Starting phenix.real_space_refine on Tue Aug 26 15:36:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wgv_37516/08_2025/8wgv_37516.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wgv_37516/08_2025/8wgv_37516.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wgv_37516/08_2025/8wgv_37516.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wgv_37516/08_2025/8wgv_37516.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wgv_37516/08_2025/8wgv_37516.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wgv_37516/08_2025/8wgv_37516.map" } resolution = 2.92 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= -0.003 sd= 0.070 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 191 5.16 5 C 24693 2.51 5 N 6350 2.21 5 O 7454 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 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: 38688 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 7773 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 993, 7762 Classifications: {'peptide': 993} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 54, 'TRANS': 938} Chain breaks: 9 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Conformer: "B" Number of residues, atoms: 993, 7762 Classifications: {'peptide': 993} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 54, 'TRANS': 938} Chain breaks: 9 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 bond proxies already assigned to first conformer: 7929 Chain: "B" Number of atoms: 7770 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 992, 7759 Classifications: {'peptide': 992} Link IDs: {'PTRANS': 54, 'TRANS': 937} Chain breaks: 8 Conformer: "B" Number of residues, atoms: 992, 7759 Classifications: {'peptide': 992} Link IDs: {'PTRANS': 54, 'TRANS': 937} Chain breaks: 8 bond proxies already assigned to first conformer: 7927 Chain: "C" Number of atoms: 7761 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 991, 7750 Classifications: {'peptide': 991} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 54, 'TRANS': 936} Chain breaks: 8 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 991, 7750 Classifications: {'peptide': 991} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 54, 'TRANS': 936} Chain breaks: 8 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 7918 Chain: "D" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "E" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "F" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "D" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "E" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "F" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AARG A 493 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 493 " occ=0.50 residue: pdb=" N AARG B 493 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG B 493 " occ=0.50 residue: pdb=" N AARG C 493 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG C 493 " occ=0.50 Time building chain proxies: 12.34, per 1000 atoms: 0.32 Number of scatterers: 38688 At special positions: 0 Unit cell: (152.848, 172.42, 241.388, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 191 16.00 O 7454 8.00 N 6350 7.00 C 24693 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=28, 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 336 " - pdb=" SG CYS A 361 " 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 662 " - pdb=" SG CYS A 671 " 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=2.02 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 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=2.02 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 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 BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 234 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A 717 " " NAG A1308 " - " ASN A 801 " " NAG A1309 " - " ASN A1074 " " NAG A1310 " - " ASN A1134 " " NAG A1311 " - " ASN A1098 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 331 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 657 " " NAG B1306 " - " ASN B 709 " " NAG B1307 " - " ASN B 717 " " NAG B1308 " - " ASN B 801 " " NAG B1309 " - " ASN B1074 " " NAG B1310 " - " ASN B1134 " " NAG B1311 " - " ASN B1098 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 234 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C 603 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 657 " " NAG C1309 " - " ASN C 709 " " NAG C1310 " - " ASN C 717 " " NAG C1311 " - " ASN C 801 " " NAG C1312 " - " ASN C1074 " " NAG C1313 " - " ASN C1134 " " NAG C1314 " - " ASN C1098 " " NAG D 701 " - " ASN D 322 " " NAG D 702 " - " ASN D 432 " " NAG D 703 " - " ASN D 103 " " NAG D 704 " - " ASN D 90 " " NAG D 705 " - " ASN D 53 " " NAG E 701 " - " ASN E 322 " " NAG E 702 " - " ASN E 432 " " NAG E 703 " - " ASN E 103 " " NAG E 704 " - " ASN E 90 " " NAG E 705 " - " ASN E 53 " " NAG F 701 " - " ASN F 322 " " NAG F 702 " - " ASN F 432 " " NAG F 703 " - " ASN F 103 " " NAG F 704 " - " ASN F 90 " " NAG F 705 " - " ASN F 53 " " NAG G 1 " - " ASN D 546 " " NAG H 1 " - " ASN E 546 " " NAG I 1 " - " ASN F 546 " Time building additional restraints: 3.36 Conformation dependent library (CDL) restraints added in 1.9 seconds Enol-peptide restraints added in 715.3 nanoseconds 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8970 Finding SS restraints... Secondary structure from input PDB file: 151 helices and 50 sheets defined 37.8% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 372 removed outlier: 3.704A pdb=" N LEU A 368 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE A 371 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 388 Processing helix chain 'A' and resid 403 through 410 removed outlier: 4.121A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.851A pdb=" N ASP A 442 " --> pdb=" O SER A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.545A pdb=" N CYS A 743 " --> pdb=" O THR A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.900A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.802A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LYS A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.673A pdb=" N ALA A 903 " --> pdb=" O PRO A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.099A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 removed outlier: 3.739A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.578A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 981 removed outlier: 3.628A pdb=" N ILE A 980 " --> pdb=" O LEU A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.671A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.967A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 364 through 368 removed outlier: 3.552A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 411 removed outlier: 3.820A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLN B 409 " --> pdb=" O GLU B 406 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA B 411 " --> pdb=" O SER B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 removed outlier: 4.186A pdb=" N TYR B 421 " --> pdb=" O ASN B 417 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASN B 422 " --> pdb=" O ILE B 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 417 through 422' Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.523A pdb=" N HIS B 505 " --> pdb=" O GLY B 502 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLN B 506 " --> pdb=" O VAL B 503 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 502 through 506' Processing helix chain 'B' and resid 542 through 546 Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.705A pdb=" N GLU B 619 " --> pdb=" O ASN B 616 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 616 through 620' Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 757 Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 827 removed outlier: 3.673A pdb=" N THR B 827 " --> pdb=" O PHE B 823 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 887 through 891 removed outlier: 4.072A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.108A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.664A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 967 removed outlier: 3.746A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ALA B 958 " --> pdb=" O HIS B 954 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 983 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.442A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 removed outlier: 4.075A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.043A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 411 removed outlier: 3.640A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 542 through 546 removed outlier: 3.783A pdb=" N GLY C 545 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.736A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 783 removed outlier: 4.061A pdb=" N THR C 761 " --> pdb=" O GLY C 757 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 827 removed outlier: 3.761A pdb=" N THR C 827 " --> pdb=" O PHE C 823 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.043A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 Processing helix chain 'C' and resid 941 through 944 Processing helix chain 'C' and resid 945 through 967 removed outlier: 4.057A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.771A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 4.036A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 27 removed outlier: 3.718A pdb=" N ALA D 25 " --> pdb=" O ILE D 21 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR D 27 " --> pdb=" O GLU D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 53 removed outlier: 3.759A pdb=" N LYS D 31 " --> pdb=" O THR D 27 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N PHE D 32 " --> pdb=" O PHE D 28 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ALA D 46 " --> pdb=" O GLN D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 59 No H-bonds generated for 'chain 'D' and resid 57 through 59' Processing helix chain 'D' and resid 60 through 65 removed outlier: 3.819A pdb=" N ASN D 64 " --> pdb=" O GLN D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 72 Processing helix chain 'D' and resid 72 through 79 removed outlier: 3.857A pdb=" N GLN D 76 " --> pdb=" O PHE D 72 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER D 77 " --> pdb=" O LEU D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 101 Processing helix chain 'D' and resid 109 through 129 removed outlier: 3.584A pdb=" N SER D 113 " --> pdb=" O SER D 109 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ARG D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ASN D 117 " --> pdb=" O SER D 113 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N THR D 118 " --> pdb=" O LYS D 114 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N TYR D 127 " --> pdb=" O MET D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 154 removed outlier: 4.398A pdb=" N ALA D 153 " --> pdb=" O ASN D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 167 removed outlier: 4.156A pdb=" N TRP D 163 " --> pdb=" O ASN D 159 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ALA D 164 " --> pdb=" O GLU D 160 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N TRP D 165 " --> pdb=" O ARG D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 189 removed outlier: 3.833A pdb=" N GLU D 181 " --> pdb=" O ARG D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 194 removed outlier: 3.740A pdb=" N ALA D 193 " --> pdb=" O MET D 190 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASN D 194 " --> pdb=" O ALA D 191 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 190 through 194' Processing helix chain 'D' and resid 198 through 200 No H-bonds generated for 'chain 'D' and resid 198 through 200' Processing helix chain 'D' and resid 201 through 206 Processing helix chain 'D' and resid 220 through 248 removed outlier: 3.959A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N VAL D 226 " --> pdb=" O LEU D 222 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N GLU D 227 " --> pdb=" O ILE D 223 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N GLU D 232 " --> pdb=" O HIS D 228 " (cutoff:3.500A) Proline residue: D 235 - end of helix removed outlier: 3.733A pdb=" N HIS D 239 " --> pdb=" O PRO D 235 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU D 240 " --> pdb=" O LEU D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 275 through 281 removed outlier: 4.127A pdb=" N SER D 280 " --> pdb=" O ASN D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 299 Processing helix chain 'D' and resid 303 through 319 removed outlier: 4.032A pdb=" N ILE D 307 " --> pdb=" O ASP D 303 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N PHE D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 331 removed outlier: 3.732A pdb=" N SER D 331 " --> pdb=" O TRP D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 385 removed outlier: 4.066A pdb=" N ALA D 372 " --> pdb=" O ASP D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 413 removed outlier: 3.594A pdb=" N ILE D 407 " --> pdb=" O ALA D 403 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU D 410 " --> pdb=" O GLU D 406 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER D 411 " --> pdb=" O ILE D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 422 removed outlier: 3.934A pdb=" N SER D 420 " --> pdb=" O LYS D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 440 removed outlier: 4.200A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ILE D 436 " --> pdb=" O ASN D 432 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N PHE D 438 " --> pdb=" O THR D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 440 through 445 Processing helix chain 'D' and resid 449 through 466 removed outlier: 3.542A pdb=" N MET D 462 " --> pdb=" O LYS D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 through 484 removed outlier: 4.037A pdb=" N MET D 474 " --> pdb=" O LYS D 470 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TRP D 477 " --> pdb=" O TRP D 473 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N TRP D 478 " --> pdb=" O MET D 474 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLU D 479 " --> pdb=" O LYS D 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 533 Processing helix chain 'D' and resid 547 through 554 removed outlier: 3.906A pdb=" N GLN D 552 " --> pdb=" O THR D 548 " (cutoff:3.500A) Processing helix chain 'D' and resid 554 through 559 Processing helix chain 'D' and resid 567 through 572 Processing helix chain 'D' and resid 581 through 598 removed outlier: 4.130A pdb=" N LEU D 585 " --> pdb=" O VAL D 581 " (cutoff:3.500A) Proline residue: D 590 - end of helix removed outlier: 3.658A pdb=" N TRP D 594 " --> pdb=" O PRO D 590 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 53 removed outlier: 4.626A pdb=" N ASP E 38 " --> pdb=" O HIS E 34 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LEU E 39 " --> pdb=" O GLU E 35 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASN E 51 " --> pdb=" O SER E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 65 removed outlier: 3.895A pdb=" N VAL E 59 " --> pdb=" O THR E 55 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLN E 60 " --> pdb=" O GLU E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 80 removed outlier: 3.667A pdb=" N GLU E 75 " --> pdb=" O ALA E 71 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA E 80 " --> pdb=" O GLN E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 101 removed outlier: 3.576A pdb=" N ALA E 99 " --> pdb=" O LEU E 95 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU E 100 " --> pdb=" O GLN E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 108 removed outlier: 3.629A pdb=" N VAL E 107 " --> pdb=" O GLY E 104 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU E 108 " --> pdb=" O SER E 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 104 through 108' Processing helix chain 'E' and resid 109 through 129 removed outlier: 3.688A pdb=" N THR E 118 " --> pdb=" O LYS E 114 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N SER E 124 " --> pdb=" O LEU E 120 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE E 126 " --> pdb=" O THR E 122 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N TYR E 127 " --> pdb=" O MET E 123 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR E 129 " --> pdb=" O THR E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 154 Processing helix chain 'E' and resid 157 through 171 removed outlier: 3.955A pdb=" N ARG E 161 " --> pdb=" O ASP E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 181 Proline residue: E 178 - end of helix Processing helix chain 'E' and resid 182 through 190 removed outlier: 3.748A pdb=" N LEU E 186 " --> pdb=" O GLU E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 207 removed outlier: 3.731A pdb=" N TYR E 207 " --> pdb=" O TRP E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 247 removed outlier: 4.539A pdb=" N GLU E 227 " --> pdb=" O ILE E 223 " (cutoff:3.500A) Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 248 through 252 removed outlier: 3.568A pdb=" N TYR E 252 " --> pdb=" O MET E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 263 through 267 removed outlier: 3.922A pdb=" N LEU E 267 " --> pdb=" O ALA E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 300 removed outlier: 3.664A pdb=" N GLN E 300 " --> pdb=" O ALA E 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 311 removed outlier: 4.033A pdb=" N LYS E 309 " --> pdb=" O GLN E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 317 removed outlier: 3.527A pdb=" N SER E 317 " --> pdb=" O LYS E 313 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 330 removed outlier: 4.031A pdb=" N TRP E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU E 329 " --> pdb=" O GLN E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 377 removed outlier: 3.618A pdb=" N THR E 371 " --> pdb=" O ASP E 367 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU E 375 " --> pdb=" O THR E 371 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N MET E 376 " --> pdb=" O ALA E 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 378 through 385 removed outlier: 3.772A pdb=" N ALA E 384 " --> pdb=" O GLN E 380 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N TYR E 385 " --> pdb=" O TYR E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 397 through 410 removed outlier: 4.137A pdb=" N GLU E 402 " --> pdb=" O GLU E 398 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA E 403 " --> pdb=" O GLY E 399 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 446 removed outlier: 3.706A pdb=" N GLU E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N PHE E 438 " --> pdb=" O THR E 434 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU E 439 " --> pdb=" O GLU E 435 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU E 440 " --> pdb=" O ILE E 436 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LYS E 441 " --> pdb=" O ASN E 437 " (cutoff:3.500A) Processing helix chain 'E' and resid 449 through 466 removed outlier: 3.805A pdb=" N TRP E 459 " --> pdb=" O MET E 455 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N ARG E 460 " --> pdb=" O LEU E 456 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N TRP E 461 " --> pdb=" O GLU E 457 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET E 462 " --> pdb=" O LYS E 458 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL E 463 " --> pdb=" O TRP E 459 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N PHE E 464 " --> pdb=" O ARG E 460 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLY E 466 " --> pdb=" O MET E 462 " (cutoff:3.500A) Processing helix chain 'E' and resid 474 through 485 removed outlier: 4.410A pdb=" N GLU E 479 " --> pdb=" O LYS E 475 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N MET E 480 " --> pdb=" O LYS E 476 " (cutoff:3.500A) Processing helix chain 'E' and resid 512 through 531 removed outlier: 3.640A pdb=" N THR E 519 " --> pdb=" O TYR E 515 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE E 523 " --> pdb=" O THR E 519 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLN E 524 " --> pdb=" O LEU E 520 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N PHE E 525 " --> pdb=" O TYR E 521 " (cutoff:3.500A) Processing helix chain 'E' and resid 548 through 559 removed outlier: 3.615A pdb=" N ARG E 559 " --> pdb=" O PHE E 555 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 573 removed outlier: 3.751A pdb=" N GLU E 571 " --> pdb=" O THR E 567 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N VAL E 573 " --> pdb=" O ALA E 569 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 586 Processing helix chain 'E' and resid 590 through 600 removed outlier: 4.250A pdb=" N TRP E 594 " --> pdb=" O PRO E 590 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ASP E 597 " --> pdb=" O THR E 593 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLN E 598 " --> pdb=" O TRP E 594 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS E 600 " --> pdb=" O LYS E 596 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 53 removed outlier: 3.750A pdb=" N GLN F 24 " --> pdb=" O THR F 20 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N HIS F 34 " --> pdb=" O ASP F 30 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU F 39 " --> pdb=" O GLU F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 64 Processing helix chain 'F' and resid 65 through 81 Processing helix chain 'F' and resid 91 through 99 Processing helix chain 'F' and resid 109 through 124 removed outlier: 3.578A pdb=" N THR F 122 " --> pdb=" O THR F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 129 Processing helix chain 'F' and resid 145 through 151 Processing helix chain 'F' and resid 157 through 173 removed outlier: 3.724A pdb=" N ARG F 161 " --> pdb=" O ASP F 157 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU F 162 " --> pdb=" O TYR F 158 " (cutoff:3.500A) Processing helix chain 'F' and resid 175 through 187 removed outlier: 4.623A pdb=" N LEU F 179 " --> pdb=" O GLN F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 193 removed outlier: 3.941A pdb=" N ALA F 191 " --> pdb=" O LYS F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 200 through 205 removed outlier: 3.612A pdb=" N GLY F 205 " --> pdb=" O ASP F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 218 through 229 removed outlier: 3.730A pdb=" N LEU F 222 " --> pdb=" O SER F 218 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ILE F 223 " --> pdb=" O ARG F 219 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU F 224 " --> pdb=" O GLY F 220 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLU F 227 " --> pdb=" O ILE F 223 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N HIS F 228 " --> pdb=" O GLU F 224 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR F 229 " --> pdb=" O ASP F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 247 removed outlier: 4.102A pdb=" N HIS F 239 " --> pdb=" O PRO F 235 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS F 247 " --> pdb=" O TYR F 243 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 279 removed outlier: 3.529A pdb=" N LEU F 278 " --> pdb=" O TRP F 275 " (cutoff:3.500A) Processing helix chain 'F' and resid 293 through 301 removed outlier: 3.858A pdb=" N ASP F 299 " --> pdb=" O ASP F 295 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLN F 300 " --> pdb=" O ALA F 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 312 removed outlier: 3.982A pdb=" N LYS F 309 " --> pdb=" O GLN F 305 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU F 312 " --> pdb=" O PHE F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 315 No H-bonds generated for 'chain 'F' and resid 313 through 315' Processing helix chain 'F' and resid 326 through 331 removed outlier: 3.592A pdb=" N ASN F 330 " --> pdb=" O GLY F 326 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER F 331 " --> pdb=" O PHE F 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 326 through 331' Processing helix chain 'F' and resid 365 through 385 removed outlier: 3.779A pdb=" N HIS F 373 " --> pdb=" O PHE F 369 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU F 375 " --> pdb=" O THR F 371 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N MET F 376 " --> pdb=" O ALA F 372 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TYR F 385 " --> pdb=" O TYR F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 393 Processing helix chain 'F' and resid 397 through 411 removed outlier: 3.777A pdb=" N HIS F 401 " --> pdb=" O ASN F 397 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N GLU F 402 " --> pdb=" O GLU F 398 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA F 403 " --> pdb=" O GLY F 399 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL F 404 " --> pdb=" O PHE F 400 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY F 405 " --> pdb=" O HIS F 401 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N MET F 408 " --> pdb=" O VAL F 404 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N SER F 409 " --> pdb=" O GLY F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 419 removed outlier: 3.527A pdb=" N LYS F 419 " --> pdb=" O PRO F 415 " (cutoff:3.500A) Processing helix chain 'F' and resid 433 through 447 removed outlier: 4.345A pdb=" N THR F 445 " --> pdb=" O LYS F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 449 through 465 removed outlier: 3.677A pdb=" N THR F 453 " --> pdb=" O THR F 449 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU F 457 " --> pdb=" O THR F 453 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LYS F 458 " --> pdb=" O TYR F 454 " (cutoff:3.500A) Processing helix chain 'F' and resid 474 through 481 removed outlier: 4.060A pdb=" N TRP F 478 " --> pdb=" O MET F 474 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU F 479 " --> pdb=" O LYS F 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 512 through 521 removed outlier: 4.116A pdb=" N ARG F 518 " --> pdb=" O ARG F 514 " (cutoff:3.500A) Processing helix chain 'F' and resid 522 through 530 removed outlier: 4.425A pdb=" N GLN F 526 " --> pdb=" O GLN F 522 " (cutoff:3.500A) Processing helix chain 'F' and resid 547 through 554 Processing helix chain 'F' and resid 554 through 560 Processing helix chain 'F' and resid 567 through 573 Processing helix chain 'F' and resid 581 through 588 removed outlier: 3.533A pdb=" N LEU F 585 " --> pdb=" O VAL F 581 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE F 588 " --> pdb=" O LEU F 584 " (cutoff:3.500A) Processing helix chain 'F' and resid 588 through 598 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.926A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 224 through 227 removed outlier: 5.992A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR A 208 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 116 through 119 Processing sheet with id=AA5, first strand: chain 'A' and resid 127 through 128 Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.619A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 357 through 358 removed outlier: 5.365A pdb=" N VAL A 511 " --> pdb=" O ILE A 434 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ILE A 434 " --> pdb=" O VAL A 511 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU A 513 " --> pdb=" O CYS A 432 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.944A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 removed outlier: 3.602A pdb=" N TYR A 453 " --> pdb=" O AARG A 493 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 539 through 542 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.159A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.561A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.057A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.531A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.306A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 30 Processing sheet with id=AC1, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.256A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 8.987A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER B 94 " --> pdb=" O ARG B 190 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 51 removed outlier: 3.805A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 54 through 55 Processing sheet with id=AC4, first strand: chain 'B' and resid 103 through 107 removed outlier: 3.780A pdb=" N ILE B 105 " --> pdb=" O GLN B 239 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 119 through 121 Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.562A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 324 through 325 removed outlier: 6.765A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.233A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 565 through 567 removed outlier: 6.613A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 653 through 655 removed outlier: 5.955A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.606A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.606A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.469A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 788 through 790 removed outlier: 5.782A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD7, first strand: chain 'C' and resid 26 through 30 removed outlier: 4.354A pdb=" N SER C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.990A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE1, first strand: chain 'C' and resid 93 through 94 removed outlier: 5.240A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 316 removed outlier: 6.690A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 378 through 379 Processing sheet with id=AE4, first strand: chain 'C' and resid 397 through 402 Processing sheet with id=AE5, first strand: chain 'C' and resid 538 through 539 Processing sheet with id=AE6, first strand: chain 'C' and resid 575 through 577 Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.057A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.463A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.486A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.486A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.502A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF3, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.345A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'D' and resid 350 through 352 removed outlier: 6.416A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 262 through 263 removed outlier: 5.590A pdb=" N LEU F 262 " --> pdb=" O VAL F 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 1365 hydrogen bonds defined for protein. 3801 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: 7.81 Time building geometry restraints manager: 4.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.26: 6343 1.26 - 1.40: 10042 1.40 - 1.54: 22810 1.54 - 1.68: 168 1.68 - 1.83: 278 Bond restraints: 39641 Sorted by residual: bond pdb=" CG PRO F 321 " pdb=" CD PRO F 321 " ideal model delta sigma weight residual 1.503 1.115 0.388 3.40e-02 8.65e+02 1.30e+02 bond pdb=" C1 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.406 1.483 -0.077 2.00e-02 2.50e+03 1.50e+01 bond pdb=" C1 NAG A1311 " pdb=" O5 NAG A1311 " ideal model delta sigma weight residual 1.406 1.482 -0.076 2.00e-02 2.50e+03 1.45e+01 bond pdb=" C1 NAG C1312 " pdb=" O5 NAG C1312 " ideal model delta sigma weight residual 1.406 1.481 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" N PRO F 321 " pdb=" CD PRO F 321 " ideal model delta sigma weight residual 1.473 1.523 -0.050 1.40e-02 5.10e+03 1.28e+01 ... (remaining 39636 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.32: 53800 4.32 - 8.64: 101 8.64 - 12.96: 4 12.96 - 17.29: 2 17.29 - 21.61: 1 Bond angle restraints: 53908 Sorted by residual: angle pdb=" N PRO F 321 " pdb=" CD PRO F 321 " pdb=" CG PRO F 321 " ideal model delta sigma weight residual 103.20 81.59 21.61 1.50e+00 4.44e-01 2.08e+02 angle pdb=" CA PRO F 321 " pdb=" N PRO F 321 " pdb=" CD PRO F 321 " ideal model delta sigma weight residual 112.00 100.57 11.43 1.40e+00 5.10e-01 6.66e+01 angle pdb=" CA PRO F 321 " pdb=" CB PRO F 321 " pdb=" CG PRO F 321 " ideal model delta sigma weight residual 104.50 90.04 14.46 1.90e+00 2.77e-01 5.80e+01 angle pdb=" N PRO F 321 " pdb=" CA PRO F 321 " pdb=" CB PRO F 321 " ideal model delta sigma weight residual 103.25 98.27 4.98 1.05e+00 9.07e-01 2.25e+01 angle pdb=" N ILE E 259 " pdb=" CA ILE E 259 " pdb=" C ILE E 259 " ideal model delta sigma weight residual 113.10 109.00 4.10 9.70e-01 1.06e+00 1.78e+01 ... (remaining 53903 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.84: 22444 24.84 - 49.67: 1343 49.67 - 74.51: 222 74.51 - 99.34: 122 99.34 - 124.18: 122 Dihedral angle restraints: 24253 sinusoidal: 10325 harmonic: 13928 Sorted by residual: dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual 93.00 177.79 -84.79 1 1.00e+01 1.00e-02 8.73e+01 dihedral pdb=" CB CYS A 743 " pdb=" SG CYS A 743 " pdb=" SG CYS A 749 " pdb=" CB CYS A 749 " ideal model delta sinusoidal sigma weight residual 93.00 173.99 -80.99 1 1.00e+01 1.00e-02 8.10e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -158.95 72.95 1 1.00e+01 1.00e-02 6.79e+01 ... (remaining 24250 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 5800 0.099 - 0.199: 283 0.199 - 0.298: 9 0.298 - 0.398: 3 0.398 - 0.497: 1 Chirality restraints: 6096 Sorted by residual: chirality pdb=" C1 NAG B1311 " pdb=" ND2 ASN B1098 " pdb=" C2 NAG B1311 " pdb=" O5 NAG B1311 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-01 2.50e+01 6.18e+00 chirality pdb=" C1 NAG E 702 " pdb=" ND2 ASN E 432 " pdb=" C2 NAG E 702 " pdb=" O5 NAG E 702 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" C1 NAG C1301 " pdb=" ND2 ASN C 61 " pdb=" C2 NAG C1301 " pdb=" O5 NAG C1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.61e+00 ... (remaining 6093 not shown) Planarity restraints: 6954 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU F 320 " 0.093 5.00e-02 4.00e+02 1.30e-01 2.70e+01 pdb=" N PRO F 321 " -0.224 5.00e-02 4.00e+02 pdb=" CA PRO F 321 " 0.065 5.00e-02 4.00e+02 pdb=" CD PRO F 321 " 0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 203 " -0.029 2.00e-02 2.50e+03 2.40e-02 1.44e+01 pdb=" CG TRP E 203 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP E 203 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP E 203 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 203 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP E 203 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP E 203 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 203 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 203 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP E 203 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 372 " 0.043 5.00e-02 4.00e+02 6.55e-02 6.87e+00 pdb=" N PRO A 373 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 373 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 373 " 0.037 5.00e-02 4.00e+02 ... (remaining 6951 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1409 2.71 - 3.26: 39758 3.26 - 3.81: 63979 3.81 - 4.35: 81396 4.35 - 4.90: 133130 Nonbonded interactions: 319672 Sorted by model distance: nonbonded pdb=" OH TYR A 756 " pdb=" OD1 ASP A 994 " model vdw 2.164 3.040 nonbonded pdb=" OG1 THR D 229 " pdb=" OD1 ASN D 580 " model vdw 2.166 3.040 nonbonded pdb=" OG1 THR A 323 " pdb=" OE1 GLU A 324 " model vdw 2.175 3.040 nonbonded pdb=" NE2 GLN B 474 " pdb=" O GLY B 476 " model vdw 2.181 3.120 nonbonded pdb=" O LYS D 441 " pdb=" OG1 THR D 445 " model vdw 2.190 3.040 ... (remaining 319667 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 25 through 140 or resid 164 through 223 or (resid 224 and \ (name N or name CA or name C or name O or name CB )) or resid 225 through 492 or \ resid 494 through 676 or resid 690 through 1311)) selection = (chain 'B' and (resid 25 through 124 or (resid 125 and (name N or name CA or nam \ e C or name O or name CB )) or resid 126 through 135 or resid 137 through 140 or \ resid 164 through 223 or (resid 224 and (name N or name CA or name C or name O \ or name CB )) or resid 225 through 492 or resid 494 through 1311)) selection = (chain 'C' and (resid 25 through 124 or (resid 125 and (name N or name CA or nam \ e C or name O or name CB )) or resid 126 through 135 or resid 137 through 492 or \ resid 494 through 676 or resid 690 through 1311)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.640 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 38.820 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6472 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.388 39726 Z= 0.181 Angle : 0.666 21.608 54135 Z= 0.330 Chirality : 0.047 0.497 6096 Planarity : 0.005 0.130 6900 Dihedral : 19.457 124.176 15199 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.27 % Favored : 91.58 % Rotamer: Outliers : 0.14 % Allowed : 0.33 % Favored : 99.52 % 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: -1.46 (0.12), residues: 4711 helix: 0.28 (0.14), residues: 1448 sheet: -0.75 (0.21), residues: 599 loop : -1.81 (0.12), residues: 2664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 355 TYR 0.019 0.001 TYR C1067 PHE 0.020 0.001 PHE E 28 TRP 0.064 0.002 TRP E 203 HIS 0.011 0.001 HIS D 228 Details of bonding type rmsd covalent geometry : bond 0.00419 (39641) covalent geometry : angle 0.64286 (53908) SS BOND : bond 0.00373 ( 28) SS BOND : angle 1.50163 ( 56) hydrogen bonds : bond 0.15083 ( 1341) hydrogen bonds : angle 6.89813 ( 3801) link_BETA1-4 : bond 0.00340 ( 3) link_BETA1-4 : angle 0.96020 ( 9) link_NAG-ASN : bond 0.00607 ( 54) link_NAG-ASN : angle 3.12923 ( 162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 4186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 329 time to evaluate : 1.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 VAL cc_start: 0.8056 (p) cc_final: 0.7670 (p) REVERT: B 200 TYR cc_start: 0.6637 (m-80) cc_final: 0.5939 (m-80) REVERT: D 383 MET cc_start: 0.4008 (ptp) cc_final: 0.3404 (tmm) REVERT: E 181 GLU cc_start: 0.4836 (tt0) cc_final: 0.4479 (tt0) REVERT: E 473 TRP cc_start: 0.2057 (m100) cc_final: 0.1730 (t60) REVERT: E 559 ARG cc_start: 0.3517 (pmt-80) cc_final: 0.2835 (tpt90) outliers start: 1 outliers final: 1 residues processed: 330 average time/residue: 0.5588 time to fit residues: 231.0815 Evaluate side-chains 219 residues out of total 4186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 218 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 277 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 432 optimal weight: 10.0000 chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 20.0000 chunk 455 optimal weight: 1.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 10.0000 chunk 470 optimal weight: 5.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN ** B1142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 ASN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4769 r_free = 0.4769 target = 0.224269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.172818 restraints weight = 93880.169| |-----------------------------------------------------------------------------| r_work (start): 0.4163 rms_B_bonded: 5.78 r_work: 0.3359 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3326 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3326 r_free = 0.3326 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3326 r_free = 0.3326 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3326 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.0827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 39726 Z= 0.144 Angle : 0.686 14.074 54135 Z= 0.325 Chirality : 0.049 0.501 6096 Planarity : 0.005 0.066 6900 Dihedral : 16.925 109.644 6310 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.72 % Favored : 92.15 % Rotamer: Outliers : 1.12 % Allowed : 7.49 % Favored : 91.38 % 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: 4711 helix: 0.25 (0.14), residues: 1508 sheet: -0.67 (0.21), residues: 611 loop : -1.79 (0.12), residues: 2592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 466 TYR 0.038 0.002 TYR F 279 PHE 0.023 0.001 PHE D 592 TRP 0.035 0.001 TRP E 203 HIS 0.007 0.001 HIS D 228 Details of bonding type rmsd covalent geometry : bond 0.00324 (39641) covalent geometry : angle 0.66149 (53908) SS BOND : bond 0.00321 ( 28) SS BOND : angle 1.44560 ( 56) hydrogen bonds : bond 0.04433 ( 1341) hydrogen bonds : angle 5.46613 ( 3801) link_BETA1-4 : bond 0.00774 ( 3) link_BETA1-4 : angle 3.15295 ( 9) link_NAG-ASN : bond 0.00600 ( 54) link_NAG-ASN : angle 3.18823 ( 162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 4186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 252 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.4109 (OUTLIER) cc_final: 0.3394 (m-80) REVERT: A 238 PHE cc_start: 0.7466 (OUTLIER) cc_final: 0.5465 (p90) REVERT: A 582 LEU cc_start: 0.7280 (OUTLIER) cc_final: 0.7055 (mm) REVERT: B 269 TYR cc_start: 0.7362 (m-10) cc_final: 0.7089 (m-10) REVERT: C 242 LEU cc_start: 0.7415 (OUTLIER) cc_final: 0.7196 (tm) REVERT: D 474 MET cc_start: 0.4019 (mmm) cc_final: 0.3023 (tpp) REVERT: E 473 TRP cc_start: 0.1698 (m-10) cc_final: 0.0980 (t60) REVERT: E 557 MET cc_start: -0.0325 (OUTLIER) cc_final: -0.0586 (ttt) REVERT: E 559 ARG cc_start: 0.3859 (pmt-80) cc_final: 0.2966 (tpt90) outliers start: 42 outliers final: 13 residues processed: 272 average time/residue: 0.5316 time to fit residues: 183.1749 Evaluate side-chains 252 residues out of total 4186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 234 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain E residue 215 TYR Chi-restraints excluded: chain E residue 557 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 338 optimal weight: 20.0000 chunk 267 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 147 optimal weight: 4.9990 chunk 83 optimal weight: 0.3980 chunk 470 optimal weight: 30.0000 chunk 157 optimal weight: 2.9990 chunk 403 optimal weight: 0.1980 chunk 387 optimal weight: 10.0000 chunk 169 optimal weight: 0.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 ASN A 196 ASN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1142 GLN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 GLN F 98 GLN ** F 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4776 r_free = 0.4776 target = 0.223552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.170477 restraints weight = 119389.043| |-----------------------------------------------------------------------------| r_work (start): 0.4154 rms_B_bonded: 5.96 r_work: 0.3400 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3357 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3357 r_free = 0.3357 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3357 r_free = 0.3357 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3357 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 39726 Z= 0.119 Angle : 0.656 12.780 54135 Z= 0.308 Chirality : 0.048 0.502 6096 Planarity : 0.004 0.066 6900 Dihedral : 12.759 104.920 6308 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.46 % Favored : 92.41 % Rotamer: Outliers : 1.07 % Allowed : 10.31 % Favored : 88.62 % 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: -1.26 (0.12), residues: 4711 helix: 0.47 (0.14), residues: 1484 sheet: -0.65 (0.21), residues: 610 loop : -1.71 (0.12), residues: 2617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1107 TYR 0.030 0.001 TYR D 41 PHE 0.025 0.001 PHE D 512 TRP 0.020 0.001 TRP E 203 HIS 0.007 0.001 HIS D 228 Details of bonding type rmsd covalent geometry : bond 0.00259 (39641) covalent geometry : angle 0.63276 (53908) SS BOND : bond 0.00247 ( 28) SS BOND : angle 1.25502 ( 56) hydrogen bonds : bond 0.03794 ( 1341) hydrogen bonds : angle 5.05527 ( 3801) link_BETA1-4 : bond 0.00933 ( 3) link_BETA1-4 : angle 3.70141 ( 9) link_NAG-ASN : bond 0.00640 ( 54) link_NAG-ASN : angle 3.07924 ( 162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 4186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 265 time to evaluate : 1.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.4336 (OUTLIER) cc_final: 0.3502 (m-80) REVERT: A 238 PHE cc_start: 0.7361 (OUTLIER) cc_final: 0.5286 (p90) REVERT: B 269 TYR cc_start: 0.7381 (m-10) cc_final: 0.7132 (m-80) REVERT: D 231 GLU cc_start: 0.5573 (pt0) cc_final: 0.5020 (tt0) REVERT: D 383 MET cc_start: 0.3041 (pp-130) cc_final: 0.2816 (ptp) REVERT: E 364 VAL cc_start: 0.0746 (OUTLIER) cc_final: 0.0503 (m) REVERT: E 557 MET cc_start: -0.0103 (OUTLIER) cc_final: -0.0365 (ttt) REVERT: E 559 ARG cc_start: 0.3974 (pmt-80) cc_final: 0.3038 (tpt90) REVERT: F 333 LEU cc_start: 0.4689 (OUTLIER) cc_final: 0.4057 (mp) outliers start: 41 outliers final: 17 residues processed: 285 average time/residue: 0.5234 time to fit residues: 190.1423 Evaluate side-chains 248 residues out of total 4186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 226 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 195 HIS Chi-restraints excluded: chain E residue 215 TYR Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 557 MET Chi-restraints excluded: chain F residue 198 ASP Chi-restraints excluded: chain F residue 333 LEU Chi-restraints excluded: chain F residue 409 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 299 optimal weight: 20.0000 chunk 204 optimal weight: 7.9990 chunk 77 optimal weight: 0.5980 chunk 262 optimal weight: 0.5980 chunk 423 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 186 optimal weight: 0.1980 chunk 381 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 147 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4777 r_free = 0.4777 target = 0.223535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.170926 restraints weight = 106161.307| |-----------------------------------------------------------------------------| r_work (start): 0.4154 rms_B_bonded: 5.75 r_work: 0.3407 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3362 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3362 r_free = 0.3362 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3362 r_free = 0.3362 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3362 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 39726 Z= 0.122 Angle : 0.651 12.717 54135 Z= 0.303 Chirality : 0.047 0.492 6096 Planarity : 0.004 0.069 6900 Dihedral : 11.180 102.720 6308 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.25 % Favored : 92.62 % Rotamer: Outliers : 1.24 % Allowed : 11.98 % Favored : 86.78 % 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: -1.20 (0.12), residues: 4711 helix: 0.53 (0.14), residues: 1481 sheet: -0.57 (0.21), residues: 604 loop : -1.69 (0.12), residues: 2626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 346 TYR 0.027 0.001 TYR B 170 PHE 0.028 0.001 PHE D 512 TRP 0.019 0.001 TRP A 104 HIS 0.006 0.001 HIS D 228 Details of bonding type rmsd covalent geometry : bond 0.00272 (39641) covalent geometry : angle 0.62574 (53908) SS BOND : bond 0.00256 ( 28) SS BOND : angle 1.25013 ( 56) hydrogen bonds : bond 0.03739 ( 1341) hydrogen bonds : angle 4.95620 ( 3801) link_BETA1-4 : bond 0.00815 ( 3) link_BETA1-4 : angle 3.99020 ( 9) link_NAG-ASN : bond 0.00629 ( 54) link_NAG-ASN : angle 3.11338 ( 162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 4186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 246 time to evaluate : 1.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.7347 (OUTLIER) cc_final: 0.5423 (p90) REVERT: A 994 ASP cc_start: 0.8227 (OUTLIER) cc_final: 0.7954 (t0) REVERT: B 269 TYR cc_start: 0.7356 (m-10) cc_final: 0.7143 (m-80) REVERT: D 181 GLU cc_start: 0.4526 (OUTLIER) cc_final: 0.3877 (tm-30) REVERT: D 231 GLU cc_start: 0.5741 (pt0) cc_final: 0.5302 (tt0) REVERT: D 474 MET cc_start: 0.4021 (mmm) cc_final: 0.2397 (tpp) REVERT: E 364 VAL cc_start: 0.0709 (OUTLIER) cc_final: 0.0486 (m) REVERT: E 557 MET cc_start: -0.0101 (OUTLIER) cc_final: -0.0392 (ttt) REVERT: E 559 ARG cc_start: 0.4012 (pmt-80) cc_final: 0.3042 (tpt90) REVERT: F 202 TYR cc_start: 0.3763 (OUTLIER) cc_final: 0.3359 (t80) REVERT: F 333 LEU cc_start: 0.4581 (OUTLIER) cc_final: 0.3950 (mp) outliers start: 49 outliers final: 17 residues processed: 271 average time/residue: 0.5520 time to fit residues: 190.6546 Evaluate side-chains 261 residues out of total 4186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 237 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 195 HIS Chi-restraints excluded: chain E residue 215 TYR Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 557 MET Chi-restraints excluded: chain F residue 34 HIS Chi-restraints excluded: chain F residue 198 ASP Chi-restraints excluded: chain F residue 202 TYR Chi-restraints excluded: chain F residue 333 LEU Chi-restraints excluded: chain F residue 409 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 229 optimal weight: 30.0000 chunk 444 optimal weight: 2.9990 chunk 458 optimal weight: 20.0000 chunk 18 optimal weight: 4.9990 chunk 410 optimal weight: 0.0980 chunk 214 optimal weight: 0.8980 chunk 346 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 423 optimal weight: 5.9990 chunk 162 optimal weight: 0.7980 chunk 158 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 277 ASN ** D 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 GLN ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 239 HIS ** F 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4773 r_free = 0.4773 target = 0.224868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.169492 restraints weight = 103231.869| |-----------------------------------------------------------------------------| r_work (start): 0.4106 rms_B_bonded: 5.76 r_work: 0.3350 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3329 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3329 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 39726 Z= 0.144 Angle : 0.657 13.679 54135 Z= 0.307 Chirality : 0.047 0.498 6096 Planarity : 0.004 0.068 6900 Dihedral : 10.159 101.119 6308 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.78 % Favored : 92.11 % Rotamer: Outliers : 1.29 % Allowed : 13.10 % Favored : 85.61 % 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: -1.21 (0.12), residues: 4711 helix: 0.53 (0.14), residues: 1479 sheet: -0.60 (0.22), residues: 592 loop : -1.70 (0.12), residues: 2640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 177 TYR 0.023 0.001 TYR B 170 PHE 0.038 0.001 PHE A 342 TRP 0.015 0.001 TRP B 436 HIS 0.006 0.001 HIS D 228 Details of bonding type rmsd covalent geometry : bond 0.00331 (39641) covalent geometry : angle 0.63101 (53908) SS BOND : bond 0.00280 ( 28) SS BOND : angle 1.31181 ( 56) hydrogen bonds : bond 0.03896 ( 1341) hydrogen bonds : angle 4.96125 ( 3801) link_BETA1-4 : bond 0.01227 ( 3) link_BETA1-4 : angle 4.23498 ( 9) link_NAG-ASN : bond 0.00620 ( 54) link_NAG-ASN : angle 3.21746 ( 162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 4186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 247 time to evaluate : 1.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.7329 (OUTLIER) cc_final: 0.5358 (p90) REVERT: A 994 ASP cc_start: 0.8229 (OUTLIER) cc_final: 0.7956 (t0) REVERT: B 269 TYR cc_start: 0.7401 (m-10) cc_final: 0.7086 (m-80) REVERT: C 740 MET cc_start: 0.8213 (mmt) cc_final: 0.7968 (mmm) REVERT: D 181 GLU cc_start: 0.4487 (OUTLIER) cc_final: 0.3875 (tm-30) REVERT: D 231 GLU cc_start: 0.5781 (pt0) cc_final: 0.5363 (tt0) REVERT: D 383 MET cc_start: 0.3585 (ptp) cc_final: 0.3111 (pp-130) REVERT: E 364 VAL cc_start: 0.0820 (OUTLIER) cc_final: 0.0592 (m) REVERT: E 557 MET cc_start: -0.0091 (OUTLIER) cc_final: -0.0375 (ttt) REVERT: E 559 ARG cc_start: 0.3868 (pmt-80) cc_final: 0.3025 (tpt90) REVERT: E 589 GLU cc_start: 0.2286 (OUTLIER) cc_final: 0.1743 (pp20) REVERT: F 202 TYR cc_start: 0.3812 (OUTLIER) cc_final: 0.3398 (t80) REVERT: F 332 MET cc_start: 0.0706 (pmm) cc_final: -0.2003 (mtp) REVERT: F 333 LEU cc_start: 0.4472 (OUTLIER) cc_final: 0.3833 (mp) REVERT: F 523 PHE cc_start: 0.2735 (m-80) cc_final: 0.2110 (m-80) outliers start: 51 outliers final: 21 residues processed: 281 average time/residue: 0.5118 time to fit residues: 183.4991 Evaluate side-chains 257 residues out of total 4186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 228 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 195 HIS Chi-restraints excluded: chain D residue 323 MET Chi-restraints excluded: chain E residue 215 TYR Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 557 MET Chi-restraints excluded: chain E residue 589 GLU Chi-restraints excluded: chain F residue 34 HIS Chi-restraints excluded: chain F residue 198 ASP Chi-restraints excluded: chain F residue 202 TYR Chi-restraints excluded: chain F residue 333 LEU Chi-restraints excluded: chain F residue 409 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 171 optimal weight: 1.9990 chunk 26 optimal weight: 8.9990 chunk 317 optimal weight: 20.0000 chunk 24 optimal weight: 6.9990 chunk 310 optimal weight: 9.9990 chunk 353 optimal weight: 0.9990 chunk 303 optimal weight: 30.0000 chunk 123 optimal weight: 0.6980 chunk 201 optimal weight: 4.9990 chunk 356 optimal weight: 2.9990 chunk 269 optimal weight: 0.8980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 505 HIS ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 134 ASN ** F 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4778 r_free = 0.4778 target = 0.224559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.172121 restraints weight = 130304.992| |-----------------------------------------------------------------------------| r_work (start): 0.4147 rms_B_bonded: 6.38 r_work: 0.3353 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3309 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3309 r_free = 0.3309 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3309 r_free = 0.3309 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3309 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 39726 Z= 0.152 Angle : 0.659 13.144 54135 Z= 0.309 Chirality : 0.047 0.509 6096 Planarity : 0.004 0.085 6900 Dihedral : 9.522 103.180 6308 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.53 % Favored : 92.36 % Rotamer: Outliers : 1.48 % Allowed : 13.75 % Favored : 84.77 % 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: -1.23 (0.12), residues: 4711 helix: 0.52 (0.14), residues: 1478 sheet: -0.64 (0.21), residues: 599 loop : -1.70 (0.12), residues: 2634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 204 TYR 0.024 0.001 TYR B 170 PHE 0.032 0.001 PHE A 342 TRP 0.022 0.001 TRP F 459 HIS 0.006 0.001 HIS D 228 Details of bonding type rmsd covalent geometry : bond 0.00351 (39641) covalent geometry : angle 0.63198 (53908) SS BOND : bond 0.00298 ( 28) SS BOND : angle 1.37253 ( 56) hydrogen bonds : bond 0.03948 ( 1341) hydrogen bonds : angle 4.96024 ( 3801) link_BETA1-4 : bond 0.01192 ( 3) link_BETA1-4 : angle 4.30165 ( 9) link_NAG-ASN : bond 0.00620 ( 54) link_NAG-ASN : angle 3.22643 ( 162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 4186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 242 time to evaluate : 1.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.7481 (OUTLIER) cc_final: 0.5477 (p90) REVERT: A 994 ASP cc_start: 0.8270 (OUTLIER) cc_final: 0.8001 (t0) REVERT: B 269 TYR cc_start: 0.7499 (m-10) cc_final: 0.7179 (m-80) REVERT: C 740 MET cc_start: 0.8258 (mmt) cc_final: 0.7987 (mmm) REVERT: D 181 GLU cc_start: 0.4504 (OUTLIER) cc_final: 0.3838 (tm-30) REVERT: D 231 GLU cc_start: 0.5684 (pt0) cc_final: 0.5207 (tt0) REVERT: D 332 MET cc_start: 0.1956 (ppp) cc_final: 0.1668 (ppp) REVERT: D 474 MET cc_start: 0.3548 (mmm) cc_final: 0.1342 (tpp) REVERT: D 512 PHE cc_start: 0.3716 (t80) cc_final: 0.3495 (t80) REVERT: E 364 VAL cc_start: 0.0906 (OUTLIER) cc_final: 0.0683 (m) REVERT: E 366 MET cc_start: 0.2085 (OUTLIER) cc_final: 0.1784 (tmt) REVERT: E 462 MET cc_start: 0.1829 (mpt) cc_final: 0.1627 (mpp) REVERT: E 557 MET cc_start: -0.0021 (OUTLIER) cc_final: -0.0319 (ttt) REVERT: E 559 ARG cc_start: 0.3959 (pmt-80) cc_final: 0.2965 (tpt90) REVERT: E 588 PHE cc_start: 0.1719 (m-80) cc_final: 0.1413 (m-10) REVERT: E 589 GLU cc_start: 0.2332 (OUTLIER) cc_final: 0.1763 (pp20) REVERT: F 202 TYR cc_start: 0.3719 (OUTLIER) cc_final: 0.3324 (t80) REVERT: F 270 MET cc_start: 0.1828 (mmt) cc_final: 0.0227 (mpp) REVERT: F 333 LEU cc_start: 0.4529 (OUTLIER) cc_final: 0.3896 (mp) REVERT: F 523 PHE cc_start: 0.2932 (m-80) cc_final: 0.2365 (m-80) outliers start: 59 outliers final: 26 residues processed: 279 average time/residue: 0.5007 time to fit residues: 179.0912 Evaluate side-chains 260 residues out of total 4186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 225 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 195 HIS Chi-restraints excluded: chain E residue 215 TYR Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 366 MET Chi-restraints excluded: chain E residue 557 MET Chi-restraints excluded: chain E residue 589 GLU Chi-restraints excluded: chain F residue 34 HIS Chi-restraints excluded: chain F residue 198 ASP Chi-restraints excluded: chain F residue 202 TYR Chi-restraints excluded: chain F residue 333 LEU Chi-restraints excluded: chain F residue 408 MET Chi-restraints excluded: chain F residue 409 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 464 optimal weight: 20.0000 chunk 277 optimal weight: 4.9990 chunk 322 optimal weight: 5.9990 chunk 62 optimal weight: 0.4980 chunk 380 optimal weight: 40.0000 chunk 106 optimal weight: 20.0000 chunk 377 optimal weight: 5.9990 chunk 245 optimal weight: 10.0000 chunk 382 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 297 optimal weight: 10.0000 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 505 HIS ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4752 r_free = 0.4752 target = 0.222056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.171950 restraints weight = 117676.867| |-----------------------------------------------------------------------------| r_work (start): 0.4166 rms_B_bonded: 6.02 r_work: 0.3350 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3289 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3289 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 39726 Z= 0.248 Angle : 0.714 14.723 54135 Z= 0.341 Chirality : 0.049 0.544 6096 Planarity : 0.004 0.069 6900 Dihedral : 9.510 105.564 6308 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.70 % Favored : 91.20 % Rotamer: Outliers : 1.48 % Allowed : 14.53 % Favored : 83.99 % 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: -1.45 (0.12), residues: 4711 helix: 0.31 (0.14), residues: 1484 sheet: -0.82 (0.21), residues: 587 loop : -1.80 (0.12), residues: 2640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 44 TYR 0.032 0.002 TYR B 265 PHE 0.032 0.002 PHE A 342 TRP 0.035 0.002 TRP E 473 HIS 0.006 0.001 HIS D 228 Details of bonding type rmsd covalent geometry : bond 0.00589 (39641) covalent geometry : angle 0.68713 (53908) SS BOND : bond 0.00433 ( 28) SS BOND : angle 1.70628 ( 56) hydrogen bonds : bond 0.04655 ( 1341) hydrogen bonds : angle 5.20760 ( 3801) link_BETA1-4 : bond 0.01146 ( 3) link_BETA1-4 : angle 4.38672 ( 9) link_NAG-ASN : bond 0.00647 ( 54) link_NAG-ASN : angle 3.37105 ( 162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 4186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 235 time to evaluate : 1.507 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.7605 (OUTLIER) cc_final: 0.5525 (p90) REVERT: A 994 ASP cc_start: 0.8262 (OUTLIER) cc_final: 0.7917 (t0) REVERT: B 269 TYR cc_start: 0.7529 (m-10) cc_final: 0.7287 (m-10) REVERT: B 754 LEU cc_start: 0.8530 (pp) cc_final: 0.8320 (pp) REVERT: B 941 THR cc_start: 0.6177 (OUTLIER) cc_final: 0.5960 (p) REVERT: C 740 MET cc_start: 0.8373 (mmt) cc_final: 0.8086 (mmm) REVERT: D 181 GLU cc_start: 0.4626 (OUTLIER) cc_final: 0.3935 (tm-30) REVERT: D 231 GLU cc_start: 0.5624 (pt0) cc_final: 0.5180 (tt0) REVERT: D 332 MET cc_start: 0.2213 (ppp) cc_final: 0.1729 (ppp) REVERT: D 383 MET cc_start: 0.3461 (ptp) cc_final: 0.2820 (pp-130) REVERT: D 474 MET cc_start: 0.3712 (mmm) cc_final: 0.1818 (tpp) REVERT: E 181 GLU cc_start: 0.4136 (tm-30) cc_final: 0.3129 (tt0) REVERT: E 270 MET cc_start: 0.1790 (ptm) cc_final: 0.1535 (ptm) REVERT: E 364 VAL cc_start: 0.0612 (OUTLIER) cc_final: 0.0360 (m) REVERT: E 366 MET cc_start: 0.2059 (OUTLIER) cc_final: 0.1686 (tmt) REVERT: E 557 MET cc_start: -0.0112 (OUTLIER) cc_final: -0.0406 (ttt) REVERT: E 559 ARG cc_start: 0.3925 (pmt-80) cc_final: 0.2936 (tpt90) REVERT: E 588 PHE cc_start: 0.1592 (m-80) cc_final: 0.1277 (m-10) REVERT: E 589 GLU cc_start: 0.2350 (OUTLIER) cc_final: 0.1786 (pp20) REVERT: F 332 MET cc_start: 0.0838 (pmm) cc_final: -0.1928 (mtp) REVERT: F 366 MET cc_start: 0.1758 (tpp) cc_final: -0.0817 (ppp) REVERT: F 467 GLU cc_start: 0.3359 (pp20) cc_final: 0.3155 (tp30) REVERT: F 523 PHE cc_start: 0.3008 (m-80) cc_final: 0.2388 (m-80) outliers start: 59 outliers final: 31 residues processed: 278 average time/residue: 0.4908 time to fit residues: 173.8202 Evaluate side-chains 260 residues out of total 4186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 221 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 195 HIS Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 215 TYR Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 366 MET Chi-restraints excluded: chain E residue 557 MET Chi-restraints excluded: chain E residue 589 GLU Chi-restraints excluded: chain F residue 34 HIS Chi-restraints excluded: chain F residue 198 ASP Chi-restraints excluded: chain F residue 409 SER Chi-restraints excluded: chain F residue 544 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 100 optimal weight: 0.6980 chunk 377 optimal weight: 8.9990 chunk 303 optimal weight: 40.0000 chunk 192 optimal weight: 0.7980 chunk 374 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 chunk 353 optimal weight: 0.8980 chunk 471 optimal weight: 3.9990 chunk 209 optimal weight: 0.5980 chunk 375 optimal weight: 0.9980 chunk 430 optimal weight: 10.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN C 913 GLN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 GLN ** D 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4771 r_free = 0.4771 target = 0.222851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.170298 restraints weight = 128045.247| |-----------------------------------------------------------------------------| r_work (start): 0.4143 rms_B_bonded: 6.26 r_work: 0.3362 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3324 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3324 r_free = 0.3324 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3324 r_free = 0.3324 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3324 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 39726 Z= 0.121 Angle : 0.653 15.132 54135 Z= 0.308 Chirality : 0.046 0.530 6096 Planarity : 0.004 0.068 6900 Dihedral : 8.981 104.011 6308 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.40 % Favored : 92.49 % Rotamer: Outliers : 1.10 % Allowed : 15.20 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.24 (0.12), residues: 4711 helix: 0.48 (0.14), residues: 1485 sheet: -0.70 (0.21), residues: 595 loop : -1.68 (0.12), residues: 2631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 995 TYR 0.027 0.001 TYR A 365 PHE 0.035 0.001 PHE A 342 TRP 0.051 0.001 TRP E 473 HIS 0.007 0.001 HIS D 228 Details of bonding type rmsd covalent geometry : bond 0.00267 (39641) covalent geometry : angle 0.62725 (53908) SS BOND : bond 0.00274 ( 28) SS BOND : angle 1.34128 ( 56) hydrogen bonds : bond 0.03774 ( 1341) hydrogen bonds : angle 4.94634 ( 3801) link_BETA1-4 : bond 0.00982 ( 3) link_BETA1-4 : angle 3.87124 ( 9) link_NAG-ASN : bond 0.00631 ( 54) link_NAG-ASN : angle 3.16547 ( 162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 4186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 235 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.4737 (m-80) cc_final: 0.4202 (t80) REVERT: A 238 PHE cc_start: 0.7477 (OUTLIER) cc_final: 0.5458 (p90) REVERT: A 994 ASP cc_start: 0.8228 (OUTLIER) cc_final: 0.7979 (t0) REVERT: B 189 LEU cc_start: 0.7701 (OUTLIER) cc_final: 0.7456 (mt) REVERT: B 269 TYR cc_start: 0.7505 (m-10) cc_final: 0.7298 (m-80) REVERT: C 740 MET cc_start: 0.8291 (mmt) cc_final: 0.7997 (mmm) REVERT: D 181 GLU cc_start: 0.4482 (OUTLIER) cc_final: 0.3839 (tm-30) REVERT: D 231 GLU cc_start: 0.5665 (pt0) cc_final: 0.5194 (tt0) REVERT: D 332 MET cc_start: 0.2210 (ppp) cc_final: 0.1692 (ppp) REVERT: D 383 MET cc_start: 0.3485 (ptp) cc_final: 0.2960 (pp-130) REVERT: D 474 MET cc_start: 0.3702 (mmm) cc_final: 0.2050 (tpp) REVERT: E 215 TYR cc_start: 0.3809 (OUTLIER) cc_final: 0.3211 (m-80) REVERT: E 364 VAL cc_start: 0.0866 (OUTLIER) cc_final: 0.0650 (m) REVERT: E 366 MET cc_start: 0.2038 (OUTLIER) cc_final: 0.1698 (tmt) REVERT: E 559 ARG cc_start: 0.3870 (pmt-80) cc_final: 0.2831 (tpt90) REVERT: E 588 PHE cc_start: 0.1578 (m-80) cc_final: 0.1289 (m-10) REVERT: F 332 MET cc_start: 0.0503 (pmm) cc_final: -0.2186 (mtp) REVERT: F 366 MET cc_start: 0.1729 (tpp) cc_final: -0.0739 (ppp) REVERT: F 467 GLU cc_start: 0.3443 (pp20) cc_final: 0.3215 (tp30) outliers start: 43 outliers final: 19 residues processed: 264 average time/residue: 0.4986 time to fit residues: 167.1182 Evaluate side-chains 250 residues out of total 4186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 224 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 215 TYR Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 366 MET Chi-restraints excluded: chain F residue 34 HIS Chi-restraints excluded: chain F residue 198 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 272 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 65 optimal weight: 0.5980 chunk 392 optimal weight: 40.0000 chunk 130 optimal weight: 7.9990 chunk 9 optimal weight: 7.9990 chunk 23 optimal weight: 0.8980 chunk 444 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 263 optimal weight: 3.9990 chunk 300 optimal weight: 20.0000 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4772 r_free = 0.4772 target = 0.222018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.175910 restraints weight = 101747.887| |-----------------------------------------------------------------------------| r_work (start): 0.4243 rms_B_bonded: 5.89 r_work: 0.3411 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3334 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3334 r_free = 0.3334 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3334 r_free = 0.3334 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3334 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 39726 Z= 0.166 Angle : 0.675 15.535 54135 Z= 0.318 Chirality : 0.047 0.523 6096 Planarity : 0.004 0.067 6900 Dihedral : 8.863 104.403 6308 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.02 % Favored : 91.88 % Rotamer: Outliers : 1.07 % Allowed : 15.73 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.29 (0.12), residues: 4711 helix: 0.44 (0.14), residues: 1484 sheet: -0.74 (0.21), residues: 596 loop : -1.70 (0.12), residues: 2631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 983 TYR 0.025 0.001 TYR A 365 PHE 0.039 0.002 PHE E 438 TRP 0.024 0.002 TRP A 104 HIS 0.009 0.001 HIS D 228 Details of bonding type rmsd covalent geometry : bond 0.00390 (39641) covalent geometry : angle 0.64659 (53908) SS BOND : bond 0.00344 ( 28) SS BOND : angle 2.40767 ( 56) hydrogen bonds : bond 0.04055 ( 1341) hydrogen bonds : angle 5.00548 ( 3801) link_BETA1-4 : bond 0.01001 ( 3) link_BETA1-4 : angle 3.72065 ( 9) link_NAG-ASN : bond 0.00610 ( 54) link_NAG-ASN : angle 3.19394 ( 162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 4186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 225 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.5010 (m-80) cc_final: 0.4470 (t80) REVERT: A 238 PHE cc_start: 0.7652 (OUTLIER) cc_final: 0.5598 (p90) REVERT: A 994 ASP cc_start: 0.8264 (OUTLIER) cc_final: 0.7942 (t0) REVERT: B 189 LEU cc_start: 0.7686 (OUTLIER) cc_final: 0.7406 (mt) REVERT: B 269 TYR cc_start: 0.7514 (m-10) cc_final: 0.7217 (m-10) REVERT: C 740 MET cc_start: 0.8244 (mmt) cc_final: 0.7968 (mmm) REVERT: C 995 ARG cc_start: 0.7919 (ttp80) cc_final: 0.7120 (ttp80) REVERT: D 181 GLU cc_start: 0.4552 (OUTLIER) cc_final: 0.3901 (tm-30) REVERT: D 231 GLU cc_start: 0.5605 (pt0) cc_final: 0.5148 (tt0) REVERT: D 332 MET cc_start: 0.1900 (ppp) cc_final: 0.1460 (ppp) REVERT: D 383 MET cc_start: 0.3544 (ptp) cc_final: 0.2954 (pp-130) REVERT: D 474 MET cc_start: 0.3867 (mmm) cc_final: 0.2247 (tpp) REVERT: E 215 TYR cc_start: 0.3665 (OUTLIER) cc_final: 0.3057 (m-80) REVERT: E 364 VAL cc_start: 0.0727 (OUTLIER) cc_final: 0.0497 (m) REVERT: E 366 MET cc_start: 0.2050 (OUTLIER) cc_final: 0.1692 (tmt) REVERT: E 559 ARG cc_start: 0.3857 (pmt-80) cc_final: 0.2744 (tpt90) REVERT: E 588 PHE cc_start: 0.1569 (m-80) cc_final: 0.1284 (m-10) REVERT: F 62 MET cc_start: 0.0422 (mpt) cc_final: -0.1468 (mtt) REVERT: F 333 LEU cc_start: 0.3504 (tt) cc_final: 0.3119 (pp) REVERT: F 366 MET cc_start: 0.1718 (tpp) cc_final: -0.0873 (ppp) REVERT: F 409 SER cc_start: 0.3301 (t) cc_final: 0.2792 (p) REVERT: F 467 GLU cc_start: 0.3353 (pp20) cc_final: 0.3106 (tp30) outliers start: 42 outliers final: 21 residues processed: 255 average time/residue: 0.5316 time to fit residues: 170.7891 Evaluate side-chains 246 residues out of total 4186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 218 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 215 TYR Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 366 MET Chi-restraints excluded: chain F residue 34 HIS Chi-restraints excluded: chain F residue 198 ASP Chi-restraints excluded: chain F residue 544 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 97 optimal weight: 4.9990 chunk 432 optimal weight: 4.9990 chunk 229 optimal weight: 30.0000 chunk 331 optimal weight: 6.9990 chunk 131 optimal weight: 4.9990 chunk 374 optimal weight: 7.9990 chunk 318 optimal weight: 8.9990 chunk 181 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 299 optimal weight: 9.9990 chunk 18 optimal weight: 3.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 ASN B 314 GLN B 755 GLN B 804 GLN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 505 HIS ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 599 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4743 r_free = 0.4743 target = 0.219867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.166050 restraints weight = 95596.559| |-----------------------------------------------------------------------------| r_work (start): 0.4104 rms_B_bonded: 5.54 r_work: 0.3328 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3288 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3288 r_free = 0.3288 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3288 r_free = 0.3288 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3288 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 39726 Z= 0.270 Angle : 0.741 16.310 54135 Z= 0.355 Chirality : 0.050 0.572 6096 Planarity : 0.005 0.068 6900 Dihedral : 9.129 106.214 6308 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.89 % Favored : 91.00 % Rotamer: Outliers : 1.03 % Allowed : 15.87 % Favored : 83.10 % 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: -1.52 (0.12), residues: 4711 helix: 0.21 (0.14), residues: 1485 sheet: -0.87 (0.21), residues: 596 loop : -1.83 (0.12), residues: 2630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 983 TYR 0.032 0.002 TYR B 265 PHE 0.035 0.002 PHE A 342 TRP 0.028 0.002 TRP F 459 HIS 0.010 0.001 HIS D 228 Details of bonding type rmsd covalent geometry : bond 0.00644 (39641) covalent geometry : angle 0.71392 (53908) SS BOND : bond 0.00475 ( 28) SS BOND : angle 2.34068 ( 56) hydrogen bonds : bond 0.04809 ( 1341) hydrogen bonds : angle 5.29622 ( 3801) link_BETA1-4 : bond 0.00987 ( 3) link_BETA1-4 : angle 3.62792 ( 9) link_NAG-ASN : bond 0.00647 ( 54) link_NAG-ASN : angle 3.38514 ( 162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9422 Ramachandran restraints generated. 4711 Oldfield, 0 Emsley, 4711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 4186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 226 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.7518 (OUTLIER) cc_final: 0.5429 (p90) REVERT: A 994 ASP cc_start: 0.8183 (OUTLIER) cc_final: 0.7861 (t0) REVERT: B 189 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7461 (mt) REVERT: B 269 TYR cc_start: 0.7561 (m-10) cc_final: 0.7169 (m-10) REVERT: C 324 GLU cc_start: 0.7939 (pm20) cc_final: 0.7471 (pm20) REVERT: C 995 ARG cc_start: 0.7903 (ttp80) cc_final: 0.7164 (ttp80) REVERT: D 181 GLU cc_start: 0.4489 (OUTLIER) cc_final: 0.3851 (tm-30) REVERT: D 231 GLU cc_start: 0.5689 (pt0) cc_final: 0.5218 (tt0) REVERT: D 332 MET cc_start: 0.2102 (ppp) cc_final: 0.1612 (ppp) REVERT: D 383 MET cc_start: 0.3335 (ptp) cc_final: 0.2757 (pp-130) REVERT: D 474 MET cc_start: 0.3923 (mmm) cc_final: 0.2536 (tpp) REVERT: E 364 VAL cc_start: 0.0611 (OUTLIER) cc_final: 0.0392 (m) REVERT: E 366 MET cc_start: 0.1997 (OUTLIER) cc_final: 0.1536 (tmt) REVERT: E 559 ARG cc_start: 0.3910 (pmt-80) cc_final: 0.2906 (tpt90) REVERT: E 588 PHE cc_start: 0.1438 (m-80) cc_final: 0.1152 (m-10) REVERT: F 62 MET cc_start: 0.0258 (mpt) cc_final: -0.1605 (mtt) REVERT: F 270 MET cc_start: 0.1653 (mmm) cc_final: 0.1018 (ptp) REVERT: F 332 MET cc_start: 0.1139 (pmm) cc_final: -0.1851 (mmm) REVERT: F 366 MET cc_start: 0.1768 (tpp) cc_final: -0.0762 (ppp) outliers start: 40 outliers final: 24 residues processed: 256 average time/residue: 0.5442 time to fit residues: 176.1987 Evaluate side-chains 246 residues out of total 4186 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 216 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 212 VAL Chi-restraints excluded: chain E residue 215 TYR Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 366 MET Chi-restraints excluded: chain F residue 34 HIS Chi-restraints excluded: chain F residue 198 ASP Chi-restraints excluded: chain F residue 544 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 170 optimal weight: 0.9990 chunk 261 optimal weight: 1.9990 chunk 325 optimal weight: 8.9990 chunk 194 optimal weight: 0.5980 chunk 401 optimal weight: 3.9990 chunk 460 optimal weight: 6.9990 chunk 238 optimal weight: 30.0000 chunk 248 optimal weight: 0.8980 chunk 270 optimal weight: 0.9980 chunk 106 optimal weight: 10.0000 chunk 279 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 599 ASN ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 472 GLN ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 578 ASN ** E 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 599 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4773 r_free = 0.4773 target = 0.222301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.173918 restraints weight = 111432.607| |-----------------------------------------------------------------------------| r_work (start): 0.4217 rms_B_bonded: 6.32 r_work: 0.3399 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3332 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3332 r_free = 0.3332 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3332 r_free = 0.3332 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3332 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 39726 Z= 0.128 Angle : 0.668 15.131 54135 Z= 0.316 Chirality : 0.047 0.542 6096 Planarity : 0.004 0.067 6900 Dihedral : 8.673 103.863 6308 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.49 % Favored : 92.41 % Rotamer: Outliers : 1.03 % Allowed : 15.97 % Favored : 83.01 % 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: -1.33 (0.12), residues: 4711 helix: 0.40 (0.14), residues: 1482 sheet: -0.77 (0.21), residues: 596 loop : -1.72 (0.12), residues: 2633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 995 TYR 0.023 0.001 TYR A 365 PHE 0.035 0.001 PHE A 342 TRP 0.027 0.001 TRP A 104 HIS 0.012 0.001 HIS D 228 Details of bonding type rmsd covalent geometry : bond 0.00288 (39641) covalent geometry : angle 0.64260 (53908) SS BOND : bond 0.00296 ( 28) SS BOND : angle 1.85980 ( 56) hydrogen bonds : bond 0.03851 ( 1341) hydrogen bonds : angle 4.99870 ( 3801) link_BETA1-4 : bond 0.00869 ( 3) link_BETA1-4 : angle 3.07126 ( 9) link_NAG-ASN : bond 0.00616 ( 54) link_NAG-ASN : angle 3.16974 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16255.48 seconds wall clock time: 276 minutes 28.07 seconds (16588.07 seconds total)