Starting phenix.real_space_refine on Tue Aug 26 05:55:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zc3_39921/08_2025/8zc3_39921.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zc3_39921/08_2025/8zc3_39921.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zc3_39921/08_2025/8zc3_39921.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zc3_39921/08_2025/8zc3_39921.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zc3_39921/08_2025/8zc3_39921.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zc3_39921/08_2025/8zc3_39921.map" } resolution = 4.69 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.037 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 144 5.16 5 C 21556 2.51 5 N 5557 2.21 5 O 6599 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: 33856 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 7778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7778 Classifications: {'peptide': 993} Link IDs: {'PTRANS': 55, 'TRANS': 937} Chain breaks: 10 Chain: "B" Number of atoms: 7790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 994, 7790 Classifications: {'peptide': 994} Link IDs: {'PTRANS': 55, 'TRANS': 938} Chain breaks: 10 Chain: "C" Number of atoms: 7778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7778 Classifications: {'peptide': 993} Link IDs: {'PTRANS': 55, 'TRANS': 937} Chain breaks: 10 Chain: "D" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1591 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 195} Chain breaks: 1 Chain: "E" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1679 Classifications: {'peptide': 221} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 208} Chain breaks: 1 Chain: "M" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1591 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 195} Chain breaks: 1 Chain: "N" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1591 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 195} Chain breaks: 1 Chain: "Q" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1679 Classifications: {'peptide': 221} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 208} Chain breaks: 1 Chain: "R" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1679 Classifications: {'peptide': 221} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 208} Chain breaks: 1 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" 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: "O" 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: "P" 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: "S" 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: "T" 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: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 7.03, per 1000 atoms: 0.21 Number of scatterers: 33856 At special positions: 0 Unit cell: (136.576, 199.936, 242.176, 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 144 16.00 O 6599 8.00 N 5557 7.00 C 21556 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 89 " distance=2.03 Simple disulfide: pdb=" SG CYS D 145 " - pdb=" SG CYS D 204 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 103 " - pdb=" SG CYS E 108 " distance=2.03 Simple disulfide: pdb=" SG CYS E 154 " - pdb=" SG CYS E 210 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 89 " distance=2.03 Simple disulfide: pdb=" SG CYS M 145 " - pdb=" SG CYS M 204 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 89 " distance=2.03 Simple disulfide: pdb=" SG CYS N 145 " - pdb=" SG CYS N 204 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 96 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 103 " - pdb=" SG CYS Q 108 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 154 " - pdb=" SG CYS Q 210 " distance=2.03 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 103 " - pdb=" SG CYS R 108 " distance=2.03 Simple disulfide: pdb=" SG CYS R 154 " - pdb=" SG CYS R 210 " 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 F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 603 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A1074 " " NAG A1308 " - " ASN A1134 " " NAG A1309 " - " ASN A 61 " " NAG A1310 " - " ASN A 234 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 709 " " NAG B1306 " - " ASN B1074 " " NAG B1307 " - " ASN B1098 " " NAG B1308 " - " ASN B1134 " " NAG B1309 " - " ASN B 343 " " NAG C1301 " - " ASN C 331 " " NAG C1302 " - " ASN C 61 " " NAG C1303 " - " ASN C 122 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 657 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " ASN C 343 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 801 " " NAG H 1 " - " ASN A1098 " " NAG I 1 " - " ASN B 122 " " NAG J 1 " - " ASN B 717 " " NAG K 1 " - " ASN B 801 " " NAG L 1 " - " ASN B 331 " " NAG O 1 " - " ASN C 717 " " NAG P 1 " - " ASN C 801 " " NAG S 1 " - " ASN C1098 " " NAG T 1 " - " ASN C1134 " Time building additional restraints: 3.00 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 476.8 nanoseconds 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8000 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 70 sheets defined 16.7% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 294 through 302 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.864A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 371 removed outlier: 3.542A pdb=" N PHE A 371 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.616A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 removed outlier: 4.263A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.992A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 916 removed outlier: 3.592A pdb=" N LEU A 916 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 removed outlier: 3.968A pdb=" N SER A 939 " --> pdb=" O GLN A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 966 removed outlier: 3.701A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 984 removed outlier: 3.592A pdb=" N LEU A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N SER A 982 " --> pdb=" O ASN A 978 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG A 983 " --> pdb=" O ASP A 979 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU A 984 " --> pdb=" O ILE A 980 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 977 through 984' Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.394A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 365 through 369 Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.685A pdb=" N LYS B 386 " --> pdb=" O SER B 383 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 383 through 387' Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 746 through 757 removed outlier: 3.832A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 781 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.676A pdb=" N ILE B 870 " --> pdb=" O THR B 866 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 913 through 919 removed outlier: 4.317A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ASN B 919 " --> pdb=" O VAL B 915 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 913 through 919' Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.846A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.972A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.813A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 4.407A 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 338 through 343 Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.531A pdb=" N LEU C 368 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N TYR C 369 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN C 370 " --> pdb=" O VAL C 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 365 through 370' Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.613A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.529A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.505A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.500A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE C 782 " --> pdb=" O THR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.739A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASN C 919 " --> pdb=" O VAL C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 967 removed outlier: 3.692A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 979 through 984 Processing helix chain 'C' and resid 991 through 1033 removed outlier: 3.581A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 138 removed outlier: 3.865A pdb=" N LEU D 136 " --> pdb=" O SER D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 199 removed outlier: 3.749A pdb=" N HIS D 199 " --> pdb=" O GLN D 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 111 removed outlier: 3.715A pdb=" N ARG E 110 " --> pdb=" O SER E 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 135 through 139 removed outlier: 3.513A pdb=" N ASN M 139 " --> pdb=" O LEU M 136 " (cutoff:3.500A) Processing helix chain 'M' and resid 192 through 199 removed outlier: 3.591A pdb=" N HIS M 199 " --> pdb=" O GLN M 195 " (cutoff:3.500A) Processing helix chain 'N' and resid 132 through 137 Processing helix chain 'N' and resid 192 through 199 Processing helix chain 'Q' and resid 87 through 91 removed outlier: 3.902A pdb=" N THR Q 91 " --> pdb=" O SER Q 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 170 through 172 No H-bonds generated for 'chain 'R' and resid 170 through 172' Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.705A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 4.257A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE B 326 " --> pdb=" O ASN B 540 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 49 through 55 removed outlier: 3.651A pdb=" N HIS A 49 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE A 55 " --> pdb=" O GLN A 271 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN A 271 " --> pdb=" O PHE A 55 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU A 276 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL A 289 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.739A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TRP A 104 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE A 119 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 140 through 141 removed outlier: 4.461A pdb=" N PHE A 140 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ARG A 158 " --> pdb=" O PHE A 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.651A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE A 598 " --> pdb=" O ALA A 609 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A 650 " --> pdb=" O PHE A 643 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE A 643 " --> pdb=" O LEU A 650 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.583A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.613A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR A 396 " --> pdb=" O SER A 514 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 removed outlier: 3.759A pdb=" N TYR A 453 " --> pdb=" O GLN A 493 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN A 493 " --> pdb=" O TYR A 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.887A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 9.446A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 712 through 721 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 712 through 721 current: chain 'A' and resid 1059 through 1077 removed outlier: 3.520A pdb=" N THR A1105 " --> pdb=" O VAL A1094 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.032A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 788 through 789 removed outlier: 6.101A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 1081 through 1083 removed outlier: 5.041A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER A1123 " --> pdb=" O ALA A1087 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.663A pdb=" N VAL B 62 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER B 31 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER B 94 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG B 190 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 49 through 55 removed outlier: 3.501A pdb=" N LEU B 277 " --> pdb=" O HIS B 49 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE B 275 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS B 278 " --> pdb=" O ASP B 287 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.517A pdb=" N PHE B 238 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLN B 239 " --> pdb=" O ILE B 105 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ILE B 105 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B 241 " --> pdb=" O GLY B 103 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 119 through 121 removed outlier: 4.252A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VAL B 127 " --> pdb=" O VAL B 120 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 140 through 141 removed outlier: 4.056A pdb=" N PHE B 140 " --> pdb=" O ARG B 158 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG B 158 " --> pdb=" O PHE B 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.007A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR B 612 " --> pdb=" O CYS B 649 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLY B 648 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.953A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE B 358 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 453 through 454 removed outlier: 4.808A pdb=" N TYR B 453 " --> pdb=" O GLN B 493 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLN B 493 " --> pdb=" O TYR B 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.149A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.644A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 733 through 735 removed outlier: 4.090A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR B 859 " --> pdb=" O SER B 735 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AC9, first strand: chain 'B' and resid 1120 through 1121 Processing sheet with id=AD1, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD2, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.746A pdb=" N THR C 29 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL C 62 " --> pdb=" O THR C 29 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 60 through 65 current: chain 'C' and resid 189 through 197 removed outlier: 4.324A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N TYR C 204 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LYS C 202 " --> pdb=" O LYS C 195 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE C 197 " --> pdb=" O TYR C 200 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.823A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE C 55 " --> pdb=" O GLN C 271 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS C 278 " --> pdb=" O ASP C 287 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.914A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TRP C 104 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE C 119 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 313 through 318 removed outlier: 6.582A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TYR C 612 " --> pdb=" O CYS C 649 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.578A pdb=" N ILE C 326 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN C 542 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG C 328 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 356 through 358 Processing sheet with id=AD8, first strand: chain 'C' and resid 399 through 402 Processing sheet with id=AD9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE1, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.810A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA C 672 " --> pdb=" O ILE C 664 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE C 664 " --> pdb=" O ALA C 672 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 712 through 713 Processing sheet with id=AE3, first strand: chain 'C' and resid 717 through 719 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 717 through 719 current: chain 'C' and resid 1059 through 1070 No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'C' and resid 733 through 735 removed outlier: 4.213A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR C 859 " --> pdb=" O SER C 735 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 1120 through 1122 removed outlier: 3.581A pdb=" N PHE C1121 " --> pdb=" O PHE C1089 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N CYS C1082 " --> pdb=" O VAL C1133 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1094 through 1097 removed outlier: 3.570A pdb=" N VAL C1094 " --> pdb=" O THR C1105 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 17 through 23 removed outlier: 3.656A pdb=" N SER D 73 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER D 66 " --> pdb=" O SER D 73 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 46 through 49 removed outlier: 3.592A pdb=" N GLN D 38 " --> pdb=" O LYS D 46 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU D 48 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLY D 98 " --> pdb=" O ASP D 93 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 125 through 129 removed outlier: 3.696A pdb=" N SER D 148 " --> pdb=" O SER D 125 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N VAL D 144 " --> pdb=" O PHE D 129 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA D 141 " --> pdb=" O LEU D 191 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE D 147 " --> pdb=" O ALA D 185 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP D 149 " --> pdb=" O TYR D 183 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N TYR D 183 " --> pdb=" O ASP D 149 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 159 through 160 removed outlier: 4.001A pdb=" N LYS D 160 " --> pdb=" O SER D 203 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER D 203 " --> pdb=" O LYS D 160 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'D' and resid 206 through 207 removed outlier: 4.635A pdb=" N VAL D 206 " --> pdb=" O VAL D 213 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL D 213 " --> pdb=" O VAL D 206 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'E' and resid 11 through 12 Processing sheet with id=AF4, first strand: chain 'E' and resid 17 through 23 removed outlier: 3.654A pdb=" N MET E 81 " --> pdb=" O VAL E 20 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N THR E 69 " --> pdb=" O GLU E 82 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 45 through 51 removed outlier: 6.943A pdb=" N TRP E 36 " --> pdb=" O MET E 48 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N TRP E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ILE E 34 " --> pdb=" O TRP E 50 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN E 33 " --> pdb=" O SER E 99 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL E 37 " --> pdb=" O PHE E 95 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 134 through 136 removed outlier: 3.660A pdb=" N LEU E 155 " --> pdb=" O PHE E 136 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER E 194 " --> pdb=" O CYS E 154 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N TYR E 190 " --> pdb=" O ASP E 158 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 165 through 168 removed outlier: 3.584A pdb=" N CYS E 210 " --> pdb=" O LYS E 223 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS E 223 " --> pdb=" O CYS E 210 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'M' and resid 9 through 11 removed outlier: 3.897A pdb=" N THR M 108 " --> pdb=" O ALA M 10 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'M' and resid 18 through 23 removed outlier: 3.771A pdb=" N SER M 71 " --> pdb=" O SER M 68 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER M 66 " --> pdb=" O SER M 73 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'M' and resid 45 through 49 removed outlier: 7.074A pdb=" N TRP M 36 " --> pdb=" O LEU M 48 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY M 98 " --> pdb=" O ASP M 93 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'M' and resid 125 through 129 removed outlier: 4.109A pdb=" N VAL M 144 " --> pdb=" O PHE M 129 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 142 through 150 current: chain 'M' and resid 183 through 185 Processing sheet with id=AG3, first strand: chain 'M' and resid 157 through 160 removed outlier: 3.640A pdb=" N LYS M 160 " --> pdb=" O SER M 203 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER M 203 " --> pdb=" O LYS M 160 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL M 206 " --> pdb=" O VAL M 213 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL M 213 " --> pdb=" O VAL M 206 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'N' and resid 17 through 23 removed outlier: 3.540A pdb=" N ILE N 76 " --> pdb=" O VAL N 18 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'N' and resid 35 through 39 removed outlier: 6.715A pdb=" N TRP N 36 " --> pdb=" O LEU N 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 45 through 49 current: chain 'N' and resid 99 through 100 Processing sheet with id=AG6, first strand: chain 'N' and resid 125 through 129 removed outlier: 4.081A pdb=" N VAL N 144 " --> pdb=" O PHE N 129 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N CYS N 145 " --> pdb=" O SER N 187 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N SER N 187 " --> pdb=" O CYS N 145 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE N 147 " --> pdb=" O ALA N 185 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA N 185 " --> pdb=" O ILE N 147 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N ALA N 184 " --> pdb=" O PRO N 175 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N SER N 186 " --> pdb=" O THR N 173 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'N' and resid 141 through 142 Processing sheet with id=AG8, first strand: chain 'N' and resid 158 through 160 removed outlier: 3.994A pdb=" N LYS N 160 " --> pdb=" O SER N 203 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER N 203 " --> pdb=" O LYS N 160 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Q' and resid 33 through 39 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 46 through 47 current: chain 'Q' and resid 116 through 117 Processing sheet with id=AH1, first strand: chain 'Q' and resid 68 through 71 removed outlier: 3.876A pdb=" N GLU Q 82 " --> pdb=" O THR Q 69 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR Q 71 " --> pdb=" O TYR Q 80 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N TYR Q 80 " --> pdb=" O THR Q 71 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'Q' and resid 150 through 152 removed outlier: 3.592A pdb=" N LEU Q 152 " --> pdb=" O VAL Q 196 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'Q' and resid 165 through 168 removed outlier: 3.566A pdb=" N THR Q 165 " --> pdb=" O ASN Q 213 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS Q 223 " --> pdb=" O CYS Q 210 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL Q 212 " --> pdb=" O VAL Q 221 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL Q 221 " --> pdb=" O VAL Q 212 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N HIS Q 214 " --> pdb=" O THR Q 219 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR Q 219 " --> pdb=" O HIS Q 214 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'R' and resid 33 through 39 removed outlier: 6.761A pdb=" N ILE R 34 " --> pdb=" O TRP R 50 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N TRP R 50 " --> pdb=" O ILE R 34 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N TRP R 36 " --> pdb=" O MET R 48 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TRP R 50 " --> pdb=" O ASN R 59 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN R 59 " --> pdb=" O TRP R 50 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 59 through 60 current: chain 'R' and resid 114 through 117 Processing sheet with id=AH5, first strand: chain 'R' and resid 68 through 72 Processing sheet with id=AH6, first strand: chain 'R' and resid 135 through 137 Processing sheet with id=AH7, first strand: chain 'R' and resid 165 through 168 removed outlier: 4.245A pdb=" N VAL R 212 " --> pdb=" O VAL R 221 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N VAL R 221 " --> pdb=" O VAL R 212 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N HIS R 214 " --> pdb=" O THR R 219 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR R 219 " --> pdb=" O HIS R 214 " (cutoff:3.500A) 880 hydrogen bonds defined for protein. 2400 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: 6.76 Time building geometry restraints manager: 3.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10669 1.34 - 1.47: 8890 1.47 - 1.60: 14918 1.60 - 1.73: 0 1.73 - 1.85: 180 Bond restraints: 34657 Sorted by residual: bond pdb=" C1 NAG B1306 " pdb=" O5 NAG B1306 " ideal model delta sigma weight residual 1.406 1.477 -0.071 2.00e-02 2.50e+03 1.28e+01 bond pdb=" CA ARG B1039 " pdb=" C ARG B1039 " ideal model delta sigma weight residual 1.523 1.487 0.036 1.23e-02 6.61e+03 8.64e+00 bond pdb=" N LYS B1038 " pdb=" CA LYS B1038 " ideal model delta sigma weight residual 1.459 1.424 0.035 1.25e-02 6.40e+03 7.78e+00 bond pdb=" CA ASP B1041 " pdb=" C ASP B1041 " ideal model delta sigma weight residual 1.525 1.487 0.038 1.40e-02 5.10e+03 7.46e+00 bond pdb=" CA SER B1037 " pdb=" C SER B1037 " ideal model delta sigma weight residual 1.523 1.494 0.029 1.21e-02 6.83e+03 5.77e+00 ... (remaining 34652 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 46427 2.43 - 4.86: 659 4.86 - 7.29: 83 7.29 - 9.73: 16 9.73 - 12.16: 4 Bond angle restraints: 47189 Sorted by residual: angle pdb=" C PHE B1042 " pdb=" N CYS B1043 " pdb=" CA CYS B1043 " ideal model delta sigma weight residual 122.95 115.65 7.30 1.44e+00 4.82e-01 2.57e+01 angle pdb=" N SER B1037 " pdb=" CA SER B1037 " pdb=" C SER B1037 " ideal model delta sigma weight residual 108.02 116.80 -8.78 1.75e+00 3.27e-01 2.52e+01 angle pdb=" C VAL A1040 " pdb=" N ASP A1041 " pdb=" CA ASP A1041 " ideal model delta sigma weight residual 121.54 131.00 -9.46 1.91e+00 2.74e-01 2.45e+01 angle pdb=" N LYS B1038 " pdb=" CA LYS B1038 " pdb=" C LYS B1038 " ideal model delta sigma weight residual 111.71 106.03 5.68 1.15e+00 7.56e-01 2.44e+01 angle pdb=" C ASN B1074 " pdb=" CA ASN B1074 " pdb=" CB ASN B1074 " ideal model delta sigma weight residual 109.53 117.43 -7.90 1.65e+00 3.67e-01 2.29e+01 ... (remaining 47184 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 19264 17.91 - 35.82: 1638 35.82 - 53.73: 262 53.73 - 71.65: 90 71.65 - 89.56: 52 Dihedral angle restraints: 21306 sinusoidal: 8877 harmonic: 12429 Sorted by residual: dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 2.99 -88.99 1 1.00e+01 1.00e-02 9.43e+01 dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual -86.00 2.93 -88.93 1 1.00e+01 1.00e-02 9.42e+01 dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual 93.00 5.05 87.95 1 1.00e+01 1.00e-02 9.26e+01 ... (remaining 21303 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.140: 5447 0.140 - 0.280: 30 0.280 - 0.420: 7 0.420 - 0.560: 1 0.560 - 0.700: 1 Chirality restraints: 5486 Sorted by residual: chirality pdb=" C1 NAG B1306 " pdb=" ND2 ASN B1074 " pdb=" C2 NAG B1306 " pdb=" O5 NAG B1306 " both_signs ideal model delta sigma weight residual False -2.40 -1.70 -0.70 2.00e-01 2.50e+01 1.22e+01 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN B 122 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.86 -0.54 2.00e-01 2.50e+01 7.35e+00 chirality pdb=" C1 NAG A1310 " pdb=" ND2 ASN A 234 " pdb=" C2 NAG A1310 " pdb=" O5 NAG A1310 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.86e+00 ... (remaining 5483 not shown) Planarity restraints: 6040 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B1074 " 0.009 2.00e-02 2.50e+03 3.77e-02 1.77e+01 pdb=" CG ASN B1074 " -0.051 2.00e-02 2.50e+03 pdb=" OD1 ASN B1074 " 0.044 2.00e-02 2.50e+03 pdb=" ND2 ASN B1074 " -0.035 2.00e-02 2.50e+03 pdb=" C1 NAG B1306 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 986 " 0.066 5.00e-02 4.00e+02 9.78e-02 1.53e+01 pdb=" N PRO B 987 " -0.169 5.00e-02 4.00e+02 pdb=" CA PRO B 987 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO B 987 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE Q 160 " -0.046 5.00e-02 4.00e+02 6.96e-02 7.75e+00 pdb=" N PRO Q 161 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO Q 161 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO Q 161 " -0.036 5.00e-02 4.00e+02 ... (remaining 6037 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 251 2.57 - 3.15: 24528 3.15 - 3.73: 49741 3.73 - 4.32: 65303 4.32 - 4.90: 108806 Nonbonded interactions: 248629 Sorted by model distance: nonbonded pdb=" CB SER Q 126 " pdb=" CE2 PHE Q 160 " model vdw 1.984 3.740 nonbonded pdb=" CB SER Q 126 " pdb=" CZ PHE Q 160 " model vdw 2.262 3.740 nonbonded pdb=" OG1 THR C 716 " pdb=" OE1 GLN C1071 " model vdw 2.267 3.040 nonbonded pdb=" OG1 THR B 108 " pdb=" O ASN B 234 " model vdw 2.282 3.040 nonbonded pdb=" O ASP A 294 " pdb=" OG SER A 297 " model vdw 2.292 3.040 ... (remaining 248624 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 142 or resid 155 through 210 or resid 216 throu \ gh 245 or resid 263 through 1309)) selection = (chain 'B' and (resid 27 through 95 or resid 100 through 245 or resid 263 throug \ h 1309)) selection = (chain 'C' and (resid 27 through 142 or resid 155 through 210 or resid 216 throu \ gh 245 or resid 263 through 1309)) } ncs_group { reference = chain 'D' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'E' selection = chain 'Q' selection = chain 'R' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'O' selection = chain 'P' selection = chain 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.220 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: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.070 Set scattering table: 0.140 Process input model: 29.460 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.100 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 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 0.071 34758 Z= 0.183 Angle : 0.704 15.032 47441 Z= 0.357 Chirality : 0.051 0.700 5486 Planarity : 0.005 0.098 6001 Dihedral : 13.975 89.558 13153 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.98 % Favored : 95.97 % Rotamer: Outliers : 0.16 % Allowed : 0.32 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % 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: -1.49 (0.12), residues: 4192 helix: 0.18 (0.19), residues: 625 sheet: 0.05 (0.18), residues: 819 loop : -1.70 (0.11), residues: 2748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Q 67 TYR 0.032 0.001 TYR C 453 PHE 0.037 0.001 PHE Q 160 TRP 0.025 0.001 TRP Q 113 HIS 0.002 0.000 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00350 (34657) covalent geometry : angle 0.68607 (47189) SS BOND : bond 0.00239 ( 51) SS BOND : angle 0.97395 ( 102) hydrogen bonds : bond 0.23613 ( 880) hydrogen bonds : angle 8.33962 ( 2400) link_BETA1-4 : bond 0.00614 ( 11) link_BETA1-4 : angle 1.95445 ( 33) link_NAG-ASN : bond 0.00660 ( 39) link_NAG-ASN : angle 3.02616 ( 117) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 379 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 THR cc_start: 0.8834 (t) cc_final: 0.7996 (m) REVERT: A 655 TYR cc_start: 0.8742 (t80) cc_final: 0.8470 (t80) REVERT: A 953 ASN cc_start: 0.8059 (t0) cc_final: 0.7834 (t0) REVERT: A 1028 LYS cc_start: 0.7871 (mttt) cc_final: 0.7457 (mttm) REVERT: A 1050 MET cc_start: 0.6712 (ptp) cc_final: 0.6398 (ptp) REVERT: B 135 PHE cc_start: 0.7946 (m-80) cc_final: 0.7534 (m-80) REVERT: B 400 PHE cc_start: 0.8025 (p90) cc_final: 0.7307 (p90) REVERT: B 759 PHE cc_start: 0.5120 (m-10) cc_final: 0.4829 (m-10) REVERT: B 1076 THR cc_start: 0.7504 (p) cc_final: 0.7300 (p) REVERT: B 1118 ASP cc_start: 0.8806 (p0) cc_final: 0.8425 (p0) REVERT: C 55 PHE cc_start: 0.7764 (m-80) cc_final: 0.7474 (m-80) REVERT: C 104 TRP cc_start: 0.6815 (m-90) cc_final: 0.6524 (m-90) REVERT: C 275 PHE cc_start: 0.8206 (m-10) cc_final: 0.7433 (m-10) REVERT: C 298 GLU cc_start: 0.8546 (tm-30) cc_final: 0.8229 (tm-30) REVERT: C 302 THR cc_start: 0.8318 (p) cc_final: 0.7952 (p) REVERT: C 455 LEU cc_start: 0.8437 (tp) cc_final: 0.8185 (tp) REVERT: C 465 GLU cc_start: 0.7892 (pt0) cc_final: 0.7662 (pt0) REVERT: C 513 LEU cc_start: 0.8491 (tp) cc_final: 0.7589 (pp) REVERT: C 562 PHE cc_start: 0.8756 (p90) cc_final: 0.8287 (p90) REVERT: C 977 LEU cc_start: 0.7306 (mm) cc_final: 0.7027 (pp) REVERT: C 978 ASN cc_start: 0.6092 (p0) cc_final: 0.5852 (p0) REVERT: C 1050 MET cc_start: 0.8274 (ppp) cc_final: 0.7636 (ppp) REVERT: E 126 SER cc_start: 0.2823 (m) cc_final: 0.2486 (t) REVERT: M 87 TYR cc_start: 0.5706 (m-80) cc_final: 0.5499 (m-80) REVERT: N 22 CYS cc_start: 0.4947 (t) cc_final: 0.4746 (t) REVERT: N 150 PHE cc_start: 0.3882 (p90) cc_final: 0.3636 (p90) REVERT: Q 31 ASP cc_start: 0.8047 (m-30) cc_final: 0.7480 (m-30) REVERT: R 70 MET cc_start: 0.8706 (mpp) cc_final: 0.8329 (mpp) REVERT: R 108 CYS cc_start: 0.4777 (p) cc_final: 0.4511 (p) REVERT: R 190 TYR cc_start: 0.6948 (m-80) cc_final: 0.6461 (m-10) outliers start: 6 outliers final: 0 residues processed: 385 average time/residue: 0.1676 time to fit residues: 111.8855 Evaluate side-chains 272 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 272 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 197 optimal weight: 10.0000 chunk 388 optimal weight: 7.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 401 optimal weight: 2.9990 chunk 424 optimal weight: 6.9990 chunk 155 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 HIS A 751 ASN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 405 ASN B 777 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN D 38 GLN D 178 GLN E 6 GLN ** E 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 ASN M 99 HIS M 137 GLN N 38 GLN N 52 ASN ** R 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.115556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.081121 restraints weight = 129938.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.083084 restraints weight = 81001.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.084459 restraints weight = 56271.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.085399 restraints weight = 42934.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.086018 restraints weight = 35236.971| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 34758 Z= 0.161 Angle : 0.576 12.332 47441 Z= 0.291 Chirality : 0.045 0.357 5486 Planarity : 0.004 0.081 6001 Dihedral : 5.769 57.749 5612 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.13 % Allowed : 4.87 % Favored : 94.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % 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: -1.01 (0.13), residues: 4192 helix: 1.30 (0.21), residues: 623 sheet: 0.03 (0.17), residues: 941 loop : -1.51 (0.12), residues: 2628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B1039 TYR 0.019 0.001 TYR B1067 PHE 0.016 0.002 PHE B1089 TRP 0.014 0.001 TRP R 113 HIS 0.006 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00348 (34657) covalent geometry : angle 0.56333 (47189) SS BOND : bond 0.00320 ( 51) SS BOND : angle 0.99862 ( 102) hydrogen bonds : bond 0.04142 ( 880) hydrogen bonds : angle 5.88899 ( 2400) link_BETA1-4 : bond 0.00240 ( 11) link_BETA1-4 : angle 1.38218 ( 33) link_NAG-ASN : bond 0.00550 ( 39) link_NAG-ASN : angle 2.28594 ( 117) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 349 time to evaluate : 1.276 Fit side-chains revert: symmetry clash REVERT: A 429 PHE cc_start: 0.7279 (t80) cc_final: 0.7063 (t80) REVERT: A 655 TYR cc_start: 0.8506 (t80) cc_final: 0.8262 (t80) REVERT: B 400 PHE cc_start: 0.7984 (p90) cc_final: 0.7213 (p90) REVERT: B 401 VAL cc_start: 0.8656 (t) cc_final: 0.7997 (p) REVERT: B 1041 ASP cc_start: 0.8597 (t0) cc_final: 0.7580 (t0) REVERT: B 1118 ASP cc_start: 0.8668 (p0) cc_final: 0.6803 (t70) REVERT: C 40 ASP cc_start: 0.8914 (p0) cc_final: 0.8682 (p0) REVERT: C 56 LEU cc_start: 0.8407 (tp) cc_final: 0.8191 (tp) REVERT: C 128 ILE cc_start: 0.7271 (mm) cc_final: 0.6980 (mm) REVERT: C 275 PHE cc_start: 0.8356 (m-10) cc_final: 0.7856 (m-10) REVERT: C 427 ASP cc_start: 0.7002 (p0) cc_final: 0.6680 (p0) REVERT: C 455 LEU cc_start: 0.8603 (tp) cc_final: 0.8295 (tp) REVERT: C 465 GLU cc_start: 0.8070 (pt0) cc_final: 0.7660 (pt0) REVERT: C 513 LEU cc_start: 0.8551 (tp) cc_final: 0.7368 (pp) REVERT: C 562 PHE cc_start: 0.8774 (p90) cc_final: 0.8355 (p90) REVERT: C 922 LEU cc_start: 0.8842 (tp) cc_final: 0.8636 (tp) REVERT: C 977 LEU cc_start: 0.7476 (mm) cc_final: 0.7160 (pt) REVERT: C 1050 MET cc_start: 0.8657 (ppp) cc_final: 0.7912 (ppp) REVERT: C 1110 TYR cc_start: 0.8145 (t80) cc_final: 0.7771 (t80) REVERT: D 5 THR cc_start: 0.3075 (m) cc_final: 0.2865 (m) REVERT: M 87 TYR cc_start: 0.5930 (m-80) cc_final: 0.5655 (m-80) REVERT: Q 31 ASP cc_start: 0.7715 (m-30) cc_final: 0.7119 (m-30) REVERT: Q 48 MET cc_start: 0.6653 (pmm) cc_final: 0.6183 (pmm) REVERT: Q 70 MET cc_start: 0.2474 (mpp) cc_final: 0.2269 (mpp) REVERT: R 70 MET cc_start: 0.8662 (mpp) cc_final: 0.8335 (mpp) REVERT: R 81 MET cc_start: 0.3737 (mpp) cc_final: 0.3369 (mpp) REVERT: R 190 TYR cc_start: 0.6811 (m-80) cc_final: 0.6480 (m-10) outliers start: 5 outliers final: 2 residues processed: 352 average time/residue: 0.1820 time to fit residues: 110.2338 Evaluate side-chains 254 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 252 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 84 optimal weight: 6.9990 chunk 384 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 136 optimal weight: 7.9990 chunk 363 optimal weight: 30.0000 chunk 195 optimal weight: 6.9990 chunk 328 optimal weight: 20.0000 chunk 388 optimal weight: 3.9990 chunk 269 optimal weight: 0.8980 chunk 294 optimal weight: 6.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 ASN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN B 955 ASN B1048 HIS B1108 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN C 394 ASN C 774 GLN C1054 GLN E 119 GLN ** E 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 ASN N 52 ASN Q 3 GLN ** R 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.111873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.078650 restraints weight = 126655.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.079166 restraints weight = 85558.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.080041 restraints weight = 66616.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.080576 restraints weight = 49113.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.080813 restraints weight = 44957.964| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 34758 Z= 0.191 Angle : 0.613 13.317 47441 Z= 0.311 Chirality : 0.046 0.350 5486 Planarity : 0.005 0.079 6001 Dihedral : 5.822 56.448 5612 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 0.08 % Allowed : 4.39 % Favored : 95.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % 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: -1.10 (0.13), residues: 4192 helix: 1.08 (0.20), residues: 637 sheet: -0.11 (0.17), residues: 895 loop : -1.49 (0.12), residues: 2660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B1039 TYR 0.026 0.002 TYR C 508 PHE 0.046 0.002 PHE A 906 TRP 0.012 0.001 TRP E 111 HIS 0.019 0.001 HIS C 954 Details of bonding type rmsd covalent geometry : bond 0.00422 (34657) covalent geometry : angle 0.59897 (47189) SS BOND : bond 0.00375 ( 51) SS BOND : angle 1.32763 ( 102) hydrogen bonds : bond 0.04603 ( 880) hydrogen bonds : angle 5.62964 ( 2400) link_BETA1-4 : bond 0.00389 ( 11) link_BETA1-4 : angle 1.60021 ( 33) link_NAG-ASN : bond 0.00420 ( 39) link_NAG-ASN : angle 2.32800 ( 117) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 336 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 655 TYR cc_start: 0.8842 (t80) cc_final: 0.8325 (t80) REVERT: B 135 PHE cc_start: 0.8058 (m-80) cc_final: 0.7724 (m-80) REVERT: B 400 PHE cc_start: 0.7971 (p90) cc_final: 0.7182 (p90) REVERT: B 401 VAL cc_start: 0.8678 (t) cc_final: 0.7868 (p) REVERT: B 498 ARG cc_start: 0.8768 (mpt180) cc_final: 0.8402 (mmt180) REVERT: B 562 PHE cc_start: 0.7712 (p90) cc_final: 0.7446 (p90) REVERT: B 655 TYR cc_start: 0.8284 (t80) cc_final: 0.8076 (t80) REVERT: B 786 LYS cc_start: 0.8689 (mmmt) cc_final: 0.8442 (mtpt) REVERT: B 1041 ASP cc_start: 0.8976 (t0) cc_final: 0.8065 (t0) REVERT: B 1118 ASP cc_start: 0.8730 (p0) cc_final: 0.8304 (p0) REVERT: C 275 PHE cc_start: 0.8439 (m-10) cc_final: 0.7966 (m-10) REVERT: C 427 ASP cc_start: 0.6591 (p0) cc_final: 0.6193 (p0) REVERT: C 455 LEU cc_start: 0.8616 (tp) cc_final: 0.8284 (tp) REVERT: C 562 PHE cc_start: 0.8705 (p90) cc_final: 0.8251 (p90) REVERT: C 751 ASN cc_start: 0.6766 (p0) cc_final: 0.6480 (m-40) REVERT: C 752 LEU cc_start: 0.8805 (pp) cc_final: 0.8419 (tp) REVERT: C 773 GLU cc_start: 0.8697 (pp20) cc_final: 0.8487 (tm-30) REVERT: C 1050 MET cc_start: 0.8877 (ppp) cc_final: 0.8044 (ppp) REVERT: C 1110 TYR cc_start: 0.8343 (t80) cc_final: 0.8015 (t80) REVERT: E 126 SER cc_start: 0.2801 (m) cc_final: 0.2460 (t) REVERT: M 87 TYR cc_start: 0.5725 (m-80) cc_final: 0.5499 (m-80) REVERT: N 22 CYS cc_start: 0.4592 (t) cc_final: 0.4365 (t) REVERT: Q 31 ASP cc_start: 0.7948 (m-30) cc_final: 0.7334 (m-30) REVERT: Q 48 MET cc_start: 0.6331 (pmm) cc_final: 0.5544 (pmm) REVERT: Q 183 VAL cc_start: 0.5817 (m) cc_final: 0.5508 (m) REVERT: R 81 MET cc_start: 0.3974 (mpp) cc_final: 0.3588 (mpp) outliers start: 3 outliers final: 0 residues processed: 339 average time/residue: 0.1819 time to fit residues: 106.2049 Evaluate side-chains 233 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 116 optimal weight: 7.9990 chunk 134 optimal weight: 10.0000 chunk 186 optimal weight: 1.9990 chunk 407 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 chunk 243 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 138 optimal weight: 9.9990 chunk 139 optimal weight: 3.9990 chunk 170 optimal weight: 4.9990 chunk 173 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 HIS A 394 ASN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B1088 HIS ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 GLN C 394 ASN C 954 HIS D 38 GLN ** M 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 ASN N 38 GLN Q 3 GLN ** R 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 211 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.111441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.084304 restraints weight = 138169.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.083279 restraints weight = 151757.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.084719 restraints weight = 121238.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.084156 restraints weight = 89952.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.084373 restraints weight = 84975.723| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 34758 Z= 0.209 Angle : 0.617 9.702 47441 Z= 0.312 Chirality : 0.046 0.359 5486 Planarity : 0.005 0.080 6001 Dihedral : 5.966 58.467 5612 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 0.08 % Allowed : 3.66 % Favored : 96.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % 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: -1.22 (0.13), residues: 4192 helix: 1.00 (0.20), residues: 631 sheet: -0.32 (0.17), residues: 925 loop : -1.53 (0.12), residues: 2636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1107 TYR 0.020 0.002 TYR M 88 PHE 0.018 0.002 PHE B 888 TRP 0.012 0.001 TRP N 92 HIS 0.008 0.001 HIS C 954 Details of bonding type rmsd covalent geometry : bond 0.00461 (34657) covalent geometry : angle 0.60211 (47189) SS BOND : bond 0.00570 ( 51) SS BOND : angle 1.37089 ( 102) hydrogen bonds : bond 0.04206 ( 880) hydrogen bonds : angle 5.59139 ( 2400) link_BETA1-4 : bond 0.00313 ( 11) link_BETA1-4 : angle 1.56906 ( 33) link_NAG-ASN : bond 0.00390 ( 39) link_NAG-ASN : angle 2.37059 ( 117) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 300 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 PHE cc_start: 0.7164 (t80) cc_final: 0.6949 (t80) REVERT: A 655 TYR cc_start: 0.8889 (t80) cc_final: 0.8201 (t80) REVERT: A 902 MET cc_start: 0.8014 (tpt) cc_final: 0.7656 (tpp) REVERT: A 1050 MET cc_start: 0.7369 (ptp) cc_final: 0.7017 (ptp) REVERT: B 135 PHE cc_start: 0.8007 (m-80) cc_final: 0.7776 (m-80) REVERT: B 378 LYS cc_start: 0.8044 (mmtt) cc_final: 0.7678 (tmtt) REVERT: B 400 PHE cc_start: 0.7981 (p90) cc_final: 0.7364 (p90) REVERT: B 401 VAL cc_start: 0.8697 (t) cc_final: 0.8124 (p) REVERT: B 498 ARG cc_start: 0.8492 (mpt180) cc_final: 0.8103 (mmt180) REVERT: B 562 PHE cc_start: 0.7780 (p90) cc_final: 0.7579 (p90) REVERT: B 655 TYR cc_start: 0.8418 (t80) cc_final: 0.8166 (t80) REVERT: B 1041 ASP cc_start: 0.8897 (t0) cc_final: 0.7985 (t0) REVERT: B 1118 ASP cc_start: 0.8524 (p0) cc_final: 0.8092 (p0) REVERT: C 390 LEU cc_start: 0.8270 (mt) cc_final: 0.8053 (mt) REVERT: C 427 ASP cc_start: 0.6648 (p0) cc_final: 0.6335 (p0) REVERT: C 455 LEU cc_start: 0.8521 (tp) cc_final: 0.8270 (tp) REVERT: C 562 PHE cc_start: 0.8702 (p90) cc_final: 0.8290 (p90) REVERT: C 751 ASN cc_start: 0.6827 (p0) cc_final: 0.6437 (m-40) REVERT: C 1050 MET cc_start: 0.8629 (ppp) cc_final: 0.8378 (ppp) REVERT: D 5 THR cc_start: 0.4134 (m) cc_final: 0.3857 (m) REVERT: E 126 SER cc_start: 0.4064 (m) cc_final: 0.3482 (t) REVERT: M 87 TYR cc_start: 0.5462 (m-80) cc_final: 0.5254 (m-80) REVERT: Q 29 PHE cc_start: 0.8150 (t80) cc_final: 0.7720 (t80) REVERT: Q 31 ASP cc_start: 0.7742 (m-30) cc_final: 0.7308 (m-30) REVERT: Q 34 ILE cc_start: 0.7713 (tp) cc_final: 0.7512 (tp) REVERT: Q 72 ARG cc_start: 0.5680 (ttm-80) cc_final: 0.5286 (ttm-80) REVERT: Q 183 VAL cc_start: 0.3906 (m) cc_final: 0.3613 (m) REVERT: R 81 MET cc_start: 0.3983 (mpp) cc_final: 0.3732 (mpp) REVERT: R 190 TYR cc_start: 0.6959 (m-80) cc_final: 0.6746 (m-80) outliers start: 3 outliers final: 1 residues processed: 302 average time/residue: 0.1879 time to fit residues: 97.1260 Evaluate side-chains 229 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 228 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 112 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 chunk 340 optimal weight: 0.0670 chunk 143 optimal weight: 6.9990 chunk 97 optimal weight: 7.9990 chunk 174 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 216 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 171 optimal weight: 2.9990 overall best weight: 1.0922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B1083 HIS C 121 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C 777 ASN D 52 ASN ** M 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 ASN Q 3 GLN Q 213 ASN ** R 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.112647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.078433 restraints weight = 126834.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.080485 restraints weight = 85473.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.081000 restraints weight = 60022.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.082019 restraints weight = 44820.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.082612 restraints weight = 35543.669| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 34758 Z= 0.102 Angle : 0.532 11.072 47441 Z= 0.263 Chirality : 0.045 0.456 5486 Planarity : 0.004 0.082 6001 Dihedral : 5.506 58.995 5612 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.05 % Allowed : 1.88 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % 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: -1.03 (0.13), residues: 4192 helix: 1.44 (0.21), residues: 625 sheet: -0.15 (0.17), residues: 914 loop : -1.49 (0.12), residues: 2653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 55 TYR 0.017 0.001 TYR C 508 PHE 0.019 0.001 PHE C 906 TRP 0.028 0.001 TRP Q 111 HIS 0.004 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00228 (34657) covalent geometry : angle 0.51494 (47189) SS BOND : bond 0.00275 ( 51) SS BOND : angle 1.08314 ( 102) hydrogen bonds : bond 0.03695 ( 880) hydrogen bonds : angle 5.22133 ( 2400) link_BETA1-4 : bond 0.00328 ( 11) link_BETA1-4 : angle 1.53002 ( 33) link_NAG-ASN : bond 0.00329 ( 39) link_NAG-ASN : angle 2.43330 ( 117) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 336 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7883 (m-30) cc_final: 0.7631 (m-30) REVERT: A 94 SER cc_start: 0.7384 (m) cc_final: 0.6895 (p) REVERT: A 655 TYR cc_start: 0.8801 (t80) cc_final: 0.8179 (t80) REVERT: A 820 ASP cc_start: 0.7782 (m-30) cc_final: 0.7477 (m-30) REVERT: A 858 LEU cc_start: 0.8905 (mm) cc_final: 0.8686 (mm) REVERT: B 135 PHE cc_start: 0.7962 (m-80) cc_final: 0.7757 (m-80) REVERT: B 400 PHE cc_start: 0.8027 (p90) cc_final: 0.7157 (p90) REVERT: B 498 ARG cc_start: 0.8598 (mpt180) cc_final: 0.8059 (mmt180) REVERT: B 655 TYR cc_start: 0.8374 (t80) cc_final: 0.8153 (t80) REVERT: B 777 ASN cc_start: 0.8624 (m-40) cc_final: 0.8174 (m110) REVERT: B 786 LYS cc_start: 0.8606 (mmmt) cc_final: 0.8357 (mtpt) REVERT: B 867 ASP cc_start: 0.8130 (p0) cc_final: 0.7889 (p0) REVERT: B 1041 ASP cc_start: 0.8886 (t0) cc_final: 0.7968 (t0) REVERT: B 1067 TYR cc_start: 0.7445 (t80) cc_final: 0.7112 (t80) REVERT: B 1118 ASP cc_start: 0.8372 (p0) cc_final: 0.7959 (p0) REVERT: C 128 ILE cc_start: 0.7226 (mm) cc_final: 0.6511 (mm) REVERT: C 275 PHE cc_start: 0.8398 (m-10) cc_final: 0.7993 (m-10) REVERT: C 286 THR cc_start: 0.8460 (p) cc_final: 0.8058 (t) REVERT: C 427 ASP cc_start: 0.6871 (p0) cc_final: 0.6627 (p0) REVERT: C 455 LEU cc_start: 0.8664 (tp) cc_final: 0.8396 (tp) REVERT: C 562 PHE cc_start: 0.8585 (p90) cc_final: 0.8117 (p90) REVERT: C 697 MET cc_start: 0.8039 (ttt) cc_final: 0.7809 (ttt) REVERT: C 751 ASN cc_start: 0.6677 (p0) cc_final: 0.6333 (m-40) REVERT: C 752 LEU cc_start: 0.8508 (pp) cc_final: 0.8097 (tp) REVERT: E 126 SER cc_start: 0.3208 (m) cc_final: 0.2879 (t) REVERT: N 22 CYS cc_start: 0.5110 (t) cc_final: 0.4841 (t) REVERT: Q 29 PHE cc_start: 0.8254 (t80) cc_final: 0.7591 (t80) REVERT: Q 31 ASP cc_start: 0.8075 (m-30) cc_final: 0.7496 (m-30) REVERT: Q 72 ARG cc_start: 0.5320 (ttm-80) cc_final: 0.4750 (ttm-80) REVERT: Q 81 MET cc_start: 0.5019 (mmm) cc_final: 0.4815 (mmm) REVERT: Q 112 MET cc_start: 0.8670 (ptt) cc_final: 0.8038 (ppp) REVERT: Q 183 VAL cc_start: 0.6048 (m) cc_final: 0.5776 (m) REVERT: R 81 MET cc_start: 0.3811 (mpp) cc_final: 0.3261 (mpp) REVERT: R 95 PHE cc_start: 0.7008 (m-80) cc_final: 0.6758 (m-80) outliers start: 2 outliers final: 0 residues processed: 338 average time/residue: 0.1924 time to fit residues: 111.5017 Evaluate side-chains 252 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 313 optimal weight: 30.0000 chunk 418 optimal weight: 30.0000 chunk 13 optimal weight: 9.9990 chunk 252 optimal weight: 2.9990 chunk 230 optimal weight: 0.9980 chunk 344 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 354 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 396 optimal weight: 9.9990 chunk 375 optimal weight: 0.9990 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 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 HIS A 394 ASN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 HIS ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 HIS ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN B 955 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C 777 ASN ** M 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 ASN Q 3 GLN ** R 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.112242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.078415 restraints weight = 126700.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.080390 restraints weight = 85197.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.080803 restraints weight = 59301.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.081553 restraints weight = 45176.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.081726 restraints weight = 41734.133| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 34758 Z= 0.114 Angle : 0.533 10.116 47441 Z= 0.265 Chirality : 0.044 0.351 5486 Planarity : 0.004 0.084 6001 Dihedral : 5.363 59.815 5612 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.11 % Allowed : 1.83 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % 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: -0.95 (0.13), residues: 4192 helix: 1.47 (0.21), residues: 631 sheet: -0.08 (0.17), residues: 898 loop : -1.43 (0.12), residues: 2663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Q 67 TYR 0.014 0.001 TYR A 380 PHE 0.012 0.001 PHE R 136 TRP 0.018 0.001 TRP Q 111 HIS 0.010 0.001 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00257 (34657) covalent geometry : angle 0.51792 (47189) SS BOND : bond 0.00295 ( 51) SS BOND : angle 1.13439 ( 102) hydrogen bonds : bond 0.03629 ( 880) hydrogen bonds : angle 5.10428 ( 2400) link_BETA1-4 : bond 0.00319 ( 11) link_BETA1-4 : angle 1.52222 ( 33) link_NAG-ASN : bond 0.00360 ( 39) link_NAG-ASN : angle 2.24147 ( 117) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 323 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7989 (m-30) cc_final: 0.7609 (m-30) REVERT: A 94 SER cc_start: 0.7461 (m) cc_final: 0.7060 (p) REVERT: A 429 PHE cc_start: 0.6997 (t80) cc_final: 0.6537 (t80) REVERT: A 655 TYR cc_start: 0.8814 (t80) cc_final: 0.8185 (t80) REVERT: A 820 ASP cc_start: 0.7997 (m-30) cc_final: 0.7709 (m-30) REVERT: A 858 LEU cc_start: 0.9003 (mm) cc_final: 0.8791 (mm) REVERT: B 135 PHE cc_start: 0.8005 (m-80) cc_final: 0.7726 (m-80) REVERT: B 400 PHE cc_start: 0.7907 (p90) cc_final: 0.7071 (p90) REVERT: B 442 ASP cc_start: 0.7928 (t0) cc_final: 0.7375 (t70) REVERT: B 498 ARG cc_start: 0.8550 (mpt180) cc_final: 0.7827 (mmt180) REVERT: B 655 TYR cc_start: 0.8447 (t80) cc_final: 0.8105 (t80) REVERT: B 660 TYR cc_start: 0.7220 (m-80) cc_final: 0.6843 (m-10) REVERT: B 777 ASN cc_start: 0.8614 (m-40) cc_final: 0.8141 (m110) REVERT: B 1036 GLN cc_start: 0.8217 (tm-30) cc_final: 0.7994 (tm-30) REVERT: B 1041 ASP cc_start: 0.8954 (t0) cc_final: 0.8067 (t0) REVERT: B 1067 TYR cc_start: 0.7480 (t80) cc_final: 0.7165 (t80) REVERT: B 1118 ASP cc_start: 0.8482 (p0) cc_final: 0.8192 (p0) REVERT: C 128 ILE cc_start: 0.7188 (mm) cc_final: 0.6202 (mm) REVERT: C 286 THR cc_start: 0.8389 (p) cc_final: 0.7965 (t) REVERT: C 429 PHE cc_start: 0.7459 (t80) cc_final: 0.7254 (t80) REVERT: C 455 LEU cc_start: 0.8663 (tp) cc_final: 0.8377 (tp) REVERT: C 498 ARG cc_start: 0.8035 (mmp80) cc_final: 0.7790 (mmm160) REVERT: C 562 PHE cc_start: 0.8679 (p90) cc_final: 0.8240 (p90) REVERT: C 751 ASN cc_start: 0.6775 (p0) cc_final: 0.6553 (m-40) REVERT: C 752 LEU cc_start: 0.8523 (pp) cc_final: 0.8245 (tp) REVERT: C 1050 MET cc_start: 0.8899 (ppp) cc_final: 0.8584 (ppp) REVERT: D 5 THR cc_start: 0.3342 (m) cc_final: 0.3127 (m) REVERT: E 126 SER cc_start: 0.3352 (m) cc_final: 0.3014 (t) REVERT: M 87 TYR cc_start: 0.5865 (m-80) cc_final: 0.5551 (m-80) REVERT: M 88 TYR cc_start: 0.6542 (m-10) cc_final: 0.5631 (m-80) REVERT: N 22 CYS cc_start: 0.5166 (t) cc_final: 0.4899 (t) REVERT: Q 29 PHE cc_start: 0.8219 (t80) cc_final: 0.7545 (t80) REVERT: Q 31 ASP cc_start: 0.8031 (m-30) cc_final: 0.7426 (m-30) REVERT: Q 72 ARG cc_start: 0.5518 (ttm-80) cc_final: 0.4928 (ttm-80) REVERT: Q 111 TRP cc_start: 0.7951 (m-10) cc_final: 0.7501 (m-10) REVERT: Q 112 MET cc_start: 0.8772 (ptt) cc_final: 0.8139 (ppp) REVERT: Q 183 VAL cc_start: 0.5764 (m) cc_final: 0.5454 (m) REVERT: R 32 TYR cc_start: 0.7688 (m-80) cc_final: 0.7471 (m-80) REVERT: R 95 PHE cc_start: 0.7118 (m-80) cc_final: 0.6816 (m-80) outliers start: 4 outliers final: 2 residues processed: 325 average time/residue: 0.1965 time to fit residues: 110.4982 Evaluate side-chains 249 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 247 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 126 optimal weight: 30.0000 chunk 43 optimal weight: 9.9990 chunk 171 optimal weight: 2.9990 chunk 416 optimal weight: 50.0000 chunk 254 optimal weight: 6.9990 chunk 342 optimal weight: 20.0000 chunk 162 optimal weight: 0.9980 chunk 184 optimal weight: 3.9990 chunk 137 optimal weight: 8.9990 chunk 155 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN D 38 GLN ** M 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 ASN M 119 GLN N 32 ASN ** Q 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.111052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.082070 restraints weight = 138295.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.080764 restraints weight = 127825.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.082203 restraints weight = 96354.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.082047 restraints weight = 78743.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.082279 restraints weight = 69766.664| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 34758 Z= 0.192 Angle : 0.615 9.786 47441 Z= 0.309 Chirality : 0.046 0.340 5486 Planarity : 0.005 0.085 6001 Dihedral : 5.745 57.493 5612 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % 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: -1.11 (0.13), residues: 4192 helix: 1.19 (0.20), residues: 631 sheet: -0.22 (0.17), residues: 941 loop : -1.50 (0.12), residues: 2620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 355 TYR 0.017 0.002 TYR C 453 PHE 0.025 0.002 PHE B 371 TRP 0.026 0.002 TRP Q 111 HIS 0.005 0.001 HIS C1083 Details of bonding type rmsd covalent geometry : bond 0.00427 (34657) covalent geometry : angle 0.59934 (47189) SS BOND : bond 0.00441 ( 51) SS BOND : angle 1.48163 ( 102) hydrogen bonds : bond 0.04128 ( 880) hydrogen bonds : angle 5.36265 ( 2400) link_BETA1-4 : bond 0.00287 ( 11) link_BETA1-4 : angle 1.65072 ( 33) link_NAG-ASN : bond 0.00412 ( 39) link_NAG-ASN : angle 2.37748 ( 117) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 310 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 SER cc_start: 0.7698 (m) cc_final: 0.7247 (p) REVERT: A 429 PHE cc_start: 0.7165 (t80) cc_final: 0.6950 (t80) REVERT: A 655 TYR cc_start: 0.8966 (t80) cc_final: 0.8174 (t80) REVERT: A 820 ASP cc_start: 0.8103 (m-30) cc_final: 0.7813 (m-30) REVERT: B 135 PHE cc_start: 0.7863 (m-80) cc_final: 0.7586 (m-80) REVERT: B 200 TYR cc_start: 0.6176 (m-10) cc_final: 0.5616 (m-80) REVERT: B 400 PHE cc_start: 0.7864 (p90) cc_final: 0.6949 (p90) REVERT: B 401 VAL cc_start: 0.8671 (t) cc_final: 0.7840 (p) REVERT: B 498 ARG cc_start: 0.8544 (mpt180) cc_final: 0.7453 (mpt180) REVERT: B 655 TYR cc_start: 0.8598 (t80) cc_final: 0.8210 (t80) REVERT: B 777 ASN cc_start: 0.8740 (m-40) cc_final: 0.8224 (m110) REVERT: B 819 GLU cc_start: 0.8889 (mt-10) cc_final: 0.8682 (mt-10) REVERT: B 902 MET cc_start: 0.8658 (mmt) cc_final: 0.8448 (mpp) REVERT: B 1041 ASP cc_start: 0.9006 (t0) cc_final: 0.8087 (t0) REVERT: B 1118 ASP cc_start: 0.8625 (p0) cc_final: 0.8414 (p0) REVERT: C 128 ILE cc_start: 0.7365 (mm) cc_final: 0.6763 (mm) REVERT: C 429 PHE cc_start: 0.7655 (t80) cc_final: 0.7383 (t80) REVERT: C 455 LEU cc_start: 0.8693 (tp) cc_final: 0.8375 (tp) REVERT: C 498 ARG cc_start: 0.7977 (mmp80) cc_final: 0.7761 (mmm160) REVERT: C 562 PHE cc_start: 0.8655 (p90) cc_final: 0.8239 (p90) REVERT: C 697 MET cc_start: 0.7994 (ttt) cc_final: 0.7764 (ttt) REVERT: C 712 ILE cc_start: 0.9009 (tt) cc_final: 0.8772 (tt) REVERT: D 5 THR cc_start: 0.3733 (m) cc_final: 0.3474 (m) REVERT: E 126 SER cc_start: 0.4058 (m) cc_final: 0.3565 (t) REVERT: N 61 GLU cc_start: 0.7612 (tm-30) cc_final: 0.7100 (pt0) REVERT: Q 29 PHE cc_start: 0.8286 (t80) cc_final: 0.7686 (t80) REVERT: Q 31 ASP cc_start: 0.8015 (m-30) cc_final: 0.7538 (m-30) REVERT: Q 48 MET cc_start: 0.6363 (pmm) cc_final: 0.5956 (pmm) REVERT: Q 70 MET cc_start: 0.3365 (mpp) cc_final: 0.0733 (tpt) REVERT: Q 72 ARG cc_start: 0.5793 (ttm-80) cc_final: 0.5333 (ttm-80) REVERT: Q 111 TRP cc_start: 0.7986 (m-10) cc_final: 0.7667 (m-10) REVERT: Q 183 VAL cc_start: 0.4535 (m) cc_final: 0.4231 (m) REVERT: R 81 MET cc_start: 0.4017 (mpp) cc_final: 0.3797 (mpp) REVERT: R 95 PHE cc_start: 0.7027 (m-80) cc_final: 0.6672 (m-80) outliers start: 0 outliers final: 0 residues processed: 310 average time/residue: 0.1752 time to fit residues: 94.1133 Evaluate side-chains 229 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 315 optimal weight: 0.8980 chunk 405 optimal weight: 7.9990 chunk 355 optimal weight: 0.9990 chunk 415 optimal weight: 9.9990 chunk 162 optimal weight: 3.9990 chunk 210 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 chunk 81 optimal weight: 10.0000 chunk 270 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 HIS ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN C 121 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C 777 ASN ** D 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN Q 3 GLN ** R 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.111745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.078948 restraints weight = 126858.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.079850 restraints weight = 92664.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.080379 restraints weight = 64199.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.080832 restraints weight = 56166.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.081160 restraints weight = 48513.573| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 34758 Z= 0.109 Angle : 0.546 10.219 47441 Z= 0.272 Chirality : 0.045 0.356 5486 Planarity : 0.004 0.084 6001 Dihedral : 5.347 57.759 5612 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.08 % Allowed : 0.75 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % 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: -0.96 (0.13), residues: 4192 helix: 1.46 (0.21), residues: 631 sheet: -0.10 (0.17), residues: 973 loop : -1.46 (0.12), residues: 2588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 905 TYR 0.014 0.001 TYR A 453 PHE 0.023 0.001 PHE C 92 TRP 0.016 0.001 TRP Q 111 HIS 0.004 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00246 (34657) covalent geometry : angle 0.53115 (47189) SS BOND : bond 0.00298 ( 51) SS BOND : angle 1.29368 ( 102) hydrogen bonds : bond 0.03673 ( 880) hydrogen bonds : angle 5.08091 ( 2400) link_BETA1-4 : bond 0.00330 ( 11) link_BETA1-4 : angle 1.57680 ( 33) link_NAG-ASN : bond 0.00357 ( 39) link_NAG-ASN : angle 2.22607 ( 117) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 336 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 SER cc_start: 0.7339 (m) cc_final: 0.7039 (p) REVERT: A 429 PHE cc_start: 0.7225 (t80) cc_final: 0.6803 (t80) REVERT: A 655 TYR cc_start: 0.8959 (t80) cc_final: 0.8220 (t80) REVERT: A 820 ASP cc_start: 0.7988 (m-30) cc_final: 0.7693 (m-30) REVERT: A 858 LEU cc_start: 0.9074 (mm) cc_final: 0.8865 (mm) REVERT: A 1065 VAL cc_start: 0.8955 (t) cc_final: 0.8565 (p) REVERT: B 135 PHE cc_start: 0.7888 (m-80) cc_final: 0.7608 (m-80) REVERT: B 200 TYR cc_start: 0.6159 (m-10) cc_final: 0.5393 (m-80) REVERT: B 400 PHE cc_start: 0.7803 (p90) cc_final: 0.6885 (p90) REVERT: B 655 TYR cc_start: 0.8537 (t80) cc_final: 0.8067 (t80) REVERT: B 774 GLN cc_start: 0.7947 (mp10) cc_final: 0.7563 (mp10) REVERT: B 777 ASN cc_start: 0.8620 (m-40) cc_final: 0.8142 (m110) REVERT: B 819 GLU cc_start: 0.8891 (mt-10) cc_final: 0.8663 (mt-10) REVERT: B 902 MET cc_start: 0.8868 (mmt) cc_final: 0.8640 (tpp) REVERT: B 1041 ASP cc_start: 0.8955 (t0) cc_final: 0.7929 (t0) REVERT: B 1050 MET cc_start: 0.7547 (tpp) cc_final: 0.6796 (tpp) REVERT: B 1067 TYR cc_start: 0.7559 (t80) cc_final: 0.7229 (t80) REVERT: C 128 ILE cc_start: 0.7557 (mm) cc_final: 0.7291 (mm) REVERT: C 429 PHE cc_start: 0.7530 (t80) cc_final: 0.7274 (t80) REVERT: C 455 LEU cc_start: 0.8627 (tp) cc_final: 0.8299 (tp) REVERT: C 562 PHE cc_start: 0.8665 (p90) cc_final: 0.8198 (p90) REVERT: C 712 ILE cc_start: 0.8980 (tt) cc_final: 0.8733 (tt) REVERT: C 752 LEU cc_start: 0.8569 (pp) cc_final: 0.8310 (tp) REVERT: C 858 LEU cc_start: 0.8622 (mm) cc_final: 0.8222 (pp) REVERT: C 1050 MET cc_start: 0.8779 (ppp) cc_final: 0.8578 (ppp) REVERT: D 5 THR cc_start: 0.3053 (m) cc_final: 0.2826 (m) REVERT: E 126 SER cc_start: 0.3579 (m) cc_final: 0.3210 (t) REVERT: M 87 TYR cc_start: 0.5621 (m-80) cc_final: 0.5369 (m-80) REVERT: N 22 CYS cc_start: 0.4642 (t) cc_final: 0.4336 (t) REVERT: Q 29 PHE cc_start: 0.8283 (t80) cc_final: 0.7551 (t80) REVERT: Q 31 ASP cc_start: 0.8157 (m-30) cc_final: 0.7654 (m-30) REVERT: Q 70 MET cc_start: 0.3031 (mpp) cc_final: 0.0742 (tpt) REVERT: Q 112 MET cc_start: 0.8462 (ptt) cc_final: 0.7741 (ppp) REVERT: Q 183 VAL cc_start: 0.5686 (m) cc_final: 0.5367 (m) REVERT: Q 190 TYR cc_start: 0.5675 (m-10) cc_final: 0.5456 (m-80) REVERT: R 43 GLN cc_start: 0.7555 (pm20) cc_final: 0.7326 (pm20) REVERT: R 81 MET cc_start: 0.3795 (mpp) cc_final: 0.3519 (mpp) REVERT: R 95 PHE cc_start: 0.7176 (m-80) cc_final: 0.6853 (m-80) outliers start: 3 outliers final: 1 residues processed: 338 average time/residue: 0.1656 time to fit residues: 97.3601 Evaluate side-chains 251 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 250 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 409 optimal weight: 20.0000 chunk 380 optimal weight: 10.0000 chunk 402 optimal weight: 5.9990 chunk 364 optimal weight: 3.9990 chunk 277 optimal weight: 1.9990 chunk 246 optimal weight: 0.8980 chunk 361 optimal weight: 0.0770 chunk 137 optimal weight: 0.4980 chunk 74 optimal weight: 1.9990 chunk 341 optimal weight: 30.0000 chunk 300 optimal weight: 10.0000 overall best weight: 1.0942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C 777 ASN D 38 GLN D 99 HIS E 6 GLN M 16 GLN ** M 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 32 ASN ** Q 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 39 GLN ** R 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.112116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.079546 restraints weight = 126919.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.079404 restraints weight = 92898.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.081256 restraints weight = 69084.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.081526 restraints weight = 46237.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.081645 restraints weight = 46371.375| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 34758 Z= 0.102 Angle : 0.536 10.037 47441 Z= 0.266 Chirality : 0.045 0.359 5486 Planarity : 0.004 0.085 6001 Dihedral : 5.135 57.473 5612 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.03 % Allowed : 0.35 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % 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: -0.87 (0.13), residues: 4192 helix: 1.54 (0.21), residues: 631 sheet: -0.05 (0.17), residues: 958 loop : -1.39 (0.12), residues: 2603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 190 TYR 0.017 0.001 TYR B 873 PHE 0.020 0.001 PHE B 371 TRP 0.015 0.001 TRP Q 111 HIS 0.003 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00233 (34657) covalent geometry : angle 0.52178 (47189) SS BOND : bond 0.00273 ( 51) SS BOND : angle 1.17682 ( 102) hydrogen bonds : bond 0.03563 ( 880) hydrogen bonds : angle 4.96801 ( 2400) link_BETA1-4 : bond 0.00327 ( 11) link_BETA1-4 : angle 1.52604 ( 33) link_NAG-ASN : bond 0.00357 ( 39) link_NAG-ASN : angle 2.17629 ( 117) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 327 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 SER cc_start: 0.7077 (m) cc_final: 0.6847 (p) REVERT: A 429 PHE cc_start: 0.7097 (t80) cc_final: 0.6800 (t80) REVERT: A 655 TYR cc_start: 0.8953 (t80) cc_final: 0.8223 (t80) REVERT: A 712 ILE cc_start: 0.7953 (tp) cc_final: 0.7694 (tp) REVERT: A 820 ASP cc_start: 0.7889 (m-30) cc_final: 0.7590 (m-30) REVERT: A 858 LEU cc_start: 0.9059 (mm) cc_final: 0.8850 (mm) REVERT: A 1065 VAL cc_start: 0.8966 (t) cc_final: 0.8626 (p) REVERT: B 135 PHE cc_start: 0.7841 (m-80) cc_final: 0.7631 (m-80) REVERT: B 200 TYR cc_start: 0.5972 (m-10) cc_final: 0.5364 (m-80) REVERT: B 400 PHE cc_start: 0.7757 (p90) cc_final: 0.7011 (p90) REVERT: B 498 ARG cc_start: 0.8455 (mpt180) cc_final: 0.7944 (mmt180) REVERT: B 655 TYR cc_start: 0.8597 (t80) cc_final: 0.8076 (t80) REVERT: B 660 TYR cc_start: 0.7232 (m-80) cc_final: 0.6831 (m-10) REVERT: B 774 GLN cc_start: 0.7905 (mp10) cc_final: 0.7593 (mp10) REVERT: B 777 ASN cc_start: 0.8624 (m-40) cc_final: 0.8157 (m110) REVERT: B 786 LYS cc_start: 0.8631 (mmmt) cc_final: 0.8420 (mtpt) REVERT: B 819 GLU cc_start: 0.8895 (mt-10) cc_final: 0.8659 (mt-10) REVERT: B 902 MET cc_start: 0.8852 (mmt) cc_final: 0.8643 (tpp) REVERT: B 977 LEU cc_start: 0.8249 (mm) cc_final: 0.8034 (mm) REVERT: B 1041 ASP cc_start: 0.8898 (t0) cc_final: 0.7900 (t0) REVERT: B 1050 MET cc_start: 0.7517 (tpp) cc_final: 0.6735 (tpp) REVERT: B 1067 TYR cc_start: 0.7485 (t80) cc_final: 0.7182 (t80) REVERT: C 128 ILE cc_start: 0.7677 (mm) cc_final: 0.7396 (mm) REVERT: C 429 PHE cc_start: 0.7446 (t80) cc_final: 0.7232 (t80) REVERT: C 455 LEU cc_start: 0.8590 (tp) cc_final: 0.8276 (tp) REVERT: C 562 PHE cc_start: 0.8605 (p90) cc_final: 0.8185 (p90) REVERT: C 752 LEU cc_start: 0.8630 (pp) cc_final: 0.8287 (tp) REVERT: C 858 LEU cc_start: 0.8640 (mm) cc_final: 0.8229 (pp) REVERT: C 900 MET cc_start: 0.7889 (mmm) cc_final: 0.7248 (ttt) REVERT: C 1050 MET cc_start: 0.8683 (ppp) cc_final: 0.8480 (ppp) REVERT: E 126 SER cc_start: 0.3618 (m) cc_final: 0.3263 (t) REVERT: M 87 TYR cc_start: 0.5427 (m-80) cc_final: 0.5057 (m-80) REVERT: M 88 TYR cc_start: 0.6732 (m-10) cc_final: 0.5924 (m-80) REVERT: N 22 CYS cc_start: 0.4878 (t) cc_final: 0.4640 (t) REVERT: Q 29 PHE cc_start: 0.8263 (t80) cc_final: 0.7561 (t80) REVERT: Q 31 ASP cc_start: 0.8157 (m-30) cc_final: 0.7651 (m-30) REVERT: Q 48 MET cc_start: 0.6621 (pmm) cc_final: 0.6253 (pmm) REVERT: Q 111 TRP cc_start: 0.8093 (m-10) cc_final: 0.7886 (m-10) REVERT: Q 112 MET cc_start: 0.8485 (ptt) cc_final: 0.7759 (ppp) REVERT: Q 183 VAL cc_start: 0.5558 (m) cc_final: 0.5228 (m) REVERT: Q 190 TYR cc_start: 0.5670 (m-10) cc_final: 0.5461 (m-80) REVERT: R 43 GLN cc_start: 0.7452 (pm20) cc_final: 0.7164 (pm20) REVERT: R 81 MET cc_start: 0.3808 (mpp) cc_final: 0.3565 (mpp) REVERT: R 94 TYR cc_start: 0.6636 (m-80) cc_final: 0.6317 (m-10) REVERT: R 95 PHE cc_start: 0.7066 (m-80) cc_final: 0.6823 (m-80) outliers start: 1 outliers final: 1 residues processed: 328 average time/residue: 0.1722 time to fit residues: 97.9085 Evaluate side-chains 251 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 250 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 233 optimal weight: 10.0000 chunk 241 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 275 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 107 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 118 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 chunk 80 optimal weight: 4.9990 chunk 357 optimal weight: 9.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 HIS ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN D 38 GLN ** M 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 3 GLN ** R 119 GLN ** 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 = 0.3818 r_free = 0.3818 target = 0.110976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.078258 restraints weight = 127583.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.078187 restraints weight = 100075.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.079238 restraints weight = 74637.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.079728 restraints weight = 57965.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.079911 restraints weight = 51202.008| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 34758 Z= 0.136 Angle : 0.560 9.837 47441 Z= 0.279 Chirality : 0.045 0.350 5486 Planarity : 0.004 0.085 6001 Dihedral : 5.201 57.297 5612 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.05 % Allowed : 0.40 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % 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: -0.92 (0.13), residues: 4192 helix: 1.44 (0.21), residues: 629 sheet: -0.05 (0.17), residues: 963 loop : -1.42 (0.12), residues: 2600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 905 TYR 0.020 0.001 TYR B 873 PHE 0.022 0.001 PHE B 371 TRP 0.020 0.001 TRP Q 111 HIS 0.004 0.001 HIS C1083 Details of bonding type rmsd covalent geometry : bond 0.00307 (34657) covalent geometry : angle 0.54527 (47189) SS BOND : bond 0.00308 ( 51) SS BOND : angle 1.27097 ( 102) hydrogen bonds : bond 0.03737 ( 880) hydrogen bonds : angle 5.02682 ( 2400) link_BETA1-4 : bond 0.00288 ( 11) link_BETA1-4 : angle 1.57077 ( 33) link_NAG-ASN : bond 0.00349 ( 39) link_NAG-ASN : angle 2.22326 ( 117) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 316 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 SER cc_start: 0.7276 (m) cc_final: 0.6863 (p) REVERT: A 429 PHE cc_start: 0.7139 (t80) cc_final: 0.6894 (t80) REVERT: A 655 TYR cc_start: 0.8898 (t80) cc_final: 0.8160 (t80) REVERT: A 820 ASP cc_start: 0.7943 (m-30) cc_final: 0.7637 (m-30) REVERT: A 1050 MET cc_start: 0.6626 (ptp) cc_final: 0.6293 (ptp) REVERT: A 1065 VAL cc_start: 0.8965 (t) cc_final: 0.8634 (p) REVERT: B 400 PHE cc_start: 0.7717 (p90) cc_final: 0.7055 (p90) REVERT: B 498 ARG cc_start: 0.8415 (mpt180) cc_final: 0.8064 (mmt90) REVERT: B 655 TYR cc_start: 0.8554 (t80) cc_final: 0.8057 (t80) REVERT: B 660 TYR cc_start: 0.7224 (m-80) cc_final: 0.6904 (m-10) REVERT: B 774 GLN cc_start: 0.7947 (mp10) cc_final: 0.7639 (mp10) REVERT: B 777 ASN cc_start: 0.8596 (m-40) cc_final: 0.8165 (m110) REVERT: B 786 LYS cc_start: 0.8632 (mmmt) cc_final: 0.8386 (mtpt) REVERT: B 819 GLU cc_start: 0.8932 (mt-10) cc_final: 0.8542 (mm-30) REVERT: B 902 MET cc_start: 0.8801 (mmt) cc_final: 0.8582 (tpp) REVERT: B 1041 ASP cc_start: 0.8891 (t0) cc_final: 0.7920 (t0) REVERT: B 1050 MET cc_start: 0.7806 (tpp) cc_final: 0.7387 (tpp) REVERT: B 1067 TYR cc_start: 0.7588 (t80) cc_final: 0.7262 (t80) REVERT: C 128 ILE cc_start: 0.7712 (mm) cc_final: 0.7439 (mm) REVERT: C 429 PHE cc_start: 0.7466 (t80) cc_final: 0.7229 (t80) REVERT: C 455 LEU cc_start: 0.8589 (tp) cc_final: 0.8339 (tp) REVERT: C 562 PHE cc_start: 0.8664 (p90) cc_final: 0.8251 (p90) REVERT: C 712 ILE cc_start: 0.9011 (tt) cc_final: 0.8764 (tt) REVERT: C 752 LEU cc_start: 0.8626 (pp) cc_final: 0.8298 (tp) REVERT: C 858 LEU cc_start: 0.8627 (mm) cc_final: 0.8283 (pp) REVERT: D 5 THR cc_start: 0.3153 (m) cc_final: 0.2915 (m) REVERT: E 126 SER cc_start: 0.3813 (m) cc_final: 0.3421 (t) REVERT: M 87 TYR cc_start: 0.5286 (m-80) cc_final: 0.4877 (m-80) REVERT: M 88 TYR cc_start: 0.6536 (m-10) cc_final: 0.5575 (m-80) REVERT: N 22 CYS cc_start: 0.4636 (t) cc_final: 0.4314 (t) REVERT: N 48 LEU cc_start: 0.8746 (tp) cc_final: 0.8542 (tp) REVERT: Q 29 PHE cc_start: 0.8274 (t80) cc_final: 0.7616 (t80) REVERT: Q 31 ASP cc_start: 0.8110 (m-30) cc_final: 0.7625 (m-30) REVERT: Q 48 MET cc_start: 0.6554 (pmm) cc_final: 0.6176 (pmm) REVERT: Q 70 MET cc_start: 0.2388 (mpp) cc_final: 0.0162 (tpp) REVERT: Q 112 MET cc_start: 0.8508 (ptt) cc_final: 0.7750 (ppp) REVERT: Q 183 VAL cc_start: 0.5221 (m) cc_final: 0.4892 (m) REVERT: Q 190 TYR cc_start: 0.5682 (m-10) cc_final: 0.5477 (m-80) REVERT: R 43 GLN cc_start: 0.7692 (pm20) cc_final: 0.7287 (pm20) REVERT: R 95 PHE cc_start: 0.7077 (m-80) cc_final: 0.6875 (m-80) outliers start: 2 outliers final: 1 residues processed: 317 average time/residue: 0.1852 time to fit residues: 101.7554 Evaluate side-chains 243 residues out of total 3716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 242 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 361 optimal weight: 6.9990 chunk 395 optimal weight: 3.9990 chunk 151 optimal weight: 8.9990 chunk 152 optimal weight: 1.9990 chunk 148 optimal weight: 5.9990 chunk 70 optimal weight: 0.0980 chunk 399 optimal weight: 4.9990 chunk 331 optimal weight: 0.9990 chunk 209 optimal weight: 0.4980 chunk 173 optimal weight: 0.9990 chunk 383 optimal weight: 8.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C 777 ASN ** E 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.112256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.078318 restraints weight = 126952.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.080616 restraints weight = 80731.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.081137 restraints weight = 52287.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.082131 restraints weight = 40730.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.082086 restraints weight = 37372.695| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 34758 Z= 0.096 Angle : 0.533 10.304 47441 Z= 0.265 Chirality : 0.045 0.360 5486 Planarity : 0.004 0.084 6001 Dihedral : 4.975 57.651 5612 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.03 % Allowed : 0.24 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % 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: -0.83 (0.13), residues: 4192 helix: 1.52 (0.21), residues: 629 sheet: 0.02 (0.17), residues: 958 loop : -1.37 (0.12), residues: 2605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Q 67 TYR 0.017 0.001 TYR B 873 PHE 0.020 0.001 PHE B 371 TRP 0.030 0.001 TRP Q 111 HIS 0.004 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00220 (34657) covalent geometry : angle 0.51947 (47189) SS BOND : bond 0.00270 ( 51) SS BOND : angle 1.16935 ( 102) hydrogen bonds : bond 0.03513 ( 880) hydrogen bonds : angle 4.87798 ( 2400) link_BETA1-4 : bond 0.00394 ( 11) link_BETA1-4 : angle 1.51943 ( 33) link_NAG-ASN : bond 0.00367 ( 39) link_NAG-ASN : angle 2.16622 ( 117) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4908.33 seconds wall clock time: 86 minutes 5.23 seconds (5165.23 seconds total)