Starting phenix.real_space_refine on Fri Feb 6 21:33:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ueb_64080/02_2026/9ueb_64080_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ueb_64080/02_2026/9ueb_64080.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ueb_64080/02_2026/9ueb_64080.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ueb_64080/02_2026/9ueb_64080.map" model { file = "/net/cci-nas-00/data/ceres_data/9ueb_64080/02_2026/9ueb_64080_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ueb_64080/02_2026/9ueb_64080_neut.cif" } resolution = 2.59 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= -0.002 sd= 0.170 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 162 5.16 5 C 17479 2.51 5 N 4529 2.21 5 O 5479 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27649 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 8999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1169, 8999 Classifications: {'peptide': 1169} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 55, 'TRANS': 1113} Chain breaks: 5 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'PHE:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 9020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1169, 9020 Classifications: {'peptide': 1169} Link IDs: {'PTRANS': 55, 'TRANS': 1113} Chain breaks: 5 Chain: "C" Number of atoms: 9014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1169, 9014 Classifications: {'peptide': 1169} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 55, 'TRANS': 1113} Chain breaks: 5 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" 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: "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: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 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: 6.67, per 1000 atoms: 0.24 Number of scatterers: 27649 At special positions: 0 Unit cell: (153.706, 147.119, 159.196, 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 162 16.00 O 5479 8.00 N 4529 7.00 C 17479 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 30 " - pdb=" SG CYS A 199 " distance=2.03 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 218 " distance=2.03 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 241 " distance=2.08 Simple disulfide: pdb=" SG CYS A 343 " - pdb=" SG CYS A 353 " distance=2.03 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 411 " distance=2.04 Simple disulfide: pdb=" SG CYS A 429 " - pdb=" SG CYS A 482 " distance=2.03 Simple disulfide: pdb=" SG CYS A 441 " - pdb=" SG CYS A 589 " distance=2.03 Simple disulfide: pdb=" SG CYS A 506 " - pdb=" SG CYS A 530 " distance=2.03 Simple disulfide: pdb=" SG CYS A 607 " - pdb=" SG CYS A 658 " distance=2.04 Simple disulfide: pdb=" SG CYS A 624 " - pdb=" SG CYS A 654 " distance=2.03 Simple disulfide: pdb=" SG CYS A 683 " - pdb=" SG CYS A 718 " distance=2.03 Simple disulfide: pdb=" SG CYS A 732 " - pdb=" SG CYS A 741 " distance=2.03 Simple disulfide: pdb=" SG CYS A 802 " - pdb=" SG CYS A 824 " distance=2.03 Simple disulfide: pdb=" SG CYS A 807 " - pdb=" SG CYS A 813 " distance=2.04 Simple disulfide: pdb=" SG CYS A 908 " - pdb=" SG CYS A 921 " distance=2.03 Simple disulfide: pdb=" SG CYS A1102 " - pdb=" SG CYS A1113 " distance=2.03 Simple disulfide: pdb=" SG CYS A1152 " - pdb=" SG CYS A1160 " distance=2.03 Simple disulfide: pdb=" SG CYS B 30 " - pdb=" SG CYS B 199 " distance=2.04 Simple disulfide: pdb=" SG CYS B 180 " - pdb=" SG CYS B 218 " distance=2.03 Simple disulfide: pdb=" SG CYS B 189 " - pdb=" SG CYS B 241 " distance=2.03 Simple disulfide: pdb=" SG CYS B 343 " - pdb=" SG CYS B 353 " distance=2.03 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 411 " distance=2.04 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 482 " distance=2.04 Simple disulfide: pdb=" SG CYS B 441 " - pdb=" SG CYS B 589 " distance=2.03 Simple disulfide: pdb=" SG CYS B 506 " - pdb=" SG CYS B 530 " distance=2.03 Simple disulfide: pdb=" SG CYS B 607 " - pdb=" SG CYS B 658 " distance=2.04 Simple disulfide: pdb=" SG CYS B 624 " - pdb=" SG CYS B 654 " distance=2.03 Simple disulfide: pdb=" SG CYS B 683 " - pdb=" SG CYS B 718 " distance=2.03 Simple disulfide: pdb=" SG CYS B 732 " - pdb=" SG CYS B 741 " distance=2.03 Simple disulfide: pdb=" SG CYS B 802 " - pdb=" SG CYS B 824 " distance=2.03 Simple disulfide: pdb=" SG CYS B 807 " - pdb=" SG CYS B 813 " distance=2.04 Simple disulfide: pdb=" SG CYS B 908 " - pdb=" SG CYS B 921 " distance=2.03 Simple disulfide: pdb=" SG CYS B1102 " - pdb=" SG CYS B1113 " distance=2.03 Simple disulfide: pdb=" SG CYS B1152 " - pdb=" SG CYS B1160 " distance=2.03 Simple disulfide: pdb=" SG CYS C 30 " - pdb=" SG CYS C 199 " distance=2.03 Simple disulfide: pdb=" SG CYS C 180 " - pdb=" SG CYS C 218 " distance=2.03 Simple disulfide: pdb=" SG CYS C 189 " - pdb=" SG CYS C 241 " distance=2.03 Simple disulfide: pdb=" SG CYS C 343 " - pdb=" SG CYS C 353 " distance=2.03 Simple disulfide: pdb=" SG CYS C 387 " - pdb=" SG CYS C 411 " distance=2.04 Simple disulfide: pdb=" SG CYS C 429 " - pdb=" SG CYS C 482 " distance=2.03 Simple disulfide: pdb=" SG CYS C 441 " - pdb=" SG CYS C 589 " distance=2.03 Simple disulfide: pdb=" SG CYS C 506 " - pdb=" SG CYS C 530 " distance=2.03 Simple disulfide: pdb=" SG CYS C 607 " - pdb=" SG CYS C 658 " distance=2.08 Simple disulfide: pdb=" SG CYS C 624 " - pdb=" SG CYS C 654 " distance=2.04 Simple disulfide: pdb=" SG CYS C 683 " - pdb=" SG CYS C 718 " distance=2.04 Simple disulfide: pdb=" SG CYS C 732 " - pdb=" SG CYS C 741 " distance=2.03 Simple disulfide: pdb=" SG CYS C 802 " - pdb=" SG CYS C 824 " distance=2.03 Simple disulfide: pdb=" SG CYS C 807 " - pdb=" SG CYS C 813 " distance=2.04 Simple disulfide: pdb=" SG CYS C 908 " - pdb=" SG CYS C 921 " distance=2.03 Simple disulfide: pdb=" SG CYS C1102 " - pdb=" SG CYS C1113 " distance=2.03 Simple disulfide: pdb=" SG CYS C1152 " - pdb=" SG CYS C1160 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " 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-ASN " NAG A1301 " - " ASN A 69 " " NAG A1302 " - " ASN A 170 " " NAG A1303 " - " ASN A 240 " " NAG A1304 " - " ASN A 130 " " NAG A1305 " - " ASN A 724 " " NAG A1306 " - " ASN A 781 " " NAG A1307 " - " ASN A 866 " " NAG A1308 " - " ASN A1211 " " NAG B1301 " - " ASN B 69 " " NAG B1302 " - " ASN B 170 " " NAG B1303 " - " ASN B 724 " " NAG B1304 " - " ASN B 781 " " NAG B1305 " - " ASN B 866 " " NAG B1306 " - " ASN B1171 " " NAG B1307 " - " ASN B1211 " " NAG B1308 " - " ASN B 240 " " NAG B1309 " - " ASN B 130 " " NAG C1301 " - " ASN C 170 " " NAG C1302 " - " ASN C 724 " " NAG C1303 " - " ASN C 781 " " NAG C1304 " - " ASN C 866 " " NAG C1305 " - " ASN C1171 " " NAG C1306 " - " ASN C1211 " " NAG C1307 " - " ASN C 69 " " NAG C1308 " - " ASN C 240 " " NAG C1309 " - " ASN C 130 " " NAG D 1 " - " ASN A 52 " " NAG E 1 " - " ASN A 226 " " NAG F 1 " - " ASN A 414 " " NAG G 1 " - " ASN B 226 " " NAG H 1 " - " ASN B 52 " " NAG I 1 " - " ASN B 414 " " NAG J 1 " - " ASN C 226 " " NAG K 1 " - " ASN C 52 " " NAG L 1 " - " ASN C 414 " Time building additional restraints: 1.96 Conformation dependent library (CDL) restraints added in 1.3 seconds 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6486 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 56 sheets defined 25.7% alpha, 27.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'A' and resid 40 through 44 Processing helix chain 'A' and resid 52 through 56 Processing helix chain 'A' and resid 109 through 113 Processing helix chain 'A' and resid 226 through 235 removed outlier: 3.841A pdb=" N TYR A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 354 Processing helix chain 'A' and resid 414 through 420 Processing helix chain 'A' and resid 433 through 438 Processing helix chain 'A' and resid 453 through 457 Processing helix chain 'A' and resid 467 through 472 Processing helix chain 'A' and resid 528 through 533 removed outlier: 3.814A pdb=" N ASN A 532 " --> pdb=" O ILE A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 632 Processing helix chain 'A' and resid 682 through 689 removed outlier: 3.615A pdb=" N ILE A 686 " --> pdb=" O ALA A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 808 Processing helix chain 'A' and resid 810 through 817 Processing helix chain 'A' and resid 818 through 821 removed outlier: 3.945A pdb=" N GLY A 821 " --> pdb=" O ARG A 818 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 818 through 821' Processing helix chain 'A' and resid 822 through 849 Processing helix chain 'A' and resid 868 through 871 Processing helix chain 'A' and resid 884 through 893 Processing helix chain 'A' and resid 903 through 912 removed outlier: 3.985A pdb=" N GLY A 912 " --> pdb=" O CYS A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 927 removed outlier: 3.505A pdb=" N GLN A 923 " --> pdb=" O LEU A 919 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N TYR A 924 " --> pdb=" O ILE A 920 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N VAL A 925 " --> pdb=" O CYS A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 936 through 946 removed outlier: 3.542A pdb=" N GLU A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 947 through 950 Processing helix chain 'A' and resid 967 through 978 Processing helix chain 'A' and resid 982 through 989 Processing helix chain 'A' and resid 989 through 1003 removed outlier: 3.601A pdb=" N ALA A1003 " --> pdb=" O GLN A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1008 removed outlier: 3.583A pdb=" N GLY A1007 " --> pdb=" O MET A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1012 through 1035 removed outlier: 3.550A pdb=" N LEU A1029 " --> pdb=" O ASN A1025 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU A1035 " --> pdb=" O LYS A1031 " (cutoff:3.500A) Processing helix chain 'A' and resid 1036 through 1038 No H-bonds generated for 'chain 'A' and resid 1036 through 1038' Processing helix chain 'A' and resid 1046 through 1054 Processing helix chain 'A' and resid 1055 through 1103 removed outlier: 3.516A pdb=" N LEU A1066 " --> pdb=" O GLN A1062 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1221 Processing helix chain 'B' and resid 213 through 218 Processing helix chain 'B' and resid 226 through 234 Processing helix chain 'B' and resid 346 through 355 Processing helix chain 'B' and resid 414 through 420 Processing helix chain 'B' and resid 433 through 439 Processing helix chain 'B' and resid 453 through 457 Processing helix chain 'B' and resid 467 through 472 Processing helix chain 'B' and resid 528 through 533 removed outlier: 3.700A pdb=" N ASN B 532 " --> pdb=" O ILE B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 629 through 632 Processing helix chain 'B' and resid 682 through 689 Processing helix chain 'B' and resid 693 through 698 removed outlier: 4.233A pdb=" N GLN B 698 " --> pdb=" O ARG B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 808 Processing helix chain 'B' and resid 810 through 817 removed outlier: 3.603A pdb=" N LEU B 816 " --> pdb=" O LYS B 812 " (cutoff:3.500A) Processing helix chain 'B' and resid 818 through 820 No H-bonds generated for 'chain 'B' and resid 818 through 820' Processing helix chain 'B' and resid 822 through 849 Processing helix chain 'B' and resid 860 through 864 removed outlier: 4.193A pdb=" N GLY B 863 " --> pdb=" O GLY B 860 " (cutoff:3.500A) Processing helix chain 'B' and resid 867 through 871 Processing helix chain 'B' and resid 884 through 893 Processing helix chain 'B' and resid 903 through 911 Processing helix chain 'B' and resid 918 through 927 removed outlier: 3.537A pdb=" N GLN B 923 " --> pdb=" O LEU B 919 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N TYR B 924 " --> pdb=" O ILE B 920 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL B 925 " --> pdb=" O CYS B 921 " (cutoff:3.500A) Processing helix chain 'B' and resid 936 through 946 removed outlier: 3.545A pdb=" N GLU B 940 " --> pdb=" O ASP B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 967 through 978 Processing helix chain 'B' and resid 982 through 989 Processing helix chain 'B' and resid 989 through 1002 Processing helix chain 'B' and resid 1003 through 1008 Processing helix chain 'B' and resid 1012 through 1035 removed outlier: 3.598A pdb=" N LEU B1029 " --> pdb=" O ASN B1025 " (cutoff:3.500A) Processing helix chain 'B' and resid 1036 through 1038 No H-bonds generated for 'chain 'B' and resid 1036 through 1038' Processing helix chain 'B' and resid 1046 through 1054 Processing helix chain 'B' and resid 1055 through 1103 Processing helix chain 'B' and resid 1217 through 1221 Processing helix chain 'C' and resid 52 through 56 Processing helix chain 'C' and resid 226 through 234 Processing helix chain 'C' and resid 273 through 275 No H-bonds generated for 'chain 'C' and resid 273 through 275' Processing helix chain 'C' and resid 346 through 355 Processing helix chain 'C' and resid 414 through 420 Processing helix chain 'C' and resid 433 through 440 Processing helix chain 'C' and resid 453 through 461 removed outlier: 5.054A pdb=" N SER C 458 " --> pdb=" O SER C 455 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N MET C 460 " --> pdb=" O LYS C 457 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN C 461 " --> pdb=" O SER C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 472 Processing helix chain 'C' and resid 528 through 533 removed outlier: 3.723A pdb=" N ASN C 532 " --> pdb=" O ILE C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 550 through 554 Processing helix chain 'C' and resid 682 through 689 removed outlier: 3.544A pdb=" N ILE C 686 " --> pdb=" O ALA C 682 " (cutoff:3.500A) Processing helix chain 'C' and resid 693 through 697 removed outlier: 3.570A pdb=" N THR C 696 " --> pdb=" O PHE C 693 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 808 Processing helix chain 'C' and resid 810 through 817 Processing helix chain 'C' and resid 822 through 849 Processing helix chain 'C' and resid 884 through 894 Processing helix chain 'C' and resid 903 through 912 removed outlier: 4.268A pdb=" N GLY C 912 " --> pdb=" O CYS C 908 " (cutoff:3.500A) Processing helix chain 'C' and resid 918 through 927 removed outlier: 4.832A pdb=" N TYR C 924 " --> pdb=" O ILE C 920 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N VAL C 925 " --> pdb=" O CYS C 921 " (cutoff:3.500A) Processing helix chain 'C' and resid 936 through 946 Processing helix chain 'C' and resid 967 through 978 Processing helix chain 'C' and resid 982 through 989 Processing helix chain 'C' and resid 989 through 1003 removed outlier: 3.604A pdb=" N ALA C1003 " --> pdb=" O GLN C 999 " (cutoff:3.500A) Processing helix chain 'C' and resid 1004 through 1008 Processing helix chain 'C' and resid 1012 through 1035 removed outlier: 3.570A pdb=" N LEU C1029 " --> pdb=" O ASN C1025 " (cutoff:3.500A) Processing helix chain 'C' and resid 1036 through 1038 No H-bonds generated for 'chain 'C' and resid 1036 through 1038' Processing helix chain 'C' and resid 1046 through 1054 Processing helix chain 'C' and resid 1055 through 1103 removed outlier: 3.594A pdb=" N LEU C1066 " --> pdb=" O GLN C1062 " (cutoff:3.500A) Processing helix chain 'C' and resid 1217 through 1221 Processing sheet with id=AA1, first strand: chain 'A' and resid 59 through 60 removed outlier: 7.047A pdb=" N ILE A 59 " --> pdb=" O MET A 282 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N LEU A 284 " --> pdb=" O ILE A 59 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N LEU A 284 " --> pdb=" O SER A 271 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N SER A 271 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA A 286 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR A 318 " --> pdb=" O ARG A 124 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 70 through 78 removed outlier: 3.590A pdb=" N ILE A 70 " --> pdb=" O PHE A 331 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLY A 76 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 325 " --> pdb=" O GLY A 76 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ARG A 339 " --> pdb=" O ASP A 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 132 through 133 removed outlier: 5.576A pdb=" N THR A 143 " --> pdb=" O ALA A 313 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 236 through 248 removed outlier: 7.758A pdb=" N GLN A 239 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N GLU A 192 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N CYS A 241 " --> pdb=" O VAL A 190 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N VAL A 190 " --> pdb=" O CYS A 241 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N PHE A 243 " --> pdb=" O TYR A 188 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR A 188 " --> pdb=" O PHE A 243 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ALA A 150 " --> pdb=" O ILE A 300 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 157 through 159 Processing sheet with id=AA6, first strand: chain 'A' and resid 210 through 211 removed outlier: 6.887A pdb=" N VAL A 210 " --> pdb=" O SER A 303 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 363 through 366 Processing sheet with id=AA8, first strand: chain 'A' and resid 377 through 380 removed outlier: 4.477A pdb=" N TYR A 652 " --> pdb=" O CYS A 624 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ILE A 643 " --> pdb=" O VAL A 655 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL A 635 " --> pdb=" O ILE A 643 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 385 through 386 removed outlier: 6.505A pdb=" N VAL A 385 " --> pdb=" O ASN A 412 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 404 through 408 removed outlier: 3.667A pdb=" N SER A 444 " --> pdb=" O GLN A 580 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU A 571 " --> pdb=" O ALA A 488 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N THR A 481 " --> pdb=" O CYS A 429 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N CYS A 429 " --> pdb=" O THR A 481 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ARG A 483 " --> pdb=" O PHE A 427 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N PHE A 427 " --> pdb=" O ARG A 483 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N PHE A 485 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 507 through 510 Processing sheet with id=AB3, first strand: chain 'A' and resid 545 through 546 Processing sheet with id=AB4, first strand: chain 'A' and resid 722 through 729 removed outlier: 7.043A pdb=" N LEU A 753 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N SER A 725 " --> pdb=" O LEU A 753 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N LEU A 755 " --> pdb=" O SER A 725 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N MET A 727 " --> pdb=" O LEU A 755 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N LEU A 740 " --> pdb=" O LEU A 736 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 764 through 765 removed outlier: 6.300A pdb=" N GLN A 764 " --> pdb=" O SER C 854 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 1117 through 1126 removed outlier: 6.989A pdb=" N VAL A1135 " --> pdb=" O ILE A1119 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N SER A1121 " --> pdb=" O PHE A1133 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N PHE A1133 " --> pdb=" O SER A1121 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N VAL A1123 " --> pdb=" O TYR A1131 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N TYR A1131 " --> pdb=" O VAL A1123 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N ASN A1125 " --> pdb=" O GLY A1129 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N GLY A1129 " --> pdb=" O ASN A1125 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N PHE A1168 " --> pdb=" O ALA A1148 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1117 through 1126 removed outlier: 6.989A pdb=" N VAL A1135 " --> pdb=" O ILE A1119 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N SER A1121 " --> pdb=" O PHE A1133 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N PHE A1133 " --> pdb=" O SER A1121 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N VAL A1123 " --> pdb=" O TYR A1131 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N TYR A1131 " --> pdb=" O VAL A1123 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N ASN A1125 " --> pdb=" O GLY A1129 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N GLY A1129 " --> pdb=" O ASN A1125 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N HIS A1142 " --> pdb=" O PRO A 779 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ASN A1144 " --> pdb=" O GLN A 777 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N GLN A 777 " --> pdb=" O ASN A1144 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N THR A1146 " --> pdb=" O VAL A 775 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL A 775 " --> pdb=" O THR A1146 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 797 through 800 removed outlier: 4.559A pdb=" N LYS A 797 " --> pdb=" O LEU A 931 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 853 through 854 Processing sheet with id=AC1, first strand: chain 'A' and resid 861 through 862 Processing sheet with id=AC2, first strand: chain 'A' and resid 963 through 964 removed outlier: 7.202A pdb=" N ASN B1141 " --> pdb=" O THR B 780 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N PHE B 782 " --> pdb=" O PRO B1139 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N PHE B 784 " --> pdb=" O TYR B1137 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N TYR B1137 " --> pdb=" O PHE B 784 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ILE B 786 " --> pdb=" O VAL B1135 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL B1135 " --> pdb=" O ILE B 786 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N GLN B 788 " --> pdb=" O PHE B1133 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N PHE B1133 " --> pdb=" O GLN B 788 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N TYR B 790 " --> pdb=" O TYR B1131 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N TYR B1131 " --> pdb=" O TYR B 790 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLN B 792 " --> pdb=" O GLY B1129 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N GLY B1129 " --> pdb=" O GLN B 792 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N TYR B1137 " --> pdb=" O HIS B1118 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N HIS B1118 " --> pdb=" O TYR B1137 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 963 through 964 removed outlier: 7.202A pdb=" N ASN B1141 " --> pdb=" O THR B 780 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N PHE B 782 " --> pdb=" O PRO B1139 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N PHE B 784 " --> pdb=" O TYR B1137 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N TYR B1137 " --> pdb=" O PHE B 784 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ILE B 786 " --> pdb=" O VAL B1135 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL B1135 " --> pdb=" O ILE B 786 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N GLN B 788 " --> pdb=" O PHE B1133 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N PHE B1133 " --> pdb=" O GLN B 788 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N TYR B 790 " --> pdb=" O TYR B1131 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N TYR B1131 " --> pdb=" O TYR B 790 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLN B 792 " --> pdb=" O GLY B1129 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N GLY B1129 " --> pdb=" O GLN B 792 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N PHE B1168 " --> pdb=" O ALA B1148 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N GLY B1186 " --> pdb=" O ASN B1191 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N ASN B1191 " --> pdb=" O GLY B1186 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 1200 through 1203 removed outlier: 3.916A pdb=" N CYS A1160 " --> pdb=" O VAL A1203 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 70 through 78 removed outlier: 3.536A pdb=" N GLY B 76 " --> pdb=" O LEU B 325 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU B 325 " --> pdb=" O GLY B 76 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ARG B 339 " --> pdb=" O ASP B 330 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 86 through 88 removed outlier: 3.617A pdb=" N ALA B 286 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N SER B 271 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N LEU B 284 " --> pdb=" O SER B 271 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 115 through 116 removed outlier: 4.175A pdb=" N ALA B 150 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LEU B 184 " --> pdb=" O TYR B 245 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N TYR B 245 " --> pdb=" O LEU B 184 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ALA B 186 " --> pdb=" O PHE B 243 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N PHE B 243 " --> pdb=" O ALA B 186 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N TYR B 188 " --> pdb=" O CYS B 241 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N CYS B 241 " --> pdb=" O TYR B 188 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 132 through 133 removed outlier: 6.094A pdb=" N THR B 143 " --> pdb=" O ALA B 313 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 157 through 158 Processing sheet with id=AD1, first strand: chain 'B' and resid 210 through 212 removed outlier: 6.659A pdb=" N VAL B 210 " --> pdb=" O SER B 303 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 363 through 366 removed outlier: 3.510A pdb=" N CYS B 718 " --> pdb=" O PHE B 678 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY B 717 " --> pdb=" O THR B 714 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 376 through 380 removed outlier: 5.815A pdb=" N GLY B 376 " --> pdb=" O GLU B 609 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ASN B 611 " --> pdb=" O GLY B 376 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N PHE B 378 " --> pdb=" O ASN B 611 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ILE B 643 " --> pdb=" O VAL B 655 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL B 635 " --> pdb=" O ILE B 643 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 385 through 386 removed outlier: 6.568A pdb=" N VAL B 385 " --> pdb=" O ASN B 412 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 404 through 408 removed outlier: 3.767A pdb=" N SER B 444 " --> pdb=" O GLN B 580 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU B 571 " --> pdb=" O ALA B 488 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N THR B 481 " --> pdb=" O CYS B 429 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N CYS B 429 " --> pdb=" O THR B 481 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ARG B 483 " --> pdb=" O PHE B 427 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N PHE B 427 " --> pdb=" O ARG B 483 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N PHE B 485 " --> pdb=" O ASN B 425 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 499 through 500 removed outlier: 3.534A pdb=" N THR B 565 " --> pdb=" O TYR B 500 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 516 through 519 removed outlier: 3.671A pdb=" N LYS B 505 " --> pdb=" O VAL B 559 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY B 554 " --> pdb=" O GLN B 551 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 722 through 729 removed outlier: 7.048A pdb=" N LEU B 753 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N SER B 725 " --> pdb=" O LEU B 753 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N LEU B 755 " --> pdb=" O SER B 725 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N MET B 727 " --> pdb=" O LEU B 755 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N LEU B 740 " --> pdb=" O LEU B 736 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 797 through 800 removed outlier: 4.514A pdb=" N LYS B 797 " --> pdb=" O LEU B 931 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 853 through 854 Processing sheet with id=AE2, first strand: chain 'B' and resid 963 through 964 removed outlier: 6.876A pdb=" N VAL C 775 " --> pdb=" O THR C1146 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N THR C1146 " --> pdb=" O VAL C 775 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLN C 777 " --> pdb=" O ASN C1144 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ASN C1144 " --> pdb=" O GLN C 777 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N HIS C1142 " --> pdb=" O PRO C 779 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL C1120 " --> pdb=" O VAL C1135 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N TYR C1137 " --> pdb=" O HIS C1118 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N HIS C1118 " --> pdb=" O TYR C1137 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 963 through 964 removed outlier: 6.876A pdb=" N VAL C 775 " --> pdb=" O THR C1146 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N THR C1146 " --> pdb=" O VAL C 775 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLN C 777 " --> pdb=" O ASN C1144 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ASN C1144 " --> pdb=" O GLN C 777 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N HIS C1142 " --> pdb=" O PRO C 779 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N THR C1146 " --> pdb=" O LEU C1170 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N PHE C1168 " --> pdb=" O ALA C1148 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 1200 through 1203 removed outlier: 3.892A pdb=" N CYS B1160 " --> pdb=" O VAL B1203 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 70 through 78 removed outlier: 3.581A pdb=" N LEU C 325 " --> pdb=" O GLY C 76 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ARG C 339 " --> pdb=" O ASP C 330 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 86 through 89 removed outlier: 3.594A pdb=" N ALA C 286 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N SER C 271 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N LEU C 284 " --> pdb=" O SER C 271 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 144 through 145 Processing sheet with id=AE8, first strand: chain 'C' and resid 236 through 248 removed outlier: 5.868A pdb=" N LEU C 238 " --> pdb=" O GLU C 192 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N GLU C 192 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ASN C 240 " --> pdb=" O VAL C 190 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N VAL C 190 " --> pdb=" O ASN C 240 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N TYR C 188 " --> pdb=" O SER C 242 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ILE C 244 " --> pdb=" O ALA C 186 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ALA C 186 " --> pdb=" O ILE C 244 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N SER C 246 " --> pdb=" O LEU C 184 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU C 184 " --> pdb=" O SER C 246 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ALA C 150 " --> pdb=" O ILE C 300 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 157 through 159 Processing sheet with id=AF1, first strand: chain 'C' and resid 210 through 212 removed outlier: 6.584A pdb=" N VAL C 210 " --> pdb=" O SER C 303 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'C' and resid 363 through 366 removed outlier: 3.530A pdb=" N GLY C 717 " --> pdb=" O THR C 714 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 378 through 380 removed outlier: 4.599A pdb=" N TYR C 652 " --> pdb=" O CYS C 624 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ILE C 643 " --> pdb=" O VAL C 655 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N VAL C 635 " --> pdb=" O ILE C 643 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 404 through 408 removed outlier: 3.648A pdb=" N SER C 444 " --> pdb=" O GLN C 580 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU C 571 " --> pdb=" O ALA C 488 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N THR C 481 " --> pdb=" O CYS C 429 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N CYS C 429 " --> pdb=" O THR C 481 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ARG C 483 " --> pdb=" O PHE C 427 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N PHE C 427 " --> pdb=" O ARG C 483 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N PHE C 485 " --> pdb=" O ASN C 425 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 411 through 413 Processing sheet with id=AF6, first strand: chain 'C' and resid 499 through 500 Processing sheet with id=AF7, first strand: chain 'C' and resid 516 through 519 removed outlier: 3.878A pdb=" N LYS C 505 " --> pdb=" O VAL C 559 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 722 through 729 removed outlier: 7.043A pdb=" N LEU C 753 " --> pdb=" O VAL C 723 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N SER C 725 " --> pdb=" O LEU C 753 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N LEU C 755 " --> pdb=" O SER C 725 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N MET C 727 " --> pdb=" O LEU C 755 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N LEU C 740 " --> pdb=" O LEU C 736 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 797 through 800 removed outlier: 4.664A pdb=" N LYS C 797 " --> pdb=" O LEU C 931 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 861 through 862 Processing sheet with id=AG2, first strand: chain 'C' and resid 1151 through 1152 removed outlier: 4.114A pdb=" N CYS C1160 " --> pdb=" O VAL C1203 " (cutoff:3.500A) 1063 hydrogen bonds defined for protein. 2835 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.18 Time building geometry restraints manager: 2.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 7841 1.33 - 1.47: 8448 1.47 - 1.62: 11759 1.62 - 1.76: 0 1.76 - 1.90: 222 Bond restraints: 28270 Sorted by residual: bond pdb=" N VAL C 372 " pdb=" CA VAL C 372 " ideal model delta sigma weight residual 1.458 1.504 -0.046 1.19e-02 7.06e+03 1.50e+01 bond pdb=" N VAL C 659 " pdb=" CA VAL C 659 " ideal model delta sigma weight residual 1.459 1.506 -0.047 1.25e-02 6.40e+03 1.43e+01 bond pdb=" C PRO C 662 " pdb=" O PRO C 662 " ideal model delta sigma weight residual 1.233 1.192 0.042 1.10e-02 8.26e+03 1.42e+01 bond pdb=" C PRO B 535 " pdb=" O PRO B 535 " ideal model delta sigma weight residual 1.237 1.192 0.045 1.26e-02 6.30e+03 1.28e+01 bond pdb=" N VAL C 661 " pdb=" CA VAL C 661 " ideal model delta sigma weight residual 1.461 1.505 -0.044 1.23e-02 6.61e+03 1.26e+01 ... (remaining 28265 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.75: 37919 2.75 - 5.49: 481 5.49 - 8.24: 37 8.24 - 10.98: 9 10.98 - 13.73: 3 Bond angle restraints: 38449 Sorted by residual: angle pdb=" N THR A 697 " pdb=" CA THR A 697 " pdb=" C THR A 697 " ideal model delta sigma weight residual 111.28 100.31 10.97 1.09e+00 8.42e-01 1.01e+02 angle pdb=" N CYS C 658 " pdb=" CA CYS C 658 " pdb=" C CYS C 658 " ideal model delta sigma weight residual 108.38 118.61 -10.23 1.35e+00 5.49e-01 5.74e+01 angle pdb=" C PHE C 370 " pdb=" CA PHE C 370 " pdb=" CB PHE C 370 " ideal model delta sigma weight residual 110.19 121.50 -11.31 1.64e+00 3.72e-01 4.76e+01 angle pdb=" N ILE C 951 " pdb=" CA ILE C 951 " pdb=" C ILE C 951 " ideal model delta sigma weight residual 111.91 106.62 5.29 8.90e-01 1.26e+00 3.53e+01 angle pdb=" CA CYS A 189 " pdb=" CB CYS A 189 " pdb=" SG CYS A 189 " ideal model delta sigma weight residual 114.40 127.21 -12.81 2.30e+00 1.89e-01 3.10e+01 ... (remaining 38444 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 15750 17.72 - 35.43: 1375 35.43 - 53.15: 195 53.15 - 70.87: 52 70.87 - 88.58: 25 Dihedral angle restraints: 17397 sinusoidal: 7227 harmonic: 10170 Sorted by residual: dihedral pdb=" C VAL C 659 " pdb=" N VAL C 659 " pdb=" CA VAL C 659 " pdb=" CB VAL C 659 " ideal model delta harmonic sigma weight residual -122.00 -149.29 27.29 0 2.50e+00 1.60e-01 1.19e+02 dihedral pdb=" CA THR A1156 " pdb=" C THR A1156 " pdb=" N PRO A1157 " pdb=" CA PRO A1157 " ideal model delta harmonic sigma weight residual -180.00 -128.41 -51.59 0 5.00e+00 4.00e-02 1.06e+02 dihedral pdb=" N VAL C 659 " pdb=" C VAL C 659 " pdb=" CA VAL C 659 " pdb=" CB VAL C 659 " ideal model delta harmonic sigma weight residual 123.40 148.23 -24.83 0 2.50e+00 1.60e-01 9.86e+01 ... (remaining 17394 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.195: 4384 0.195 - 0.390: 26 0.390 - 0.585: 2 0.585 - 0.780: 1 0.780 - 0.975: 1 Chirality restraints: 4414 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.21e+02 chirality pdb=" C1 NAG L 2 " pdb=" O4 NAG L 1 " pdb=" C2 NAG L 2 " pdb=" O5 NAG L 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 7.44e+01 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.50 0.10 2.00e-02 2.50e+03 2.48e+01 ... (remaining 4411 not shown) Planarity restraints: 4992 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1309 " 0.271 2.00e-02 2.50e+03 2.27e-01 6.42e+02 pdb=" C7 NAG B1309 " -0.070 2.00e-02 2.50e+03 pdb=" C8 NAG B1309 " 0.179 2.00e-02 2.50e+03 pdb=" N2 NAG B1309 " -0.383 2.00e-02 2.50e+03 pdb=" O7 NAG B1309 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1308 " -0.252 2.00e-02 2.50e+03 2.18e-01 5.93e+02 pdb=" C7 NAG A1308 " 0.055 2.00e-02 2.50e+03 pdb=" C8 NAG A1308 " -0.155 2.00e-02 2.50e+03 pdb=" N2 NAG A1308 " 0.382 2.00e-02 2.50e+03 pdb=" O7 NAG A1308 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1308 " -0.252 2.00e-02 2.50e+03 2.14e-01 5.70e+02 pdb=" C7 NAG B1308 " 0.063 2.00e-02 2.50e+03 pdb=" C8 NAG B1308 " -0.166 2.00e-02 2.50e+03 pdb=" N2 NAG B1308 " 0.364 2.00e-02 2.50e+03 pdb=" O7 NAG B1308 " -0.010 2.00e-02 2.50e+03 ... (remaining 4989 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 427 2.66 - 3.22: 25112 3.22 - 3.78: 42147 3.78 - 4.34: 61263 4.34 - 4.90: 98336 Nonbonded interactions: 227285 Sorted by model distance: nonbonded pdb=" OG1 THR A 585 " pdb=" OG SER A 587 " model vdw 2.105 3.040 nonbonded pdb=" O PRO C 79 " pdb=" OH TYR C 327 " model vdw 2.129 3.040 nonbonded pdb=" OD1 ASP B 541 " pdb=" OG SER B 563 " model vdw 2.132 3.040 nonbonded pdb=" OG1 THR C 585 " pdb=" OG SER C 587 " model vdw 2.143 3.040 nonbonded pdb=" OG SER A 155 " pdb=" O GLY A 293 " model vdw 2.159 3.040 ... (remaining 227280 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' selection = (chain 'B' and (resid 18 through 41 or (resid 42 and (name N or name CA or name \ C or name O or name CB )) or resid 43 through 44 or (resid 45 and (name N or nam \ e CA or name C or name O or name CB )) or resid 46 through 214 or (resid 215 and \ (name N or name CA or name C or name O or name CB )) or resid 216 through 694 o \ r (resid 695 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 96 through 1308)) selection = (chain 'C' and (resid 18 through 44 or (resid 45 and (name N or name CA or name \ C or name O or name CB )) or resid 46 through 214 or (resid 215 and (name N or n \ ame CA or name C or name O or name CB )) or resid 216 through 694 or (resid 695 \ and (name N or name CA or name C or name O or name CB )) or resid 696 through 13 \ 08)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 27.650 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 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 : 0.005 0.092 28365 Z= 0.247 Angle : 0.785 13.728 38683 Z= 0.441 Chirality : 0.057 0.975 4414 Planarity : 0.011 0.227 4957 Dihedral : 13.286 88.583 10758 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.82 % Favored : 94.12 % Rotamer: Outliers : 0.27 % Allowed : 0.43 % Favored : 99.30 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.21 % Twisted General : 0.09 % 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 are not related in a simple way. whole: -1.29 (0.13), residues: 3471 helix: 0.33 (0.19), residues: 765 sheet: -0.45 (0.19), residues: 723 loop : -1.53 (0.13), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 656 TYR 0.032 0.002 TYR C 442 PHE 0.025 0.002 PHE A 358 TRP 0.015 0.002 TRP A 185 HIS 0.010 0.001 HIS B 373 Details of bonding type rmsd covalent geometry : bond 0.00453 (28270) covalent geometry : angle 0.75816 (38449) SS BOND : bond 0.00993 ( 51) SS BOND : angle 2.00445 ( 102) hydrogen bonds : bond 0.19344 ( 1037) hydrogen bonds : angle 8.02641 ( 2835) link_BETA1-4 : bond 0.00767 ( 9) link_BETA1-4 : angle 3.41188 ( 27) link_NAG-ASN : bond 0.00478 ( 35) link_NAG-ASN : angle 3.13090 ( 105) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 3015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 364 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 651 ASN cc_start: 0.8400 (m110) cc_final: 0.7888 (m110) REVERT: A 1181 GLN cc_start: 0.8614 (tp-100) cc_final: 0.8360 (tp-100) REVERT: B 113 LYS cc_start: 0.7029 (mttp) cc_final: 0.6766 (mtpt) REVERT: B 549 LEU cc_start: 0.7235 (pp) cc_final: 0.7034 (pp) REVERT: B 727 MET cc_start: 0.8207 (ptm) cc_final: 0.8002 (ptp) REVERT: B 1086 GLU cc_start: 0.7672 (tm-30) cc_final: 0.7436 (tm-30) REVERT: B 1221 LEU cc_start: 0.8480 (mt) cc_final: 0.8199 (mt) outliers start: 8 outliers final: 3 residues processed: 367 average time/residue: 0.6282 time to fit residues: 270.9002 Evaluate side-chains 297 residues out of total 3015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 294 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 660 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 3.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 ASN A 632 GLN A 862 ASN A 903 GLN A 999 GLN ** B 691 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1214 ASN C 580 GLN C 631 GLN C 762 GLN C 777 GLN C 844 ASN C 855 GLN C 903 GLN C 999 GLN C1080 GLN C1081 GLN C1142 HIS C1214 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.178160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.136339 restraints weight = 30482.814| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.15 r_work: 0.3391 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.0845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 28365 Z= 0.170 Angle : 0.664 11.428 38683 Z= 0.350 Chirality : 0.047 0.444 4414 Planarity : 0.005 0.070 4957 Dihedral : 6.845 58.947 4709 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.65 % Favored : 94.30 % Rotamer: Outliers : 1.46 % Allowed : 6.28 % Favored : 92.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.21 % Twisted General : 0.09 % 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 are not related in a simple way. whole: -1.06 (0.14), residues: 3471 helix: 0.54 (0.19), residues: 783 sheet: -0.33 (0.19), residues: 753 loop : -1.41 (0.13), residues: 1935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 695 TYR 0.025 0.002 TYR C 442 PHE 0.027 0.002 PHE C 169 TRP 0.014 0.002 TRP A 185 HIS 0.010 0.001 HIS B 373 Details of bonding type rmsd covalent geometry : bond 0.00382 (28270) covalent geometry : angle 0.64521 (38449) SS BOND : bond 0.00648 ( 51) SS BOND : angle 1.49103 ( 102) hydrogen bonds : bond 0.05913 ( 1037) hydrogen bonds : angle 6.10408 ( 2835) link_BETA1-4 : bond 0.00514 ( 9) link_BETA1-4 : angle 2.05707 ( 27) link_NAG-ASN : bond 0.00480 ( 35) link_NAG-ASN : angle 2.62762 ( 105) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 3015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 309 time to evaluate : 1.089 Fit side-chains revert: symmetry clash REVERT: A 273 ARG cc_start: 0.7030 (mtp85) cc_final: 0.6807 (mtp180) REVERT: A 423 MET cc_start: 0.8297 (tpt) cc_final: 0.7955 (tmm) REVERT: A 460 MET cc_start: 0.9007 (mtm) cc_final: 0.8677 (mtp) REVERT: A 651 ASN cc_start: 0.8242 (m110) cc_final: 0.7772 (m110) REVERT: A 652 TYR cc_start: 0.7240 (t80) cc_final: 0.6967 (t80) REVERT: B 113 LYS cc_start: 0.7276 (mttp) cc_final: 0.7054 (mtpp) REVERT: B 164 VAL cc_start: 0.7240 (m) cc_final: 0.7033 (p) REVERT: B 549 LEU cc_start: 0.7082 (pp) cc_final: 0.6819 (pp) REVERT: B 1086 GLU cc_start: 0.8134 (tm-30) cc_final: 0.7818 (tm-30) REVERT: B 1221 LEU cc_start: 0.8381 (mt) cc_final: 0.8029 (mt) REVERT: C 540 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.8046 (tp40) REVERT: C 727 MET cc_start: 0.8298 (ptm) cc_final: 0.8079 (ptp) REVERT: C 1214 ASN cc_start: 0.7695 (m-40) cc_final: 0.7380 (m110) outliers start: 44 outliers final: 22 residues processed: 332 average time/residue: 0.6137 time to fit residues: 240.9681 Evaluate side-chains 300 residues out of total 3015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 277 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 837 MET Chi-restraints excluded: chain A residue 1010 THR Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 698 GLN Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 767 SER Chi-restraints excluded: chain B residue 837 MET Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 493 THR Chi-restraints excluded: chain C residue 540 GLN Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 660 SER Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 767 SER Chi-restraints excluded: chain C residue 837 MET Chi-restraints excluded: chain C residue 1010 THR Chi-restraints excluded: chain C residue 1108 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 34 optimal weight: 8.9990 chunk 284 optimal weight: 0.3980 chunk 339 optimal weight: 3.9990 chunk 272 optimal weight: 5.9990 chunk 302 optimal weight: 6.9990 chunk 174 optimal weight: 5.9990 chunk 233 optimal weight: 0.2980 chunk 243 optimal weight: 2.9990 chunk 134 optimal weight: 30.0000 chunk 63 optimal weight: 4.9990 chunk 224 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1110 ASN ** B 691 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 GLN B1012 ASN B1080 GLN B1081 GLN B1214 ASN C 580 GLN C 631 GLN C 762 GLN C 844 ASN C 903 GLN C 999 GLN C1080 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.177575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.135910 restraints weight = 30488.948| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.18 r_work: 0.3379 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 28365 Z= 0.185 Angle : 0.659 10.609 38683 Z= 0.346 Chirality : 0.047 0.455 4414 Planarity : 0.005 0.066 4957 Dihedral : 6.743 59.930 4709 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.62 % Favored : 94.32 % Rotamer: Outliers : 2.19 % Allowed : 8.24 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.21 % Twisted General : 0.09 % 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 are not related in a simple way. whole: -1.01 (0.13), residues: 3471 helix: 0.51 (0.19), residues: 801 sheet: -0.29 (0.18), residues: 753 loop : -1.37 (0.13), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 656 TYR 0.020 0.002 TYR C 610 PHE 0.025 0.002 PHE C 545 TRP 0.014 0.001 TRP A 185 HIS 0.009 0.001 HIS B 373 Details of bonding type rmsd covalent geometry : bond 0.00428 (28270) covalent geometry : angle 0.64109 (38449) SS BOND : bond 0.00721 ( 51) SS BOND : angle 1.66045 ( 102) hydrogen bonds : bond 0.05803 ( 1037) hydrogen bonds : angle 5.90819 ( 2835) link_BETA1-4 : bond 0.00250 ( 9) link_BETA1-4 : angle 1.95740 ( 27) link_NAG-ASN : bond 0.00454 ( 35) link_NAG-ASN : angle 2.45483 ( 105) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 3015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 293 time to evaluate : 1.008 Fit side-chains REVERT: A 273 ARG cc_start: 0.7017 (mtp85) cc_final: 0.6781 (mtp180) REVERT: A 292 ASP cc_start: 0.8227 (OUTLIER) cc_final: 0.8002 (m-30) REVERT: A 423 MET cc_start: 0.8465 (tpt) cc_final: 0.8087 (tmm) REVERT: A 460 MET cc_start: 0.9034 (mtm) cc_final: 0.8738 (mtp) REVERT: A 651 ASN cc_start: 0.8255 (m110) cc_final: 0.7826 (m110) REVERT: A 652 TYR cc_start: 0.7242 (t80) cc_final: 0.6954 (t80) REVERT: A 939 MET cc_start: 0.9029 (ttm) cc_final: 0.8781 (ttt) REVERT: B 423 MET cc_start: 0.8269 (tpt) cc_final: 0.7989 (tmm) REVERT: B 549 LEU cc_start: 0.7142 (pp) cc_final: 0.6877 (pp) REVERT: B 1086 GLU cc_start: 0.8222 (tm-30) cc_final: 0.7968 (tm-30) REVERT: B 1221 LEU cc_start: 0.8404 (mt) cc_final: 0.8050 (mt) REVERT: C 540 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.8025 (tp40) REVERT: C 573 MET cc_start: 0.9171 (OUTLIER) cc_final: 0.8948 (mtm) REVERT: C 727 MET cc_start: 0.8290 (ptm) cc_final: 0.8074 (ptp) REVERT: C 1058 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7032 (mm-30) REVERT: C 1154 THR cc_start: 0.8353 (m) cc_final: 0.7988 (p) outliers start: 66 outliers final: 38 residues processed: 323 average time/residue: 0.5826 time to fit residues: 223.6494 Evaluate side-chains 327 residues out of total 3015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 285 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 565 THR Chi-restraints excluded: chain A residue 689 MET Chi-restraints excluded: chain A residue 837 MET Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 1010 THR Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1060 GLU Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 698 GLN Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 767 SER Chi-restraints excluded: chain B residue 840 GLU Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 460 MET Chi-restraints excluded: chain C residue 493 THR Chi-restraints excluded: chain C residue 540 GLN Chi-restraints excluded: chain C residue 557 ILE Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 573 MET Chi-restraints excluded: chain C residue 660 SER Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 767 SER Chi-restraints excluded: chain C residue 837 MET Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 1010 THR Chi-restraints excluded: chain C residue 1058 GLU Chi-restraints excluded: chain C residue 1108 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 30 optimal weight: 7.9990 chunk 26 optimal weight: 0.4980 chunk 233 optimal weight: 0.0020 chunk 154 optimal weight: 0.9990 chunk 147 optimal weight: 1.9990 chunk 318 optimal weight: 5.9990 chunk 155 optimal weight: 0.8980 chunk 58 optimal weight: 8.9990 chunk 209 optimal weight: 0.7980 chunk 55 optimal weight: 9.9990 chunk 196 optimal weight: 4.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 281 ASN ** B 691 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 GLN B1012 ASN B1080 GLN B1141 ASN B1214 ASN C 580 GLN C 631 GLN C 762 GLN C 829 GLN C 844 ASN ** C1059 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1080 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.181650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.140600 restraints weight = 30573.989| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 2.26 r_work: 0.3457 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.078 28365 Z= 0.112 Angle : 0.560 10.278 38683 Z= 0.295 Chirality : 0.044 0.438 4414 Planarity : 0.004 0.059 4957 Dihedral : 6.182 59.814 4708 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.75 % Favored : 95.22 % Rotamer: Outliers : 1.96 % Allowed : 10.33 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.21 % Twisted General : 0.06 % 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 are not related in a simple way. whole: -0.72 (0.14), residues: 3471 helix: 0.99 (0.19), residues: 783 sheet: -0.15 (0.19), residues: 729 loop : -1.25 (0.13), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 483 TYR 0.023 0.001 TYR C 610 PHE 0.025 0.001 PHE A 358 TRP 0.012 0.001 TRP A 185 HIS 0.006 0.001 HIS B 373 Details of bonding type rmsd covalent geometry : bond 0.00234 (28270) covalent geometry : angle 0.54336 (38449) SS BOND : bond 0.00786 ( 51) SS BOND : angle 1.42878 ( 102) hydrogen bonds : bond 0.04429 ( 1037) hydrogen bonds : angle 5.48787 ( 2835) link_BETA1-4 : bond 0.00386 ( 9) link_BETA1-4 : angle 1.68216 ( 27) link_NAG-ASN : bond 0.00458 ( 35) link_NAG-ASN : angle 2.15049 ( 105) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 3015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 315 time to evaluate : 1.036 Fit side-chains revert: symmetry clash REVERT: A 273 ARG cc_start: 0.6901 (mtp85) cc_final: 0.6693 (mtp180) REVERT: A 423 MET cc_start: 0.8216 (tpt) cc_final: 0.7901 (tmm) REVERT: A 460 MET cc_start: 0.8997 (mtm) cc_final: 0.8613 (mtp) REVERT: A 651 ASN cc_start: 0.8241 (m110) cc_final: 0.7903 (m110) REVERT: A 939 MET cc_start: 0.8913 (ttm) cc_final: 0.8678 (ttt) REVERT: A 1057 VAL cc_start: 0.7954 (OUTLIER) cc_final: 0.7728 (t) REVERT: B 423 MET cc_start: 0.8029 (tpt) cc_final: 0.7763 (tmm) REVERT: B 1086 GLU cc_start: 0.8193 (tm-30) cc_final: 0.7989 (tm-30) REVERT: C 245 TYR cc_start: 0.8126 (m-80) cc_final: 0.7915 (m-80) REVERT: C 540 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.7976 (tp40) REVERT: C 610 TYR cc_start: 0.7327 (p90) cc_final: 0.7092 (p90) REVERT: C 689 MET cc_start: 0.6065 (ptm) cc_final: 0.5827 (tmt) REVERT: C 727 MET cc_start: 0.8240 (ptm) cc_final: 0.8024 (ptp) REVERT: C 1154 THR cc_start: 0.8202 (m) cc_final: 0.7870 (p) outliers start: 59 outliers final: 25 residues processed: 340 average time/residue: 0.5776 time to fit residues: 234.0228 Evaluate side-chains 304 residues out of total 3015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 277 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 689 MET Chi-restraints excluded: chain A residue 1010 THR Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 460 MET Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 767 SER Chi-restraints excluded: chain B residue 837 MET Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 493 THR Chi-restraints excluded: chain C residue 540 GLN Chi-restraints excluded: chain C residue 557 ILE Chi-restraints excluded: chain C residue 690 LEU Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 767 SER Chi-restraints excluded: chain C residue 837 MET Chi-restraints excluded: chain C residue 1010 THR Chi-restraints excluded: chain C residue 1108 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 48 optimal weight: 3.9990 chunk 206 optimal weight: 8.9990 chunk 225 optimal weight: 8.9990 chunk 312 optimal weight: 8.9990 chunk 264 optimal weight: 8.9990 chunk 8 optimal weight: 0.7980 chunk 122 optimal weight: 4.9990 chunk 152 optimal weight: 0.0770 chunk 155 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 139 optimal weight: 4.9990 overall best weight: 1.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 691 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 GLN B1012 ASN B1080 GLN B1142 HIS B1214 ASN C 580 GLN C 631 GLN C 762 GLN C 844 ASN C1012 ASN C1080 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.179994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.138208 restraints weight = 30383.744| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 2.25 r_work: 0.3418 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 28365 Z= 0.139 Angle : 0.584 10.213 38683 Z= 0.306 Chirality : 0.045 0.432 4414 Planarity : 0.005 0.058 4957 Dihedral : 6.194 59.898 4706 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.24 % Favored : 94.73 % Rotamer: Outliers : 2.19 % Allowed : 10.93 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.21 % Twisted General : 0.09 % 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 are not related in a simple way. whole: -0.67 (0.14), residues: 3471 helix: 1.03 (0.19), residues: 783 sheet: -0.18 (0.19), residues: 723 loop : -1.18 (0.13), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 656 TYR 0.019 0.001 TYR C 610 PHE 0.021 0.002 PHE A 358 TRP 0.012 0.001 TRP A 185 HIS 0.006 0.001 HIS B 373 Details of bonding type rmsd covalent geometry : bond 0.00316 (28270) covalent geometry : angle 0.56796 (38449) SS BOND : bond 0.00685 ( 51) SS BOND : angle 1.42839 ( 102) hydrogen bonds : bond 0.04810 ( 1037) hydrogen bonds : angle 5.47825 ( 2835) link_BETA1-4 : bond 0.00271 ( 9) link_BETA1-4 : angle 1.73226 ( 27) link_NAG-ASN : bond 0.00406 ( 35) link_NAG-ASN : angle 2.16800 ( 105) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 3015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 276 time to evaluate : 0.812 Fit side-chains revert: symmetry clash REVERT: A 273 ARG cc_start: 0.6938 (mtp85) cc_final: 0.6725 (mtp180) REVERT: A 423 MET cc_start: 0.8315 (tpt) cc_final: 0.8021 (tmm) REVERT: A 460 MET cc_start: 0.9018 (mtm) cc_final: 0.8679 (mtp) REVERT: A 651 ASN cc_start: 0.8270 (m110) cc_final: 0.7936 (m110) REVERT: A 939 MET cc_start: 0.8976 (ttm) cc_final: 0.8711 (ttt) REVERT: B 423 MET cc_start: 0.8211 (tpt) cc_final: 0.7951 (mmm) REVERT: B 1086 GLU cc_start: 0.8179 (tm-30) cc_final: 0.7963 (tm-30) REVERT: C 540 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.7954 (tp40) REVERT: C 727 MET cc_start: 0.8251 (ptm) cc_final: 0.8039 (ptp) REVERT: C 991 LYS cc_start: 0.8279 (mmtm) cc_final: 0.8042 (mtpt) REVERT: C 1154 THR cc_start: 0.8225 (m) cc_final: 0.7892 (p) outliers start: 66 outliers final: 38 residues processed: 316 average time/residue: 0.5721 time to fit residues: 215.1815 Evaluate side-chains 307 residues out of total 3015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 268 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 689 MET Chi-restraints excluded: chain A residue 1010 THR Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 460 MET Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 767 SER Chi-restraints excluded: chain B residue 837 MET Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 189 CYS Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain C residue 460 MET Chi-restraints excluded: chain C residue 493 THR Chi-restraints excluded: chain C residue 540 GLN Chi-restraints excluded: chain C residue 557 ILE Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 690 LEU Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 767 SER Chi-restraints excluded: chain C residue 837 MET Chi-restraints excluded: chain C residue 944 THR Chi-restraints excluded: chain C residue 1010 THR Chi-restraints excluded: chain C residue 1108 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 292 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 49 optimal weight: 0.1980 chunk 275 optimal weight: 5.9990 chunk 263 optimal weight: 4.9990 chunk 294 optimal weight: 5.9990 chunk 126 optimal weight: 20.0000 chunk 308 optimal weight: 8.9990 chunk 224 optimal weight: 7.9990 chunk 32 optimal weight: 0.0470 chunk 258 optimal weight: 7.9990 overall best weight: 2.6484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 691 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 GLN B1012 ASN B1080 GLN B1141 ASN B1214 ASN C 580 GLN C 762 GLN C 844 ASN C1012 ASN C1080 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.177066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.132061 restraints weight = 30408.821| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.32 r_work: 0.3360 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 28365 Z= 0.212 Angle : 0.674 11.285 38683 Z= 0.351 Chirality : 0.049 0.462 4414 Planarity : 0.005 0.060 4957 Dihedral : 6.583 59.473 4706 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.62 % Favored : 94.32 % Rotamer: Outliers : 2.52 % Allowed : 11.23 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.21 % Twisted General : 0.09 % 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 are not related in a simple way. whole: -0.86 (0.13), residues: 3471 helix: 0.69 (0.19), residues: 801 sheet: -0.23 (0.19), residues: 720 loop : -1.26 (0.13), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 656 TYR 0.025 0.002 TYR C 610 PHE 0.025 0.002 PHE C 545 TRP 0.012 0.001 TRP A 185 HIS 0.008 0.001 HIS B 373 Details of bonding type rmsd covalent geometry : bond 0.00497 (28270) covalent geometry : angle 0.65757 (38449) SS BOND : bond 0.00735 ( 51) SS BOND : angle 1.59300 ( 102) hydrogen bonds : bond 0.05836 ( 1037) hydrogen bonds : angle 5.70997 ( 2835) link_BETA1-4 : bond 0.00258 ( 9) link_BETA1-4 : angle 1.94210 ( 27) link_NAG-ASN : bond 0.00394 ( 35) link_NAG-ASN : angle 2.33086 ( 105) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 3015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 278 time to evaluate : 1.080 Fit side-chains revert: symmetry clash REVERT: A 423 MET cc_start: 0.8372 (tpt) cc_final: 0.8066 (tmm) REVERT: A 460 MET cc_start: 0.9042 (mtm) cc_final: 0.8776 (mtp) REVERT: A 651 ASN cc_start: 0.8282 (m110) cc_final: 0.7812 (m110) REVERT: A 939 MET cc_start: 0.9040 (OUTLIER) cc_final: 0.8720 (ttt) REVERT: A 999 GLN cc_start: 0.8384 (OUTLIER) cc_final: 0.8172 (tt0) REVERT: A 1052 LYS cc_start: 0.6766 (OUTLIER) cc_final: 0.6156 (ttpp) REVERT: A 1058 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7021 (mm-30) REVERT: B 423 MET cc_start: 0.8382 (tpt) cc_final: 0.8118 (mmm) REVERT: B 549 LEU cc_start: 0.7159 (pp) cc_final: 0.6928 (pp) REVERT: B 695 ARG cc_start: 0.7089 (ttp-170) cc_final: 0.6513 (ttp-170) REVERT: B 777 GLN cc_start: 0.8946 (OUTLIER) cc_final: 0.8652 (mm110) REVERT: B 1086 GLU cc_start: 0.8228 (tm-30) cc_final: 0.8022 (tm-30) REVERT: C 540 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.8001 (tp40) REVERT: C 573 MET cc_start: 0.9176 (OUTLIER) cc_final: 0.8857 (mtm) REVERT: C 727 MET cc_start: 0.8300 (ptm) cc_final: 0.8088 (ptp) REVERT: C 991 LYS cc_start: 0.8285 (mmtm) cc_final: 0.8049 (mtpt) REVERT: C 1058 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7046 (mm-30) REVERT: C 1154 THR cc_start: 0.8282 (m) cc_final: 0.7951 (p) outliers start: 76 outliers final: 46 residues processed: 326 average time/residue: 0.5158 time to fit residues: 200.0780 Evaluate side-chains 322 residues out of total 3015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 268 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LYS Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 689 MET Chi-restraints excluded: chain A residue 837 MET Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 939 MET Chi-restraints excluded: chain A residue 999 GLN Chi-restraints excluded: chain A residue 1010 THR Chi-restraints excluded: chain A residue 1052 LYS Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1058 GLU Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 207 THR Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 663 LEU Chi-restraints excluded: chain B residue 686 ILE Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 767 SER Chi-restraints excluded: chain B residue 777 GLN Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 951 ILE Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 189 CYS Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain C residue 460 MET Chi-restraints excluded: chain C residue 493 THR Chi-restraints excluded: chain C residue 540 GLN Chi-restraints excluded: chain C residue 557 ILE Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 573 MET Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 690 LEU Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 767 SER Chi-restraints excluded: chain C residue 837 MET Chi-restraints excluded: chain C residue 944 THR Chi-restraints excluded: chain C residue 1010 THR Chi-restraints excluded: chain C residue 1058 GLU Chi-restraints excluded: chain C residue 1108 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 26 optimal weight: 0.1980 chunk 165 optimal weight: 0.9980 chunk 115 optimal weight: 8.9990 chunk 92 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 86 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 chunk 280 optimal weight: 0.2980 chunk 204 optimal weight: 0.9980 chunk 274 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 903 GLN ** A1059 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 691 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 698 GLN B1012 ASN B1080 GLN B1141 ASN B1214 ASN ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN C 631 GLN C 762 GLN C 844 ASN C1012 ASN ** C1059 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1080 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.181079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.139770 restraints weight = 30362.653| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.30 r_work: 0.3425 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.075 28365 Z= 0.114 Angle : 0.561 11.089 38683 Z= 0.295 Chirality : 0.044 0.416 4414 Planarity : 0.004 0.057 4957 Dihedral : 6.112 59.736 4706 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.90 % Favored : 95.07 % Rotamer: Outliers : 2.03 % Allowed : 12.13 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.21 % Twisted General : 0.09 % 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 are not related in a simple way. whole: -0.62 (0.14), residues: 3471 helix: 1.09 (0.19), residues: 783 sheet: -0.20 (0.19), residues: 723 loop : -1.14 (0.13), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 483 TYR 0.024 0.001 TYR C 610 PHE 0.023 0.001 PHE A 358 TRP 0.012 0.001 TRP A 185 HIS 0.006 0.001 HIS B 373 Details of bonding type rmsd covalent geometry : bond 0.00240 (28270) covalent geometry : angle 0.54510 (38449) SS BOND : bond 0.01088 ( 51) SS BOND : angle 1.39377 ( 102) hydrogen bonds : bond 0.04498 ( 1037) hydrogen bonds : angle 5.41073 ( 2835) link_BETA1-4 : bond 0.00324 ( 9) link_BETA1-4 : angle 1.65288 ( 27) link_NAG-ASN : bond 0.00403 ( 35) link_NAG-ASN : angle 2.10225 ( 105) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 3015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 279 time to evaluate : 0.792 Fit side-chains revert: symmetry clash REVERT: A 423 MET cc_start: 0.8245 (tpt) cc_final: 0.8007 (mmm) REVERT: A 460 MET cc_start: 0.9010 (mtm) cc_final: 0.8644 (mtp) REVERT: A 651 ASN cc_start: 0.8203 (m110) cc_final: 0.7881 (m110) REVERT: A 939 MET cc_start: 0.8974 (ttm) cc_final: 0.8706 (ttt) REVERT: B 423 MET cc_start: 0.8251 (tpt) cc_final: 0.8021 (mmm) REVERT: B 1086 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7995 (tm-30) REVERT: C 540 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.7958 (tp40) REVERT: C 591 MET cc_start: 0.7904 (OUTLIER) cc_final: 0.7020 (mmt) REVERT: C 727 MET cc_start: 0.8238 (ptm) cc_final: 0.8013 (ptp) REVERT: C 991 LYS cc_start: 0.8260 (mmtm) cc_final: 0.8034 (mtpt) REVERT: C 1154 THR cc_start: 0.8198 (m) cc_final: 0.7872 (p) outliers start: 61 outliers final: 37 residues processed: 315 average time/residue: 0.5497 time to fit residues: 206.7256 Evaluate side-chains 307 residues out of total 3015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 268 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 689 MET Chi-restraints excluded: chain A residue 837 MET Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 1010 THR Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 767 SER Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 1004 MET Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain C residue 493 THR Chi-restraints excluded: chain C residue 540 GLN Chi-restraints excluded: chain C residue 557 ILE Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 591 MET Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 690 LEU Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 767 SER Chi-restraints excluded: chain C residue 837 MET Chi-restraints excluded: chain C residue 944 THR Chi-restraints excluded: chain C residue 1010 THR Chi-restraints excluded: chain C residue 1108 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 56 optimal weight: 2.9990 chunk 276 optimal weight: 0.6980 chunk 112 optimal weight: 7.9990 chunk 322 optimal weight: 0.0060 chunk 174 optimal weight: 7.9990 chunk 21 optimal weight: 9.9990 chunk 281 optimal weight: 0.6980 chunk 242 optimal weight: 1.9990 chunk 115 optimal weight: 8.9990 chunk 274 optimal weight: 0.6980 chunk 108 optimal weight: 8.9990 overall best weight: 0.8198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 171 HIS ** B 691 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 822 GLN B1012 ASN B1080 GLN B1214 ASN ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN C 762 GLN C 844 ASN C1012 ASN ** C1059 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1080 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.181488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.140466 restraints weight = 30505.215| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 2.23 r_work: 0.3444 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 28365 Z= 0.115 Angle : 0.557 10.904 38683 Z= 0.292 Chirality : 0.044 0.422 4414 Planarity : 0.004 0.055 4957 Dihedral : 5.942 59.362 4706 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.21 % Favored : 94.76 % Rotamer: Outliers : 1.86 % Allowed : 12.69 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.21 % Twisted General : 0.06 % 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 are not related in a simple way. whole: -0.51 (0.14), residues: 3471 helix: 1.19 (0.19), residues: 783 sheet: -0.05 (0.19), residues: 705 loop : -1.10 (0.13), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 483 TYR 0.023 0.001 TYR C 610 PHE 0.021 0.001 PHE A 358 TRP 0.012 0.001 TRP A 185 HIS 0.005 0.001 HIS B 373 Details of bonding type rmsd covalent geometry : bond 0.00249 (28270) covalent geometry : angle 0.54207 (38449) SS BOND : bond 0.00610 ( 51) SS BOND : angle 1.30343 ( 102) hydrogen bonds : bond 0.04401 ( 1037) hydrogen bonds : angle 5.30924 ( 2835) link_BETA1-4 : bond 0.00320 ( 9) link_BETA1-4 : angle 1.61804 ( 27) link_NAG-ASN : bond 0.00364 ( 35) link_NAG-ASN : angle 2.11608 ( 105) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 3015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 284 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 423 MET cc_start: 0.8331 (tpt) cc_final: 0.8044 (mmm) REVERT: A 460 MET cc_start: 0.8996 (mtm) cc_final: 0.8636 (mtp) REVERT: A 651 ASN cc_start: 0.8233 (m110) cc_final: 0.7888 (m110) REVERT: A 939 MET cc_start: 0.8952 (ttm) cc_final: 0.8683 (ttt) REVERT: B 695 ARG cc_start: 0.7064 (ttp-170) cc_final: 0.6442 (ttt-90) REVERT: C 540 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.7892 (tp40) REVERT: C 689 MET cc_start: 0.6053 (ptm) cc_final: 0.5848 (tmt) REVERT: C 727 MET cc_start: 0.8270 (ptm) cc_final: 0.8063 (ptp) REVERT: C 751 SER cc_start: 0.8040 (m) cc_final: 0.7609 (t) REVERT: C 991 LYS cc_start: 0.8267 (mmtm) cc_final: 0.8042 (mtpt) REVERT: C 1005 GLN cc_start: 0.7016 (pp30) cc_final: 0.6767 (pt0) REVERT: C 1154 THR cc_start: 0.8183 (m) cc_final: 0.7857 (p) outliers start: 56 outliers final: 36 residues processed: 316 average time/residue: 0.5525 time to fit residues: 208.5163 Evaluate side-chains 311 residues out of total 3015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 274 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 689 MET Chi-restraints excluded: chain A residue 837 MET Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 1010 THR Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 767 SER Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 1004 MET Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain C residue 442 TYR Chi-restraints excluded: chain C residue 493 THR Chi-restraints excluded: chain C residue 540 GLN Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 690 LEU Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 767 SER Chi-restraints excluded: chain C residue 837 MET Chi-restraints excluded: chain C residue 944 THR Chi-restraints excluded: chain C residue 1010 THR Chi-restraints excluded: chain C residue 1108 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 232 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 208 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 281 optimal weight: 0.9980 chunk 198 optimal weight: 0.4980 chunk 273 optimal weight: 3.9990 chunk 201 optimal weight: 6.9990 chunk 44 optimal weight: 0.0060 chunk 126 optimal weight: 1.9990 chunk 296 optimal weight: 0.8980 overall best weight: 0.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 381 GLN A 631 GLN A 674 HIS ** A1059 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1080 GLN A1081 GLN ** B 691 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1012 ASN B1080 GLN B1214 ASN C 202 ASN C 580 GLN C 631 GLN C 762 GLN C 844 ASN C1012 ASN C1080 GLN C1110 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.181823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.141221 restraints weight = 30394.407| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.12 r_work: 0.3447 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 28365 Z= 0.115 Angle : 0.555 10.830 38683 Z= 0.291 Chirality : 0.044 0.422 4414 Planarity : 0.004 0.054 4957 Dihedral : 5.838 58.709 4706 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.01 % Favored : 94.96 % Rotamer: Outliers : 1.63 % Allowed : 13.49 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.21 % Twisted General : 0.03 % 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 are not related in a simple way. whole: -0.43 (0.14), residues: 3471 helix: 1.24 (0.19), residues: 783 sheet: 0.14 (0.19), residues: 672 loop : -1.09 (0.13), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 483 TYR 0.023 0.001 TYR B 610 PHE 0.020 0.001 PHE A 358 TRP 0.011 0.001 TRP A 185 HIS 0.006 0.001 HIS B 373 Details of bonding type rmsd covalent geometry : bond 0.00251 (28270) covalent geometry : angle 0.54154 (38449) SS BOND : bond 0.00564 ( 51) SS BOND : angle 1.23206 ( 102) hydrogen bonds : bond 0.04337 ( 1037) hydrogen bonds : angle 5.25566 ( 2835) link_BETA1-4 : bond 0.00296 ( 9) link_BETA1-4 : angle 1.57252 ( 27) link_NAG-ASN : bond 0.00374 ( 35) link_NAG-ASN : angle 2.02259 ( 105) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 3015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 286 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 183 ARG cc_start: 0.7178 (ttm170) cc_final: 0.6956 (ttp80) REVERT: A 423 MET cc_start: 0.8265 (tpt) cc_final: 0.7982 (mmm) REVERT: A 460 MET cc_start: 0.8990 (mtm) cc_final: 0.8598 (mtp) REVERT: A 651 ASN cc_start: 0.8216 (m110) cc_final: 0.7879 (m110) REVERT: A 939 MET cc_start: 0.8949 (ttm) cc_final: 0.8682 (ttt) REVERT: B 517 GLU cc_start: 0.7178 (tm-30) cc_final: 0.6854 (tm-30) REVERT: B 695 ARG cc_start: 0.7208 (ttp-170) cc_final: 0.6651 (ttp-170) REVERT: C 540 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.7880 (tp40) REVERT: C 727 MET cc_start: 0.8262 (ptm) cc_final: 0.8049 (ptp) REVERT: C 751 SER cc_start: 0.8032 (m) cc_final: 0.7610 (t) REVERT: C 991 LYS cc_start: 0.8268 (mmtm) cc_final: 0.8043 (mtpt) REVERT: C 1005 GLN cc_start: 0.7024 (pp30) cc_final: 0.6772 (pt0) REVERT: C 1154 THR cc_start: 0.8165 (m) cc_final: 0.7841 (p) outliers start: 49 outliers final: 36 residues processed: 315 average time/residue: 0.5649 time to fit residues: 211.6659 Evaluate side-chains 311 residues out of total 3015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 274 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 689 MET Chi-restraints excluded: chain A residue 837 MET Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 1010 THR Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 155 SER Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 767 SER Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 1004 MET Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain C residue 442 TYR Chi-restraints excluded: chain C residue 493 THR Chi-restraints excluded: chain C residue 540 GLN Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 690 LEU Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 767 SER Chi-restraints excluded: chain C residue 837 MET Chi-restraints excluded: chain C residue 944 THR Chi-restraints excluded: chain C residue 1010 THR Chi-restraints excluded: chain C residue 1108 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 132 optimal weight: 7.9990 chunk 202 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 14 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 333 optimal weight: 2.9990 chunk 141 optimal weight: 0.8980 chunk 239 optimal weight: 0.0970 chunk 235 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1059 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 691 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1080 GLN B1214 ASN C 580 GLN C 762 GLN C 844 ASN C1012 ASN C1080 GLN C1110 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.182446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.141552 restraints weight = 30555.045| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.35 r_work: 0.3443 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.081 28365 Z= 0.111 Angle : 0.549 10.726 38683 Z= 0.289 Chirality : 0.044 0.409 4414 Planarity : 0.004 0.084 4957 Dihedral : 5.747 58.293 4706 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.13 % Favored : 94.84 % Rotamer: Outliers : 1.46 % Allowed : 13.75 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.21 % 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 are not related in a simple way. whole: -0.40 (0.14), residues: 3471 helix: 1.29 (0.19), residues: 783 sheet: 0.13 (0.19), residues: 672 loop : -1.07 (0.13), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 483 TYR 0.025 0.001 TYR B 610 PHE 0.020 0.001 PHE A 358 TRP 0.010 0.001 TRP A 185 HIS 0.005 0.001 HIS B 373 Details of bonding type rmsd covalent geometry : bond 0.00240 (28270) covalent geometry : angle 0.53435 (38449) SS BOND : bond 0.00666 ( 51) SS BOND : angle 1.38607 ( 102) hydrogen bonds : bond 0.04230 ( 1037) hydrogen bonds : angle 5.20551 ( 2835) link_BETA1-4 : bond 0.00299 ( 9) link_BETA1-4 : angle 1.53340 ( 27) link_NAG-ASN : bond 0.00380 ( 35) link_NAG-ASN : angle 1.97248 ( 105) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6942 Ramachandran restraints generated. 3471 Oldfield, 0 Emsley, 3471 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 3015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 283 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 183 ARG cc_start: 0.7102 (ttm170) cc_final: 0.6887 (ttp80) REVERT: A 423 MET cc_start: 0.8389 (tpt) cc_final: 0.8111 (mmm) REVERT: A 460 MET cc_start: 0.9004 (mtm) cc_final: 0.8594 (mtp) REVERT: A 591 MET cc_start: 0.8331 (mmt) cc_final: 0.8124 (mmt) REVERT: A 651 ASN cc_start: 0.8195 (m110) cc_final: 0.7877 (m110) REVERT: A 852 HIS cc_start: 0.8103 (m-70) cc_final: 0.7796 (m90) REVERT: A 939 MET cc_start: 0.8952 (ttm) cc_final: 0.8680 (ttt) REVERT: B 330 ASP cc_start: 0.7184 (t70) cc_final: 0.6967 (p0) REVERT: B 695 ARG cc_start: 0.6909 (ttp-170) cc_final: 0.6293 (ttp-170) REVERT: C 540 GLN cc_start: 0.8247 (OUTLIER) cc_final: 0.7887 (tp40) REVERT: C 727 MET cc_start: 0.8266 (ptm) cc_final: 0.8058 (ptp) REVERT: C 991 LYS cc_start: 0.8266 (mmtm) cc_final: 0.8040 (mtpt) REVERT: C 1005 GLN cc_start: 0.6989 (pp30) cc_final: 0.6764 (pt0) REVERT: C 1154 THR cc_start: 0.8135 (m) cc_final: 0.7799 (p) outliers start: 44 outliers final: 36 residues processed: 312 average time/residue: 0.5510 time to fit residues: 204.4620 Evaluate side-chains 313 residues out of total 3015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 276 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 689 MET Chi-restraints excluded: chain A residue 837 MET Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 1010 THR Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 416 THR Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 767 SER Chi-restraints excluded: chain B residue 944 THR Chi-restraints excluded: chain B residue 1004 MET Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 189 CYS Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain C residue 442 TYR Chi-restraints excluded: chain C residue 493 THR Chi-restraints excluded: chain C residue 540 GLN Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 561 VAL Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 690 LEU Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 767 SER Chi-restraints excluded: chain C residue 837 MET Chi-restraints excluded: chain C residue 944 THR Chi-restraints excluded: chain C residue 1108 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 236 optimal weight: 0.7980 chunk 268 optimal weight: 3.9990 chunk 164 optimal weight: 0.9980 chunk 253 optimal weight: 7.9990 chunk 175 optimal weight: 6.9990 chunk 316 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 181 optimal weight: 4.9990 chunk 179 optimal weight: 1.9990 chunk 284 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 691 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1012 ASN B1080 GLN B1214 ASN C 580 GLN C 762 GLN C 844 ASN C1080 GLN C1110 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.179704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.137893 restraints weight = 30239.545| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 2.24 r_work: 0.3409 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 28365 Z= 0.159 Angle : 0.606 10.843 38683 Z= 0.318 Chirality : 0.046 0.400 4414 Planarity : 0.005 0.082 4957 Dihedral : 6.027 59.376 4706 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 1.83 % Allowed : 13.55 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.21 % Twisted General : 0.09 % 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 are not related in a simple way. whole: -0.51 (0.14), residues: 3471 helix: 1.14 (0.19), residues: 783 sheet: 0.09 (0.19), residues: 672 loop : -1.12 (0.13), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 656 TYR 0.026 0.002 TYR B 610 PHE 0.019 0.002 PHE A 236 TRP 0.009 0.001 TRP B 956 HIS 0.007 0.001 HIS B 373 Details of bonding type rmsd covalent geometry : bond 0.00367 (28270) covalent geometry : angle 0.59124 (38449) SS BOND : bond 0.00707 ( 51) SS BOND : angle 1.52287 ( 102) hydrogen bonds : bond 0.05009 ( 1037) hydrogen bonds : angle 5.39685 ( 2835) link_BETA1-4 : bond 0.00251 ( 9) link_BETA1-4 : angle 1.66276 ( 27) link_NAG-ASN : bond 0.00366 ( 35) link_NAG-ASN : angle 2.06871 ( 105) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11406.13 seconds wall clock time: 194 minutes 32.48 seconds (11672.48 seconds total)