) REVERT: E 456 LEU cc_start: 0.8175 (tt) cc_final: 0.7928 (tt) REVERT: E 457 GLU cc_start: 0.8379 (mm-30) cc_final: 0.7740 (mm-30) REVERT: E 461 TRP cc_start: 0.6548 (m-10) cc_final: 0.6189 (m-10) REVERT: E 478 TRP cc_start: 0.3485 (m100) cc_final: 0.1667 (m-90) REVERT: E 520 LEU cc_start: 0.8309 (mp) cc_final: 0.7968 (mp) REVERT: E 554 LEU cc_start: 0.8085 (tp) cc_final: 0.7851 (tp) REVERT: E 557 MET cc_start: 0.5045 (tmm) cc_final: 0.4839 (tmm) REVERT: E 562 LYS cc_start: 0.7935 (tttt) cc_final: 0.7577 (tttt) REVERT: E 571 GLU cc_start: 0.7084 (tt0) cc_final: 0.6734 (pt0) REVERT: F 323 MET cc_start: -0.0767 (mmt) cc_final: -0.1487 (mmp) REVERT: F 557 MET cc_start: 0.5644 (tmm) cc_final: 0.5419 (tmm) outliers start: 79 outliers final: 42 residues processed: 765 average time/residue: 0.2251 time to fit residues: 281.3245 Evaluate side-chains 746 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 697 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 774 GLN Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain E residue 42 GLN Chi-restraints excluded: chain E residue 60 GLN Chi-restraints excluded: chain E residue 64 ASN Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 392 LEU Chi-restraints excluded: chain F residue 199 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 335 optimal weight: 0.8980 chunk 201 optimal weight: 0.8980 chunk 228 optimal weight: 0.6980 chunk 110 optimal weight: 6.9990 chunk 28 optimal weight: 20.0000 chunk 245 optimal weight: 20.0000 chunk 115 optimal weight: 2.9990 chunk 421 optimal weight: 40.0000 chunk 301 optimal weight: 0.1980 chunk 203 optimal weight: 0.9990 chunk 365 optimal weight: 10.0000 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 787 GLN A 957 GLN B 30 ASN B 314 GLN B 703 ASN ** B 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN C 755 GLN C 925 ASN C 949 GLN ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 ASN ** E 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.221700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.156099 restraints weight = 53707.275| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 3.09 r_work: 0.3476 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 35123 Z= 0.155 Angle : 0.593 20.304 47876 Z= 0.288 Chirality : 0.045 0.336 5405 Planarity : 0.004 0.049 6115 Dihedral : 4.421 50.668 5392 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.56 % Allowed : 13.52 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.13), residues: 4213 helix: 1.09 (0.14), residues: 1348 sheet: -0.36 (0.19), residues: 637 loop : -1.67 (0.12), residues: 2228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 765 TYR 0.017 0.001 TYR B1138 PHE 0.024 0.001 PHE A 643 TRP 0.037 0.001 TRP E 566 HIS 0.008 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00348 (35050) covalent geometry : angle 0.55536 (47695) SS BOND : bond 0.00456 ( 32) SS BOND : angle 1.67595 ( 64) hydrogen bonds : bond 0.03745 ( 1343) hydrogen bonds : angle 4.49689 ( 3702) metal coordination : bond 0.00035 ( 2) link_NAG-ASN : bond 0.00794 ( 39) link_NAG-ASN : angle 4.07590 ( 117) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8426 Ramachandran restraints generated. 4213 Oldfield, 0 Emsley, 4213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8426 Ramachandran restraints generated. 4213 Oldfield, 0 Emsley, 4213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 799 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 704 time to evaluate : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.7625 (t0) cc_final: 0.7381 (t0) REVERT: A 190 ARG cc_start: 0.7445 (mtt180) cc_final: 0.7017 (mtt180) REVERT: A 206 LYS cc_start: 0.8364 (tppt) cc_final: 0.7995 (tppt) REVERT: A 227 VAL cc_start: 0.7718 (p) cc_final: 0.7464 (t) REVERT: A 273 ARG cc_start: 0.7301 (mmt90) cc_final: 0.7024 (mtp85) REVERT: A 289 VAL cc_start: 0.8804 (t) cc_final: 0.8410 (p) REVERT: A 291 CYS cc_start: 0.6451 (m) cc_final: 0.6242 (m) REVERT: A 299 THR cc_start: 0.8455 (m) cc_final: 0.8099 (p) REVERT: A 535 LYS cc_start: 0.8162 (OUTLIER) cc_final: 0.7843 (mmtp) REVERT: A 537 LYS cc_start: 0.8193 (ttmt) cc_final: 0.7912 (mtpt) REVERT: A 542 ASN cc_start: 0.8641 (t0) cc_final: 0.8327 (t0) REVERT: A 574 ASP cc_start: 0.7262 (p0) cc_final: 0.7020 (p0) REVERT: A 646 ARG cc_start: 0.7488 (mmt180) cc_final: 0.7216 (tmt170) REVERT: A 710 ASN cc_start: 0.8172 (p0) cc_final: 0.7586 (p0) REVERT: A 737 ASP cc_start: 0.7128 (t0) cc_final: 0.6771 (t0) REVERT: A 774 GLN cc_start: 0.8069 (mm-40) cc_final: 0.7847 (mm-40) REVERT: A 781 VAL cc_start: 0.8594 (OUTLIER) cc_final: 0.8371 (p) REVERT: A 884 SER cc_start: 0.8847 (m) cc_final: 0.8575 (p) REVERT: A 950 ASP cc_start: 0.7583 (t0) cc_final: 0.7276 (t0) REVERT: A 976 VAL cc_start: 0.8636 (m) cc_final: 0.8397 (p) REVERT: A 1019 ARG cc_start: 0.7671 (ttp80) cc_final: 0.7459 (ttp80) REVERT: A 1029 MET cc_start: 0.8372 (tpp) cc_final: 0.8004 (ttm) REVERT: A 1030 SER cc_start: 0.8741 (t) cc_final: 0.8492 (m) REVERT: A 1083 HIS cc_start: 0.8009 (t-170) cc_final: 0.7591 (t-170) REVERT: A 1105 THR cc_start: 0.8484 (t) cc_final: 0.7964 (p) REVERT: A 1110 TYR cc_start: 0.8619 (t80) cc_final: 0.8290 (t80) REVERT: A 1123 SER cc_start: 0.8732 (t) cc_final: 0.8510 (t) REVERT: A 1130 ILE cc_start: 0.8745 (OUTLIER) cc_final: 0.8408 (mt) REVERT: B 30 ASN cc_start: 0.8004 (OUTLIER) cc_final: 0.7783 (p0) REVERT: B 41 LYS cc_start: 0.8462 (mtmm) cc_final: 0.8255 (mtpt) REVERT: B 58 PHE cc_start: 0.8537 (m-10) cc_final: 0.8288 (m-10) REVERT: B 198 ASP cc_start: 0.7553 (t0) cc_final: 0.7048 (t0) REVERT: B 233 ILE cc_start: 0.7881 (OUTLIER) cc_final: 0.7469 (mp) REVERT: B 269 TYR cc_start: 0.8024 (m-80) cc_final: 0.7695 (m-80) REVERT: B 305 SER cc_start: 0.8809 (m) cc_final: 0.8558 (t) REVERT: B 317 ASN cc_start: 0.8204 (m-40) cc_final: 0.7967 (m-40) REVERT: B 353 TRP cc_start: 0.7018 (p-90) cc_final: 0.6360 (p-90) REVERT: B 488 CYS cc_start: 0.1410 (OUTLIER) cc_final: 0.1147 (t) REVERT: B 552 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8353 (mt) REVERT: B 599 THR cc_start: 0.8445 (OUTLIER) cc_final: 0.8132 (p) REVERT: B 603 ASN cc_start: 0.7975 (t0) cc_final: 0.7499 (t0) REVERT: B 607 GLN cc_start: 0.8328 (mt0) cc_final: 0.8050 (mt0) REVERT: B 658 ASN cc_start: 0.8551 (OUTLIER) cc_final: 0.8181 (p0) REVERT: B 663 ASP cc_start: 0.7889 (p0) cc_final: 0.7541 (p0) REVERT: B 703 ASN cc_start: 0.8385 (t0) cc_final: 0.7948 (t0) REVERT: B 704 SER cc_start: 0.8470 (m) cc_final: 0.8011 (p) REVERT: B 710 ASN cc_start: 0.8136 (p0) cc_final: 0.7936 (p0) REVERT: B 755 GLN cc_start: 0.8095 (tm-30) cc_final: 0.7811 (tm-30) REVERT: B 808 ASP cc_start: 0.7705 (t0) cc_final: 0.7423 (t0) REVERT: B 814 LYS cc_start: 0.7927 (mmmt) cc_final: 0.7630 (mmmt) REVERT: B 907 ASN cc_start: 0.8358 (t0) cc_final: 0.7991 (t0) REVERT: B 947 LYS cc_start: 0.8621 (mttt) cc_final: 0.8255 (mtpp) REVERT: B 955 ASN cc_start: 0.7841 (m-40) cc_final: 0.7626 (m-40) REVERT: B 969 LYS cc_start: 0.8461 (ptpt) cc_final: 0.8104 (ptpp) REVERT: B 996 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8283 (mp) REVERT: B 1017 GLU cc_start: 0.7771 (tp30) cc_final: 0.7241 (tp30) REVERT: B 1019 ARG cc_start: 0.7768 (ttm110) cc_final: 0.7487 (ttp80) REVERT: B 1027 THR cc_start: 0.8354 (m) cc_final: 0.8042 (t) REVERT: B 1031 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7867 (mt-10) REVERT: B 1084 ASP cc_start: 0.7770 (t0) cc_final: 0.7269 (t0) REVERT: B 1123 SER cc_start: 0.8211 (t) cc_final: 0.7916 (t) REVERT: C 58 PHE cc_start: 0.8183 (m-10) cc_final: 0.7882 (m-80) REVERT: C 104 TRP cc_start: 0.7916 (m-90) cc_final: 0.7574 (m-90) REVERT: C 158 ARG cc_start: 0.6708 (mmm-85) cc_final: 0.6405 (mmt90) REVERT: C 281 GLU cc_start: 0.7998 (pp20) cc_final: 0.7711 (pp20) REVERT: C 304 LYS cc_start: 0.8801 (ttmt) cc_final: 0.8551 (ttmm) REVERT: C 316 SER cc_start: 0.8545 (t) cc_final: 0.8193 (p) REVERT: C 319 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7697 (mtp85) REVERT: C 383 SER cc_start: 0.9059 (m) cc_final: 0.8770 (p) REVERT: C 642 VAL cc_start: 0.8930 (t) cc_final: 0.8663 (p) REVERT: C 663 ASP cc_start: 0.8004 (m-30) cc_final: 0.7682 (m-30) REVERT: C 710 ASN cc_start: 0.8125 (p0) cc_final: 0.7645 (p0) REVERT: C 921 LYS cc_start: 0.8361 (mmtm) cc_final: 0.8077 (mmtm) REVERT: C 984 LEU cc_start: 0.7684 (tp) cc_final: 0.7393 (tp) REVERT: C 1001 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8392 (tt) REVERT: C 1051 SER cc_start: 0.8288 (t) cc_final: 0.8073 (m) REVERT: C 1094 VAL cc_start: 0.8245 (m) cc_final: 0.7502 (t) REVERT: E 32 PHE cc_start: 0.7983 (t80) cc_final: 0.7430 (t80) REVERT: E 39 LEU cc_start: 0.7798 (mt) cc_final: 0.7557 (mt) REVERT: E 48 TRP cc_start: 0.6997 (t-100) cc_final: 0.6761 (t-100) REVERT: E 60 GLN cc_start: 0.7966 (OUTLIER) cc_final: 0.7704 (mp10) REVERT: E 64 ASN cc_start: 0.7159 (OUTLIER) cc_final: 0.6940 (p0) REVERT: E 73 LEU cc_start: 0.8070 (tp) cc_final: 0.7799 (tp) REVERT: E 76 GLN cc_start: 0.7721 (mm-40) cc_final: 0.7335 (mm-40) REVERT: E 82 MET cc_start: 0.7036 (mtt) cc_final: 0.6434 (mpp) REVERT: E 91 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7761 (pp) REVERT: E 123 MET cc_start: 0.8576 (mtt) cc_final: 0.8250 (mpp) REVERT: E 243 TYR cc_start: 0.5972 (t80) cc_final: 0.5602 (t80) REVERT: E 306 ARG cc_start: 0.7382 (tpp80) cc_final: 0.7052 (ttm-80) REVERT: E 355 ASP cc_start: 0.6689 (t0) cc_final: 0.6242 (t0) REVERT: E 366 MET cc_start: 0.7102 (mmt) cc_final: 0.6606 (mpp) REVERT: E 388 GLN cc_start: 0.7044 (mm-40) cc_final: 0.6805 (mm-40) REVERT: E 400 PHE cc_start: 0.7576 (m-80) cc_final: 0.7074 (m-80) REVERT: E 406 GLU cc_start: 0.7290 (mt-10) cc_final: 0.7000 (mm-30) REVERT: E 444 LEU cc_start: 0.7790 (mt) cc_final: 0.7295 (pp) REVERT: E 454 TYR cc_start: 0.7132 (t80) cc_final: 0.6711 (t80) REVERT: E 455 MET cc_start: 0.8585 (ppp) cc_final: 0.8188 (ppp) REVERT: E 457 GLU cc_start: 0.8419 (mm-30) cc_final: 0.7747 (mm-30) REVERT: E 458 LYS cc_start: 0.7109 (mppt) cc_final: 0.6897 (mppt) REVERT: E 461 TRP cc_start: 0.6610 (m-10) cc_final: 0.6226 (m-10) REVERT: E 554 LEU cc_start: 0.8065 (tp) cc_final: 0.7826 (tp) REVERT: E 557 MET cc_start: 0.5154 (tmm) cc_final: 0.4758 (tmm) REVERT: E 571 GLU cc_start: 0.7073 (tt0) cc_final: 0.6743 (pt0) REVERT: F 557 MET cc_start: 0.5666 (tmm) cc_final: 0.5447 (tmm) outliers start: 95 outliers final: 55 residues processed: 753 average time/residue: 0.2280 time to fit residues: 279.9261 Evaluate side-chains 756 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 685 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 535 LYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 658 ASN Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 973 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain E residue 35 GLU Chi-restraints excluded: chain E residue 42 GLN Chi-restraints excluded: chain E residue 60 GLN Chi-restraints excluded: chain E residue 64 ASN Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain E residue 392 LEU Chi-restraints excluded: chain F residue 199 TYR Chi-restraints excluded: chain F residue 376 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 35 optimal weight: 10.0000 chunk 371 optimal weight: 20.0000 chunk 217 optimal weight: 2.9990 chunk 180 optimal weight: 0.5980 chunk 338 optimal weight: 8.9990 chunk 210 optimal weight: 0.6980 chunk 67 optimal weight: 0.5980 chunk 363 optimal weight: 10.0000 chunk 204 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 215 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN ** B 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 856 ASN C 360 ASN C 755 GLN C 774 GLN C 949 GLN E 194 ASN ** E 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.221504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.156079 restraints weight = 53408.495| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 3.11 r_work: 0.3470 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 35123 Z= 0.153 Angle : 0.609 19.808 47876 Z= 0.294 Chirality : 0.045 0.335 5405 Planarity : 0.004 0.060 6115 Dihedral : 4.455 50.692 5392 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.05 % Allowed : 14.06 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.70 (0.13), residues: 4213 helix: 1.17 (0.14), residues: 1351 sheet: -0.27 (0.19), residues: 618 loop : -1.61 (0.12), residues: 2244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 983 TYR 0.021 0.001 TYR C 655 PHE 0.023 0.001 PHE A1075 TRP 0.041 0.001 TRP E 566 HIS 0.007 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00342 (35050) covalent geometry : angle 0.55941 (47695) SS BOND : bond 0.00376 ( 32) SS BOND : angle 1.63853 ( 64) hydrogen bonds : bond 0.03663 ( 1343) hydrogen bonds : angle 4.49472 ( 3702) metal coordination : bond 0.00084 ( 2) link_NAG-ASN : bond 0.00816 ( 39) link_NAG-ASN : angle 4.77983 ( 117) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8426 Ramachandran restraints generated. 4213 Oldfield, 0 Emsley, 4213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8426 Ramachandran restraints generated. 4213 Oldfield, 0 Emsley, 4213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 815 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 702 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.7666 (t0) cc_final: 0.7421 (t0) REVERT: A 190 ARG cc_start: 0.7376 (mtt180) cc_final: 0.6969 (mtt180) REVERT: A 227 VAL cc_start: 0.7694 (p) cc_final: 0.7459 (t) REVERT: A 273 ARG cc_start: 0.7313 (mmt90) cc_final: 0.6940 (mmt90) REVERT: A 289 VAL cc_start: 0.8807 (t) cc_final: 0.8410 (p) REVERT: A 299 THR cc_start: 0.8443 (m) cc_final: 0.8093 (p) REVERT: A 537 LYS cc_start: 0.8163 (ttmt) cc_final: 0.7907 (mtpt) REVERT: A 542 ASN cc_start: 0.8653 (t0) cc_final: 0.8341 (t0) REVERT: A 565 PHE cc_start: 0.7666 (m-10) cc_final: 0.7424 (m-10) REVERT: A 574 ASP cc_start: 0.7303 (p0) cc_final: 0.7059 (p0) REVERT: A 615 VAL cc_start: 0.8199 (p) cc_final: 0.7951 (m) REVERT: A 646 ARG cc_start: 0.7541 (mmt180) cc_final: 0.7264 (tmt170) REVERT: A 655 TYR cc_start: 0.8413 (t80) cc_final: 0.7975 (t80) REVERT: A 710 ASN cc_start: 0.8070 (p0) cc_final: 0.7728 (p0) REVERT: A 737 ASP cc_start: 0.7203 (t0) cc_final: 0.6948 (t0) REVERT: A 774 GLN cc_start: 0.8073 (mm-40) cc_final: 0.7849 (mm-40) REVERT: A 884 SER cc_start: 0.8820 (m) cc_final: 0.8572 (p) REVERT: A 950 ASP cc_start: 0.7563 (t0) cc_final: 0.7251 (t0) REVERT: A 957 GLN cc_start: 0.8221 (tt0) cc_final: 0.7974 (tt0) REVERT: A 976 VAL cc_start: 0.8631 (m) cc_final: 0.8424 (p) REVERT: A 979 ASP cc_start: 0.7092 (t0) cc_final: 0.6780 (t0) REVERT: A 983 ARG cc_start: 0.8000 (ttm170) cc_final: 0.7785 (ttm170) REVERT: A 1030 SER cc_start: 0.8774 (t) cc_final: 0.8525 (m) REVERT: A 1105 THR cc_start: 0.8481 (t) cc_final: 0.7982 (p) REVERT: A 1110 TYR cc_start: 0.8611 (t80) cc_final: 0.8406 (t80) REVERT: A 1123 SER cc_start: 0.8705 (t) cc_final: 0.8496 (t) REVERT: A 1130 ILE cc_start: 0.8755 (OUTLIER) cc_final: 0.8433 (mt) REVERT: B 58 PHE cc_start: 0.8561 (m-10) cc_final: 0.8351 (m-10) REVERT: B 198 ASP cc_start: 0.7661 (t0) cc_final: 0.7150 (t0) REVERT: B 233 ILE cc_start: 0.7961 (OUTLIER) cc_final: 0.7555 (mp) REVERT: B 305 SER cc_start: 0.8835 (m) cc_final: 0.8595 (t) REVERT: B 321 GLN cc_start: 0.7715 (mm-40) cc_final: 0.7419 (mm110) REVERT: B 353 TRP cc_start: 0.7021 (p-90) cc_final: 0.6315 (p-90) REVERT: B 488 CYS cc_start: 0.1452 (OUTLIER) cc_final: 0.1187 (t) REVERT: B 552 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8344 (mt) REVERT: B 599 THR cc_start: 0.8404 (OUTLIER) cc_final: 0.8082 (p) REVERT: B 603 ASN cc_start: 0.7977 (t0) cc_final: 0.7491 (t0) REVERT: B 607 GLN cc_start: 0.8345 (mt0) cc_final: 0.8097 (mt0) REVERT: B 703 ASN cc_start: 0.8367 (t0) cc_final: 0.7938 (t0) REVERT: B 710 ASN cc_start: 0.8152 (p0) cc_final: 0.7801 (p0) REVERT: B 755 GLN cc_start: 0.8146 (tm-30) cc_final: 0.7873 (tm-30) REVERT: B 814 LYS cc_start: 0.7907 (mmmt) cc_final: 0.7598 (mmmt) REVERT: B 907 ASN cc_start: 0.8360 (t0) cc_final: 0.8014 (t0) REVERT: B 947 LYS cc_start: 0.8636 (mttt) cc_final: 0.8276 (mtpp) REVERT: B 955 ASN cc_start: 0.7838 (m-40) cc_final: 0.7633 (m110) REVERT: B 969 LYS cc_start: 0.8430 (ptpt) cc_final: 0.8071 (ptpp) REVERT: B 996 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8287 (mp) REVERT: B 1017 GLU cc_start: 0.7822 (tp30) cc_final: 0.7568 (tp30) REVERT: B 1019 ARG cc_start: 0.7747 (ttm110) cc_final: 0.7468 (ttp80) REVERT: B 1027 THR cc_start: 0.8342 (m) cc_final: 0.8046 (t) REVERT: B 1031 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7885 (mt-10) REVERT: B 1084 ASP cc_start: 0.7776 (t0) cc_final: 0.7280 (t0) REVERT: B 1123 SER cc_start: 0.8213 (t) cc_final: 0.7916 (t) REVERT: C 58 PHE cc_start: 0.8215 (m-10) cc_final: 0.7888 (m-80) REVERT: C 104 TRP cc_start: 0.7948 (m-90) cc_final: 0.7614 (m-90) REVERT: C 281 GLU cc_start: 0.7972 (pp20) cc_final: 0.7696 (pp20) REVERT: C 304 LYS cc_start: 0.8804 (ttmt) cc_final: 0.8561 (ttmm) REVERT: C 383 SER cc_start: 0.9033 (m) cc_final: 0.8747 (p) REVERT: C 536 ASN cc_start: 0.8311 (m110) cc_final: 0.8096 (m-40) REVERT: C 563 GLN cc_start: 0.7750 (OUTLIER) cc_final: 0.7537 (tt0) REVERT: C 642 VAL cc_start: 0.8943 (OUTLIER) cc_final: 0.8668 (p) REVERT: C 646 ARG cc_start: 0.8004 (mtp180) cc_final: 0.7727 (mtp180) REVERT: C 663 ASP cc_start: 0.8020 (m-30) cc_final: 0.7690 (m-30) REVERT: C 670 ILE cc_start: 0.8868 (OUTLIER) cc_final: 0.8604 (mt) REVERT: C 710 ASN cc_start: 0.8161 (p0) cc_final: 0.7693 (p0) REVERT: C 748 GLU cc_start: 0.7510 (pm20) cc_final: 0.7027 (pt0) REVERT: C 921 LYS cc_start: 0.8358 (mmtm) cc_final: 0.8059 (mmtm) REVERT: C 984 LEU cc_start: 0.7698 (tp) cc_final: 0.7368 (tp) REVERT: C 995 ARG cc_start: 0.8506 (ttm170) cc_final: 0.8122 (ttm170) REVERT: C 1001 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8422 (tt) REVERT: C 1051 SER cc_start: 0.8285 (t) cc_final: 0.8061 (m) REVERT: C 1144 GLU cc_start: 0.8105 (tp30) cc_final: 0.7790 (tp30) REVERT: E 32 PHE cc_start: 0.7976 (t80) cc_final: 0.7396 (t80) REVERT: E 33 ASN cc_start: 0.7465 (t160) cc_final: 0.7179 (t0) REVERT: E 39 LEU cc_start: 0.7814 (mt) cc_final: 0.7593 (mt) REVERT: E 48 TRP cc_start: 0.6979 (t-100) cc_final: 0.6751 (t-100) REVERT: E 60 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.7723 (mp10) REVERT: E 73 LEU cc_start: 0.8103 (tp) cc_final: 0.7827 (tp) REVERT: E 76 GLN cc_start: 0.7691 (mm-40) cc_final: 0.7308 (mm-40) REVERT: E 82 MET cc_start: 0.7095 (mtt) cc_final: 0.6464 (mpp) REVERT: E 91 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7759 (pp) REVERT: E 123 MET cc_start: 0.8621 (mtt) cc_final: 0.8261 (mpp) REVERT: E 208 GLU cc_start: 0.6739 (tm-30) cc_final: 0.6499 (tm-30) REVERT: E 243 TYR cc_start: 0.5993 (t80) cc_final: 0.5628 (t80) REVERT: E 306 ARG cc_start: 0.7391 (tpp80) cc_final: 0.7081 (ttm-80) REVERT: E 355 ASP cc_start: 0.6704 (t0) cc_final: 0.6249 (t0) REVERT: E 360 MET cc_start: 0.4280 (tpt) cc_final: 0.3164 (tpt) REVERT: E 388 GLN cc_start: 0.7094 (mm-40) cc_final: 0.6880 (mm-40) REVERT: E 394 ASN cc_start: 0.6708 (p0) cc_final: 0.6035 (p0) REVERT: E 400 PHE cc_start: 0.7576 (m-80) cc_final: 0.7165 (m-80) REVERT: E 406 GLU cc_start: 0.7253 (mt-10) cc_final: 0.6974 (mm-30) REVERT: E 444 LEU cc_start: 0.7769 (mt) cc_final: 0.7254 (pp) REVERT: E 454 TYR cc_start: 0.7173 (t80) cc_final: 0.6860 (t80) REVERT: E 455 MET cc_start: 0.8586 (ppp) cc_final: 0.7880 (ppp) REVERT: E 456 LEU cc_start: 0.8174 (tt) cc_final: 0.7710 (mt) REVERT: E 457 GLU cc_start: 0.8412 (mm-30) cc_final: 0.7680 (mm-30) REVERT: E 461 TRP cc_start: 0.6673 (m-10) cc_final: 0.6279 (m-10) REVERT: E 557 MET cc_start: 0.5170 (tmm) cc_final: 0.4810 (tmm) REVERT: E 562 LYS cc_start: 0.7828 (tttt) cc_final: 0.7513 (tttt) REVERT: E 571 GLU cc_start: 0.7056 (tt0) cc_final: 0.6716 (pt0) REVERT: F 557 MET cc_start: 0.5656 (tmm) cc_final: 0.5439 (tmm) outliers start: 113 outliers final: 65 residues processed: 759 average time/residue: 0.2259 time to fit residues: 279.5283 Evaluate side-chains 766 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 688 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 774 GLN Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1055 SER Chi-restraints excluded: chain C residue 1111 GLU Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1120 THR Chi-restraints excluded: chain E residue 35 GLU Chi-restraints excluded: chain E residue 42 GLN Chi-restraints excluded: chain E residue 60 GLN Chi-restraints excluded: chain E residue 64 ASN Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain F residue 376 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 198 optimal weight: 0.9990 chunk 171 optimal weight: 0.0970 chunk 293 optimal weight: 0.9990 chunk 233 optimal weight: 0.9990 chunk 28 optimal weight: 20.0000 chunk 129 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 319 optimal weight: 10.0000 chunk 117 optimal weight: 0.9990 chunk 239 optimal weight: 7.9990 chunk 361 optimal weight: 0.5980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 787 GLN B 703 ASN B 856 ASN C 317 ASN C 755 GLN C 774 GLN C 949 GLN E 121 ASN ** E 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.221043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.156171 restraints weight = 53508.626| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 2.95 r_work: 0.3476 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.4223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 35123 Z= 0.155 Angle : 0.609 19.178 47876 Z= 0.297 Chirality : 0.045 0.333 5405 Planarity : 0.004 0.046 6115 Dihedral : 4.366 51.812 5392 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.94 % Allowed : 14.49 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.13), residues: 4213 helix: 1.26 (0.14), residues: 1357 sheet: -0.33 (0.19), residues: 647 loop : -1.53 (0.13), residues: 2209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 765 TYR 0.020 0.001 TYR B 904 PHE 0.023 0.001 PHE B 92 TRP 0.055 0.001 TRP E 566 HIS 0.007 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00350 (35050) covalent geometry : angle 0.56828 (47695) SS BOND : bond 0.00363 ( 32) SS BOND : angle 1.71687 ( 64) hydrogen bonds : bond 0.03710 ( 1343) hydrogen bonds : angle 4.51005 ( 3702) metal coordination : bond 0.00087 ( 2) link_NAG-ASN : bond 0.00788 ( 39) link_NAG-ASN : angle 4.32712 ( 117) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8426 Ramachandran restraints generated. 4213 Oldfield, 0 Emsley, 4213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8426 Ramachandran restraints generated. 4213 Oldfield, 0 Emsley, 4213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 813 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 704 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ASP cc_start: 0.7749 (t0) cc_final: 0.7506 (t0) REVERT: A 42 VAL cc_start: 0.8230 (t) cc_final: 0.7774 (m) REVERT: A 190 ARG cc_start: 0.7368 (mtt180) cc_final: 0.6966 (mtt180) REVERT: A 227 VAL cc_start: 0.7778 (p) cc_final: 0.7556 (t) REVERT: A 273 ARG cc_start: 0.7301 (mmt90) cc_final: 0.7016 (mtp85) REVERT: A 289 VAL cc_start: 0.8801 (t) cc_final: 0.8388 (p) REVERT: A 299 THR cc_start: 0.8469 (m) cc_final: 0.8123 (p) REVERT: A 321 GLN cc_start: 0.8265 (mm-40) cc_final: 0.8062 (mm-40) REVERT: A 537 LYS cc_start: 0.8193 (ttmt) cc_final: 0.7960 (ttpp) REVERT: A 542 ASN cc_start: 0.8647 (t0) cc_final: 0.8328 (t0) REVERT: A 559 PHE cc_start: 0.8267 (m-10) cc_final: 0.8008 (m-10) REVERT: A 574 ASP cc_start: 0.7287 (p0) cc_final: 0.7044 (p0) REVERT: A 615 VAL cc_start: 0.8279 (p) cc_final: 0.8065 (m) REVERT: A 646 ARG cc_start: 0.7716 (mmt180) cc_final: 0.7409 (tmt170) REVERT: A 655 TYR cc_start: 0.8409 (t80) cc_final: 0.8127 (t80) REVERT: A 710 ASN cc_start: 0.8079 (p0) cc_final: 0.7753 (p0) REVERT: A 737 ASP cc_start: 0.7307 (t0) cc_final: 0.6889 (t0) REVERT: A 774 GLN cc_start: 0.8075 (mm-40) cc_final: 0.7852 (mm-40) REVERT: A 884 SER cc_start: 0.8802 (m) cc_final: 0.8553 (p) REVERT: A 950 ASP cc_start: 0.7511 (t0) cc_final: 0.7224 (t0) REVERT: A 976 VAL cc_start: 0.8622 (m) cc_final: 0.8408 (p) REVERT: A 979 ASP cc_start: 0.7192 (t0) cc_final: 0.6849 (t0) REVERT: A 1030 SER cc_start: 0.8791 (t) cc_final: 0.8542 (m) REVERT: A 1094 VAL cc_start: 0.8190 (m) cc_final: 0.7309 (t) REVERT: A 1105 THR cc_start: 0.8566 (t) cc_final: 0.8092 (p) REVERT: A 1110 TYR cc_start: 0.8620 (t80) cc_final: 0.8356 (t80) REVERT: A 1130 ILE cc_start: 0.8795 (OUTLIER) cc_final: 0.8488 (mt) REVERT: B 58 PHE cc_start: 0.8603 (m-10) cc_final: 0.8393 (m-10) REVERT: B 198 ASP cc_start: 0.7739 (t0) cc_final: 0.7221 (t0) REVERT: B 233 ILE cc_start: 0.8047 (OUTLIER) cc_final: 0.7631 (mp) REVERT: B 305 SER cc_start: 0.8827 (m) cc_final: 0.8602 (t) REVERT: B 317 ASN cc_start: 0.8177 (m110) cc_final: 0.7943 (m-40) REVERT: B 321 GLN cc_start: 0.7709 (mm-40) cc_final: 0.7446 (mm110) REVERT: B 353 TRP cc_start: 0.7007 (p-90) cc_final: 0.6344 (p-90) REVERT: B 488 CYS cc_start: 0.1533 (OUTLIER) cc_final: 0.1272 (t) REVERT: B 599 THR cc_start: 0.8388 (OUTLIER) cc_final: 0.8068 (p) REVERT: B 603 ASN cc_start: 0.7754 (t0) cc_final: 0.7293 (t0) REVERT: B 607 GLN cc_start: 0.8344 (mt0) cc_final: 0.8110 (mt0) REVERT: B 642 VAL cc_start: 0.8997 (t) cc_final: 0.8666 (p) REVERT: B 698 SER cc_start: 0.8667 (t) cc_final: 0.8264 (p) REVERT: B 703 ASN cc_start: 0.8374 (t0) cc_final: 0.7925 (t0) REVERT: B 710 ASN cc_start: 0.8124 (p0) cc_final: 0.7765 (p0) REVERT: B 730 SER cc_start: 0.8790 (t) cc_final: 0.8542 (m) REVERT: B 737 ASP cc_start: 0.7484 (m-30) cc_final: 0.6882 (t0) REVERT: B 755 GLN cc_start: 0.8140 (tm-30) cc_final: 0.7921 (tm-30) REVERT: B 790 LYS cc_start: 0.8502 (mttp) cc_final: 0.7991 (mttp) REVERT: B 808 ASP cc_start: 0.7797 (t0) cc_final: 0.7498 (t0) REVERT: B 814 LYS cc_start: 0.7851 (mmmt) cc_final: 0.7559 (mmmt) REVERT: B 904 TYR cc_start: 0.7465 (m-10) cc_final: 0.7161 (m-10) REVERT: B 907 ASN cc_start: 0.8358 (t0) cc_final: 0.8004 (t0) REVERT: B 947 LYS cc_start: 0.8562 (mttt) cc_final: 0.8214 (mtpp) REVERT: B 955 ASN cc_start: 0.7849 (m-40) cc_final: 0.7628 (m110) REVERT: B 963 VAL cc_start: 0.8992 (m) cc_final: 0.8665 (t) REVERT: B 969 LYS cc_start: 0.8411 (ptpt) cc_final: 0.8062 (ptpp) REVERT: B 996 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8303 (mp) REVERT: B 1017 GLU cc_start: 0.7828 (tp30) cc_final: 0.7567 (tp30) REVERT: B 1019 ARG cc_start: 0.7704 (ttm110) cc_final: 0.7442 (ttp80) REVERT: B 1027 THR cc_start: 0.8328 (m) cc_final: 0.8096 (t) REVERT: B 1031 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7841 (mt-10) REVERT: B 1084 ASP cc_start: 0.7770 (t0) cc_final: 0.7267 (t0) REVERT: B 1123 SER cc_start: 0.8181 (t) cc_final: 0.7884 (t) REVERT: C 58 PHE cc_start: 0.8236 (m-10) cc_final: 0.7926 (m-80) REVERT: C 104 TRP cc_start: 0.7931 (m-90) cc_final: 0.7580 (m-90) REVERT: C 281 GLU cc_start: 0.7972 (pp20) cc_final: 0.7681 (pp20) REVERT: C 304 LYS cc_start: 0.8791 (ttmt) cc_final: 0.8538 (ttmm) REVERT: C 309 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7372 (mm-30) REVERT: C 317 ASN cc_start: 0.7558 (m-40) cc_final: 0.7027 (m-40) REVERT: C 383 SER cc_start: 0.8983 (m) cc_final: 0.8674 (p) REVERT: C 429 PHE cc_start: 0.6628 (t80) cc_final: 0.6302 (t80) REVERT: C 436 TRP cc_start: 0.8003 (p90) cc_final: 0.7685 (p90) REVERT: C 488 CYS cc_start: 0.2324 (OUTLIER) cc_final: 0.0889 (p) REVERT: C 538 CYS cc_start: 0.6924 (m) cc_final: 0.6569 (m) REVERT: C 559 PHE cc_start: 0.8393 (m-10) cc_final: 0.7971 (m-80) REVERT: C 642 VAL cc_start: 0.8930 (OUTLIER) cc_final: 0.8593 (p) REVERT: C 646 ARG cc_start: 0.8080 (mtp180) cc_final: 0.7822 (mtp180) REVERT: C 651 ILE cc_start: 0.8463 (pt) cc_final: 0.7996 (mm) REVERT: C 663 ASP cc_start: 0.7981 (m-30) cc_final: 0.7652 (m-30) REVERT: C 670 ILE cc_start: 0.8866 (OUTLIER) cc_final: 0.8593 (mt) REVERT: C 699 LEU cc_start: 0.8591 (mm) cc_final: 0.8374 (mm) REVERT: C 710 ASN cc_start: 0.8193 (p0) cc_final: 0.7789 (p0) REVERT: C 748 GLU cc_start: 0.7549 (pm20) cc_final: 0.7140 (pt0) REVERT: C 921 LYS cc_start: 0.8308 (mmtm) cc_final: 0.8012 (mmtm) REVERT: C 983 ARG cc_start: 0.7776 (ttt180) cc_final: 0.7437 (mtp85) REVERT: C 984 LEU cc_start: 0.7706 (tp) cc_final: 0.7371 (tp) REVERT: C 995 ARG cc_start: 0.8492 (ttm170) cc_final: 0.8131 (ttm170) REVERT: C 1001 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8443 (tt) REVERT: C 1051 SER cc_start: 0.8342 (t) cc_final: 0.8118 (m) REVERT: C 1107 ARG cc_start: 0.7866 (mtt90) cc_final: 0.7548 (mtt90) REVERT: C 1111 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7619 (tt0) REVERT: E 32 PHE cc_start: 0.7971 (t80) cc_final: 0.7361 (t80) REVERT: E 33 ASN cc_start: 0.7459 (t160) cc_final: 0.7172 (t0) REVERT: E 39 LEU cc_start: 0.7835 (mt) cc_final: 0.7619 (mt) REVERT: E 48 TRP cc_start: 0.6983 (t-100) cc_final: 0.6697 (t-100) REVERT: E 60 GLN cc_start: 0.7964 (OUTLIER) cc_final: 0.7748 (mp10) REVERT: E 73 LEU cc_start: 0.8115 (tp) cc_final: 0.7851 (tp) REVERT: E 76 GLN cc_start: 0.7735 (mm-40) cc_final: 0.7317 (mm-40) REVERT: E 82 MET cc_start: 0.7088 (mtt) cc_final: 0.6459 (mpp) REVERT: E 91 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7782 (pp) REVERT: E 123 MET cc_start: 0.8649 (mtt) cc_final: 0.8298 (mpp) REVERT: E 243 TYR cc_start: 0.6040 (t80) cc_final: 0.5679 (t80) REVERT: E 306 ARG cc_start: 0.7340 (tpp80) cc_final: 0.7051 (ttm-80) REVERT: E 355 ASP cc_start: 0.6664 (t0) cc_final: 0.6232 (t0) REVERT: E 366 MET cc_start: 0.6880 (mmt) cc_final: 0.6652 (mpp) REVERT: E 369 PHE cc_start: 0.7624 (t80) cc_final: 0.7375 (t80) REVERT: E 388 GLN cc_start: 0.7154 (mm-40) cc_final: 0.6918 (mm-40) REVERT: E 400 PHE cc_start: 0.7560 (m-80) cc_final: 0.7150 (m-80) REVERT: E 406 GLU cc_start: 0.7204 (mt-10) cc_final: 0.6952 (mm-30) REVERT: E 444 LEU cc_start: 0.7712 (mt) cc_final: 0.7185 (pp) REVERT: E 454 TYR cc_start: 0.7197 (t80) cc_final: 0.6893 (t80) REVERT: E 455 MET cc_start: 0.8634 (ppp) cc_final: 0.7971 (ppp) REVERT: E 456 LEU cc_start: 0.8132 (tt) cc_final: 0.7736 (mt) REVERT: E 457 GLU cc_start: 0.8478 (mm-30) cc_final: 0.7805 (mm-30) REVERT: E 461 TRP cc_start: 0.6600 (m-10) cc_final: 0.6236 (m-10) REVERT: E 557 MET cc_start: 0.5231 (tmm) cc_final: 0.4834 (tmm) REVERT: E 571 GLU cc_start: 0.6995 (tt0) cc_final: 0.6786 (tt0) REVERT: F 557 MET cc_start: 0.5596 (tmm) cc_final: 0.5387 (tmm) outliers start: 109 outliers final: 70 residues processed: 758 average time/residue: 0.2272 time to fit residues: 280.5263 Evaluate side-chains 775 residues out of total 3742 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 692 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 748 GLU Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 787 GLN Chi-restraints excluded: chain A residue 790 LYS Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 966 LEU Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 1120 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 659 SER Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 887 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 997 ILE Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1082 CYS Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 356 LYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 488 CYS Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 641 ASN Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 670 ILE Chi-restraints excluded: chain C residue 698 SER Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 816 SER Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1111 GLU Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain E residue 35 GLU Chi-restraints excluded: chain E residue 42 GLN Chi-restraints excluded: chain E residue 60 GLN Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 91 LEU Chi-restraints excluded: chain E residue 283 VAL Chi-restraints excluded: chain F residue 376 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 64.1534 > 50: distance: 25 - 47: 18.717 distance: 30 - 55: 17.524 distance: 43 - 47: 20.051 distance: 47 - 48: 21.071 distance: 48 - 49: 27.489 distance: 48 - 51: 20.943 distance: 49 - 50: 9.958 distance: 49 - 55: 28.224 distance: 50 - 76: 17.612 distance: 51 - 52: 19.654 distance: 52 - 53: 18.410 distance: 52 - 54: 18.006 distance: 55 - 56: 28.488 distance: 56 - 57: 12.981 distance: 56 - 59: 12.834 distance: 57 - 58: 43.615 distance: 57 - 63: 13.650 distance: 59 - 60: 42.486 distance: 60 - 61: 33.324 distance: 61 - 62: 6.446 distance: 63 - 64: 10.585 distance: 64 - 65: 21.722 distance: 64 - 67: 35.172 distance: 65 - 66: 5.883 distance: 65 - 71: 41.982 distance: 67 - 68: 41.840 distance: 68 - 69: 15.235 distance: 68 - 70: 7.434 distance: 71 - 72: 33.376 distance: 72 - 73: 8.006 distance: 72 - 75: 32.930 distance: 73 - 74: 27.822 distance: 73 - 76: 28.050 distance: 76 - 77: 3.736 distance: 77 - 78: 17.751 distance: 77 - 80: 32.717 distance: 78 - 79: 16.881 distance: 78 - 88: 14.674 distance: 80 - 81: 23.849 distance: 81 - 82: 12.589 distance: 81 - 83: 26.397 distance: 82 - 84: 26.490 distance: 83 - 85: 28.272 distance: 84 - 86: 27.007 distance: 85 - 86: 19.147 distance: 86 - 87: 21.168 distance: 88 - 89: 3.879 distance: 88 - 94: 40.029 distance: 89 - 90: 28.350 distance: 89 - 92: 42.841 distance: 90 - 91: 18.473 distance: 90 - 95: 36.998 distance: 92 - 93: 15.333 distance: 95 - 96: 41.605 distance: 96 - 97: 19.820 distance: 96 - 99: 8.462 distance: 97 - 98: 4.234 distance: 97 - 101: 17.121 distance: 99 - 100: 11.770 distance: 102 - 103: 7.074 distance: 102 - 105: 10.807 distance: 103 - 104: 9.053 distance: 103 - 113: 24.095 distance: 105 - 106: 30.855 distance: 106 - 107: 6.282 distance: 106 - 108: 21.258 distance: 107 - 109: 8.668 distance: 108 - 110: 24.721 distance: 109 - 111: 7.521 distance: 110 - 111: 11.266 distance: 111 - 112: 15.635 distance: 113 - 114: 22.070 distance: 114 - 115: 23.812 distance: 114 - 117: 35.245 distance: 115 - 116: 8.705 distance: 117 - 118: 38.354 distance: 118 - 120: 7.877 distance: 122 - 123: 26.250 distance: 122 - 125: 13.495 distance: 123 - 124: 25.048 distance: 123 - 127: 20.169 distance: 125 - 126: 27.559