Starting phenix.real_space_refine on Mon May 26 21:17:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sak_40272/05_2025/8sak_40272_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sak_40272/05_2025/8sak_40272.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sak_40272/05_2025/8sak_40272.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sak_40272/05_2025/8sak_40272.map" model { file = "/net/cci-nas-00/data/ceres_data/8sak_40272/05_2025/8sak_40272_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sak_40272/05_2025/8sak_40272_neut.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.010 sd= 1.190 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 165 5.16 5 C 18077 2.51 5 N 4638 2.21 5 O 5642 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.89s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 28522 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 8662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1121, 8662 Classifications: {'peptide': 1121} Link IDs: {'PCIS': 2, 'PTRANS': 55, 'TRANS': 1063} Chain breaks: 8 Chain: "B" Number of atoms: 8684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1124, 8684 Classifications: {'peptide': 1124} Link IDs: {'PCIS': 2, 'PTRANS': 55, 'TRANS': 1066} Chain breaks: 8 Chain: "C" Number of atoms: 8634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1117, 8634 Classifications: {'peptide': 1117} Link IDs: {'PCIS': 2, 'PTRANS': 55, 'TRANS': 1059} Chain breaks: 9 Chain: "H" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 997 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 124} Chain: "L" Number of atoms: 782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 782 Classifications: {'peptide': 105} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 98} 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: "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: "Q" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" 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: "X" 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: "c" 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: "h" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: "n" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "y" 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: "1" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "5" 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: "7" 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: 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: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 17.57, per 1000 atoms: 0.62 Number of scatterers: 28522 At special positions: 0 Unit cell: (141.644, 140.811, 203.301, 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 165 16.00 O 5642 8.00 N 4638 7.00 C 18077 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 189 " - pdb=" SG CYS A 241 " distance=2.03 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=2.03 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=2.03 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=2.03 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 482 " distance=2.03 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=2.03 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=2.03 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=2.04 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 624 " - pdb=" SG CYS C 654 " distance=2.03 Simple disulfide: pdb=" SG CYS C 683 " - pdb=" SG CYS C 718 " distance=2.03 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=2.03 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 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 100 " - pdb=" SG CYS H 100E" distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 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 ALPHA1-3 " BMA t 3 " - " MAN t 4 " ALPHA1-6 " BMA t 3 " - " MAN t 5 " BETA1-4 " NAG 1 1 " - " NAG 1 2 " " NAG 5 1 " - " NAG 5 2 " " NAG 7 1 " - " NAG 7 2 " " NAG E 1 " - " NAG E 2 " " NAG K 1 " - " NAG K 2 " " NAG Q 1 " - " NAG Q 2 " " NAG U 1 " - " NAG U 2 " " NAG X 1 " - " NAG X 2 " " NAG c 1 " - " NAG c 2 " " NAG f 1 " - " NAG f 2 " " NAG h 1 " - " NAG h 2 " " NAG l 1 " - " NAG l 2 " " NAG n 1 " - " NAG n 2 " " NAG p 1 " - " NAG p 2 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG y 1 " - " NAG y 2 " BETA1-6 " NAG 1 1 " - " FUC 1 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG Q 1 " - " FUC Q 3 " " NAG h 1 " - " FUC h 3 " NAG-ASN " NAG 1 1 " - " ASN C 623 " " NAG 5 1 " - " ASN C 866 " " NAG 7 1 " - " ASN C1211 " " NAG A1301 " - " ASN A 37 " " NAG A1302 " - " ASN A 69 " " NAG A1303 " - " ASN A 159 " " NAG A1304 " - " ASN A 170 " " NAG A1305 " - " ASN A 240 " " NAG A1306 " - " ASN A 248 " " NAG A1307 " - " ASN A 414 " " NAG A1308 " - " ASN A 724 " " NAG A1309 " - " ASN A1211 " " NAG B1301 " - " ASN B 69 " " NAG B1302 " - " ASN B 159 " " NAG B1303 " - " ASN B 170 " " NAG B1304 " - " ASN B 248 " " NAG B1305 " - " ASN B 724 " " NAG C1301 " - " ASN C 69 " " NAG C1302 " - " ASN C 159 " " NAG C1303 " - " ASN C 240 " " NAG C1304 " - " ASN C 724 " " NAG E 1 " - " ASN A 52 " " NAG K 1 " - " ASN A 226 " " NAG Q 1 " - " ASN A 623 " " NAG U 1 " - " ASN A 866 " " NAG X 1 " - " ASN B 52 " " NAG c 1 " - " ASN B 226 " " NAG f 1 " - " ASN B 414 " " NAG h 1 " - " ASN B 623 " " NAG l 1 " - " ASN B 866 " " NAG n 1 " - " ASN B1211 " " NAG p 1 " - " ASN C 52 " " NAG t 1 " - " ASN C 170 " " NAG y 1 " - " ASN C 226 " Time building additional restraints: 7.57 Conformation dependent library (CDL) restraints added in 3.4 seconds 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6632 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 63 sheets defined 25.7% alpha, 31.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.85 Creating SS restraints... Processing helix chain 'A' and resid 52 through 56 Processing helix chain 'A' and resid 226 through 235 removed outlier: 4.084A pdb=" N TYR A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 356 Processing helix chain 'A' and resid 389 through 394 Processing helix chain 'A' and resid 414 through 422 removed outlier: 3.518A pdb=" N LEU A 418 " --> pdb=" O ASN A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 440 Processing helix chain 'A' and resid 453 through 461 removed outlier: 4.704A pdb=" N SER A 458 " --> pdb=" O SER A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 472 removed outlier: 3.611A pdb=" N GLN A 470 " --> pdb=" O GLY A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 534 removed outlier: 3.705A pdb=" N ASN A 532 " --> pdb=" O ILE A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 554 Processing helix chain 'A' and resid 600 through 604 removed outlier: 3.992A pdb=" N LEU A 604 " --> pdb=" O THR A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 689 removed outlier: 3.836A 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 818 removed outlier: 3.715A pdb=" N LEU A 816 " --> pdb=" O LYS A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 820 through 848 Processing helix chain 'A' and resid 884 through 894 Processing helix chain 'A' and resid 903 through 911 Processing helix chain 'A' and resid 917 through 927 removed outlier: 3.710A pdb=" N GLN A 923 " --> pdb=" O LEU A 919 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N TYR A 924 " --> pdb=" O ILE A 920 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N VAL A 925 " --> pdb=" O CYS A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 936 through 946 Processing helix chain 'A' and resid 967 through 979 Processing helix chain 'A' and resid 982 through 989 Processing helix chain 'A' and resid 989 through 1004 removed outlier: 3.596A pdb=" N ALA A 994 " --> pdb=" O GLN A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 1012 through 1035 removed outlier: 3.511A pdb=" N GLN A1019 " --> pdb=" O PHE A1015 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A1029 " --> pdb=" O ASN A1025 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A1032 " --> pdb=" O ALA A1028 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1054 Processing helix chain 'A' and resid 1057 through 1103 removed outlier: 3.748A pdb=" N ALA A1061 " --> pdb=" O PRO A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1221 Processing helix chain 'B' and resid 40 through 44 Processing helix chain 'B' and resid 226 through 234 Processing helix chain 'B' and resid 346 through 355 Processing helix chain 'B' and resid 389 through 394 Processing helix chain 'B' and resid 414 through 422 Processing helix chain 'B' and resid 433 through 439 Processing helix chain 'B' and resid 453 through 461 removed outlier: 4.953A pdb=" N SER B 458 " --> pdb=" O SER B 455 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET B 460 " --> pdb=" O LYS B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 472 Processing helix chain 'B' and resid 528 through 533 removed outlier: 3.979A pdb=" N ASN B 532 " --> pdb=" O ILE B 529 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE B 533 " --> pdb=" O CYS B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 554 removed outlier: 3.730A pdb=" N GLY B 554 " --> pdb=" O GLN B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 689 removed outlier: 3.575A pdb=" N ILE B 686 " --> pdb=" O ALA B 682 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR B 688 " --> pdb=" O GLU B 684 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 808 Processing helix chain 'B' and resid 810 through 818 Processing helix chain 'B' and resid 820 through 850 removed outlier: 3.533A pdb=" N MET B 837 " --> pdb=" O GLY B 833 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLN B 838 " --> pdb=" O ALA B 834 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 893 Processing helix chain 'B' and resid 903 through 911 Processing helix chain 'B' and resid 917 through 922 Processing helix chain 'B' and resid 922 through 927 Processing helix chain 'B' and resid 936 through 949 removed outlier: 3.671A pdb=" N LEU B 947 " --> pdb=" O TYR B 943 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU B 948 " --> pdb=" O THR B 944 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLY B 949 " --> pdb=" O SER B 945 " (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 1004 removed outlier: 3.572A pdb=" N MET B1004 " --> pdb=" O ALA B1000 " (cutoff:3.500A) Processing helix chain 'B' and resid 1005 through 1007 No H-bonds generated for 'chain 'B' and resid 1005 through 1007' Processing helix chain 'B' and resid 1012 through 1035 removed outlier: 3.503A pdb=" N LEU B1032 " --> pdb=" O ALA B1028 " (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 1057 through 1103 removed outlier: 3.514A pdb=" N SER B1096 " --> pdb=" O ALA B1092 " (cutoff:3.500A) Processing helix chain 'B' and resid 1196 through 1198 No H-bonds generated for 'chain 'B' and resid 1196 through 1198' Processing helix chain 'B' and resid 1217 through 1221 Processing helix chain 'C' and resid 40 through 45 removed outlier: 3.928A pdb=" N LYS C 45 " --> pdb=" O GLU C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 112 removed outlier: 4.442A pdb=" N ALA C 111 " --> pdb=" O SER C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 235 removed outlier: 3.877A pdb=" N TYR C 235 " --> pdb=" O SER C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 356 removed outlier: 3.586A pdb=" N GLN C 350 " --> pdb=" O ASP C 346 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU C 351 " --> pdb=" O ASP C 347 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR C 355 " --> pdb=" O LEU C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 394 Processing helix chain 'C' and resid 414 through 422 Processing helix chain 'C' and resid 433 through 440 Processing helix chain 'C' and resid 453 through 461 removed outlier: 3.730A pdb=" N LYS C 457 " --> pdb=" O LEU C 454 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N SER C 458 " --> pdb=" O SER C 455 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN C 461 " --> pdb=" O SER C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 472 removed outlier: 3.635A pdb=" N GLN C 470 " --> pdb=" O GLY C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 528 through 533 removed outlier: 3.824A pdb=" N ASN C 532 " --> pdb=" O ILE C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 550 through 554 removed outlier: 3.513A pdb=" N GLY C 554 " --> pdb=" O GLN C 551 " (cutoff:3.500A) Processing helix chain 'C' and resid 682 through 690 removed outlier: 4.062A pdb=" N ILE C 686 " --> pdb=" O ALA C 682 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU C 690 " --> pdb=" O ILE C 686 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 808 Processing helix chain 'C' and resid 810 through 817 removed outlier: 3.640A pdb=" N LEU C 816 " --> pdb=" O LYS C 812 " (cutoff:3.500A) Processing helix chain 'C' and resid 820 through 849 Processing helix chain 'C' and resid 884 through 894 Processing helix chain 'C' and resid 903 through 911 Processing helix chain 'C' and resid 917 through 922 Processing helix chain 'C' and resid 922 through 927 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 1004 removed outlier: 3.550A pdb=" N MET C1004 " --> pdb=" O ALA C1000 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1007 No H-bonds generated for 'chain 'C' and resid 1005 through 1007' Processing helix chain 'C' and resid 1012 through 1036 removed outlier: 3.545A pdb=" N LEU C1032 " --> pdb=" O ALA C1028 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU C1036 " --> pdb=" O LEU C1032 " (cutoff:3.500A) Processing helix chain 'C' and resid 1046 through 1054 Processing helix chain 'C' and resid 1057 through 1103 removed outlier: 3.592A pdb=" N ALA C1061 " --> pdb=" O PRO C1057 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU C1066 " --> pdb=" O GLN C1062 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN C1093 " --> pdb=" O ALA C1089 " (cutoff:3.500A) Processing helix chain 'C' and resid 1217 through 1221 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.516A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.772A pdb=" N VAL L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 35 Processing sheet with id=AA2, first strand: chain 'A' and resid 66 through 67 removed outlier: 6.439A pdb=" N SER A 66 " --> pdb=" O TYR C 636 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL C 635 " --> pdb=" O ILE C 643 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ILE C 643 " --> pdb=" O VAL C 655 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 70 through 78 removed outlier: 4.350A pdb=" N ARG A 339 " --> pdb=" O ASP A 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 86 through 89 removed outlier: 3.624A pdb=" N ALA A 286 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N SER A 271 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N LEU A 284 " --> pdb=" O SER A 271 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 115 through 116 removed outlier: 4.172A pdb=" N ALA A 150 " --> pdb=" O ILE A 300 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 115 through 116 removed outlier: 4.172A pdb=" N ALA A 150 " --> pdb=" O ILE A 300 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 156 through 159 removed outlier: 4.501A pdb=" N SER A 156 " --> pdb=" O PHE A 169 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 210 through 211 removed outlier: 6.909A pdb=" N VAL A 210 " --> pdb=" O SER A 303 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 363 through 367 removed outlier: 4.436A pdb=" N LEU A 663 " --> pdb=" O VAL A 367 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER A 673 " --> pdb=" O ASP A 668 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 377 through 380 removed outlier: 6.700A pdb=" N PHE A 378 " --> pdb=" O ASN A 611 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N TYR A 652 " --> pdb=" O CYS A 624 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ILE A 643 " --> pdb=" O VAL A 655 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL A 635 " --> pdb=" O ILE A 643 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 385 through 386 removed outlier: 6.248A pdb=" N VAL A 385 " --> pdb=" O ASN A 412 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 404 through 408 removed outlier: 3.723A pdb=" N SER A 444 " --> pdb=" O GLN A 580 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N THR A 481 " --> pdb=" O CYS A 429 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N CYS A 429 " --> pdb=" O THR A 481 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ARG A 483 " --> pdb=" O PHE A 427 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N PHE A 427 " --> pdb=" O ARG A 483 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N PHE A 485 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 517 through 519 removed outlier: 6.054A pdb=" N VAL A 561 " --> pdb=" O SER A 504 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N CYS A 506 " --> pdb=" O VAL A 559 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL A 559 " --> pdb=" O CYS A 506 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ARG A 508 " --> pdb=" O ILE A 557 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ILE A 557 " --> pdb=" O ARG A 508 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLY A 556 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP A 543 " --> pdb=" O GLY A 562 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 723 through 729 removed outlier: 4.314A pdb=" N SER A 725 " --> pdb=" O LEU A 755 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N THR A 757 " --> pdb=" O SER A 725 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N MET A 727 " --> pdb=" O THR A 757 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 764 through 765 removed outlier: 5.827A pdb=" N GLN A 764 " --> pdb=" O SER B 854 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1117 through 1126 removed outlier: 6.465A pdb=" N HIS A1118 " --> pdb=" O TYR A1137 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N TYR A1137 " --> pdb=" O HIS A1118 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL A1120 " --> pdb=" O VAL A1135 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N THR A1146 " --> pdb=" O LEU A1170 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N PHE A1168 " --> pdb=" O ALA A1148 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1117 through 1126 removed outlier: 6.465A pdb=" N HIS A1118 " --> pdb=" O TYR A1137 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N TYR A1137 " --> pdb=" O HIS A1118 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL A1120 " --> pdb=" O VAL A1135 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU A 789 " --> pdb=" O PHE A1132 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ASN A 781 " --> pdb=" O THR A1140 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N HIS A1142 " --> pdb=" O PRO A 779 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ASN A1144 " --> pdb=" O GLN A 777 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N GLN A 777 " --> pdb=" O ASN A1144 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N THR A1146 " --> pdb=" O VAL A 775 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL A 775 " --> pdb=" O THR A1146 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 798 through 800 Processing sheet with id=AC1, first strand: chain 'A' and resid 853 through 854 Processing sheet with id=AC2, first strand: chain 'A' and resid 861 through 862 Processing sheet with id=AC3, first strand: chain 'A' and resid 1200 through 1203 removed outlier: 4.062A pdb=" N CYS A1160 " --> pdb=" O VAL A1203 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 33 through 34 Processing sheet with id=AC5, first strand: chain 'B' and resid 70 through 78 removed outlier: 3.511A pdb=" N VAL B 341 " --> pdb=" O LEU B 328 " (cutoff:3.500A) removed outlier: 4.598A 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 90 removed outlier: 3.815A pdb=" N ALA B 315 " --> pdb=" O TYR B 90 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA B 286 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N SER B 271 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 5.235A 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: 4.497A pdb=" N ALA B 150 " --> pdb=" O ILE B 300 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 115 through 116 removed outlier: 4.497A pdb=" N ALA B 150 " --> pdb=" O ILE B 300 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 156 through 159 removed outlier: 4.443A pdb=" N SER B 156 " --> pdb=" O PHE B 169 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 210 through 211 removed outlier: 6.541A 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 367 removed outlier: 3.537A pdb=" N VAL B 367 " --> pdb=" O LEU B 663 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU B 663 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 377 through 380 removed outlier: 4.657A pdb=" N TYR B 652 " --> pdb=" O CYS B 624 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ILE B 643 " --> pdb=" O VAL B 655 " (cutoff:3.500A) removed outlier: 6.415A 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: 6.213A 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: 3.603A pdb=" N SER B 444 " --> pdb=" O GLN B 580 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N THR B 487 " --> pdb=" O VAL B 424 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N VAL B 424 " --> pdb=" O THR B 487 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 518 through 519 removed outlier: 6.534A pdb=" N VAL B 561 " --> pdb=" O SER B 504 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N CYS B 506 " --> pdb=" O VAL B 559 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL B 559 " --> pdb=" O CYS B 506 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ARG B 508 " --> pdb=" O ILE B 557 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ILE B 557 " --> pdb=" O ARG B 508 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY B 556 " --> pdb=" O LEU B 549 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 518 through 519 removed outlier: 6.534A pdb=" N VAL B 561 " --> pdb=" O SER B 504 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N CYS B 506 " --> pdb=" O VAL B 559 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL B 559 " --> pdb=" O CYS B 506 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ARG B 508 " --> pdb=" O ILE B 557 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ILE B 557 " --> pdb=" O ARG B 508 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP B 543 " --> pdb=" O GLY B 562 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR H 99 " --> pdb=" O TYR H 100F" (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 722 through 729 removed outlier: 6.523A pdb=" N VAL B 723 " --> pdb=" O LEU B 755 " (cutoff:3.500A) removed outlier: 8.791A pdb=" N THR B 757 " --> pdb=" O VAL B 723 " (cutoff:3.500A) removed outlier: 10.621A pdb=" N SER B 725 " --> pdb=" O THR B 757 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 764 through 765 removed outlier: 5.959A pdb=" N GLN B 764 " --> pdb=" O SER C 854 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'B' and resid 1117 through 1126 removed outlier: 6.327A pdb=" N HIS B1118 " --> pdb=" O TYR B1137 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N TYR B1137 " --> pdb=" O HIS B1118 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N PHE B1168 " --> pdb=" O ALA B1148 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 1117 through 1126 removed outlier: 6.327A pdb=" N HIS B1118 " --> pdb=" O TYR B1137 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N TYR B1137 " --> pdb=" O HIS B1118 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N GLY B1129 " --> pdb=" O GLN B 792 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N GLN B 792 " --> pdb=" O GLY B1129 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N TYR B1131 " --> pdb=" O TYR B 790 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N TYR B 790 " --> pdb=" O TYR B1131 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N PHE B1133 " --> pdb=" O GLN B 788 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLN B 788 " --> pdb=" O PHE B1133 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL B1135 " --> pdb=" O ILE B 786 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE B 786 " --> pdb=" O VAL B1135 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N TYR B1137 " --> pdb=" O PHE B 784 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N PHE B 784 " --> pdb=" O TYR B1137 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N PHE B 782 " --> pdb=" O PRO B1139 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ASN B1141 " --> pdb=" O THR B 780 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE C 963 " --> pdb=" O GLN B 777 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 797 through 799 removed outlier: 4.506A pdb=" N LYS B 797 " --> pdb=" O LEU B 931 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 861 through 862 Processing sheet with id=AE5, first strand: chain 'B' and resid 1200 through 1203 removed outlier: 3.873A pdb=" N CYS B1160 " --> pdb=" O VAL B1203 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 33 through 34 Processing sheet with id=AE7, first strand: chain 'C' and resid 70 through 79 removed outlier: 6.504A pdb=" N VAL C 267 " --> pdb=" O THR C 287 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N THR C 287 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LEU C 269 " --> pdb=" O PHE C 285 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 86 through 89 removed outlier: 4.579A pdb=" N ARG C 339 " --> pdb=" O ASP C 330 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 115 through 116 removed outlier: 4.590A pdb=" N ALA C 150 " --> pdb=" O ILE C 300 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 115 through 116 removed outlier: 4.590A pdb=" N ALA C 150 " --> pdb=" O ILE C 300 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 156 through 159 removed outlier: 4.522A pdb=" N SER C 156 " --> pdb=" O PHE C 169 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG C 167 " --> pdb=" O GLY C 158 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 210 through 211 removed outlier: 6.724A pdb=" N VAL C 210 " --> pdb=" O SER C 303 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'C' and resid 363 through 367 removed outlier: 4.512A pdb=" N LEU C 663 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 385 through 386 removed outlier: 6.287A pdb=" N VAL C 385 " --> pdb=" O ASN C 412 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N CYS C 589 " --> pdb=" O CYS C 411 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 404 through 408 removed outlier: 7.329A pdb=" N THR C 481 " --> pdb=" O CYS C 429 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N CYS C 429 " --> pdb=" O THR C 481 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ARG C 483 " --> pdb=" O PHE C 427 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N PHE C 427 " --> pdb=" O ARG C 483 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N PHE C 485 " --> pdb=" O ASN C 425 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 517 through 519 removed outlier: 5.433A pdb=" N SER C 501 " --> pdb=" O THR C 565 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N THR C 565 " --> pdb=" O SER C 501 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ILE C 503 " --> pdb=" O SER C 563 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N SER C 563 " --> pdb=" O ILE C 503 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 722 through 729 removed outlier: 6.599A pdb=" N VAL C 723 " --> pdb=" O LEU C 755 " (cutoff:3.500A) removed outlier: 8.905A pdb=" N THR C 757 " --> pdb=" O VAL C 723 " (cutoff:3.500A) removed outlier: 10.830A pdb=" N SER C 725 " --> pdb=" O THR C 757 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 774 through 792 removed outlier: 6.812A pdb=" N ASN C1141 " --> pdb=" O THR C 780 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N PHE C 782 " --> pdb=" O PRO C1139 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N PHE C 784 " --> pdb=" O TYR C1137 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N TYR C1137 " --> pdb=" O PHE C 784 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE C 786 " --> pdb=" O VAL C1135 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL C1135 " --> pdb=" O ILE C 786 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLN C 788 " --> pdb=" O PHE C1133 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N PHE C1133 " --> pdb=" O GLN C 788 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N TYR C 790 " --> pdb=" O TYR C1131 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N TYR C1131 " --> pdb=" O TYR C 790 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLN C 792 " --> pdb=" O GLY C1129 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N GLY C1129 " --> pdb=" O GLN C 792 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N GLY C1129 " --> pdb=" O ASN C1125 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ASN C1125 " --> pdb=" O GLY C1129 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N TYR C1131 " --> pdb=" O VAL C1123 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N VAL C1123 " --> pdb=" O TYR C1131 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N PHE C1133 " --> pdb=" O SER C1121 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N SER C1121 " --> pdb=" O PHE C1133 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N VAL C1135 " --> pdb=" O ILE C1119 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR C1117 " --> pdb=" O TYR C1137 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 774 through 792 removed outlier: 6.812A pdb=" N ASN C1141 " --> pdb=" O THR C 780 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N PHE C 782 " --> pdb=" O PRO C1139 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N PHE C 784 " --> pdb=" O TYR C1137 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N TYR C1137 " --> pdb=" O PHE C 784 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE C 786 " --> pdb=" O VAL C1135 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL C1135 " --> pdb=" O ILE C 786 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLN C 788 " --> pdb=" O PHE C1133 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N PHE C1133 " --> pdb=" O GLN C 788 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N TYR C 790 " --> pdb=" O TYR C1131 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N TYR C1131 " --> pdb=" O TYR C 790 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLN C 792 " --> pdb=" O GLY C1129 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N GLY C1129 " --> pdb=" O GLN C 792 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N PHE C1168 " --> pdb=" O ALA C1148 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N GLY C1186 " --> pdb=" O ASN C1191 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N ASN C1191 " --> pdb=" O GLY C1186 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 798 through 800 Processing sheet with id=AG3, first strand: chain 'C' and resid 861 through 862 Processing sheet with id=AG4, first strand: chain 'C' and resid 1200 through 1203 removed outlier: 4.047A pdb=" N CYS C1160 " --> pdb=" O VAL C1203 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'H' and resid 4 through 7 removed outlier: 3.613A pdb=" N LEU H 5 " --> pdb=" O ALA H 23 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AG7, first strand: chain 'H' and resid 57 through 59 removed outlier: 5.175A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'L' and resid 5 through 6 removed outlier: 12.152A pdb=" N CYS L 23 " --> pdb=" O THR L 74 " (cutoff:3.500A) removed outlier: 11.051A pdb=" N THR L 74 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 11.431A pdb=" N ALA L 25 " --> pdb=" O SER L 72 " (cutoff:3.500A) removed outlier: 11.544A pdb=" N SER L 72 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 10.636A pdb=" N GLN L 27 " --> pdb=" O GLU L 70 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N GLU L 70 " --> pdb=" O GLN L 27 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY L 68 " --> pdb=" O VAL L 29 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'L' and resid 45 through 48 removed outlier: 6.372A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 1208 hydrogen bonds defined for protein. 3231 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: 13.92 Time building geometry restraints manager: 8.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9064 1.34 - 1.46: 7200 1.46 - 1.58: 12683 1.58 - 1.70: 2 1.70 - 1.82: 225 Bond restraints: 29174 Sorted by residual: bond pdb=" C1 MAN t 5 " pdb=" O5 MAN t 5 " ideal model delta sigma weight residual 1.399 1.482 -0.083 2.00e-02 2.50e+03 1.70e+01 bond pdb=" C1 NAG Q 1 " pdb=" O5 NAG Q 1 " ideal model delta sigma weight residual 1.406 1.478 -0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" CA VAL H 2 " pdb=" CB VAL H 2 " ideal model delta sigma weight residual 1.537 1.580 -0.044 1.21e-02 6.83e+03 1.30e+01 bond pdb=" C1 MAN t 5 " pdb=" C2 MAN t 5 " ideal model delta sigma weight residual 1.526 1.586 -0.060 2.00e-02 2.50e+03 9.03e+00 bond pdb=" C5 MAN t 5 " pdb=" O5 MAN t 5 " ideal model delta sigma weight residual 1.418 1.477 -0.059 2.00e-02 2.50e+03 8.56e+00 ... (remaining 29169 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 38533 1.32 - 2.64: 898 2.64 - 3.96: 199 3.96 - 5.28: 23 5.28 - 6.60: 14 Bond angle restraints: 39667 Sorted by residual: angle pdb=" C ASN A 170 " pdb=" CA ASN A 170 " pdb=" CB ASN A 170 " ideal model delta sigma weight residual 115.79 111.23 4.56 1.19e+00 7.06e-01 1.47e+01 angle pdb=" CB GLN H 3 " pdb=" CG GLN H 3 " pdb=" CD GLN H 3 " ideal model delta sigma weight residual 112.60 119.11 -6.51 1.70e+00 3.46e-01 1.47e+01 angle pdb=" OE1 GLN H 3 " pdb=" CD GLN H 3 " pdb=" NE2 GLN H 3 " ideal model delta sigma weight residual 122.60 118.86 3.74 1.00e+00 1.00e+00 1.40e+01 angle pdb=" CA VAL H 2 " pdb=" CB VAL H 2 " pdb=" CG1 VAL H 2 " ideal model delta sigma weight residual 110.40 116.34 -5.94 1.70e+00 3.46e-01 1.22e+01 angle pdb=" N ILE C 849 " pdb=" CA ILE C 849 " pdb=" C ILE C 849 " ideal model delta sigma weight residual 111.91 109.26 2.65 8.90e-01 1.26e+00 8.88e+00 ... (remaining 39662 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.33: 17431 24.33 - 48.65: 470 48.65 - 72.98: 75 72.98 - 97.31: 29 97.31 - 121.63: 43 Dihedral angle restraints: 18048 sinusoidal: 7648 harmonic: 10400 Sorted by residual: dihedral pdb=" C2 FUC Q 3 " pdb=" C1 FUC Q 3 " pdb=" O5 FUC Q 3 " pdb=" C5 FUC Q 3 " ideal model delta sinusoidal sigma weight residual 57.68 -63.95 121.63 1 3.00e+01 1.11e-03 1.63e+01 dihedral pdb=" C2 MAN t 4 " pdb=" C1 MAN t 4 " pdb=" O5 MAN t 4 " pdb=" C5 MAN t 4 " ideal model delta sinusoidal sigma weight residual -57.62 61.85 -119.47 1 3.00e+01 1.11e-03 1.59e+01 dihedral pdb=" C1 NAG Q 1 " pdb=" C5 NAG Q 1 " pdb=" O5 NAG Q 1 " pdb=" C4 NAG Q 1 " ideal model delta sinusoidal sigma weight residual -64.11 53.83 -117.94 1 3.00e+01 1.11e-03 1.57e+01 ... (remaining 18045 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 4396 0.101 - 0.202: 171 0.202 - 0.303: 3 0.303 - 0.404: 1 0.404 - 0.505: 2 Chirality restraints: 4573 Sorted by residual: chirality pdb=" C1 NAG A1303 " pdb=" ND2 ASN A 159 " pdb=" C2 NAG A1303 " pdb=" O5 NAG A1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-01 2.50e+01 6.37e+00 chirality pdb=" C1 NAG 5 1 " pdb=" ND2 ASN C 866 " pdb=" C2 NAG 5 1 " pdb=" O5 NAG 5 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.82e+00 chirality pdb=" C1 NAG A1304 " pdb=" ND2 ASN A 170 " pdb=" C2 NAG A1304 " pdb=" O5 NAG A1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.82e+00 ... (remaining 4570 not shown) Planarity restraints: 5112 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1302 " 0.337 2.00e-02 2.50e+03 2.92e-01 1.07e+03 pdb=" C7 NAG A1302 " -0.078 2.00e-02 2.50e+03 pdb=" C8 NAG A1302 " 0.099 2.00e-02 2.50e+03 pdb=" N2 NAG A1302 " -0.520 2.00e-02 2.50e+03 pdb=" O7 NAG A1302 " 0.163 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A 61 " -0.029 5.00e-02 4.00e+02 4.44e-02 3.16e+00 pdb=" N PRO A 62 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 62 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 62 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR C 61 " 0.029 5.00e-02 4.00e+02 4.34e-02 3.01e+00 pdb=" N PRO C 62 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO C 62 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 62 " 0.024 5.00e-02 4.00e+02 ... (remaining 5109 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 931 2.71 - 3.26: 27837 3.26 - 3.81: 45340 3.81 - 4.35: 57766 4.35 - 4.90: 98573 Nonbonded interactions: 230447 Sorted by model distance: nonbonded pdb=" OG SER L 7 " pdb=" OG SER L 22 " model vdw 2.167 3.040 nonbonded pdb=" OG SER A 384 " pdb=" OD1 ASN A 412 " model vdw 2.181 3.040 nonbonded pdb=" O ASN C 532 " pdb=" O6 NAG A1304 " model vdw 2.208 3.040 nonbonded pdb=" OE1 GLN C 788 " pdb=" OH TYR C1131 " model vdw 2.213 3.040 nonbonded pdb=" OD1 ASP C 109 " pdb=" OG1 THR C 112 " model vdw 2.218 3.040 ... (remaining 230442 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 '1' selection = chain 'Q' selection = chain 'h' } ncs_group { reference = chain '5' selection = chain '7' selection = chain 'E' selection = chain 'K' selection = chain 'U' selection = chain 'X' selection = chain 'c' selection = chain 'f' selection = chain 'l' selection = chain 'n' selection = chain 'p' selection = chain 'y' } ncs_group { reference = (chain 'A' and (resid 18 through 591 or resid 596 through 1222 or resid 1301 thr \ ough 1304)) selection = (chain 'B' and (resid 18 through 253 or resid 257 through 591 or resid 596 throu \ gh 1222 or resid 1301 through 1304)) selection = chain 'C' } 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: 2.690 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: 0.030 Extract box with map and model: 1.140 Check model and map are aligned: 0.220 Set scattering table: 0.260 Process input model: 67.820 Find NCS groups from input model: 1.760 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 29281 Z= 0.176 Angle : 0.537 15.306 39937 Z= 0.257 Chirality : 0.044 0.505 4573 Planarity : 0.006 0.292 5078 Dihedral : 13.233 121.632 11263 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.03 % Allowed : 5.36 % Favored : 92.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.14), residues: 3538 helix: 0.21 (0.19), residues: 705 sheet: 0.24 (0.18), residues: 838 loop : -0.45 (0.13), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 47 HIS 0.004 0.001 HIS L 49 PHE 0.014 0.001 PHE B 285 TYR 0.015 0.001 TYR L 89 ARG 0.003 0.000 ARG B1084 Details of bonding type rmsd link_NAG-ASN : bond 0.00436 ( 34) link_NAG-ASN : angle 2.82606 ( 102) link_ALPHA1-6 : bond 0.01900 ( 1) link_ALPHA1-6 : angle 2.72602 ( 3) link_BETA1-4 : bond 0.00769 ( 17) link_BETA1-4 : angle 2.52387 ( 51) link_ALPHA1-3 : bond 0.00451 ( 1) link_ALPHA1-3 : angle 1.91601 ( 3) hydrogen bonds : bond 0.24760 ( 1122) hydrogen bonds : angle 8.83930 ( 3231) link_BETA1-6 : bond 0.00439 ( 3) link_BETA1-6 : angle 1.43333 ( 9) SS BOND : bond 0.00222 ( 51) SS BOND : angle 0.71328 ( 102) covalent geometry : bond 0.00374 (29174) covalent geometry : angle 0.50906 (39667) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1046 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 983 time to evaluate : 3.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8405 (mtpp) cc_final: 0.8092 (mtpp) REVERT: A 86 GLU cc_start: 0.6867 (mt-10) cc_final: 0.6660 (mt-10) REVERT: A 112 THR cc_start: 0.8113 (m) cc_final: 0.7655 (p) REVERT: A 233 LYS cc_start: 0.8250 (mtmt) cc_final: 0.8012 (mtmt) REVERT: A 296 TYR cc_start: 0.8120 (m-80) cc_final: 0.7740 (m-80) REVERT: A 346 ASP cc_start: 0.7798 (p0) cc_final: 0.7512 (p0) REVERT: A 347 ASP cc_start: 0.7417 (m-30) cc_final: 0.7049 (p0) REVERT: A 348 LEU cc_start: 0.8450 (tp) cc_final: 0.8169 (tp) REVERT: A 386 GLU cc_start: 0.6597 (mm-30) cc_final: 0.6236 (mm-30) REVERT: A 412 ASN cc_start: 0.7814 (m110) cc_final: 0.7323 (m-40) REVERT: A 430 ASP cc_start: 0.7667 (p0) cc_final: 0.7404 (p0) REVERT: A 456 MET cc_start: 0.7745 (OUTLIER) cc_final: 0.7168 (mmt) REVERT: A 460 MET cc_start: 0.8503 (OUTLIER) cc_final: 0.8238 (mtp) REVERT: A 518 THR cc_start: 0.7667 (m) cc_final: 0.7387 (t) REVERT: A 528 SER cc_start: 0.8378 (t) cc_final: 0.8159 (p) REVERT: A 545 PHE cc_start: 0.8412 (m-80) cc_final: 0.7864 (m-80) REVERT: A 557 ILE cc_start: 0.7878 (mt) cc_final: 0.7669 (mm) REVERT: A 570 THR cc_start: 0.7640 (p) cc_final: 0.7432 (t) REVERT: A 613 TYR cc_start: 0.8491 (m-80) cc_final: 0.7874 (m-80) REVERT: A 681 VAL cc_start: 0.8222 (OUTLIER) cc_final: 0.7900 (m) REVERT: A 724 ASN cc_start: 0.6645 (t0) cc_final: 0.6377 (p0) REVERT: A 743 VAL cc_start: 0.8596 (t) cc_final: 0.8241 (m) REVERT: A 800 VAL cc_start: 0.8375 (m) cc_final: 0.8171 (t) REVERT: A 803 LYS cc_start: 0.8198 (ttmm) cc_final: 0.7871 (ttmm) REVERT: A 884 SER cc_start: 0.8040 (p) cc_final: 0.7482 (p) REVERT: A 888 ASP cc_start: 0.7245 (m-30) cc_final: 0.6769 (m-30) REVERT: A 893 LYS cc_start: 0.8509 (tppt) cc_final: 0.8151 (tppp) REVERT: A 910 LYS cc_start: 0.7548 (mtpt) cc_final: 0.7348 (mtpt) REVERT: A 929 LYS cc_start: 0.8078 (ttpt) cc_final: 0.7814 (ttpp) REVERT: A 963 PHE cc_start: 0.8041 (m-80) cc_final: 0.7615 (m-80) REVERT: A 974 TYR cc_start: 0.7784 (m-10) cc_final: 0.7477 (m-10) REVERT: A 976 MET cc_start: 0.8346 (mtp) cc_final: 0.8111 (mtm) REVERT: A 982 THR cc_start: 0.7937 (m) cc_final: 0.7614 (p) REVERT: A 996 LYS cc_start: 0.8327 (mmtp) cc_final: 0.8119 (mmmt) REVERT: A 997 PHE cc_start: 0.7985 (t80) cc_final: 0.7783 (t80) REVERT: A 1052 LYS cc_start: 0.7752 (ttpp) cc_final: 0.7489 (ttpp) REVERT: A 1053 ARG cc_start: 0.7915 (mmm-85) cc_final: 0.7588 (mtt180) REVERT: A 1121 SER cc_start: 0.8246 (t) cc_final: 0.7955 (m) REVERT: A 1143 VAL cc_start: 0.8131 (OUTLIER) cc_final: 0.7899 (m) REVERT: A 1144 ASN cc_start: 0.7513 (OUTLIER) cc_final: 0.7300 (p0) REVERT: A 1168 PHE cc_start: 0.8164 (m-10) cc_final: 0.7959 (m-10) REVERT: A 1195 ILE cc_start: 0.8441 (mm) cc_final: 0.8015 (mt) REVERT: A 1201 ARG cc_start: 0.7351 (ttp80) cc_final: 0.7128 (ttt-90) REVERT: A 1207 VAL cc_start: 0.7874 (m) cc_final: 0.7632 (t) REVERT: A 1208 LYS cc_start: 0.7877 (ptpp) cc_final: 0.7665 (ptpp) REVERT: B 19 VAL cc_start: 0.7545 (t) cc_final: 0.7307 (m) REVERT: B 44 ASN cc_start: 0.6910 (t0) cc_final: 0.6429 (t0) REVERT: B 65 LYS cc_start: 0.7756 (mtmm) cc_final: 0.7547 (mttm) REVERT: B 86 GLU cc_start: 0.7330 (tp30) cc_final: 0.7128 (tp30) REVERT: B 147 ILE cc_start: 0.7867 (tt) cc_final: 0.7646 (mp) REVERT: B 236 PHE cc_start: 0.8098 (m-80) cc_final: 0.7728 (m-80) REVERT: B 239 GLN cc_start: 0.7965 (pt0) cc_final: 0.7763 (pt0) REVERT: B 281 ASN cc_start: 0.7813 (m110) cc_final: 0.7602 (m-40) REVERT: B 333 VAL cc_start: 0.8549 (t) cc_final: 0.8276 (m) REVERT: B 334 ASP cc_start: 0.7888 (p0) cc_final: 0.7588 (p0) REVERT: B 367 VAL cc_start: 0.8342 (t) cc_final: 0.7939 (m) REVERT: B 425 ASN cc_start: 0.7974 (t0) cc_final: 0.7650 (t0) REVERT: B 442 TYR cc_start: 0.8389 (OUTLIER) cc_final: 0.7867 (p90) REVERT: B 459 TYR cc_start: 0.8303 (m-80) cc_final: 0.7937 (m-80) REVERT: B 491 ASN cc_start: 0.7351 (t0) cc_final: 0.7093 (t0) REVERT: B 492 LEU cc_start: 0.8190 (mt) cc_final: 0.7944 (mp) REVERT: B 498 SER cc_start: 0.8640 (t) cc_final: 0.8184 (p) REVERT: B 515 HIS cc_start: 0.7507 (p90) cc_final: 0.7217 (p90) REVERT: B 516 ILE cc_start: 0.8682 (mt) cc_final: 0.8241 (mm) REVERT: B 591 MET cc_start: 0.7083 (mmt) cc_final: 0.6825 (mmt) REVERT: B 592 MET cc_start: 0.5636 (mmm) cc_final: 0.5402 (mmm) REVERT: B 609 GLU cc_start: 0.6822 (tp30) cc_final: 0.6518 (tp30) REVERT: B 624 CYS cc_start: 0.6199 (m) cc_final: 0.5957 (m) REVERT: B 651 ASN cc_start: 0.7597 (m-40) cc_final: 0.7368 (m110) REVERT: B 656 ARG cc_start: 0.7419 (mmm160) cc_final: 0.7181 (mtp85) REVERT: B 672 ASN cc_start: 0.7908 (t0) cc_final: 0.7569 (t0) REVERT: B 681 VAL cc_start: 0.8609 (OUTLIER) cc_final: 0.8277 (p) REVERT: B 684 GLU cc_start: 0.6754 (tm-30) cc_final: 0.6423 (tm-30) REVERT: B 817 LEU cc_start: 0.8284 (tp) cc_final: 0.7974 (tt) REVERT: B 819 GLU cc_start: 0.7093 (mm-30) cc_final: 0.6892 (mm-30) REVERT: B 826 LYS cc_start: 0.7941 (mttm) cc_final: 0.7709 (mptm) REVERT: B 839 ASP cc_start: 0.7240 (m-30) cc_final: 0.7028 (m-30) REVERT: B 844 ASN cc_start: 0.7668 (t0) cc_final: 0.7158 (t0) REVERT: B 850 LYS cc_start: 0.8081 (ttmt) cc_final: 0.7871 (ttmt) REVERT: B 881 SER cc_start: 0.8235 (t) cc_final: 0.7956 (p) REVERT: B 925 VAL cc_start: 0.8332 (t) cc_final: 0.8072 (m) REVERT: B 939 MET cc_start: 0.7920 (ttm) cc_final: 0.7681 (mtp) REVERT: B 943 TYR cc_start: 0.8471 (m-80) cc_final: 0.8190 (m-80) REVERT: B 1058 GLU cc_start: 0.7272 (tt0) cc_final: 0.7041 (tt0) REVERT: B 1085 SER cc_start: 0.8496 (t) cc_final: 0.8151 (p) REVERT: B 1086 GLU cc_start: 0.7474 (mt-10) cc_final: 0.7210 (mt-10) REVERT: B 1094 LEU cc_start: 0.8319 (tp) cc_final: 0.8111 (tt) REVERT: B 1098 LYS cc_start: 0.7816 (mttm) cc_final: 0.7535 (mttp) REVERT: B 1183 TYR cc_start: 0.8159 (m-80) cc_final: 0.7784 (m-80) REVERT: B 1208 LYS cc_start: 0.7791 (ptpt) cc_final: 0.7238 (ptpt) REVERT: B 1210 GLU cc_start: 0.7455 (mm-30) cc_final: 0.7203 (tp30) REVERT: C 49 MET cc_start: 0.7916 (tpt) cc_final: 0.7600 (tpp) REVERT: C 80 LYS cc_start: 0.8269 (mtmt) cc_final: 0.8048 (mttm) REVERT: C 171 HIS cc_start: 0.8242 (m-70) cc_final: 0.7959 (m90) REVERT: C 174 LEU cc_start: 0.8435 (mm) cc_final: 0.8235 (mt) REVERT: C 192 GLU cc_start: 0.7601 (tt0) cc_final: 0.7205 (tt0) REVERT: C 228 THR cc_start: 0.7675 (p) cc_final: 0.7092 (p) REVERT: C 282 MET cc_start: 0.8846 (mtm) cc_final: 0.8613 (mtp) REVERT: C 338 ARG cc_start: 0.7531 (mtt-85) cc_final: 0.7322 (mpt180) REVERT: C 347 ASP cc_start: 0.7781 (t0) cc_final: 0.7492 (t0) REVERT: C 350 GLN cc_start: 0.6911 (tp40) cc_final: 0.6574 (tp40) REVERT: C 372 VAL cc_start: 0.8081 (OUTLIER) cc_final: 0.7816 (p) REVERT: C 377 GLN cc_start: 0.7834 (tt0) cc_final: 0.7513 (tt0) REVERT: C 380 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7363 (mt-10) REVERT: C 381 GLN cc_start: 0.7278 (OUTLIER) cc_final: 0.6874 (mp10) REVERT: C 412 ASN cc_start: 0.7359 (m110) cc_final: 0.6966 (m110) REVERT: C 423 MET cc_start: 0.7700 (tpt) cc_final: 0.7268 (tpt) REVERT: C 539 SER cc_start: 0.8138 (m) cc_final: 0.7858 (p) REVERT: C 540 GLN cc_start: 0.7363 (mt0) cc_final: 0.6957 (mt0) REVERT: C 543 ASP cc_start: 0.7671 (m-30) cc_final: 0.7411 (m-30) REVERT: C 608 VAL cc_start: 0.7855 (m) cc_final: 0.7645 (t) REVERT: C 613 TYR cc_start: 0.8253 (m-80) cc_final: 0.7726 (m-80) REVERT: C 622 ILE cc_start: 0.8037 (mm) cc_final: 0.7812 (mp) REVERT: C 636 TYR cc_start: 0.8071 (m-80) cc_final: 0.7850 (m-80) REVERT: C 651 ASN cc_start: 0.7976 (m110) cc_final: 0.7401 (m-40) REVERT: C 653 TYR cc_start: 0.8010 (m-80) cc_final: 0.7667 (m-80) REVERT: C 668 ASP cc_start: 0.8060 (t70) cc_final: 0.7834 (t0) REVERT: C 672 ASN cc_start: 0.7831 (t0) cc_final: 0.7438 (t0) REVERT: C 803 LYS cc_start: 0.8041 (ttpp) cc_final: 0.7741 (ttmt) REVERT: C 811 GLN cc_start: 0.7414 (mt0) cc_final: 0.7194 (mt0) REVERT: C 814 GLU cc_start: 0.6989 (mt-10) cc_final: 0.6708 (mm-30) REVERT: C 816 LEU cc_start: 0.7956 (mp) cc_final: 0.7412 (mt) REVERT: C 836 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7930 (tp) REVERT: C 840 GLU cc_start: 0.7590 (mt-10) cc_final: 0.7389 (mt-10) REVERT: C 871 GLN cc_start: 0.7512 (mt0) cc_final: 0.7072 (mt0) REVERT: C 887 GLU cc_start: 0.7590 (tt0) cc_final: 0.7362 (tt0) REVERT: C 906 ASP cc_start: 0.8289 (m-30) cc_final: 0.8085 (m-30) REVERT: C 909 MET cc_start: 0.7299 (mtp) cc_final: 0.6944 (mtp) REVERT: C 910 LYS cc_start: 0.8168 (mtpt) cc_final: 0.7782 (mttp) REVERT: C 929 LYS cc_start: 0.7594 (ttpt) cc_final: 0.7348 (ttmt) REVERT: C 939 MET cc_start: 0.8021 (ttm) cc_final: 0.7714 (ttt) REVERT: C 945 SER cc_start: 0.8005 (m) cc_final: 0.7720 (p) REVERT: C 950 SER cc_start: 0.8066 (p) cc_final: 0.7817 (m) REVERT: C 984 GLN cc_start: 0.7503 (tt0) cc_final: 0.7175 (tt0) REVERT: C 1035 GLU cc_start: 0.7363 (tp30) cc_final: 0.7149 (tp30) REVERT: C 1060 GLU cc_start: 0.7755 (mp0) cc_final: 0.7060 (mp0) REVERT: C 1064 ASP cc_start: 0.7603 (m-30) cc_final: 0.7307 (m-30) REVERT: C 1086 GLU cc_start: 0.7515 (mt-10) cc_final: 0.7240 (mt-10) REVERT: C 1101 GLU cc_start: 0.7532 (mm-30) cc_final: 0.7049 (mm-30) REVERT: C 1108 LYS cc_start: 0.8169 (mmmt) cc_final: 0.7848 (mtmm) REVERT: C 1125 ASN cc_start: 0.8376 (m-40) cc_final: 0.7930 (m-40) REVERT: C 1197 MET cc_start: 0.8137 (mmm) cc_final: 0.7887 (mmm) REVERT: C 1201 ARG cc_start: 0.7327 (ptp90) cc_final: 0.6835 (ptp90) REVERT: C 1206 ASP cc_start: 0.7554 (t0) cc_final: 0.7133 (t0) REVERT: L 67 SER cc_start: 0.7634 (t) cc_final: 0.7371 (m) outliers start: 63 outliers final: 18 residues processed: 1012 average time/residue: 1.1022 time to fit residues: 1345.5222 Evaluate side-chains 840 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 812 time to evaluate : 3.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 442 TYR Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1144 ASN Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain B residue 442 TYR Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 888 ASP Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 381 GLN Chi-restraints excluded: chain C residue 515 HIS Chi-restraints excluded: chain C residue 573 MET Chi-restraints excluded: chain C residue 624 CYS Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain L residue 101 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 302 optimal weight: 5.9990 chunk 271 optimal weight: 3.9990 chunk 150 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 183 optimal weight: 0.6980 chunk 144 optimal weight: 2.9990 chunk 280 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 170 optimal weight: 3.9990 chunk 208 optimal weight: 1.9990 chunk 325 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 87 GLN A 350 GLN A 461 GLN ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 GLN A 548 GLN A 611 ASN A 691 HIS A 733 GLN A 792 GLN A 871 GLN A 923 GLN A 995 ASN B 119 ASN B 262 GLN B 410 ASN B 412 ASN B 461 GLN B 580 GLN B 611 ASN B 641 ASN B 685 HIS B 731 ASN B 733 GLN ** B 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 GLN B 822 GLN B 838 GLN B 858 ASN B 938 ASN B 989 ASN B 998 ASN B1059 GLN B1125 ASN C 87 GLN C 263 ASN C 268 HIS C 461 GLN C 472 ASN ** C 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 631 GLN C 641 ASN C 752 GLN C 804 GLN C 815 GLN C 835 ASN C 892 ASN C 970 GLN C 983 GLN C 984 GLN C1012 ASN C1027 GLN C1141 ASN C1214 ASN Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.147220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.125593 restraints weight = 41127.060| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.87 r_work: 0.3163 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.092 29281 Z= 0.330 Angle : 0.742 14.457 39937 Z= 0.375 Chirality : 0.052 0.479 4573 Planarity : 0.006 0.098 5078 Dihedral : 11.641 116.385 5077 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 5.23 % Allowed : 11.55 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.13), residues: 3538 helix: 0.73 (0.18), residues: 739 sheet: 0.06 (0.17), residues: 888 loop : -0.49 (0.13), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP H 47 HIS 0.010 0.002 HIS L 87 PHE 0.039 0.003 PHE L 97 TYR 0.037 0.003 TYR L 89 ARG 0.009 0.001 ARG A1084 Details of bonding type rmsd link_NAG-ASN : bond 0.00837 ( 34) link_NAG-ASN : angle 3.26490 ( 102) link_ALPHA1-6 : bond 0.01193 ( 1) link_ALPHA1-6 : angle 1.88709 ( 3) link_BETA1-4 : bond 0.00695 ( 17) link_BETA1-4 : angle 2.35642 ( 51) link_ALPHA1-3 : bond 0.00545 ( 1) link_ALPHA1-3 : angle 2.80148 ( 3) hydrogen bonds : bond 0.06277 ( 1122) hydrogen bonds : angle 5.99818 ( 3231) link_BETA1-6 : bond 0.00796 ( 3) link_BETA1-6 : angle 1.70545 ( 9) SS BOND : bond 0.00773 ( 51) SS BOND : angle 1.58292 ( 102) covalent geometry : bond 0.00769 (29174) covalent geometry : angle 0.71565 (39667) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1021 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 859 time to evaluate : 3.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: 0.8462 (mmp) cc_final: 0.8115 (mmm) REVERT: A 55 LYS cc_start: 0.8552 (mtpp) cc_final: 0.8238 (mtpp) REVERT: A 75 GLN cc_start: 0.7755 (mm-40) cc_final: 0.7295 (mm-40) REVERT: A 175 LEU cc_start: 0.8319 (mt) cc_final: 0.8116 (mt) REVERT: A 211 PHE cc_start: 0.8623 (p90) cc_final: 0.8384 (p90) REVERT: A 242 SER cc_start: 0.8350 (OUTLIER) cc_final: 0.8090 (t) REVERT: A 256 GLU cc_start: 0.7996 (tp30) cc_final: 0.7579 (tp30) REVERT: A 296 TYR cc_start: 0.8340 (m-80) cc_final: 0.7784 (m-80) REVERT: A 302 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.6976 (mtp85) REVERT: A 326 THR cc_start: 0.8257 (t) cc_final: 0.7993 (m) REVERT: A 375 ARG cc_start: 0.7527 (mtp85) cc_final: 0.7273 (mtp85) REVERT: A 386 GLU cc_start: 0.6703 (mm-30) cc_final: 0.6328 (mm-30) REVERT: A 412 ASN cc_start: 0.8139 (m110) cc_final: 0.7506 (m-40) REVERT: A 430 ASP cc_start: 0.7803 (p0) cc_final: 0.7535 (p0) REVERT: A 460 MET cc_start: 0.8401 (tpp) cc_final: 0.7997 (mmt) REVERT: A 518 THR cc_start: 0.8103 (m) cc_final: 0.7777 (t) REVERT: A 521 VAL cc_start: 0.8287 (t) cc_final: 0.8042 (m) REVERT: A 539 SER cc_start: 0.8351 (t) cc_final: 0.8118 (m) REVERT: A 606 VAL cc_start: 0.8234 (OUTLIER) cc_final: 0.8021 (p) REVERT: A 613 TYR cc_start: 0.8624 (m-80) cc_final: 0.8115 (m-80) REVERT: A 681 VAL cc_start: 0.8318 (OUTLIER) cc_final: 0.8040 (m) REVERT: A 720 ILE cc_start: 0.8523 (pt) cc_final: 0.8191 (mt) REVERT: A 743 VAL cc_start: 0.8711 (t) cc_final: 0.8351 (m) REVERT: A 776 VAL cc_start: 0.8496 (m) cc_final: 0.8249 (p) REVERT: A 803 LYS cc_start: 0.8325 (ttmm) cc_final: 0.8104 (ttmm) REVERT: A 836 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7899 (tt) REVERT: A 891 PHE cc_start: 0.8272 (m-80) cc_final: 0.7979 (m-80) REVERT: A 893 LYS cc_start: 0.8553 (tppt) cc_final: 0.8241 (tppp) REVERT: A 910 LYS cc_start: 0.7830 (mtpt) cc_final: 0.7507 (mtpt) REVERT: A 982 THR cc_start: 0.8319 (OUTLIER) cc_final: 0.7802 (p) REVERT: A 1052 LYS cc_start: 0.7936 (ttpp) cc_final: 0.7683 (ttpp) REVERT: A 1053 ARG cc_start: 0.8249 (mmm-85) cc_final: 0.7867 (mtt180) REVERT: A 1082 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8305 (tt) REVERT: A 1143 VAL cc_start: 0.8307 (OUTLIER) cc_final: 0.8037 (m) REVERT: A 1144 ASN cc_start: 0.7804 (p0) cc_final: 0.7560 (p0) REVERT: A 1163 PRO cc_start: 0.8386 (Cg_endo) cc_final: 0.8123 (Cg_exo) REVERT: A 1193 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7445 (mt-10) REVERT: A 1195 ILE cc_start: 0.8565 (mm) cc_final: 0.8253 (mt) REVERT: A 1201 ARG cc_start: 0.7798 (ttp80) cc_final: 0.7434 (ttp80) REVERT: A 1208 LYS cc_start: 0.8060 (ptpp) cc_final: 0.7860 (ptpp) REVERT: B 44 ASN cc_start: 0.7145 (t0) cc_final: 0.6540 (t0) REVERT: B 46 GLN cc_start: 0.7504 (mp10) cc_final: 0.7182 (mm-40) REVERT: B 65 LYS cc_start: 0.8037 (mtmm) cc_final: 0.7784 (mttm) REVERT: B 88 TYR cc_start: 0.8441 (m-80) cc_final: 0.7998 (m-80) REVERT: B 112 THR cc_start: 0.8438 (m) cc_final: 0.8114 (p) REVERT: B 114 VAL cc_start: 0.8271 (t) cc_final: 0.8060 (p) REVERT: B 167 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.7621 (ttt-90) REVERT: B 178 ASP cc_start: 0.7249 (t0) cc_final: 0.6741 (t70) REVERT: B 182 THR cc_start: 0.8111 (p) cc_final: 0.7831 (p) REVERT: B 190 VAL cc_start: 0.7878 (OUTLIER) cc_final: 0.7644 (m) REVERT: B 236 PHE cc_start: 0.8249 (m-80) cc_final: 0.7969 (m-80) REVERT: B 423 MET cc_start: 0.7947 (OUTLIER) cc_final: 0.7321 (ttp) REVERT: B 442 TYR cc_start: 0.8529 (OUTLIER) cc_final: 0.7874 (p90) REVERT: B 492 LEU cc_start: 0.8333 (mt) cc_final: 0.8078 (mp) REVERT: B 498 SER cc_start: 0.8613 (t) cc_final: 0.8186 (p) REVERT: B 516 ILE cc_start: 0.8715 (mt) cc_final: 0.8448 (mm) REVERT: B 586 ASN cc_start: 0.8182 (m-40) cc_final: 0.7952 (m110) REVERT: B 591 MET cc_start: 0.7162 (mmt) cc_final: 0.6917 (mmt) REVERT: B 592 MET cc_start: 0.5606 (mmm) cc_final: 0.5350 (mmm) REVERT: B 609 GLU cc_start: 0.7037 (tp30) cc_final: 0.6729 (tp30) REVERT: B 649 ASP cc_start: 0.7344 (p0) cc_final: 0.7062 (p0) REVERT: B 651 ASN cc_start: 0.7819 (m-40) cc_final: 0.7601 (m110) REVERT: B 653 TYR cc_start: 0.8461 (m-10) cc_final: 0.8193 (m-10) REVERT: B 656 ARG cc_start: 0.7914 (mmm160) cc_final: 0.7667 (mmm160) REVERT: B 672 ASN cc_start: 0.7992 (t0) cc_final: 0.7695 (t0) REVERT: B 676 THR cc_start: 0.8186 (OUTLIER) cc_final: 0.7799 (p) REVERT: B 681 VAL cc_start: 0.8480 (OUTLIER) cc_final: 0.8216 (p) REVERT: B 684 GLU cc_start: 0.7200 (tm-30) cc_final: 0.6856 (tm-30) REVERT: B 691 HIS cc_start: 0.6012 (OUTLIER) cc_final: 0.5801 (m-70) REVERT: B 736 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8164 (mm) REVERT: B 775 VAL cc_start: 0.8560 (t) cc_final: 0.8352 (p) REVERT: B 803 LYS cc_start: 0.8509 (ttmm) cc_final: 0.8201 (ttpt) REVERT: B 817 LEU cc_start: 0.8277 (tp) cc_final: 0.7952 (tt) REVERT: B 826 LYS cc_start: 0.8346 (mttm) cc_final: 0.8066 (mtpm) REVERT: B 844 ASN cc_start: 0.7835 (t0) cc_final: 0.7153 (t0) REVERT: B 850 LYS cc_start: 0.8204 (ttmt) cc_final: 0.8002 (ttmt) REVERT: B 884 SER cc_start: 0.8356 (m) cc_final: 0.7879 (t) REVERT: B 925 VAL cc_start: 0.8327 (t) cc_final: 0.8058 (m) REVERT: B 991 LYS cc_start: 0.8170 (mtpp) cc_final: 0.7881 (mtpp) REVERT: B 1019 GLN cc_start: 0.8139 (mm110) cc_final: 0.7848 (tp40) REVERT: B 1058 GLU cc_start: 0.7359 (tt0) cc_final: 0.7133 (tt0) REVERT: B 1086 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7608 (mt-10) REVERT: B 1094 LEU cc_start: 0.8290 (tp) cc_final: 0.7977 (tt) REVERT: B 1098 LYS cc_start: 0.8089 (mttm) cc_final: 0.7874 (mttp) REVERT: B 1153 ASN cc_start: 0.7710 (p0) cc_final: 0.7477 (p0) REVERT: B 1169 VAL cc_start: 0.7968 (m) cc_final: 0.7483 (p) REVERT: B 1197 MET cc_start: 0.8470 (tpp) cc_final: 0.8258 (mmm) REVERT: B 1208 LYS cc_start: 0.7952 (ptpt) cc_final: 0.7381 (ptpt) REVERT: C 80 LYS cc_start: 0.8579 (mtmt) cc_final: 0.8334 (mttm) REVERT: C 178 ASP cc_start: 0.7027 (t0) cc_final: 0.6638 (m-30) REVERT: C 238 LEU cc_start: 0.8254 (mt) cc_final: 0.8013 (mp) REVERT: C 258 PHE cc_start: 0.8579 (t80) cc_final: 0.8338 (t80) REVERT: C 302 ARG cc_start: 0.8057 (OUTLIER) cc_final: 0.7621 (ttp80) REVERT: C 338 ARG cc_start: 0.7970 (mtt-85) cc_final: 0.7679 (mtt180) REVERT: C 350 GLN cc_start: 0.7039 (tp40) cc_final: 0.6688 (tp40) REVERT: C 372 VAL cc_start: 0.8058 (OUTLIER) cc_final: 0.7786 (p) REVERT: C 379 ILE cc_start: 0.8439 (mm) cc_final: 0.8158 (mm) REVERT: C 380 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7446 (mt-10) REVERT: C 381 GLN cc_start: 0.7231 (OUTLIER) cc_final: 0.6794 (mp10) REVERT: C 409 THR cc_start: 0.7410 (p) cc_final: 0.7129 (m) REVERT: C 456 MET cc_start: 0.8139 (mmt) cc_final: 0.7127 (mmt) REVERT: C 464 SER cc_start: 0.8231 (OUTLIER) cc_final: 0.7795 (m) REVERT: C 540 GLN cc_start: 0.7984 (mt0) cc_final: 0.7692 (mt0) REVERT: C 543 ASP cc_start: 0.7709 (m-30) cc_final: 0.7497 (m-30) REVERT: C 613 TYR cc_start: 0.8318 (m-80) cc_final: 0.8036 (m-80) REVERT: C 633 ARG cc_start: 0.7893 (ttm170) cc_final: 0.7550 (mtm-85) REVERT: C 653 TYR cc_start: 0.8223 (m-80) cc_final: 0.7806 (m-80) REVERT: C 672 ASN cc_start: 0.8178 (t0) cc_final: 0.7801 (t0) REVERT: C 673 SER cc_start: 0.8400 (p) cc_final: 0.8190 (m) REVERT: C 871 GLN cc_start: 0.7811 (mt0) cc_final: 0.7343 (mt0) REVERT: C 880 TYR cc_start: 0.7757 (m-80) cc_final: 0.7527 (m-80) REVERT: C 939 MET cc_start: 0.8178 (ttm) cc_final: 0.7952 (ttm) REVERT: C 971 SER cc_start: 0.7994 (OUTLIER) cc_final: 0.7501 (p) REVERT: C 972 ILE cc_start: 0.8406 (OUTLIER) cc_final: 0.8124 (mp) REVERT: C 976 MET cc_start: 0.8594 (mtt) cc_final: 0.8390 (mtm) REVERT: C 989 ASN cc_start: 0.8339 (m-40) cc_final: 0.8120 (m-40) REVERT: C 1035 GLU cc_start: 0.7617 (tp30) cc_final: 0.7408 (tp30) REVERT: C 1060 GLU cc_start: 0.7812 (mp0) cc_final: 0.7250 (mp0) REVERT: C 1064 ASP cc_start: 0.7796 (m-30) cc_final: 0.7558 (m-30) REVERT: C 1086 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7432 (mt-10) REVERT: C 1101 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7384 (mm-30) REVERT: C 1108 LYS cc_start: 0.8323 (mmmt) cc_final: 0.8114 (mtmt) REVERT: C 1152 CYS cc_start: 0.6691 (OUTLIER) cc_final: 0.6054 (p) REVERT: C 1189 PHE cc_start: 0.8614 (t80) cc_final: 0.8362 (t80) REVERT: C 1201 ARG cc_start: 0.7577 (ptp90) cc_final: 0.7036 (ptp90) REVERT: H 24 VAL cc_start: 0.8279 (OUTLIER) cc_final: 0.8001 (t) REVERT: L 12 SER cc_start: 0.8032 (t) cc_final: 0.7820 (t) REVERT: L 49 HIS cc_start: 0.7048 (p90) cc_final: 0.6106 (p90) outliers start: 162 outliers final: 65 residues processed: 922 average time/residue: 1.1815 time to fit residues: 1305.4300 Evaluate side-chains 881 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 792 time to evaluate : 3.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 68 SER Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 302 ARG Chi-restraints excluded: chain A residue 327 TYR Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 442 TYR Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 578 SER Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 630 LYS Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain B residue 167 ARG Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 423 MET Chi-restraints excluded: chain B residue 442 TYR Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 691 HIS Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 889 LEU Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 909 MET Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 1080 GLN Chi-restraints excluded: chain B residue 1140 THR Chi-restraints excluded: chain B residue 1146 THR Chi-restraints excluded: chain B residue 1207 VAL Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 302 ARG Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 381 GLN Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 464 SER Chi-restraints excluded: chain C residue 515 HIS Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain C residue 528 SER Chi-restraints excluded: chain C residue 624 CYS Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 671 THR Chi-restraints excluded: chain C residue 685 HIS Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 849 ILE Chi-restraints excluded: chain C residue 962 SER Chi-restraints excluded: chain C residue 971 SER Chi-restraints excluded: chain C residue 972 ILE Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1142 HIS Chi-restraints excluded: chain C residue 1145 VAL Chi-restraints excluded: chain C residue 1152 CYS Chi-restraints excluded: chain C residue 1196 THR Chi-restraints excluded: chain C residue 1221 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 100 CYS Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 50 SER Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 101 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 259 optimal weight: 0.8980 chunk 327 optimal weight: 1.9990 chunk 135 optimal weight: 0.4980 chunk 227 optimal weight: 1.9990 chunk 332 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 305 optimal weight: 0.0970 chunk 226 optimal weight: 4.9990 chunk 299 optimal weight: 5.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 611 ASN A 685 HIS A 892 ASN A 995 ASN A1023 ASN B 281 ASN B 461 GLN B 822 GLN B 838 GLN B 938 ASN B 989 ASN B1125 ASN ** B1215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 ASN C 268 HIS C 402 ASN C 461 GLN C 631 GLN C 641 ASN C 651 ASN C 804 GLN C 838 GLN C 852 HIS C 938 ASN C1141 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.148461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.126825 restraints weight = 41040.585| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.74 r_work: 0.3209 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 29281 Z= 0.148 Angle : 0.619 14.011 39937 Z= 0.305 Chirality : 0.046 0.606 4573 Planarity : 0.004 0.051 5078 Dihedral : 10.130 115.105 5058 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 4.45 % Allowed : 14.55 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.14), residues: 3538 helix: 1.31 (0.19), residues: 736 sheet: 0.25 (0.17), residues: 846 loop : -0.44 (0.13), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 47 HIS 0.005 0.001 HIS B 81 PHE 0.019 0.001 PHE C 243 TYR 0.023 0.001 TYR L 89 ARG 0.006 0.000 ARG C 656 Details of bonding type rmsd link_NAG-ASN : bond 0.00767 ( 34) link_NAG-ASN : angle 3.49430 ( 102) link_ALPHA1-6 : bond 0.01085 ( 1) link_ALPHA1-6 : angle 0.87385 ( 3) link_BETA1-4 : bond 0.00650 ( 17) link_BETA1-4 : angle 2.26300 ( 51) link_ALPHA1-3 : bond 0.00968 ( 1) link_ALPHA1-3 : angle 2.37798 ( 3) hydrogen bonds : bond 0.04943 ( 1122) hydrogen bonds : angle 5.47873 ( 3231) link_BETA1-6 : bond 0.00714 ( 3) link_BETA1-6 : angle 1.48644 ( 9) SS BOND : bond 0.00517 ( 51) SS BOND : angle 1.79242 ( 102) covalent geometry : bond 0.00336 (29174) covalent geometry : angle 0.58213 (39667) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 973 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 835 time to evaluate : 3.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: 0.8389 (mmp) cc_final: 0.8134 (mmm) REVERT: A 55 LYS cc_start: 0.8536 (mtpp) cc_final: 0.8209 (mttp) REVERT: A 75 GLN cc_start: 0.7616 (mm110) cc_final: 0.7261 (mm110) REVERT: A 210 VAL cc_start: 0.8458 (m) cc_final: 0.8202 (t) REVERT: A 211 PHE cc_start: 0.8574 (p90) cc_final: 0.8369 (p90) REVERT: A 242 SER cc_start: 0.8240 (OUTLIER) cc_final: 0.7947 (p) REVERT: A 256 GLU cc_start: 0.7998 (tp30) cc_final: 0.7596 (tp30) REVERT: A 296 TYR cc_start: 0.8262 (m-80) cc_final: 0.7777 (m-80) REVERT: A 386 GLU cc_start: 0.6630 (mm-30) cc_final: 0.6238 (mm-30) REVERT: A 412 ASN cc_start: 0.8065 (m110) cc_final: 0.7343 (m-40) REVERT: A 430 ASP cc_start: 0.7714 (p0) cc_final: 0.7492 (p0) REVERT: A 460 MET cc_start: 0.8409 (tpp) cc_final: 0.8035 (mmt) REVERT: A 505 LYS cc_start: 0.8239 (ttmm) cc_final: 0.7837 (tttm) REVERT: A 518 THR cc_start: 0.8024 (m) cc_final: 0.7772 (t) REVERT: A 521 VAL cc_start: 0.8192 (t) cc_final: 0.7951 (m) REVERT: A 539 SER cc_start: 0.8338 (t) cc_final: 0.8091 (m) REVERT: A 606 VAL cc_start: 0.8190 (m) cc_final: 0.7969 (p) REVERT: A 611 ASN cc_start: 0.7905 (t0) cc_final: 0.7578 (t0) REVERT: A 613 TYR cc_start: 0.8551 (m-80) cc_final: 0.7989 (m-80) REVERT: A 616 SER cc_start: 0.8424 (p) cc_final: 0.8157 (m) REVERT: A 681 VAL cc_start: 0.8241 (OUTLIER) cc_final: 0.7956 (m) REVERT: A 720 ILE cc_start: 0.8522 (pt) cc_final: 0.8169 (mt) REVERT: A 743 VAL cc_start: 0.8660 (t) cc_final: 0.8302 (m) REVERT: A 776 VAL cc_start: 0.8504 (m) cc_final: 0.8255 (p) REVERT: A 784 PHE cc_start: 0.8451 (m-80) cc_final: 0.7955 (m-80) REVERT: A 803 LYS cc_start: 0.8208 (ttmm) cc_final: 0.7985 (ttmm) REVERT: A 812 LYS cc_start: 0.7896 (tppp) cc_final: 0.7642 (mmmm) REVERT: A 836 LEU cc_start: 0.8043 (tp) cc_final: 0.7824 (tt) REVERT: A 891 PHE cc_start: 0.8216 (m-80) cc_final: 0.7921 (m-80) REVERT: A 910 LYS cc_start: 0.7693 (mtpt) cc_final: 0.7391 (mtpt) REVERT: A 963 PHE cc_start: 0.8117 (m-80) cc_final: 0.7719 (m-80) REVERT: A 982 THR cc_start: 0.8246 (OUTLIER) cc_final: 0.7764 (p) REVERT: A 1020 ASP cc_start: 0.7621 (m-30) cc_final: 0.7385 (m-30) REVERT: A 1052 LYS cc_start: 0.7854 (ttpp) cc_final: 0.7608 (ttpp) REVERT: A 1060 GLU cc_start: 0.7516 (mt-10) cc_final: 0.7252 (mp0) REVERT: A 1143 VAL cc_start: 0.8255 (OUTLIER) cc_final: 0.7978 (m) REVERT: A 1144 ASN cc_start: 0.7783 (p0) cc_final: 0.7521 (p0) REVERT: A 1193 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7314 (mt-10) REVERT: A 1201 ARG cc_start: 0.7768 (ttp80) cc_final: 0.7392 (ttp80) REVERT: B 31 LYS cc_start: 0.7900 (mmtm) cc_final: 0.7627 (mmmm) REVERT: B 44 ASN cc_start: 0.7032 (t0) cc_final: 0.6502 (t0) REVERT: B 55 LYS cc_start: 0.8012 (mttp) cc_final: 0.7678 (mttm) REVERT: B 65 LYS cc_start: 0.7927 (mtmm) cc_final: 0.7637 (mttm) REVERT: B 112 THR cc_start: 0.8402 (m) cc_final: 0.8136 (p) REVERT: B 114 VAL cc_start: 0.8233 (t) cc_final: 0.8019 (p) REVERT: B 167 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7636 (ttt-90) REVERT: B 178 ASP cc_start: 0.7086 (t0) cc_final: 0.6705 (t70) REVERT: B 182 THR cc_start: 0.7954 (p) cc_final: 0.7719 (p) REVERT: B 190 VAL cc_start: 0.7721 (p) cc_final: 0.7514 (m) REVERT: B 442 TYR cc_start: 0.8485 (OUTLIER) cc_final: 0.8013 (p90) REVERT: B 492 LEU cc_start: 0.8287 (mt) cc_final: 0.8017 (mp) REVERT: B 498 SER cc_start: 0.8568 (t) cc_final: 0.8161 (p) REVERT: B 516 ILE cc_start: 0.8753 (mt) cc_final: 0.8523 (mm) REVERT: B 586 ASN cc_start: 0.8130 (m-40) cc_final: 0.7911 (m110) REVERT: B 592 MET cc_start: 0.5417 (mmm) cc_final: 0.5193 (mmm) REVERT: B 609 GLU cc_start: 0.6953 (tp30) cc_final: 0.6657 (tp30) REVERT: B 624 CYS cc_start: 0.6543 (m) cc_final: 0.6291 (m) REVERT: B 625 THR cc_start: 0.8430 (m) cc_final: 0.8208 (t) REVERT: B 672 ASN cc_start: 0.7980 (t0) cc_final: 0.7692 (t0) REVERT: B 676 THR cc_start: 0.8200 (OUTLIER) cc_final: 0.7802 (p) REVERT: B 681 VAL cc_start: 0.8457 (OUTLIER) cc_final: 0.8222 (p) REVERT: B 684 GLU cc_start: 0.7293 (tm-30) cc_final: 0.6983 (tm-30) REVERT: B 775 VAL cc_start: 0.8507 (t) cc_final: 0.8280 (p) REVERT: B 800 VAL cc_start: 0.8411 (m) cc_final: 0.8143 (t) REVERT: B 803 LYS cc_start: 0.8387 (ttmm) cc_final: 0.8065 (ttpt) REVERT: B 817 LEU cc_start: 0.8202 (tp) cc_final: 0.7896 (tt) REVERT: B 826 LYS cc_start: 0.8250 (mttm) cc_final: 0.8031 (mptp) REVERT: B 836 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7565 (mt) REVERT: B 844 ASN cc_start: 0.7731 (t0) cc_final: 0.7047 (t0) REVERT: B 850 LYS cc_start: 0.8204 (ttmt) cc_final: 0.7973 (ttmt) REVERT: B 864 ASP cc_start: 0.7724 (OUTLIER) cc_final: 0.7389 (m-30) REVERT: B 884 SER cc_start: 0.8299 (m) cc_final: 0.7752 (t) REVERT: B 925 VAL cc_start: 0.8237 (t) cc_final: 0.8008 (m) REVERT: B 991 LYS cc_start: 0.8170 (mtpp) cc_final: 0.7718 (mmtm) REVERT: B 1019 GLN cc_start: 0.7985 (mm110) cc_final: 0.7682 (tp40) REVERT: B 1094 LEU cc_start: 0.8258 (tp) cc_final: 0.7947 (tt) REVERT: B 1153 ASN cc_start: 0.7615 (p0) cc_final: 0.7395 (p0) REVERT: B 1169 VAL cc_start: 0.7932 (m) cc_final: 0.7393 (p) REVERT: B 1197 MET cc_start: 0.8388 (tpp) cc_final: 0.8039 (mmm) REVERT: B 1208 LYS cc_start: 0.7858 (ptpt) cc_final: 0.7237 (ptpt) REVERT: C 80 LYS cc_start: 0.8532 (mtmt) cc_final: 0.8267 (mttm) REVERT: C 83 ASP cc_start: 0.7777 (t0) cc_final: 0.7524 (t0) REVERT: C 178 ASP cc_start: 0.6980 (t0) cc_final: 0.6599 (m-30) REVERT: C 183 ARG cc_start: 0.7599 (ttp80) cc_final: 0.7173 (mtm180) REVERT: C 190 VAL cc_start: 0.8231 (t) cc_final: 0.8015 (m) REVERT: C 238 LEU cc_start: 0.8219 (mt) cc_final: 0.7983 (mp) REVERT: C 256 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7555 (mt-10) REVERT: C 258 PHE cc_start: 0.8572 (t80) cc_final: 0.8174 (t80) REVERT: C 338 ARG cc_start: 0.7916 (mtt-85) cc_final: 0.7649 (mtt180) REVERT: C 350 GLN cc_start: 0.6986 (tp40) cc_final: 0.6695 (tp40) REVERT: C 372 VAL cc_start: 0.8045 (OUTLIER) cc_final: 0.7802 (p) REVERT: C 379 ILE cc_start: 0.8373 (mm) cc_final: 0.8156 (mm) REVERT: C 380 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7225 (mt-10) REVERT: C 381 GLN cc_start: 0.7153 (OUTLIER) cc_final: 0.6685 (mp10) REVERT: C 456 MET cc_start: 0.7835 (mmt) cc_final: 0.6660 (mmt) REVERT: C 464 SER cc_start: 0.8251 (t) cc_final: 0.7804 (m) REVERT: C 540 GLN cc_start: 0.7876 (mt0) cc_final: 0.7575 (mt0) REVERT: C 543 ASP cc_start: 0.7643 (m-30) cc_final: 0.7443 (m-30) REVERT: C 613 TYR cc_start: 0.8255 (m-80) cc_final: 0.8052 (m-80) REVERT: C 653 TYR cc_start: 0.8160 (m-80) cc_final: 0.7706 (m-80) REVERT: C 663 LEU cc_start: 0.8363 (mt) cc_final: 0.8159 (mm) REVERT: C 669 LYS cc_start: 0.8200 (ttpp) cc_final: 0.7944 (ttmm) REVERT: C 672 ASN cc_start: 0.8141 (t0) cc_final: 0.7780 (t0) REVERT: C 780 THR cc_start: 0.8255 (OUTLIER) cc_final: 0.8019 (m) REVERT: C 871 GLN cc_start: 0.7715 (mt0) cc_final: 0.7202 (mt0) REVERT: C 893 LYS cc_start: 0.8326 (mmtm) cc_final: 0.7937 (mppt) REVERT: C 894 VAL cc_start: 0.8230 (t) cc_final: 0.8013 (p) REVERT: C 939 MET cc_start: 0.8134 (ttm) cc_final: 0.7934 (ttm) REVERT: C 971 SER cc_start: 0.7940 (OUTLIER) cc_final: 0.7461 (p) REVERT: C 972 ILE cc_start: 0.8375 (mm) cc_final: 0.8095 (mp) REVERT: C 976 MET cc_start: 0.8552 (mtt) cc_final: 0.8349 (mtm) REVERT: C 981 ILE cc_start: 0.7997 (mt) cc_final: 0.7762 (mt) REVERT: C 1060 GLU cc_start: 0.7772 (mp0) cc_final: 0.7190 (mp0) REVERT: C 1064 ASP cc_start: 0.7717 (m-30) cc_final: 0.7447 (m-30) REVERT: C 1086 GLU cc_start: 0.7687 (mt-10) cc_final: 0.7394 (mt-10) REVERT: C 1101 GLU cc_start: 0.7685 (mm-30) cc_final: 0.7249 (mm-30) REVERT: C 1108 LYS cc_start: 0.8264 (mmmt) cc_final: 0.8049 (mtmm) REVERT: C 1189 PHE cc_start: 0.8605 (t80) cc_final: 0.8312 (t80) REVERT: C 1193 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7392 (mt-10) REVERT: C 1197 MET cc_start: 0.8331 (tpp) cc_final: 0.7931 (tpp) REVERT: C 1201 ARG cc_start: 0.7453 (ptp90) cc_final: 0.6937 (ptp90) REVERT: L 10 THR cc_start: 0.7924 (m) cc_final: 0.7714 (p) REVERT: L 39 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8064 (mptp) outliers start: 138 outliers final: 65 residues processed: 892 average time/residue: 1.1775 time to fit residues: 1261.8410 Evaluate side-chains 877 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 797 time to evaluate : 2.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 442 TYR Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 578 SER Chi-restraints excluded: chain A residue 618 ARG Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 837 MET Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain B residue 167 ARG Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 330 ASP Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 442 TYR Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 685 HIS Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 822 GLN Chi-restraints excluded: chain B residue 836 LEU Chi-restraints excluded: chain B residue 864 ASP Chi-restraints excluded: chain B residue 889 LEU Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 1013 LEU Chi-restraints excluded: chain B residue 1080 GLN Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain B residue 1140 THR Chi-restraints excluded: chain B residue 1142 HIS Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 381 GLN Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 442 TYR Chi-restraints excluded: chain C residue 515 HIS Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain C residue 624 CYS Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 671 THR Chi-restraints excluded: chain C residue 685 HIS Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 780 THR Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 822 GLN Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 944 THR Chi-restraints excluded: chain C residue 971 SER Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1145 VAL Chi-restraints excluded: chain C residue 1196 THR Chi-restraints excluded: chain C residue 1216 LEU Chi-restraints excluded: chain C residue 1221 LEU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 39 LYS Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain L residue 101 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 20 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 330 optimal weight: 0.9980 chunk 293 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 149 optimal weight: 3.9990 chunk 334 optimal weight: 0.3980 chunk 103 optimal weight: 0.6980 chunk 310 optimal weight: 8.9990 chunk 222 optimal weight: 4.9990 chunk 171 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 685 HIS A 828 ASN A 892 ASN A1125 ASN B 461 GLN B 515 HIS B 580 GLN B 822 GLN B 838 GLN B 989 ASN B1038 ASN C 461 GLN C 631 GLN C 641 ASN C 651 ASN C 838 GLN C 923 GLN C1059 GLN C1141 ASN C1191 ASN L 6 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.148613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.126510 restraints weight = 41315.733| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.76 r_work: 0.3192 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 29281 Z= 0.163 Angle : 0.621 13.663 39937 Z= 0.308 Chirality : 0.047 0.490 4573 Planarity : 0.004 0.051 5078 Dihedral : 9.623 110.069 5055 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 4.78 % Allowed : 15.81 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.14), residues: 3538 helix: 1.46 (0.19), residues: 730 sheet: 0.30 (0.17), residues: 861 loop : -0.43 (0.13), residues: 1947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP H 47 HIS 0.005 0.001 HIS B 81 PHE 0.018 0.001 PHE A 782 TYR 0.022 0.001 TYR L 89 ARG 0.004 0.000 ARG B 302 Details of bonding type rmsd link_NAG-ASN : bond 0.00498 ( 34) link_NAG-ASN : angle 3.21989 ( 102) link_ALPHA1-6 : bond 0.00596 ( 1) link_ALPHA1-6 : angle 1.16669 ( 3) link_BETA1-4 : bond 0.00631 ( 17) link_BETA1-4 : angle 2.24425 ( 51) link_ALPHA1-3 : bond 0.00740 ( 1) link_ALPHA1-3 : angle 2.54576 ( 3) hydrogen bonds : bond 0.04649 ( 1122) hydrogen bonds : angle 5.29925 ( 3231) link_BETA1-6 : bond 0.00755 ( 3) link_BETA1-6 : angle 1.51635 ( 9) SS BOND : bond 0.00522 ( 51) SS BOND : angle 2.25833 ( 102) covalent geometry : bond 0.00374 (29174) covalent geometry : angle 0.58352 (39667) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 972 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 824 time to evaluate : 3.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 GLN cc_start: 0.7391 (mp10) cc_final: 0.6982 (mp10) REVERT: A 49 MET cc_start: 0.8436 (mmp) cc_final: 0.8164 (mmm) REVERT: A 55 LYS cc_start: 0.8592 (mtpp) cc_final: 0.8223 (mttp) REVERT: A 75 GLN cc_start: 0.7661 (mm110) cc_final: 0.7457 (mm110) REVERT: A 241 CYS cc_start: 0.6910 (m) cc_final: 0.6680 (m) REVERT: A 242 SER cc_start: 0.8276 (OUTLIER) cc_final: 0.8039 (p) REVERT: A 256 GLU cc_start: 0.8033 (tp30) cc_final: 0.7652 (tp30) REVERT: A 296 TYR cc_start: 0.8289 (m-80) cc_final: 0.7814 (m-80) REVERT: A 375 ARG cc_start: 0.7458 (mtp85) cc_final: 0.7198 (mtp85) REVERT: A 386 GLU cc_start: 0.6671 (mm-30) cc_final: 0.6059 (mm-30) REVERT: A 412 ASN cc_start: 0.8153 (m110) cc_final: 0.7454 (m-40) REVERT: A 439 ARG cc_start: 0.8304 (ptt-90) cc_final: 0.8059 (ptt90) REVERT: A 460 MET cc_start: 0.8387 (tpp) cc_final: 0.8060 (mmt) REVERT: A 518 THR cc_start: 0.8100 (m) cc_final: 0.7860 (t) REVERT: A 521 VAL cc_start: 0.8213 (t) cc_final: 0.7974 (m) REVERT: A 539 SER cc_start: 0.8382 (t) cc_final: 0.8124 (m) REVERT: A 606 VAL cc_start: 0.8244 (m) cc_final: 0.7993 (p) REVERT: A 611 ASN cc_start: 0.7937 (t0) cc_final: 0.7609 (t0) REVERT: A 613 TYR cc_start: 0.8595 (m-80) cc_final: 0.8054 (m-80) REVERT: A 616 SER cc_start: 0.8446 (p) cc_final: 0.8164 (m) REVERT: A 681 VAL cc_start: 0.8284 (OUTLIER) cc_final: 0.7994 (m) REVERT: A 720 ILE cc_start: 0.8555 (pt) cc_final: 0.8213 (mt) REVERT: A 743 VAL cc_start: 0.8675 (t) cc_final: 0.8360 (m) REVERT: A 776 VAL cc_start: 0.8480 (m) cc_final: 0.8209 (p) REVERT: A 784 PHE cc_start: 0.8473 (m-80) cc_final: 0.8005 (m-80) REVERT: A 812 LYS cc_start: 0.7903 (tppp) cc_final: 0.7659 (mmmm) REVERT: A 891 PHE cc_start: 0.8174 (m-80) cc_final: 0.7935 (m-80) REVERT: A 910 LYS cc_start: 0.7728 (mtpt) cc_final: 0.7434 (mtpt) REVERT: A 1052 LYS cc_start: 0.7872 (ttpp) cc_final: 0.7643 (ttpp) REVERT: A 1082 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8300 (tt) REVERT: A 1143 VAL cc_start: 0.8290 (OUTLIER) cc_final: 0.8026 (m) REVERT: A 1144 ASN cc_start: 0.7787 (p0) cc_final: 0.7488 (p0) REVERT: A 1159 ARG cc_start: 0.7908 (OUTLIER) cc_final: 0.7501 (ttp80) REVERT: A 1193 GLU cc_start: 0.7882 (mt-10) cc_final: 0.7498 (mt-10) REVERT: A 1201 ARG cc_start: 0.7820 (ttp80) cc_final: 0.7590 (ttp80) REVERT: A 1206 ASP cc_start: 0.7290 (t0) cc_final: 0.7074 (t70) REVERT: B 44 ASN cc_start: 0.7017 (t0) cc_final: 0.6557 (t0) REVERT: B 65 LYS cc_start: 0.7929 (mtmm) cc_final: 0.7670 (mttm) REVERT: B 112 THR cc_start: 0.8436 (m) cc_final: 0.8170 (p) REVERT: B 114 VAL cc_start: 0.8277 (t) cc_final: 0.8077 (p) REVERT: B 167 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7658 (ttt-90) REVERT: B 178 ASP cc_start: 0.7130 (t0) cc_final: 0.6758 (t70) REVERT: B 190 VAL cc_start: 0.7789 (p) cc_final: 0.7574 (m) REVERT: B 240 ASN cc_start: 0.7876 (m110) cc_final: 0.7547 (m-40) REVERT: B 410 ASN cc_start: 0.7720 (t0) cc_final: 0.7478 (t0) REVERT: B 442 TYR cc_start: 0.8488 (OUTLIER) cc_final: 0.7943 (p90) REVERT: B 492 LEU cc_start: 0.8352 (mt) cc_final: 0.8086 (mp) REVERT: B 498 SER cc_start: 0.8595 (t) cc_final: 0.8206 (p) REVERT: B 586 ASN cc_start: 0.8143 (m-40) cc_final: 0.7895 (m110) REVERT: B 592 MET cc_start: 0.5391 (mmm) cc_final: 0.5177 (mmm) REVERT: B 609 GLU cc_start: 0.7050 (tp30) cc_final: 0.6797 (tp30) REVERT: B 624 CYS cc_start: 0.6401 (m) cc_final: 0.6138 (m) REVERT: B 625 THR cc_start: 0.8427 (m) cc_final: 0.8224 (t) REVERT: B 672 ASN cc_start: 0.8033 (t0) cc_final: 0.7749 (t0) REVERT: B 676 THR cc_start: 0.8212 (OUTLIER) cc_final: 0.7831 (p) REVERT: B 681 VAL cc_start: 0.8063 (OUTLIER) cc_final: 0.7846 (p) REVERT: B 684 GLU cc_start: 0.6908 (tm-30) cc_final: 0.6527 (tm-30) REVERT: B 775 VAL cc_start: 0.8506 (t) cc_final: 0.8299 (p) REVERT: B 800 VAL cc_start: 0.8398 (m) cc_final: 0.8135 (t) REVERT: B 803 LYS cc_start: 0.8451 (ttmm) cc_final: 0.8137 (ttpt) REVERT: B 817 LEU cc_start: 0.8174 (tp) cc_final: 0.7842 (tt) REVERT: B 844 ASN cc_start: 0.7867 (t0) cc_final: 0.7289 (t0) REVERT: B 850 LYS cc_start: 0.8208 (ttmt) cc_final: 0.7950 (ttmt) REVERT: B 864 ASP cc_start: 0.7774 (OUTLIER) cc_final: 0.7527 (m-30) REVERT: B 925 VAL cc_start: 0.8238 (t) cc_final: 0.8016 (m) REVERT: B 991 LYS cc_start: 0.8185 (mtpp) cc_final: 0.7809 (mmtm) REVERT: B 1019 GLN cc_start: 0.8061 (mm110) cc_final: 0.7768 (tp40) REVERT: B 1094 LEU cc_start: 0.8254 (tp) cc_final: 0.7974 (tt) REVERT: B 1153 ASN cc_start: 0.7629 (p0) cc_final: 0.7339 (p0) REVERT: B 1169 VAL cc_start: 0.7950 (m) cc_final: 0.7382 (p) REVERT: B 1197 MET cc_start: 0.8453 (tpp) cc_final: 0.8135 (mmm) REVERT: B 1208 LYS cc_start: 0.7879 (ptpt) cc_final: 0.7273 (ptpt) REVERT: B 1210 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7466 (mm-30) REVERT: C 80 LYS cc_start: 0.8578 (mtmt) cc_final: 0.8319 (mttm) REVERT: C 83 ASP cc_start: 0.7853 (t0) cc_final: 0.7602 (t0) REVERT: C 178 ASP cc_start: 0.6996 (t0) cc_final: 0.6583 (m-30) REVERT: C 190 VAL cc_start: 0.8255 (t) cc_final: 0.8050 (m) REVERT: C 238 LEU cc_start: 0.8191 (mt) cc_final: 0.7969 (mp) REVERT: C 256 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7769 (tt0) REVERT: C 258 PHE cc_start: 0.8565 (t80) cc_final: 0.8299 (t80) REVERT: C 338 ARG cc_start: 0.7957 (mtt-85) cc_final: 0.7680 (mtt180) REVERT: C 350 GLN cc_start: 0.7054 (tp40) cc_final: 0.6775 (tp40) REVERT: C 372 VAL cc_start: 0.8027 (m) cc_final: 0.7799 (p) REVERT: C 379 ILE cc_start: 0.8376 (mm) cc_final: 0.8130 (mm) REVERT: C 380 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7554 (mt-10) REVERT: C 381 GLN cc_start: 0.7231 (OUTLIER) cc_final: 0.6762 (mp10) REVERT: C 456 MET cc_start: 0.7848 (mmt) cc_final: 0.6773 (mmt) REVERT: C 464 SER cc_start: 0.8275 (OUTLIER) cc_final: 0.7844 (m) REVERT: C 495 THR cc_start: 0.8550 (t) cc_final: 0.8162 (p) REVERT: C 540 GLN cc_start: 0.7969 (mt0) cc_final: 0.7668 (mt0) REVERT: C 543 ASP cc_start: 0.7690 (m-30) cc_final: 0.7481 (m-30) REVERT: C 653 TYR cc_start: 0.8198 (m-80) cc_final: 0.7710 (m-80) REVERT: C 669 LYS cc_start: 0.8262 (ttpp) cc_final: 0.7979 (ttmm) REVERT: C 672 ASN cc_start: 0.8164 (t0) cc_final: 0.7787 (t0) REVERT: C 754 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.7745 (mt0) REVERT: C 780 THR cc_start: 0.8263 (OUTLIER) cc_final: 0.8019 (m) REVERT: C 814 GLU cc_start: 0.7350 (mt-10) cc_final: 0.7111 (mm-30) REVERT: C 836 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7828 (tp) REVERT: C 871 GLN cc_start: 0.7745 (mt0) cc_final: 0.7350 (mt0) REVERT: C 893 LYS cc_start: 0.8313 (mmtm) cc_final: 0.7911 (mppt) REVERT: C 940 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7689 (mt-10) REVERT: C 971 SER cc_start: 0.7982 (OUTLIER) cc_final: 0.7469 (p) REVERT: C 972 ILE cc_start: 0.8414 (mm) cc_final: 0.8134 (mp) REVERT: C 984 GLN cc_start: 0.7585 (tt0) cc_final: 0.6452 (tt0) REVERT: C 988 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.6885 (mp0) REVERT: C 1060 GLU cc_start: 0.7826 (mp0) cc_final: 0.7399 (mp0) REVERT: C 1064 ASP cc_start: 0.7751 (m-30) cc_final: 0.7504 (m-30) REVERT: C 1086 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7460 (mt-10) REVERT: C 1101 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7318 (mm-30) REVERT: C 1108 LYS cc_start: 0.8277 (mmmt) cc_final: 0.8076 (mtmm) REVERT: C 1193 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7453 (mt-10) REVERT: C 1197 MET cc_start: 0.8348 (tpp) cc_final: 0.7910 (tpp) REVERT: C 1201 ARG cc_start: 0.7505 (ptp90) cc_final: 0.6995 (ptp90) outliers start: 148 outliers final: 75 residues processed: 879 average time/residue: 1.2078 time to fit residues: 1265.0734 Evaluate side-chains 892 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 800 time to evaluate : 3.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 442 TYR Chi-restraints excluded: chain A residue 578 SER Chi-restraints excluded: chain A residue 618 ARG Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 630 LYS Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 837 MET Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 1027 GLN Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1142 HIS Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1159 ARG Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1197 MET Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 167 ARG Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 442 TYR Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 665 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 864 ASP Chi-restraints excluded: chain B residue 889 LEU Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 909 MET Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 992 LEU Chi-restraints excluded: chain B residue 1080 GLN Chi-restraints excluded: chain B residue 1140 THR Chi-restraints excluded: chain B residue 1142 HIS Chi-restraints excluded: chain B residue 1207 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 381 GLN Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 442 TYR Chi-restraints excluded: chain C residue 464 SER Chi-restraints excluded: chain C residue 515 HIS Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 671 THR Chi-restraints excluded: chain C residue 754 GLN Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 775 VAL Chi-restraints excluded: chain C residue 780 THR Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 837 MET Chi-restraints excluded: chain C residue 944 THR Chi-restraints excluded: chain C residue 962 SER Chi-restraints excluded: chain C residue 971 SER Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1142 HIS Chi-restraints excluded: chain C residue 1145 VAL Chi-restraints excluded: chain C residue 1196 THR Chi-restraints excluded: chain C residue 1216 LEU Chi-restraints excluded: chain C residue 1221 LEU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 39 LYS Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain L residue 101 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 87 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 274 optimal weight: 2.9990 chunk 231 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 184 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 287 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 170 optimal weight: 3.9990 chunk 340 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 GLN A 162 ASN ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 828 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 381 GLN B 461 GLN ** B 838 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 990 GLN B1038 ASN B1125 ASN C 162 ASN C 631 GLN C 641 ASN C 685 HIS C 738 GLN C 838 GLN ** C 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1141 ASN ** C1215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.146465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.124392 restraints weight = 40952.597| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.79 r_work: 0.3151 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.085 29281 Z= 0.324 Angle : 0.725 13.579 39937 Z= 0.364 Chirality : 0.052 0.542 4573 Planarity : 0.005 0.057 5078 Dihedral : 9.620 110.178 5053 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 5.49 % Allowed : 16.23 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.13), residues: 3538 helix: 1.07 (0.19), residues: 740 sheet: 0.15 (0.17), residues: 881 loop : -0.62 (0.13), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP H 47 HIS 0.010 0.002 HIS L 91 PHE 0.028 0.002 PHE L 97 TYR 0.034 0.002 TYR L 89 ARG 0.008 0.001 ARG A1084 Details of bonding type rmsd link_NAG-ASN : bond 0.00861 ( 34) link_NAG-ASN : angle 3.41887 ( 102) link_ALPHA1-6 : bond 0.00243 ( 1) link_ALPHA1-6 : angle 1.35180 ( 3) link_BETA1-4 : bond 0.00701 ( 17) link_BETA1-4 : angle 2.39021 ( 51) link_ALPHA1-3 : bond 0.00610 ( 1) link_ALPHA1-3 : angle 2.18040 ( 3) hydrogen bonds : bond 0.05577 ( 1122) hydrogen bonds : angle 5.54705 ( 3231) link_BETA1-6 : bond 0.00665 ( 3) link_BETA1-6 : angle 1.44236 ( 9) SS BOND : bond 0.00562 ( 51) SS BOND : angle 2.20929 ( 102) covalent geometry : bond 0.00754 (29174) covalent geometry : angle 0.69155 (39667) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 990 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 820 time to evaluate : 3.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 GLN cc_start: 0.7354 (mp10) cc_final: 0.6984 (mp10) REVERT: A 49 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.8146 (mmm) REVERT: A 75 GLN cc_start: 0.7649 (mm110) cc_final: 0.7368 (mm110) REVERT: A 242 SER cc_start: 0.8360 (OUTLIER) cc_final: 0.8129 (p) REVERT: A 256 GLU cc_start: 0.7961 (tp30) cc_final: 0.7556 (tp30) REVERT: A 296 TYR cc_start: 0.8297 (m-80) cc_final: 0.7852 (m-80) REVERT: A 375 ARG cc_start: 0.7460 (mtp85) cc_final: 0.7147 (mtp85) REVERT: A 439 ARG cc_start: 0.8338 (ptt-90) cc_final: 0.8071 (ptt90) REVERT: A 460 MET cc_start: 0.8371 (tpp) cc_final: 0.8048 (mmt) REVERT: A 518 THR cc_start: 0.8130 (m) cc_final: 0.7842 (t) REVERT: A 521 VAL cc_start: 0.8338 (t) cc_final: 0.8095 (m) REVERT: A 539 SER cc_start: 0.8396 (t) cc_final: 0.8088 (m) REVERT: A 608 VAL cc_start: 0.7778 (OUTLIER) cc_final: 0.7480 (t) REVERT: A 681 VAL cc_start: 0.8343 (OUTLIER) cc_final: 0.8074 (m) REVERT: A 720 ILE cc_start: 0.8512 (pt) cc_final: 0.8212 (mt) REVERT: A 743 VAL cc_start: 0.8697 (t) cc_final: 0.8327 (p) REVERT: A 776 VAL cc_start: 0.8517 (m) cc_final: 0.8215 (p) REVERT: A 812 LYS cc_start: 0.7974 (tppp) cc_final: 0.7724 (mmmm) REVERT: A 910 LYS cc_start: 0.7839 (mtpt) cc_final: 0.7559 (mtpt) REVERT: A 1036 LEU cc_start: 0.8347 (mt) cc_final: 0.8129 (mt) REVERT: A 1052 LYS cc_start: 0.7910 (ttpp) cc_final: 0.7653 (ttpp) REVERT: A 1060 GLU cc_start: 0.7598 (mt-10) cc_final: 0.7394 (mp0) REVERT: A 1082 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8323 (tt) REVERT: A 1090 ARG cc_start: 0.7659 (OUTLIER) cc_final: 0.7434 (mtp180) REVERT: A 1143 VAL cc_start: 0.8302 (OUTLIER) cc_final: 0.8037 (m) REVERT: A 1144 ASN cc_start: 0.7905 (p0) cc_final: 0.7617 (p0) REVERT: A 1159 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.7559 (ttp80) REVERT: A 1193 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7436 (mt-10) REVERT: A 1201 ARG cc_start: 0.7770 (ttp80) cc_final: 0.7385 (ttp80) REVERT: B 44 ASN cc_start: 0.7136 (t0) cc_final: 0.6658 (t0) REVERT: B 65 LYS cc_start: 0.8023 (mtmm) cc_final: 0.7760 (mttp) REVERT: B 112 THR cc_start: 0.8447 (m) cc_final: 0.8215 (p) REVERT: B 114 VAL cc_start: 0.8272 (t) cc_final: 0.8032 (p) REVERT: B 167 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7596 (ttt-90) REVERT: B 178 ASP cc_start: 0.7136 (t0) cc_final: 0.6770 (t70) REVERT: B 190 VAL cc_start: 0.7822 (p) cc_final: 0.7576 (m) REVERT: B 240 ASN cc_start: 0.7903 (m110) cc_final: 0.7589 (m-40) REVERT: B 350 GLN cc_start: 0.8170 (tt0) cc_final: 0.7644 (tt0) REVERT: B 374 SER cc_start: 0.8211 (t) cc_final: 0.7937 (p) REVERT: B 423 MET cc_start: 0.7892 (OUTLIER) cc_final: 0.7292 (tpp) REVERT: B 442 TYR cc_start: 0.8484 (OUTLIER) cc_final: 0.7748 (p90) REVERT: B 492 LEU cc_start: 0.8400 (mt) cc_final: 0.8142 (mp) REVERT: B 498 SER cc_start: 0.8569 (t) cc_final: 0.8188 (p) REVERT: B 586 ASN cc_start: 0.8166 (m-40) cc_final: 0.7933 (m110) REVERT: B 609 GLU cc_start: 0.7039 (tp30) cc_final: 0.6807 (tp30) REVERT: B 624 CYS cc_start: 0.6550 (m) cc_final: 0.6337 (m) REVERT: B 676 THR cc_start: 0.8157 (OUTLIER) cc_final: 0.7794 (p) REVERT: B 803 LYS cc_start: 0.8409 (ttmm) cc_final: 0.8033 (ttpp) REVERT: B 817 LEU cc_start: 0.8195 (tp) cc_final: 0.7838 (tt) REVERT: B 836 LEU cc_start: 0.7842 (mp) cc_final: 0.7557 (mt) REVERT: B 864 ASP cc_start: 0.7811 (OUTLIER) cc_final: 0.7554 (m-30) REVERT: B 925 VAL cc_start: 0.8228 (t) cc_final: 0.7956 (m) REVERT: B 991 LYS cc_start: 0.8134 (mtpp) cc_final: 0.7734 (mmtm) REVERT: B 1019 GLN cc_start: 0.8122 (mm110) cc_final: 0.7845 (tp40) REVERT: B 1094 LEU cc_start: 0.8256 (tp) cc_final: 0.7961 (tt) REVERT: B 1153 ASN cc_start: 0.7659 (p0) cc_final: 0.7369 (p0) REVERT: B 1197 MET cc_start: 0.8363 (tpp) cc_final: 0.8155 (mmm) REVERT: B 1208 LYS cc_start: 0.7815 (ptpt) cc_final: 0.7212 (ptpt) REVERT: B 1210 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7495 (mm-30) REVERT: C 80 LYS cc_start: 0.8552 (mtmt) cc_final: 0.8284 (mttp) REVERT: C 183 ARG cc_start: 0.7433 (mtm180) cc_final: 0.6937 (ttp-170) REVERT: C 190 VAL cc_start: 0.8299 (t) cc_final: 0.8049 (m) REVERT: C 225 THR cc_start: 0.7935 (p) cc_final: 0.7236 (t) REVERT: C 302 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7502 (ttp80) REVERT: C 350 GLN cc_start: 0.7227 (tp40) cc_final: 0.6845 (tp40) REVERT: C 372 VAL cc_start: 0.8029 (m) cc_final: 0.7811 (p) REVERT: C 380 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7298 (mt-10) REVERT: C 381 GLN cc_start: 0.7231 (OUTLIER) cc_final: 0.6748 (mp10) REVERT: C 423 MET cc_start: 0.7829 (OUTLIER) cc_final: 0.7234 (tpt) REVERT: C 456 MET cc_start: 0.7910 (mmt) cc_final: 0.6488 (mmt) REVERT: C 464 SER cc_start: 0.8279 (t) cc_final: 0.7916 (m) REVERT: C 540 GLN cc_start: 0.7963 (mt0) cc_final: 0.7605 (mt0) REVERT: C 543 ASP cc_start: 0.7723 (m-30) cc_final: 0.7463 (m-30) REVERT: C 601 THR cc_start: 0.8160 (p) cc_final: 0.7888 (m) REVERT: C 653 TYR cc_start: 0.8239 (m-80) cc_final: 0.7594 (m-80) REVERT: C 669 LYS cc_start: 0.8326 (ttpp) cc_final: 0.8053 (ttmm) REVERT: C 672 ASN cc_start: 0.8180 (t0) cc_final: 0.7747 (t0) REVERT: C 780 THR cc_start: 0.8285 (OUTLIER) cc_final: 0.8063 (m) REVERT: C 871 GLN cc_start: 0.7769 (mt0) cc_final: 0.7304 (mt0) REVERT: C 884 SER cc_start: 0.8069 (m) cc_final: 0.7816 (p) REVERT: C 893 LYS cc_start: 0.8370 (mmtm) cc_final: 0.8162 (mmtm) REVERT: C 971 SER cc_start: 0.7947 (OUTLIER) cc_final: 0.7424 (p) REVERT: C 972 ILE cc_start: 0.8374 (OUTLIER) cc_final: 0.8055 (mp) REVERT: C 988 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7000 (mp0) REVERT: C 1060 GLU cc_start: 0.7847 (mp0) cc_final: 0.7315 (mp0) REVERT: C 1064 ASP cc_start: 0.7805 (m-30) cc_final: 0.7529 (m-30) REVERT: C 1086 GLU cc_start: 0.7737 (mt-10) cc_final: 0.7407 (mt-10) REVERT: C 1098 LYS cc_start: 0.7983 (ttmm) cc_final: 0.7760 (tttm) REVERT: C 1101 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7315 (mm-30) REVERT: C 1160 CYS cc_start: 0.6804 (m) cc_final: 0.6478 (m) REVERT: C 1193 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7501 (mt-10) REVERT: C 1201 ARG cc_start: 0.7492 (ptp90) cc_final: 0.6975 (ptp90) REVERT: H 24 VAL cc_start: 0.8233 (m) cc_final: 0.7959 (t) REVERT: L 10 THR cc_start: 0.7931 (m) cc_final: 0.7715 (p) outliers start: 170 outliers final: 100 residues processed: 895 average time/residue: 1.1872 time to fit residues: 1274.1691 Evaluate side-chains 921 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 801 time to evaluate : 3.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 442 TYR Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 578 SER Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 618 ARG Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 630 LYS Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 724 ASN Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 789 GLU Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 837 MET Chi-restraints excluded: chain A residue 840 GLU Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1090 ARG Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1159 ARG Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1208 LYS Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 167 ARG Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 423 MET Chi-restraints excluded: chain B residue 442 TYR Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 685 HIS Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 864 ASP Chi-restraints excluded: chain B residue 889 LEU Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 909 MET Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 992 LEU Chi-restraints excluded: chain B residue 1013 LEU Chi-restraints excluded: chain B residue 1035 GLU Chi-restraints excluded: chain B residue 1045 SER Chi-restraints excluded: chain B residue 1080 GLN Chi-restraints excluded: chain B residue 1140 THR Chi-restraints excluded: chain B residue 1207 VAL Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 298 THR Chi-restraints excluded: chain C residue 302 ARG Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 381 GLN Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 423 MET Chi-restraints excluded: chain C residue 442 TYR Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 515 HIS Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 665 VAL Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 671 THR Chi-restraints excluded: chain C residue 673 SER Chi-restraints excluded: chain C residue 754 GLN Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 775 VAL Chi-restraints excluded: chain C residue 780 THR Chi-restraints excluded: chain C residue 822 GLN Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 857 LEU Chi-restraints excluded: chain C residue 944 THR Chi-restraints excluded: chain C residue 962 SER Chi-restraints excluded: chain C residue 971 SER Chi-restraints excluded: chain C residue 972 ILE Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1035 GLU Chi-restraints excluded: chain C residue 1145 VAL Chi-restraints excluded: chain C residue 1196 THR Chi-restraints excluded: chain C residue 1221 LEU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 39 LYS Chi-restraints excluded: chain L residue 50 SER Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 101 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 279 optimal weight: 0.8980 chunk 138 optimal weight: 1.9990 chunk 205 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 223 optimal weight: 0.8980 chunk 332 optimal weight: 0.7980 chunk 302 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 107 optimal weight: 0.2980 chunk 50 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 611 ASN A 685 HIS A 828 ASN A 995 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 713 GLN B 838 GLN B1038 ASN C 162 ASN C 631 GLN C 641 ASN ** C 685 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 838 GLN C1141 ASN C1191 ASN L 6 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.148536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.125680 restraints weight = 41140.211| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.83 r_work: 0.3207 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 29281 Z= 0.156 Angle : 0.631 13.170 39937 Z= 0.311 Chirality : 0.047 0.519 4573 Planarity : 0.005 0.053 5078 Dihedral : 9.066 106.350 5052 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 4.49 % Allowed : 18.20 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.14), residues: 3538 helix: 1.47 (0.19), residues: 734 sheet: 0.35 (0.17), residues: 836 loop : -0.57 (0.13), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 47 HIS 0.006 0.001 HIS B 81 PHE 0.016 0.001 PHE C 331 TYR 0.023 0.001 TYR B 653 ARG 0.006 0.000 ARG B 818 Details of bonding type rmsd link_NAG-ASN : bond 0.00678 ( 34) link_NAG-ASN : angle 3.28080 ( 102) link_ALPHA1-6 : bond 0.00529 ( 1) link_ALPHA1-6 : angle 1.28753 ( 3) link_BETA1-4 : bond 0.00624 ( 17) link_BETA1-4 : angle 2.27618 ( 51) link_ALPHA1-3 : bond 0.00926 ( 1) link_ALPHA1-3 : angle 2.58950 ( 3) hydrogen bonds : bond 0.04543 ( 1122) hydrogen bonds : angle 5.24683 ( 3231) link_BETA1-6 : bond 0.00707 ( 3) link_BETA1-6 : angle 1.49813 ( 9) SS BOND : bond 0.00550 ( 51) SS BOND : angle 2.45524 ( 102) covalent geometry : bond 0.00357 (29174) covalent geometry : angle 0.59145 (39667) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 941 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 802 time to evaluate : 2.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 GLN cc_start: 0.7363 (mp10) cc_final: 0.6975 (mp10) REVERT: A 49 MET cc_start: 0.8323 (mmp) cc_final: 0.8055 (mmm) REVERT: A 210 VAL cc_start: 0.8491 (OUTLIER) cc_final: 0.8251 (t) REVERT: A 242 SER cc_start: 0.8227 (OUTLIER) cc_final: 0.8022 (p) REVERT: A 256 GLU cc_start: 0.7911 (tp30) cc_final: 0.7482 (tp30) REVERT: A 296 TYR cc_start: 0.8221 (m-80) cc_final: 0.7817 (m-80) REVERT: A 375 ARG cc_start: 0.7468 (mtp85) cc_final: 0.7137 (mtp85) REVERT: A 439 ARG cc_start: 0.8287 (ptt-90) cc_final: 0.8010 (ptt90) REVERT: A 460 MET cc_start: 0.8365 (tpp) cc_final: 0.8032 (mmt) REVERT: A 518 THR cc_start: 0.8074 (m) cc_final: 0.7801 (t) REVERT: A 521 VAL cc_start: 0.8206 (t) cc_final: 0.7937 (m) REVERT: A 539 SER cc_start: 0.8360 (t) cc_final: 0.8040 (m) REVERT: A 608 VAL cc_start: 0.7699 (OUTLIER) cc_final: 0.7428 (t) REVERT: A 611 ASN cc_start: 0.7999 (t0) cc_final: 0.7747 (t0) REVERT: A 613 TYR cc_start: 0.8613 (m-80) cc_final: 0.8148 (m-80) REVERT: A 616 SER cc_start: 0.8374 (p) cc_final: 0.8120 (m) REVERT: A 681 VAL cc_start: 0.8170 (OUTLIER) cc_final: 0.7912 (m) REVERT: A 689 MET cc_start: 0.7087 (mtm) cc_final: 0.6379 (ppp) REVERT: A 720 ILE cc_start: 0.8503 (pt) cc_final: 0.8131 (mp) REVERT: A 743 VAL cc_start: 0.8656 (t) cc_final: 0.8290 (p) REVERT: A 776 VAL cc_start: 0.8493 (m) cc_final: 0.8225 (p) REVERT: A 811 GLN cc_start: 0.6881 (tm-30) cc_final: 0.6557 (tm-30) REVERT: A 812 LYS cc_start: 0.7858 (tppp) cc_final: 0.7629 (mmmm) REVERT: A 902 MET cc_start: 0.8312 (ttp) cc_final: 0.8050 (ttt) REVERT: A 910 LYS cc_start: 0.7772 (mtpt) cc_final: 0.7515 (mtpt) REVERT: A 1036 LEU cc_start: 0.8357 (mt) cc_final: 0.8125 (mt) REVERT: A 1082 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8274 (tt) REVERT: A 1143 VAL cc_start: 0.8286 (OUTLIER) cc_final: 0.8013 (m) REVERT: A 1144 ASN cc_start: 0.7888 (p0) cc_final: 0.7576 (p0) REVERT: A 1159 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7553 (ttp80) REVERT: A 1193 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7385 (mt-10) REVERT: A 1201 ARG cc_start: 0.7774 (ttp80) cc_final: 0.7377 (ttp80) REVERT: B 44 ASN cc_start: 0.7077 (t0) cc_final: 0.6614 (t0) REVERT: B 65 LYS cc_start: 0.7948 (mtmm) cc_final: 0.7701 (mttp) REVERT: B 70 ILE cc_start: 0.8022 (OUTLIER) cc_final: 0.7710 (OUTLIER) REVERT: B 112 THR cc_start: 0.8467 (m) cc_final: 0.8215 (p) REVERT: B 114 VAL cc_start: 0.8235 (t) cc_final: 0.8015 (p) REVERT: B 167 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7612 (ttt-90) REVERT: B 178 ASP cc_start: 0.7007 (t0) cc_final: 0.6510 (t70) REVERT: B 190 VAL cc_start: 0.7717 (p) cc_final: 0.7503 (m) REVERT: B 347 ASP cc_start: 0.7631 (OUTLIER) cc_final: 0.7310 (p0) REVERT: B 374 SER cc_start: 0.8218 (t) cc_final: 0.7972 (p) REVERT: B 410 ASN cc_start: 0.7710 (t0) cc_final: 0.7463 (t0) REVERT: B 442 TYR cc_start: 0.8475 (OUTLIER) cc_final: 0.7909 (p90) REVERT: B 492 LEU cc_start: 0.8232 (mt) cc_final: 0.7969 (mp) REVERT: B 498 SER cc_start: 0.8568 (t) cc_final: 0.8198 (p) REVERT: B 586 ASN cc_start: 0.8134 (m-40) cc_final: 0.7876 (m110) REVERT: B 609 GLU cc_start: 0.6976 (tp30) cc_final: 0.6701 (tp30) REVERT: B 676 THR cc_start: 0.8170 (OUTLIER) cc_final: 0.7712 (p) REVERT: B 787 THR cc_start: 0.8696 (OUTLIER) cc_final: 0.8321 (p) REVERT: B 800 VAL cc_start: 0.8369 (m) cc_final: 0.7994 (t) REVERT: B 803 LYS cc_start: 0.8499 (ttmm) cc_final: 0.8080 (ttpp) REVERT: B 836 LEU cc_start: 0.7724 (mp) cc_final: 0.7447 (mt) REVERT: B 864 ASP cc_start: 0.7718 (OUTLIER) cc_final: 0.7450 (m-30) REVERT: B 910 LYS cc_start: 0.7709 (mmpt) cc_final: 0.7355 (tppp) REVERT: B 925 VAL cc_start: 0.8244 (t) cc_final: 0.8016 (m) REVERT: B 991 LYS cc_start: 0.8090 (mtpp) cc_final: 0.7737 (mmtm) REVERT: B 1019 GLN cc_start: 0.8064 (mm110) cc_final: 0.7764 (tp40) REVERT: B 1094 LEU cc_start: 0.8213 (tp) cc_final: 0.7920 (tt) REVERT: B 1153 ASN cc_start: 0.7569 (p0) cc_final: 0.7271 (p0) REVERT: B 1208 LYS cc_start: 0.7744 (ptpt) cc_final: 0.7108 (ptpt) REVERT: B 1210 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7391 (mm-30) REVERT: C 46 GLN cc_start: 0.7755 (mt0) cc_final: 0.7545 (mt0) REVERT: C 49 MET cc_start: 0.8235 (tpp) cc_final: 0.7917 (mmp) REVERT: C 80 LYS cc_start: 0.8467 (mtmt) cc_final: 0.8200 (mttp) REVERT: C 83 ASP cc_start: 0.7874 (t0) cc_final: 0.7637 (t0) REVERT: C 183 ARG cc_start: 0.7419 (mtm180) cc_final: 0.7097 (ttp-170) REVERT: C 190 VAL cc_start: 0.8226 (t) cc_final: 0.8001 (m) REVERT: C 225 THR cc_start: 0.7796 (p) cc_final: 0.7267 (t) REVERT: C 350 GLN cc_start: 0.7218 (tp40) cc_final: 0.6807 (tp40) REVERT: C 372 VAL cc_start: 0.8019 (m) cc_final: 0.7803 (p) REVERT: C 381 GLN cc_start: 0.7304 (OUTLIER) cc_final: 0.6783 (mp10) REVERT: C 423 MET cc_start: 0.7724 (tpt) cc_final: 0.7154 (tpt) REVERT: C 456 MET cc_start: 0.7774 (mmt) cc_final: 0.6383 (mmt) REVERT: C 464 SER cc_start: 0.8267 (t) cc_final: 0.7909 (m) REVERT: C 540 GLN cc_start: 0.7884 (mt0) cc_final: 0.7549 (mt0) REVERT: C 543 ASP cc_start: 0.7735 (m-30) cc_final: 0.7470 (m-30) REVERT: C 601 THR cc_start: 0.8078 (p) cc_final: 0.7819 (m) REVERT: C 653 TYR cc_start: 0.8175 (m-80) cc_final: 0.7480 (m-80) REVERT: C 669 LYS cc_start: 0.8200 (ttpp) cc_final: 0.7877 (ttmm) REVERT: C 672 ASN cc_start: 0.8121 (t0) cc_final: 0.7739 (t0) REVERT: C 754 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.7639 (mt0) REVERT: C 780 THR cc_start: 0.8270 (OUTLIER) cc_final: 0.8054 (m) REVERT: C 871 GLN cc_start: 0.7752 (mt0) cc_final: 0.7332 (mt0) REVERT: C 884 SER cc_start: 0.7983 (m) cc_final: 0.7727 (p) REVERT: C 894 VAL cc_start: 0.8012 (t) cc_final: 0.7771 (p) REVERT: C 971 SER cc_start: 0.7900 (OUTLIER) cc_final: 0.7380 (p) REVERT: C 972 ILE cc_start: 0.8287 (mm) cc_final: 0.8019 (mp) REVERT: C 988 GLU cc_start: 0.7501 (OUTLIER) cc_final: 0.6848 (mp0) REVERT: C 1012 ASN cc_start: 0.7296 (t0) cc_final: 0.7078 (m-40) REVERT: C 1060 GLU cc_start: 0.7771 (mp0) cc_final: 0.7286 (mp0) REVERT: C 1064 ASP cc_start: 0.7692 (m-30) cc_final: 0.7410 (m-30) REVERT: C 1086 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7461 (mt-10) REVERT: C 1101 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7287 (mm-30) REVERT: C 1160 CYS cc_start: 0.6672 (m) cc_final: 0.6326 (m) REVERT: C 1193 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7360 (mt-10) REVERT: C 1197 MET cc_start: 0.8256 (tpp) cc_final: 0.7884 (tpp) REVERT: C 1201 ARG cc_start: 0.7490 (ptp90) cc_final: 0.6937 (ptp90) REVERT: H 20 LEU cc_start: 0.8650 (mt) cc_final: 0.8447 (mt) REVERT: L 4 MET cc_start: 0.7761 (mmm) cc_final: 0.7288 (mmm) REVERT: L 10 THR cc_start: 0.7821 (m) cc_final: 0.7607 (p) outliers start: 139 outliers final: 74 residues processed: 861 average time/residue: 1.1886 time to fit residues: 1220.0686 Evaluate side-chains 871 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 779 time to evaluate : 3.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 242 SER Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 442 TYR Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 618 ARG Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 724 ASN Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 837 MET Chi-restraints excluded: chain A residue 840 GLU Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 1027 GLN Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1159 ARG Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1208 LYS Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 167 ARG Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 442 TYR Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 685 HIS Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 811 GLN Chi-restraints excluded: chain B residue 864 ASP Chi-restraints excluded: chain B residue 889 LEU Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 909 MET Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 992 LEU Chi-restraints excluded: chain B residue 1013 LEU Chi-restraints excluded: chain B residue 1035 GLU Chi-restraints excluded: chain B residue 1140 THR Chi-restraints excluded: chain B residue 1142 HIS Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 339 ARG Chi-restraints excluded: chain C residue 381 GLN Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 442 TYR Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 515 HIS Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 671 THR Chi-restraints excluded: chain C residue 754 GLN Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 775 VAL Chi-restraints excluded: chain C residue 780 THR Chi-restraints excluded: chain C residue 822 GLN Chi-restraints excluded: chain C residue 889 LEU Chi-restraints excluded: chain C residue 944 THR Chi-restraints excluded: chain C residue 962 SER Chi-restraints excluded: chain C residue 971 SER Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1145 VAL Chi-restraints excluded: chain C residue 1216 LEU Chi-restraints excluded: chain C residue 1221 LEU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 100 CYS Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 39 LYS Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 93 SER Chi-restraints excluded: chain L residue 101 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 280 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 286 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 278 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 218 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 192 optimal weight: 0.9990 chunk 177 optimal weight: 1.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 GLN ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 685 HIS A 828 ASN A 995 ASN A1125 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 240 ASN B 713 GLN ** B 838 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1038 ASN B1125 ASN C 162 ASN C 631 GLN C 641 ASN C 685 HIS C 838 GLN C 970 GLN C1141 ASN L 6 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.147493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.124364 restraints weight = 41353.378| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.82 r_work: 0.3194 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.108 29281 Z= 0.242 Angle : 0.697 13.116 39937 Z= 0.346 Chirality : 0.050 0.568 4573 Planarity : 0.005 0.055 5078 Dihedral : 8.813 104.098 5050 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 4.71 % Allowed : 18.65 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.13), residues: 3538 helix: 1.27 (0.19), residues: 734 sheet: 0.14 (0.17), residues: 860 loop : -0.60 (0.13), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP H 47 HIS 0.014 0.001 HIS B 691 PHE 0.022 0.002 PHE L 97 TYR 0.030 0.002 TYR B 653 ARG 0.006 0.001 ARG B 547 Details of bonding type rmsd link_NAG-ASN : bond 0.00640 ( 34) link_NAG-ASN : angle 3.33460 ( 102) link_ALPHA1-6 : bond 0.00310 ( 1) link_ALPHA1-6 : angle 1.42981 ( 3) link_BETA1-4 : bond 0.00631 ( 17) link_BETA1-4 : angle 2.34703 ( 51) link_ALPHA1-3 : bond 0.00812 ( 1) link_ALPHA1-3 : angle 2.59219 ( 3) hydrogen bonds : bond 0.05005 ( 1122) hydrogen bonds : angle 5.34649 ( 3231) link_BETA1-6 : bond 0.00694 ( 3) link_BETA1-6 : angle 1.55045 ( 9) SS BOND : bond 0.00736 ( 51) SS BOND : angle 3.19430 ( 102) covalent geometry : bond 0.00567 (29174) covalent geometry : angle 0.65293 (39667) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 949 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 803 time to evaluate : 2.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 GLN cc_start: 0.7358 (mp10) cc_final: 0.6967 (mp10) REVERT: A 49 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.8039 (mmm) REVERT: A 55 LYS cc_start: 0.8491 (mtpp) cc_final: 0.8204 (mtpp) REVERT: A 75 GLN cc_start: 0.7525 (mm110) cc_final: 0.7222 (mm110) REVERT: A 210 VAL cc_start: 0.8496 (OUTLIER) cc_final: 0.8255 (t) REVERT: A 238 LEU cc_start: 0.8118 (mt) cc_final: 0.7871 (OUTLIER) REVERT: A 256 GLU cc_start: 0.7894 (tp30) cc_final: 0.7469 (tp30) REVERT: A 295 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.7973 (mmtp) REVERT: A 296 TYR cc_start: 0.8211 (m-80) cc_final: 0.7794 (m-80) REVERT: A 375 ARG cc_start: 0.7421 (mtp85) cc_final: 0.7141 (mtp85) REVERT: A 439 ARG cc_start: 0.8314 (ptt-90) cc_final: 0.8042 (ptt90) REVERT: A 460 MET cc_start: 0.8327 (tpp) cc_final: 0.7991 (mmt) REVERT: A 518 THR cc_start: 0.8060 (m) cc_final: 0.7799 (t) REVERT: A 521 VAL cc_start: 0.8196 (t) cc_final: 0.7931 (m) REVERT: A 539 SER cc_start: 0.8359 (t) cc_final: 0.8023 (m) REVERT: A 608 VAL cc_start: 0.7720 (OUTLIER) cc_final: 0.7438 (t) REVERT: A 681 VAL cc_start: 0.8239 (OUTLIER) cc_final: 0.8003 (m) REVERT: A 689 MET cc_start: 0.7075 (mtm) cc_final: 0.6377 (ppp) REVERT: A 743 VAL cc_start: 0.8648 (t) cc_final: 0.8291 (p) REVERT: A 754 GLN cc_start: 0.8022 (OUTLIER) cc_final: 0.7750 (mt0) REVERT: A 776 VAL cc_start: 0.8508 (m) cc_final: 0.8237 (p) REVERT: A 811 GLN cc_start: 0.6932 (tm-30) cc_final: 0.6625 (tm-30) REVERT: A 812 LYS cc_start: 0.7896 (tppp) cc_final: 0.7634 (mmmm) REVERT: A 902 MET cc_start: 0.8317 (ttp) cc_final: 0.8116 (ttt) REVERT: A 910 LYS cc_start: 0.7788 (mtpt) cc_final: 0.7533 (mtpt) REVERT: A 1036 LEU cc_start: 0.8339 (mt) cc_final: 0.8127 (mt) REVERT: A 1082 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8248 (tt) REVERT: A 1143 VAL cc_start: 0.8267 (OUTLIER) cc_final: 0.8005 (m) REVERT: A 1144 ASN cc_start: 0.7915 (p0) cc_final: 0.7615 (p0) REVERT: A 1193 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7333 (mt-10) REVERT: A 1195 ILE cc_start: 0.8552 (mm) cc_final: 0.8233 (mt) REVERT: A 1201 ARG cc_start: 0.7721 (ttp80) cc_final: 0.7314 (ttp80) REVERT: B 44 ASN cc_start: 0.7110 (t0) cc_final: 0.6515 (t0) REVERT: B 65 LYS cc_start: 0.7970 (mtmm) cc_final: 0.7751 (mttp) REVERT: B 70 ILE cc_start: 0.8021 (OUTLIER) cc_final: 0.7705 (OUTLIER) REVERT: B 112 THR cc_start: 0.8449 (m) cc_final: 0.8201 (p) REVERT: B 114 VAL cc_start: 0.8213 (t) cc_final: 0.7983 (p) REVERT: B 167 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7564 (ttt-90) REVERT: B 178 ASP cc_start: 0.6975 (t0) cc_final: 0.6575 (t70) REVERT: B 182 THR cc_start: 0.7978 (p) cc_final: 0.7676 (p) REVERT: B 190 VAL cc_start: 0.7711 (p) cc_final: 0.7490 (m) REVERT: B 347 ASP cc_start: 0.7644 (OUTLIER) cc_final: 0.7285 (p0) REVERT: B 374 SER cc_start: 0.8213 (t) cc_final: 0.7927 (p) REVERT: B 442 TYR cc_start: 0.8449 (OUTLIER) cc_final: 0.7717 (p90) REVERT: B 492 LEU cc_start: 0.8362 (mt) cc_final: 0.8100 (mp) REVERT: B 498 SER cc_start: 0.8584 (t) cc_final: 0.8218 (p) REVERT: B 586 ASN cc_start: 0.8155 (m-40) cc_final: 0.7906 (m110) REVERT: B 609 GLU cc_start: 0.6945 (tp30) cc_final: 0.6658 (tp30) REVERT: B 676 THR cc_start: 0.8153 (OUTLIER) cc_final: 0.7680 (p) REVERT: B 787 THR cc_start: 0.8691 (OUTLIER) cc_final: 0.8331 (p) REVERT: B 800 VAL cc_start: 0.8320 (m) cc_final: 0.8109 (t) REVERT: B 803 LYS cc_start: 0.8368 (ttmm) cc_final: 0.7973 (ttpp) REVERT: B 818 ARG cc_start: 0.7470 (mtm180) cc_final: 0.7254 (ttp-170) REVERT: B 836 LEU cc_start: 0.7673 (OUTLIER) cc_final: 0.7418 (mt) REVERT: B 864 ASP cc_start: 0.7762 (OUTLIER) cc_final: 0.7471 (m-30) REVERT: B 884 SER cc_start: 0.8368 (m) cc_final: 0.7939 (p) REVERT: B 925 VAL cc_start: 0.8200 (t) cc_final: 0.7974 (m) REVERT: B 991 LYS cc_start: 0.8060 (mtpp) cc_final: 0.7677 (mmtm) REVERT: B 1019 GLN cc_start: 0.8069 (mm110) cc_final: 0.7761 (tp40) REVERT: B 1094 LEU cc_start: 0.8183 (tp) cc_final: 0.7883 (tt) REVERT: B 1153 ASN cc_start: 0.7594 (p0) cc_final: 0.7281 (p0) REVERT: B 1208 LYS cc_start: 0.7703 (ptpt) cc_final: 0.7088 (ptpt) REVERT: B 1210 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7373 (mm-30) REVERT: C 46 GLN cc_start: 0.7799 (mt0) cc_final: 0.7570 (mt0) REVERT: C 49 MET cc_start: 0.8231 (tpp) cc_final: 0.7903 (mmp) REVERT: C 80 LYS cc_start: 0.8445 (mtmt) cc_final: 0.8164 (mttp) REVERT: C 190 VAL cc_start: 0.8213 (t) cc_final: 0.7962 (m) REVERT: C 302 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7411 (ttp80) REVERT: C 350 GLN cc_start: 0.7196 (tp40) cc_final: 0.6814 (tp40) REVERT: C 372 VAL cc_start: 0.8011 (m) cc_final: 0.7805 (p) REVERT: C 381 GLN cc_start: 0.7327 (OUTLIER) cc_final: 0.6779 (mp10) REVERT: C 423 MET cc_start: 0.7765 (OUTLIER) cc_final: 0.7121 (tpt) REVERT: C 456 MET cc_start: 0.7813 (mmt) cc_final: 0.6444 (mmt) REVERT: C 464 SER cc_start: 0.8274 (t) cc_final: 0.7909 (m) REVERT: C 495 THR cc_start: 0.8518 (t) cc_final: 0.8111 (p) REVERT: C 540 GLN cc_start: 0.7841 (mt0) cc_final: 0.7462 (mt0) REVERT: C 543 ASP cc_start: 0.7720 (m-30) cc_final: 0.7398 (m-30) REVERT: C 546 THR cc_start: 0.8050 (m) cc_final: 0.7833 (t) REVERT: C 601 THR cc_start: 0.8063 (p) cc_final: 0.7837 (m) REVERT: C 653 TYR cc_start: 0.8184 (m-80) cc_final: 0.7486 (m-80) REVERT: C 669 LYS cc_start: 0.8217 (ttpp) cc_final: 0.7884 (ttmm) REVERT: C 672 ASN cc_start: 0.8137 (t0) cc_final: 0.7754 (t0) REVERT: C 780 THR cc_start: 0.8261 (OUTLIER) cc_final: 0.8047 (m) REVERT: C 871 GLN cc_start: 0.7801 (mt0) cc_final: 0.7299 (mt0) REVERT: C 884 SER cc_start: 0.8027 (m) cc_final: 0.7796 (p) REVERT: C 894 VAL cc_start: 0.7975 (t) cc_final: 0.7718 (p) REVERT: C 911 GLN cc_start: 0.7803 (tt0) cc_final: 0.7544 (tt0) REVERT: C 971 SER cc_start: 0.7926 (OUTLIER) cc_final: 0.7381 (p) REVERT: C 972 ILE cc_start: 0.8290 (mm) cc_final: 0.7992 (mp) REVERT: C 988 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.6851 (mp0) REVERT: C 1012 ASN cc_start: 0.7335 (t0) cc_final: 0.7132 (m-40) REVERT: C 1060 GLU cc_start: 0.7809 (mp0) cc_final: 0.7258 (mp0) REVERT: C 1064 ASP cc_start: 0.7715 (m-30) cc_final: 0.7423 (m-30) REVERT: C 1086 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7427 (mt-10) REVERT: C 1101 GLU cc_start: 0.7655 (mm-30) cc_final: 0.7261 (mm-30) REVERT: C 1160 CYS cc_start: 0.6604 (m) cc_final: 0.6271 (m) REVERT: C 1193 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7421 (mt-10) REVERT: C 1197 MET cc_start: 0.8245 (tpp) cc_final: 0.7832 (tpp) REVERT: C 1201 ARG cc_start: 0.7476 (ptp90) cc_final: 0.6903 (ptp90) REVERT: H 89 VAL cc_start: 0.8077 (p) cc_final: 0.7716 (t) REVERT: L 10 THR cc_start: 0.7910 (m) cc_final: 0.7680 (p) REVERT: L 12 SER cc_start: 0.7830 (t) cc_final: 0.7583 (m) REVERT: L 49 HIS cc_start: 0.6793 (OUTLIER) cc_final: 0.6538 (t70) outliers start: 146 outliers final: 88 residues processed: 870 average time/residue: 1.2379 time to fit residues: 1286.1541 Evaluate side-chains 893 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 784 time to evaluate : 3.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 295 LYS Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 442 TYR Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 618 ARG Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 630 LYS Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 724 ASN Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 754 GLN Chi-restraints excluded: chain A residue 789 GLU Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 837 MET Chi-restraints excluded: chain A residue 840 GLU Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1027 GLN Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 167 ARG Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 442 TYR Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 685 HIS Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 836 LEU Chi-restraints excluded: chain B residue 864 ASP Chi-restraints excluded: chain B residue 889 LEU Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 909 MET Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 992 LEU Chi-restraints excluded: chain B residue 1013 LEU Chi-restraints excluded: chain B residue 1035 GLU Chi-restraints excluded: chain B residue 1045 SER Chi-restraints excluded: chain B residue 1140 THR Chi-restraints excluded: chain B residue 1142 HIS Chi-restraints excluded: chain B residue 1161 ILE Chi-restraints excluded: chain B residue 1207 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 302 ARG Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 381 GLN Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 423 MET Chi-restraints excluded: chain C residue 442 TYR Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain C residue 588 VAL Chi-restraints excluded: chain C residue 665 VAL Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 671 THR Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 754 GLN Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 775 VAL Chi-restraints excluded: chain C residue 780 THR Chi-restraints excluded: chain C residue 822 GLN Chi-restraints excluded: chain C residue 889 LEU Chi-restraints excluded: chain C residue 944 THR Chi-restraints excluded: chain C residue 962 SER Chi-restraints excluded: chain C residue 971 SER Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1142 HIS Chi-restraints excluded: chain C residue 1145 VAL Chi-restraints excluded: chain C residue 1221 LEU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 100 CYS Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 39 LYS Chi-restraints excluded: chain L residue 49 HIS Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 101 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 171 optimal weight: 1.9990 chunk 262 optimal weight: 0.5980 chunk 127 optimal weight: 0.7980 chunk 223 optimal weight: 1.9990 chunk 185 optimal weight: 0.9990 chunk 151 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 265 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 611 ASN A 685 HIS A 995 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 685 HIS B 713 GLN B 838 GLN B1038 ASN C 162 ASN C 461 GLN C 631 GLN C 641 ASN C 685 HIS C 838 GLN C 938 ASN C 970 GLN C1141 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.148039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.124523 restraints weight = 41511.281| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.91 r_work: 0.3209 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 29281 Z= 0.197 Angle : 0.676 12.891 39937 Z= 0.333 Chirality : 0.048 0.615 4573 Planarity : 0.005 0.054 5078 Dihedral : 8.275 103.559 5048 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 4.45 % Allowed : 19.01 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.14), residues: 3538 helix: 1.39 (0.19), residues: 728 sheet: 0.17 (0.18), residues: 842 loop : -0.60 (0.13), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP H 47 HIS 0.009 0.001 HIS B 691 PHE 0.021 0.002 PHE C 243 TYR 0.030 0.002 TYR B 653 ARG 0.005 0.000 ARG B 547 Details of bonding type rmsd link_NAG-ASN : bond 0.00667 ( 34) link_NAG-ASN : angle 3.43697 ( 102) link_ALPHA1-6 : bond 0.00437 ( 1) link_ALPHA1-6 : angle 1.37821 ( 3) link_BETA1-4 : bond 0.00624 ( 17) link_BETA1-4 : angle 2.34139 ( 51) link_ALPHA1-3 : bond 0.00982 ( 1) link_ALPHA1-3 : angle 2.73134 ( 3) hydrogen bonds : bond 0.04701 ( 1122) hydrogen bonds : angle 5.28052 ( 3231) link_BETA1-6 : bond 0.00781 ( 3) link_BETA1-6 : angle 1.58119 ( 9) SS BOND : bond 0.00800 ( 51) SS BOND : angle 3.14705 ( 102) covalent geometry : bond 0.00464 (29174) covalent geometry : angle 0.62881 (39667) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 936 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 798 time to evaluate : 3.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 GLN cc_start: 0.7318 (mp10) cc_final: 0.6923 (mp10) REVERT: A 49 MET cc_start: 0.8278 (OUTLIER) cc_final: 0.8023 (mmm) REVERT: A 55 LYS cc_start: 0.8453 (mtpp) cc_final: 0.8161 (mtpp) REVERT: A 75 GLN cc_start: 0.7512 (mm110) cc_final: 0.7198 (mm110) REVERT: A 210 VAL cc_start: 0.8440 (OUTLIER) cc_final: 0.8208 (t) REVERT: A 242 SER cc_start: 0.8184 (t) cc_final: 0.7875 (p) REVERT: A 256 GLU cc_start: 0.7840 (tp30) cc_final: 0.7431 (tp30) REVERT: A 295 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.7951 (mmtp) REVERT: A 296 TYR cc_start: 0.8171 (m-80) cc_final: 0.7759 (m-80) REVERT: A 415 LEU cc_start: 0.7814 (tp) cc_final: 0.7584 (tt) REVERT: A 439 ARG cc_start: 0.8275 (ptt-90) cc_final: 0.8002 (ptt90) REVERT: A 460 MET cc_start: 0.8322 (tpp) cc_final: 0.7999 (mmt) REVERT: A 518 THR cc_start: 0.8011 (m) cc_final: 0.7754 (t) REVERT: A 521 VAL cc_start: 0.8164 (t) cc_final: 0.7899 (m) REVERT: A 539 SER cc_start: 0.8352 (t) cc_final: 0.8013 (m) REVERT: A 608 VAL cc_start: 0.7749 (OUTLIER) cc_final: 0.7395 (t) REVERT: A 681 VAL cc_start: 0.8191 (OUTLIER) cc_final: 0.7942 (m) REVERT: A 689 MET cc_start: 0.7127 (mtm) cc_final: 0.6421 (ppp) REVERT: A 720 ILE cc_start: 0.8441 (pt) cc_final: 0.8075 (mp) REVERT: A 743 VAL cc_start: 0.8613 (t) cc_final: 0.8285 (p) REVERT: A 754 GLN cc_start: 0.7969 (OUTLIER) cc_final: 0.7699 (mt0) REVERT: A 776 VAL cc_start: 0.8490 (m) cc_final: 0.8210 (p) REVERT: A 812 LYS cc_start: 0.7831 (tppp) cc_final: 0.7572 (mmmm) REVERT: A 910 LYS cc_start: 0.7742 (mtpt) cc_final: 0.7475 (mtpt) REVERT: A 1036 LEU cc_start: 0.8336 (mt) cc_final: 0.8114 (mt) REVERT: A 1060 GLU cc_start: 0.7479 (mt-10) cc_final: 0.7204 (mp0) REVERT: A 1082 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8211 (tt) REVERT: A 1143 VAL cc_start: 0.8261 (OUTLIER) cc_final: 0.7986 (m) REVERT: A 1144 ASN cc_start: 0.7916 (p0) cc_final: 0.7624 (p0) REVERT: A 1193 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7231 (mt-10) REVERT: A 1195 ILE cc_start: 0.8508 (mm) cc_final: 0.8173 (mt) REVERT: A 1201 ARG cc_start: 0.7668 (ttp80) cc_final: 0.7241 (ttp80) REVERT: B 44 ASN cc_start: 0.6962 (t0) cc_final: 0.6510 (t0) REVERT: B 65 LYS cc_start: 0.7950 (mtmm) cc_final: 0.7737 (mttp) REVERT: B 70 ILE cc_start: 0.7983 (OUTLIER) cc_final: 0.7661 (OUTLIER) REVERT: B 112 THR cc_start: 0.8428 (m) cc_final: 0.8184 (p) REVERT: B 114 VAL cc_start: 0.8211 (t) cc_final: 0.7984 (p) REVERT: B 167 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7520 (ttt-90) REVERT: B 178 ASP cc_start: 0.6953 (t0) cc_final: 0.6549 (t70) REVERT: B 190 VAL cc_start: 0.7640 (p) cc_final: 0.7417 (m) REVERT: B 347 ASP cc_start: 0.7602 (OUTLIER) cc_final: 0.7303 (p0) REVERT: B 374 SER cc_start: 0.8209 (t) cc_final: 0.7974 (p) REVERT: B 410 ASN cc_start: 0.7683 (t0) cc_final: 0.7437 (t0) REVERT: B 442 TYR cc_start: 0.8432 (OUTLIER) cc_final: 0.7700 (p90) REVERT: B 498 SER cc_start: 0.8539 (t) cc_final: 0.8222 (p) REVERT: B 586 ASN cc_start: 0.8141 (m-40) cc_final: 0.7865 (m110) REVERT: B 609 GLU cc_start: 0.6903 (tp30) cc_final: 0.6599 (tp30) REVERT: B 624 CYS cc_start: 0.6180 (m) cc_final: 0.5967 (m) REVERT: B 676 THR cc_start: 0.8141 (OUTLIER) cc_final: 0.7683 (p) REVERT: B 787 THR cc_start: 0.8680 (OUTLIER) cc_final: 0.8315 (p) REVERT: B 800 VAL cc_start: 0.8278 (m) cc_final: 0.8076 (t) REVERT: B 803 LYS cc_start: 0.8287 (ttmm) cc_final: 0.7924 (ttmm) REVERT: B 818 ARG cc_start: 0.7400 (mtm180) cc_final: 0.7197 (ttp-170) REVERT: B 822 GLN cc_start: 0.6584 (pm20) cc_final: 0.6359 (pt0) REVERT: B 826 LYS cc_start: 0.7971 (mptp) cc_final: 0.7709 (mmtm) REVERT: B 836 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7351 (mt) REVERT: B 864 ASP cc_start: 0.7719 (OUTLIER) cc_final: 0.7427 (m-30) REVERT: B 910 LYS cc_start: 0.7629 (mmpt) cc_final: 0.7426 (mmpt) REVERT: B 925 VAL cc_start: 0.8193 (t) cc_final: 0.7972 (m) REVERT: B 991 LYS cc_start: 0.8028 (mtpp) cc_final: 0.7642 (mmtm) REVERT: B 1019 GLN cc_start: 0.8024 (mm110) cc_final: 0.7744 (tp40) REVERT: B 1094 LEU cc_start: 0.8146 (tp) cc_final: 0.7846 (tt) REVERT: B 1153 ASN cc_start: 0.7554 (p0) cc_final: 0.7251 (p0) REVERT: B 1208 LYS cc_start: 0.7691 (ptpt) cc_final: 0.7053 (ptpt) REVERT: B 1210 GLU cc_start: 0.7716 (mm-30) cc_final: 0.7350 (mm-30) REVERT: C 35 MET cc_start: 0.7401 (OUTLIER) cc_final: 0.7187 (mmt) REVERT: C 45 LYS cc_start: 0.8326 (mtmt) cc_final: 0.8010 (mtmm) REVERT: C 46 GLN cc_start: 0.7777 (mt0) cc_final: 0.7545 (mt0) REVERT: C 49 MET cc_start: 0.8241 (tpp) cc_final: 0.7910 (mmp) REVERT: C 80 LYS cc_start: 0.8413 (mtmt) cc_final: 0.8115 (mttp) REVERT: C 183 ARG cc_start: 0.7469 (ttp-170) cc_final: 0.6933 (ttp-170) REVERT: C 190 VAL cc_start: 0.8171 (t) cc_final: 0.7943 (m) REVERT: C 225 THR cc_start: 0.7871 (p) cc_final: 0.7225 (t) REVERT: C 302 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7195 (ttp80) REVERT: C 347 ASP cc_start: 0.7350 (t0) cc_final: 0.7106 (t0) REVERT: C 350 GLN cc_start: 0.7187 (tp40) cc_final: 0.6804 (tp40) REVERT: C 380 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7349 (mt-10) REVERT: C 423 MET cc_start: 0.7743 (tpt) cc_final: 0.7111 (tpt) REVERT: C 456 MET cc_start: 0.7739 (mmt) cc_final: 0.6390 (mmt) REVERT: C 464 SER cc_start: 0.8247 (t) cc_final: 0.7866 (m) REVERT: C 540 GLN cc_start: 0.7813 (mt0) cc_final: 0.7423 (mt0) REVERT: C 543 ASP cc_start: 0.7708 (m-30) cc_final: 0.7376 (m-30) REVERT: C 653 TYR cc_start: 0.8158 (m-80) cc_final: 0.7449 (m-80) REVERT: C 663 LEU cc_start: 0.8330 (mt) cc_final: 0.8088 (mm) REVERT: C 669 LYS cc_start: 0.8172 (ttpp) cc_final: 0.7840 (ttmm) REVERT: C 672 ASN cc_start: 0.8120 (t0) cc_final: 0.7737 (t0) REVERT: C 754 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.7613 (mt0) REVERT: C 871 GLN cc_start: 0.7816 (mt0) cc_final: 0.7320 (mt0) REVERT: C 884 SER cc_start: 0.7992 (m) cc_final: 0.7763 (p) REVERT: C 892 ASN cc_start: 0.8123 (OUTLIER) cc_final: 0.7877 (m110) REVERT: C 894 VAL cc_start: 0.7949 (t) cc_final: 0.7687 (p) REVERT: C 962 SER cc_start: 0.8043 (OUTLIER) cc_final: 0.7814 (t) REVERT: C 971 SER cc_start: 0.7885 (OUTLIER) cc_final: 0.7335 (p) REVERT: C 972 ILE cc_start: 0.8250 (mm) cc_final: 0.7949 (mp) REVERT: C 988 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.6744 (mp0) REVERT: C 1012 ASN cc_start: 0.7233 (t0) cc_final: 0.6942 (m-40) REVERT: C 1060 GLU cc_start: 0.7774 (mp0) cc_final: 0.7198 (mp0) REVERT: C 1064 ASP cc_start: 0.7642 (m-30) cc_final: 0.7342 (m-30) REVERT: C 1086 GLU cc_start: 0.7700 (mt-10) cc_final: 0.7397 (mt-10) REVERT: C 1101 GLU cc_start: 0.7606 (mm-30) cc_final: 0.7200 (mm-30) REVERT: C 1193 GLU cc_start: 0.7611 (mt-10) cc_final: 0.7377 (mt-10) REVERT: C 1197 MET cc_start: 0.8236 (tpp) cc_final: 0.7835 (tpp) REVERT: C 1201 ARG cc_start: 0.7424 (ptp90) cc_final: 0.6835 (ptp90) REVERT: L 10 THR cc_start: 0.7899 (m) cc_final: 0.7655 (p) REVERT: L 12 SER cc_start: 0.7809 (t) cc_final: 0.7544 (m) outliers start: 138 outliers final: 85 residues processed: 864 average time/residue: 1.1872 time to fit residues: 1221.4506 Evaluate side-chains 888 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 781 time to evaluate : 2.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 295 LYS Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 442 TYR Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 618 ARG Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 724 ASN Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 754 GLN Chi-restraints excluded: chain A residue 789 GLU Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain A residue 837 MET Chi-restraints excluded: chain A residue 840 GLU Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1027 GLN Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1205 GLN Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 167 ARG Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 442 TYR Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 539 SER Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 836 LEU Chi-restraints excluded: chain B residue 864 ASP Chi-restraints excluded: chain B residue 889 LEU Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 909 MET Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 992 LEU Chi-restraints excluded: chain B residue 1013 LEU Chi-restraints excluded: chain B residue 1035 GLU Chi-restraints excluded: chain B residue 1140 THR Chi-restraints excluded: chain B residue 1142 HIS Chi-restraints excluded: chain B residue 1161 ILE Chi-restraints excluded: chain B residue 1207 VAL Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 302 ARG Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 339 ARG Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 442 TYR Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain C residue 588 VAL Chi-restraints excluded: chain C residue 665 VAL Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 671 THR Chi-restraints excluded: chain C residue 673 SER Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 754 GLN Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 775 VAL Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 822 GLN Chi-restraints excluded: chain C residue 857 LEU Chi-restraints excluded: chain C residue 892 ASN Chi-restraints excluded: chain C residue 944 THR Chi-restraints excluded: chain C residue 962 SER Chi-restraints excluded: chain C residue 971 SER Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1108 LYS Chi-restraints excluded: chain C residue 1145 VAL Chi-restraints excluded: chain C residue 1221 LEU Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 39 LYS Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 101 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 95 optimal weight: 2.9990 chunk 193 optimal weight: 0.9980 chunk 195 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 338 optimal weight: 0.4980 chunk 257 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 611 ASN A 685 HIS A 995 ASN A1125 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 GLN B 685 HIS ** B 838 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1038 ASN B1125 ASN C 162 ASN C 461 GLN C 631 GLN C 641 ASN C 685 HIS C 838 GLN C 858 ASN C 923 GLN C 938 ASN C 970 GLN C1141 ASN L 6 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.147696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.124875 restraints weight = 41296.413| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.78 r_work: 0.3204 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 29281 Z= 0.232 Angle : 0.710 22.529 39937 Z= 0.350 Chirality : 0.050 0.850 4573 Planarity : 0.005 0.055 5078 Dihedral : 8.062 101.764 5045 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 4.36 % Allowed : 19.33 % Favored : 76.31 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.13), residues: 3538 helix: 1.29 (0.19), residues: 734 sheet: 0.12 (0.17), residues: 846 loop : -0.62 (0.13), residues: 1958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP H 47 HIS 0.008 0.001 HIS B 691 PHE 0.022 0.002 PHE C 243 TYR 0.029 0.002 TYR B 653 ARG 0.005 0.000 ARG A1084 Details of bonding type rmsd link_NAG-ASN : bond 0.00554 ( 34) link_NAG-ASN : angle 4.16429 ( 102) link_ALPHA1-6 : bond 0.00412 ( 1) link_ALPHA1-6 : angle 1.37650 ( 3) link_BETA1-4 : bond 0.00654 ( 17) link_BETA1-4 : angle 2.41867 ( 51) link_ALPHA1-3 : bond 0.00991 ( 1) link_ALPHA1-3 : angle 2.87277 ( 3) hydrogen bonds : bond 0.04929 ( 1122) hydrogen bonds : angle 5.30452 ( 3231) link_BETA1-6 : bond 0.00742 ( 3) link_BETA1-6 : angle 1.64931 ( 9) SS BOND : bond 0.00711 ( 51) SS BOND : angle 3.17589 ( 102) covalent geometry : bond 0.00545 (29174) covalent geometry : angle 0.65402 (39667) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 925 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 790 time to evaluate : 3.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 GLN cc_start: 0.7342 (mp10) cc_final: 0.6953 (mp10) REVERT: A 49 MET cc_start: 0.8270 (OUTLIER) cc_final: 0.8031 (mmm) REVERT: A 55 LYS cc_start: 0.8465 (mtpp) cc_final: 0.8178 (mtpp) REVERT: A 75 GLN cc_start: 0.7562 (mm110) cc_final: 0.7285 (mm110) REVERT: A 210 VAL cc_start: 0.8478 (OUTLIER) cc_final: 0.8244 (t) REVERT: A 242 SER cc_start: 0.8136 (t) cc_final: 0.7764 (p) REVERT: A 256 GLU cc_start: 0.7858 (tp30) cc_final: 0.7457 (tp30) REVERT: A 295 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.7962 (mmtp) REVERT: A 296 TYR cc_start: 0.8192 (m-80) cc_final: 0.7778 (m-80) REVERT: A 428 SER cc_start: 0.8230 (t) cc_final: 0.7961 (p) REVERT: A 439 ARG cc_start: 0.8285 (ptt-90) cc_final: 0.8014 (ptt90) REVERT: A 460 MET cc_start: 0.8319 (tpp) cc_final: 0.7987 (mmt) REVERT: A 518 THR cc_start: 0.8038 (m) cc_final: 0.7782 (t) REVERT: A 521 VAL cc_start: 0.8196 (t) cc_final: 0.7937 (m) REVERT: A 539 SER cc_start: 0.8364 (t) cc_final: 0.8019 (m) REVERT: A 608 VAL cc_start: 0.7674 (OUTLIER) cc_final: 0.7406 (t) REVERT: A 615 VAL cc_start: 0.8248 (t) cc_final: 0.7801 (p) REVERT: A 681 VAL cc_start: 0.8197 (OUTLIER) cc_final: 0.7947 (m) REVERT: A 689 MET cc_start: 0.7119 (mtm) cc_final: 0.6465 (ppp) REVERT: A 743 VAL cc_start: 0.8629 (t) cc_final: 0.8310 (p) REVERT: A 754 GLN cc_start: 0.8008 (OUTLIER) cc_final: 0.7740 (mt0) REVERT: A 776 VAL cc_start: 0.8495 (m) cc_final: 0.8219 (p) REVERT: A 812 LYS cc_start: 0.7864 (tppp) cc_final: 0.7605 (mmmm) REVERT: A 910 LYS cc_start: 0.7763 (mtpt) cc_final: 0.7494 (mtpt) REVERT: A 1019 GLN cc_start: 0.8152 (tp-100) cc_final: 0.7844 (tp40) REVERT: A 1036 LEU cc_start: 0.8339 (mt) cc_final: 0.8129 (mt) REVERT: A 1060 GLU cc_start: 0.7506 (mt-10) cc_final: 0.7235 (mp0) REVERT: A 1082 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8234 (tt) REVERT: A 1143 VAL cc_start: 0.8303 (OUTLIER) cc_final: 0.8029 (m) REVERT: A 1144 ASN cc_start: 0.7959 (p0) cc_final: 0.7666 (p0) REVERT: A 1193 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7331 (mt-10) REVERT: A 1195 ILE cc_start: 0.8525 (mm) cc_final: 0.8207 (mt) REVERT: A 1201 ARG cc_start: 0.7674 (ttp80) cc_final: 0.7267 (ttp80) REVERT: B 44 ASN cc_start: 0.6982 (t0) cc_final: 0.6534 (t0) REVERT: B 112 THR cc_start: 0.8431 (m) cc_final: 0.8207 (p) REVERT: B 114 VAL cc_start: 0.8211 (t) cc_final: 0.7983 (p) REVERT: B 167 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7536 (ttt-90) REVERT: B 178 ASP cc_start: 0.6946 (t0) cc_final: 0.6560 (t70) REVERT: B 190 VAL cc_start: 0.7646 (p) cc_final: 0.7415 (m) REVERT: B 347 ASP cc_start: 0.7607 (OUTLIER) cc_final: 0.7301 (p0) REVERT: B 374 SER cc_start: 0.8214 (t) cc_final: 0.7983 (p) REVERT: B 442 TYR cc_start: 0.8436 (OUTLIER) cc_final: 0.7715 (p90) REVERT: B 498 SER cc_start: 0.8544 (t) cc_final: 0.8226 (p) REVERT: B 553 GLU cc_start: 0.7020 (OUTLIER) cc_final: 0.6767 (tp30) REVERT: B 586 ASN cc_start: 0.8156 (m-40) cc_final: 0.7869 (m110) REVERT: B 609 GLU cc_start: 0.6945 (tp30) cc_final: 0.6641 (tp30) REVERT: B 676 THR cc_start: 0.8151 (OUTLIER) cc_final: 0.7682 (p) REVERT: B 787 THR cc_start: 0.8694 (OUTLIER) cc_final: 0.8335 (p) REVERT: B 800 VAL cc_start: 0.8301 (m) cc_final: 0.8080 (t) REVERT: B 803 LYS cc_start: 0.8266 (ttmm) cc_final: 0.7967 (mmmt) REVERT: B 822 GLN cc_start: 0.6620 (pm20) cc_final: 0.6380 (pt0) REVERT: B 826 LYS cc_start: 0.8018 (mptp) cc_final: 0.7692 (mmtm) REVERT: B 836 LEU cc_start: 0.7613 (OUTLIER) cc_final: 0.7364 (mt) REVERT: B 864 ASP cc_start: 0.7741 (OUTLIER) cc_final: 0.7444 (m-30) REVERT: B 925 VAL cc_start: 0.8201 (t) cc_final: 0.7969 (m) REVERT: B 991 LYS cc_start: 0.8047 (mtpp) cc_final: 0.7661 (mmtm) REVERT: B 1019 GLN cc_start: 0.8043 (mm110) cc_final: 0.7768 (tp40) REVERT: B 1094 LEU cc_start: 0.8150 (tp) cc_final: 0.7852 (tt) REVERT: B 1153 ASN cc_start: 0.7555 (p0) cc_final: 0.7248 (p0) REVERT: B 1208 LYS cc_start: 0.7693 (ptpt) cc_final: 0.7054 (ptpt) REVERT: B 1210 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7363 (mm-30) REVERT: C 35 MET cc_start: 0.7487 (OUTLIER) cc_final: 0.7233 (mmt) REVERT: C 45 LYS cc_start: 0.8324 (mtmt) cc_final: 0.8009 (mtmm) REVERT: C 46 GLN cc_start: 0.7790 (mt0) cc_final: 0.7558 (mt0) REVERT: C 80 LYS cc_start: 0.8427 (mtmt) cc_final: 0.8132 (mttp) REVERT: C 183 ARG cc_start: 0.7463 (ttp-170) cc_final: 0.6960 (ttp-170) REVERT: C 190 VAL cc_start: 0.8189 (t) cc_final: 0.7948 (m) REVERT: C 225 THR cc_start: 0.7923 (p) cc_final: 0.7456 (t) REVERT: C 256 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7641 (mm-30) REVERT: C 302 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.7269 (ttp80) REVERT: C 347 ASP cc_start: 0.7337 (t0) cc_final: 0.7082 (t0) REVERT: C 350 GLN cc_start: 0.7202 (tp40) cc_final: 0.6817 (tp40) REVERT: C 423 MET cc_start: 0.7745 (OUTLIER) cc_final: 0.7124 (tpt) REVERT: C 456 MET cc_start: 0.7789 (mmt) cc_final: 0.6881 (mmt) REVERT: C 464 SER cc_start: 0.8250 (t) cc_final: 0.7882 (m) REVERT: C 540 GLN cc_start: 0.7872 (mt0) cc_final: 0.7475 (mt0) REVERT: C 543 ASP cc_start: 0.7705 (m-30) cc_final: 0.7373 (m-30) REVERT: C 546 THR cc_start: 0.7982 (m) cc_final: 0.7776 (t) REVERT: C 653 TYR cc_start: 0.8159 (m-80) cc_final: 0.7527 (m-80) REVERT: C 663 LEU cc_start: 0.8364 (mt) cc_final: 0.8130 (mm) REVERT: C 669 LYS cc_start: 0.8186 (ttpp) cc_final: 0.7848 (ttmm) REVERT: C 672 ASN cc_start: 0.8119 (t0) cc_final: 0.7715 (t0) REVERT: C 858 ASN cc_start: 0.7254 (t0) cc_final: 0.6835 (t0) REVERT: C 871 GLN cc_start: 0.7836 (mt0) cc_final: 0.7415 (mt0) REVERT: C 884 SER cc_start: 0.8017 (m) cc_final: 0.7788 (p) REVERT: C 892 ASN cc_start: 0.8148 (OUTLIER) cc_final: 0.7914 (m110) REVERT: C 894 VAL cc_start: 0.7946 (t) cc_final: 0.7673 (p) REVERT: C 962 SER cc_start: 0.8045 (OUTLIER) cc_final: 0.7844 (t) REVERT: C 971 SER cc_start: 0.7924 (OUTLIER) cc_final: 0.7389 (p) REVERT: C 972 ILE cc_start: 0.8264 (mm) cc_final: 0.7973 (mp) REVERT: C 988 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.6733 (mp0) REVERT: C 1012 ASN cc_start: 0.7311 (t0) cc_final: 0.7011 (m-40) REVERT: C 1060 GLU cc_start: 0.7774 (mp0) cc_final: 0.7208 (mp0) REVERT: C 1064 ASP cc_start: 0.7697 (m-30) cc_final: 0.7398 (m-30) REVERT: C 1086 GLU cc_start: 0.7695 (mt-10) cc_final: 0.7403 (mt-10) REVERT: C 1101 GLU cc_start: 0.7622 (mm-30) cc_final: 0.7234 (mm-30) REVERT: C 1193 GLU cc_start: 0.7638 (mt-10) cc_final: 0.7403 (mt-10) REVERT: C 1197 MET cc_start: 0.8249 (tpp) cc_final: 0.7825 (tpp) REVERT: H 89 VAL cc_start: 0.8118 (p) cc_final: 0.7745 (t) REVERT: L 10 THR cc_start: 0.7903 (m) cc_final: 0.7658 (p) REVERT: L 12 SER cc_start: 0.7807 (t) cc_final: 0.7571 (m) outliers start: 135 outliers final: 90 residues processed: 851 average time/residue: 1.2312 time to fit residues: 1251.4267 Evaluate side-chains 900 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 787 time to evaluate : 3.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 240 ASN Chi-restraints excluded: chain A residue 295 LYS Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 442 TYR Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 618 ARG Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 724 ASN Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 754 GLN Chi-restraints excluded: chain A residue 789 GLU Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain A residue 840 GLU Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1027 GLN Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1205 GLN Chi-restraints excluded: chain A residue 1208 LYS Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 167 ARG Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 442 TYR Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 553 GLU Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 743 VAL Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 836 LEU Chi-restraints excluded: chain B residue 849 ILE Chi-restraints excluded: chain B residue 864 ASP Chi-restraints excluded: chain B residue 889 LEU Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 992 LEU Chi-restraints excluded: chain B residue 1013 LEU Chi-restraints excluded: chain B residue 1035 GLU Chi-restraints excluded: chain B residue 1045 SER Chi-restraints excluded: chain B residue 1140 THR Chi-restraints excluded: chain B residue 1161 ILE Chi-restraints excluded: chain B residue 1207 VAL Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 302 ARG Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 339 ARG Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 423 MET Chi-restraints excluded: chain C residue 442 TYR Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain C residue 588 VAL Chi-restraints excluded: chain C residue 665 VAL Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 671 THR Chi-restraints excluded: chain C residue 673 SER Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 754 GLN Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 775 VAL Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 822 GLN Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 849 ILE Chi-restraints excluded: chain C residue 857 LEU Chi-restraints excluded: chain C residue 889 LEU Chi-restraints excluded: chain C residue 892 ASN Chi-restraints excluded: chain C residue 944 THR Chi-restraints excluded: chain C residue 962 SER Chi-restraints excluded: chain C residue 971 SER Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1035 GLU Chi-restraints excluded: chain C residue 1145 VAL Chi-restraints excluded: chain C residue 1221 LEU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 39 LYS Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 101 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 289 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 284 optimal weight: 0.6980 chunk 74 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 279 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 169 optimal weight: 0.5980 chunk 121 optimal weight: 0.6980 chunk 276 optimal weight: 5.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 611 ASN A 685 HIS A 995 ASN A1125 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 GLN B 713 GLN B 838 GLN B1038 ASN B1125 ASN C 162 ASN C 461 GLN C 631 GLN C 641 ASN C 685 HIS C 838 GLN C 938 ASN C 970 GLN C1141 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.148690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.125871 restraints weight = 41079.497| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.75 r_work: 0.3222 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 29281 Z= 0.159 Angle : 0.661 16.087 39937 Z= 0.325 Chirality : 0.047 0.557 4573 Planarity : 0.005 0.053 5078 Dihedral : 7.769 102.107 5045 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.52 % Allowed : 20.39 % Favored : 76.09 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.14), residues: 3538 helix: 1.50 (0.19), residues: 730 sheet: 0.23 (0.18), residues: 829 loop : -0.58 (0.13), residues: 1979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 47 HIS 0.008 0.001 HIS B 691 PHE 0.020 0.001 PHE C 243 TYR 0.025 0.001 TYR B 653 ARG 0.005 0.000 ARG B 547 Details of bonding type rmsd link_NAG-ASN : bond 0.00482 ( 34) link_NAG-ASN : angle 3.78667 ( 102) link_ALPHA1-6 : bond 0.00568 ( 1) link_ALPHA1-6 : angle 1.30595 ( 3) link_BETA1-4 : bond 0.00672 ( 17) link_BETA1-4 : angle 2.39006 ( 51) link_ALPHA1-3 : bond 0.01300 ( 1) link_ALPHA1-3 : angle 2.88934 ( 3) hydrogen bonds : bond 0.04475 ( 1122) hydrogen bonds : angle 5.16497 ( 3231) link_BETA1-6 : bond 0.00805 ( 3) link_BETA1-6 : angle 1.66323 ( 9) SS BOND : bond 0.00681 ( 51) SS BOND : angle 2.82884 ( 102) covalent geometry : bond 0.00371 (29174) covalent geometry : angle 0.61124 (39667) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7076 Ramachandran restraints generated. 3538 Oldfield, 0 Emsley, 3538 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 898 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 789 time to evaluate : 3.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 GLN cc_start: 0.7365 (mp10) cc_final: 0.6987 (mp10) REVERT: A 49 MET cc_start: 0.8259 (OUTLIER) cc_final: 0.8035 (mmm) REVERT: A 55 LYS cc_start: 0.8515 (mtpp) cc_final: 0.8239 (mtpp) REVERT: A 75 GLN cc_start: 0.7491 (mm110) cc_final: 0.7157 (mm110) REVERT: A 113 LYS cc_start: 0.7728 (mtpt) cc_final: 0.7459 (mppt) REVERT: A 152 MET cc_start: 0.8023 (ttp) cc_final: 0.7784 (ptp) REVERT: A 210 VAL cc_start: 0.8467 (OUTLIER) cc_final: 0.8232 (t) REVERT: A 256 GLU cc_start: 0.7883 (tp30) cc_final: 0.7514 (tp30) REVERT: A 296 TYR cc_start: 0.8208 (m-80) cc_final: 0.7817 (m-80) REVERT: A 375 ARG cc_start: 0.7459 (mtp85) cc_final: 0.7211 (mtp85) REVERT: A 439 ARG cc_start: 0.8305 (ptt-90) cc_final: 0.7948 (ptt90) REVERT: A 460 MET cc_start: 0.8350 (tpp) cc_final: 0.8013 (mmt) REVERT: A 518 THR cc_start: 0.8053 (m) cc_final: 0.7815 (t) REVERT: A 521 VAL cc_start: 0.8162 (t) cc_final: 0.7915 (m) REVERT: A 539 SER cc_start: 0.8367 (t) cc_final: 0.8034 (m) REVERT: A 608 VAL cc_start: 0.7780 (OUTLIER) cc_final: 0.7443 (t) REVERT: A 615 VAL cc_start: 0.8301 (t) cc_final: 0.7842 (p) REVERT: A 681 VAL cc_start: 0.8176 (OUTLIER) cc_final: 0.7921 (m) REVERT: A 689 MET cc_start: 0.7132 (mtm) cc_final: 0.6497 (ppp) REVERT: A 743 VAL cc_start: 0.8647 (t) cc_final: 0.8351 (p) REVERT: A 754 GLN cc_start: 0.7948 (OUTLIER) cc_final: 0.7697 (mt0) REVERT: A 766 LEU cc_start: 0.8274 (tp) cc_final: 0.7926 (tt) REVERT: A 776 VAL cc_start: 0.8507 (m) cc_final: 0.8230 (p) REVERT: A 812 LYS cc_start: 0.7837 (tppp) cc_final: 0.7593 (mmmm) REVERT: A 1036 LEU cc_start: 0.8385 (mt) cc_final: 0.8132 (mt) REVERT: A 1060 GLU cc_start: 0.7527 (mt-10) cc_final: 0.7261 (mp0) REVERT: A 1082 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8265 (tt) REVERT: A 1143 VAL cc_start: 0.8301 (OUTLIER) cc_final: 0.8027 (m) REVERT: A 1144 ASN cc_start: 0.7919 (p0) cc_final: 0.7642 (p0) REVERT: A 1165 ASP cc_start: 0.6337 (p0) cc_final: 0.6131 (p0) REVERT: A 1193 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7332 (mt-10) REVERT: A 1195 ILE cc_start: 0.8513 (mm) cc_final: 0.8187 (mt) REVERT: A 1201 ARG cc_start: 0.7714 (ttp80) cc_final: 0.7302 (ttp80) REVERT: A 1205 GLN cc_start: 0.7627 (OUTLIER) cc_final: 0.7298 (mm-40) REVERT: B 44 ASN cc_start: 0.6960 (t0) cc_final: 0.6506 (t0) REVERT: B 65 LYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7746 (mttm) REVERT: B 70 ILE cc_start: 0.7992 (OUTLIER) cc_final: 0.7684 (OUTLIER) REVERT: B 112 THR cc_start: 0.8433 (m) cc_final: 0.8218 (p) REVERT: B 114 VAL cc_start: 0.8195 (t) cc_final: 0.7990 (p) REVERT: B 178 ASP cc_start: 0.6949 (t0) cc_final: 0.6570 (t70) REVERT: B 190 VAL cc_start: 0.7687 (p) cc_final: 0.7483 (m) REVERT: B 347 ASP cc_start: 0.7577 (OUTLIER) cc_final: 0.7328 (p0) REVERT: B 374 SER cc_start: 0.8212 (t) cc_final: 0.7961 (p) REVERT: B 410 ASN cc_start: 0.7652 (t0) cc_final: 0.7366 (t0) REVERT: B 442 TYR cc_start: 0.8466 (OUTLIER) cc_final: 0.7817 (p90) REVERT: B 498 SER cc_start: 0.8535 (t) cc_final: 0.8220 (p) REVERT: B 553 GLU cc_start: 0.6970 (OUTLIER) cc_final: 0.6761 (tp30) REVERT: B 586 ASN cc_start: 0.8133 (m-40) cc_final: 0.7840 (m110) REVERT: B 609 GLU cc_start: 0.6963 (tp30) cc_final: 0.6685 (tp30) REVERT: B 676 THR cc_start: 0.8157 (OUTLIER) cc_final: 0.7707 (p) REVERT: B 787 THR cc_start: 0.8695 (OUTLIER) cc_final: 0.8359 (p) REVERT: B 826 LYS cc_start: 0.7880 (mptp) cc_final: 0.7594 (mmtm) REVERT: B 836 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.7361 (mt) REVERT: B 864 ASP cc_start: 0.7702 (OUTLIER) cc_final: 0.7348 (m-30) REVERT: B 939 MET cc_start: 0.7870 (mtp) cc_final: 0.7608 (ttt) REVERT: B 991 LYS cc_start: 0.8083 (mtpp) cc_final: 0.7670 (mmtm) REVERT: B 1019 GLN cc_start: 0.7980 (mm110) cc_final: 0.7712 (tp40) REVERT: B 1071 LEU cc_start: 0.8283 (mt) cc_final: 0.8072 (mm) REVERT: B 1094 LEU cc_start: 0.8197 (tp) cc_final: 0.7902 (tt) REVERT: B 1153 ASN cc_start: 0.7569 (p0) cc_final: 0.7268 (p0) REVERT: B 1208 LYS cc_start: 0.7696 (ptpt) cc_final: 0.7097 (ptpt) REVERT: B 1210 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7374 (mm-30) REVERT: C 35 MET cc_start: 0.7469 (OUTLIER) cc_final: 0.7231 (mmt) REVERT: C 45 LYS cc_start: 0.8315 (mtmt) cc_final: 0.8016 (mtmm) REVERT: C 46 GLN cc_start: 0.7782 (mt0) cc_final: 0.7566 (mt0) REVERT: C 80 LYS cc_start: 0.8449 (mtmt) cc_final: 0.8173 (mttp) REVERT: C 178 ASP cc_start: 0.6970 (t0) cc_final: 0.6691 (m-30) REVERT: C 183 ARG cc_start: 0.7468 (ttp-170) cc_final: 0.6944 (ttp-170) REVERT: C 190 VAL cc_start: 0.8205 (t) cc_final: 0.7999 (m) REVERT: C 225 THR cc_start: 0.8090 (p) cc_final: 0.7536 (t) REVERT: C 256 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7664 (mm-30) REVERT: C 302 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7234 (ttp80) REVERT: C 347 ASP cc_start: 0.7385 (t0) cc_final: 0.7118 (t0) REVERT: C 350 GLN cc_start: 0.7197 (tp40) cc_final: 0.6828 (tp40) REVERT: C 380 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7484 (mt-10) REVERT: C 423 MET cc_start: 0.7735 (OUTLIER) cc_final: 0.7139 (tpt) REVERT: C 456 MET cc_start: 0.7769 (mmt) cc_final: 0.6997 (mmt) REVERT: C 464 SER cc_start: 0.8240 (t) cc_final: 0.7868 (m) REVERT: C 540 GLN cc_start: 0.7884 (mt0) cc_final: 0.7530 (mt0) REVERT: C 543 ASP cc_start: 0.7716 (m-30) cc_final: 0.7434 (m-30) REVERT: C 653 TYR cc_start: 0.8153 (m-80) cc_final: 0.7478 (m-80) REVERT: C 663 LEU cc_start: 0.8357 (mt) cc_final: 0.8146 (mm) REVERT: C 669 LYS cc_start: 0.8202 (ttpp) cc_final: 0.7869 (ttmm) REVERT: C 672 ASN cc_start: 0.8146 (t0) cc_final: 0.7745 (t0) REVERT: C 754 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.7637 (mt0) REVERT: C 858 ASN cc_start: 0.7278 (t0) cc_final: 0.6970 (t0) REVERT: C 871 GLN cc_start: 0.7846 (mt0) cc_final: 0.7429 (mt0) REVERT: C 884 SER cc_start: 0.7989 (m) cc_final: 0.7771 (p) REVERT: C 893 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7613 (mptt) REVERT: C 894 VAL cc_start: 0.7968 (t) cc_final: 0.7706 (p) REVERT: C 962 SER cc_start: 0.8056 (OUTLIER) cc_final: 0.7848 (t) REVERT: C 971 SER cc_start: 0.7940 (OUTLIER) cc_final: 0.7418 (p) REVERT: C 972 ILE cc_start: 0.8322 (mm) cc_final: 0.8034 (mp) REVERT: C 988 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.6723 (mp0) REVERT: C 1012 ASN cc_start: 0.7256 (t0) cc_final: 0.7011 (m-40) REVERT: C 1060 GLU cc_start: 0.7741 (mp0) cc_final: 0.7220 (mp0) REVERT: C 1064 ASP cc_start: 0.7688 (m-30) cc_final: 0.7419 (m-30) REVERT: C 1065 ARG cc_start: 0.7851 (mtt-85) cc_final: 0.7616 (mtt90) REVERT: C 1086 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7420 (mt-10) REVERT: C 1101 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7260 (mm-30) REVERT: C 1193 GLU cc_start: 0.7612 (mt-10) cc_final: 0.7399 (mt-10) REVERT: C 1197 MET cc_start: 0.8205 (tpp) cc_final: 0.7812 (tpp) REVERT: L 10 THR cc_start: 0.7830 (m) cc_final: 0.7588 (p) REVERT: L 12 SER cc_start: 0.7715 (t) cc_final: 0.7465 (m) outliers start: 109 outliers final: 71 residues processed: 840 average time/residue: 1.2366 time to fit residues: 1233.6886 Evaluate side-chains 872 residues out of total 3099 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 777 time to evaluate : 2.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 442 TYR Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 618 ARG Chi-restraints excluded: chain A residue 622 ILE Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 681 VAL Chi-restraints excluded: chain A residue 724 ASN Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 754 GLN Chi-restraints excluded: chain A residue 789 GLU Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain A residue 840 GLU Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 1027 GLN Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1143 VAL Chi-restraints excluded: chain A residue 1169 VAL Chi-restraints excluded: chain A residue 1205 GLN Chi-restraints excluded: chain A residue 1208 LYS Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 292 ASP Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 442 TYR Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 553 GLU Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 612 LEU Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 787 THR Chi-restraints excluded: chain B residue 836 LEU Chi-restraints excluded: chain B residue 864 ASP Chi-restraints excluded: chain B residue 889 LEU Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 957 THR Chi-restraints excluded: chain B residue 992 LEU Chi-restraints excluded: chain B residue 1013 LEU Chi-restraints excluded: chain B residue 1035 GLU Chi-restraints excluded: chain B residue 1140 THR Chi-restraints excluded: chain B residue 1161 ILE Chi-restraints excluded: chain B residue 1207 VAL Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 302 ARG Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 339 ARG Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 423 MET Chi-restraints excluded: chain C residue 442 TYR Chi-restraints excluded: chain C residue 515 HIS Chi-restraints excluded: chain C residue 522 ILE Chi-restraints excluded: chain C residue 588 VAL Chi-restraints excluded: chain C residue 665 VAL Chi-restraints excluded: chain C residue 670 THR Chi-restraints excluded: chain C residue 671 THR Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 754 GLN Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 775 VAL Chi-restraints excluded: chain C residue 819 GLU Chi-restraints excluded: chain C residue 893 LYS Chi-restraints excluded: chain C residue 944 THR Chi-restraints excluded: chain C residue 962 SER Chi-restraints excluded: chain C residue 971 SER Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1142 HIS Chi-restraints excluded: chain C residue 1145 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain H residue 109 VAL Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 39 LYS Chi-restraints excluded: chain L residue 101 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 37 optimal weight: 1.9990 chunk 189 optimal weight: 2.9990 chunk 198 optimal weight: 6.9990 chunk 249 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 338 optimal weight: 0.3980 chunk 337 optimal weight: 0.9980 chunk 229 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 291 optimal weight: 0.9980 chunk 222 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 611 ASN A 685 HIS A 995 ASN A1125 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 GLN B 685 HIS B 713 GLN B 838 GLN B1038 ASN B1125 ASN C 162 ASN C 631 GLN C 641 ASN C 685 HIS C 838 GLN C 923 GLN C 938 ASN C 970 GLN C1141 ASN L 6 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.148600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.125645 restraints weight = 41058.655| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.76 r_work: 0.3220 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.188 29281 Z= 0.214 Angle : 0.779 59.199 39937 Z= 0.414 Chirality : 0.051 1.124 4573 Planarity : 0.005 0.053 5078 Dihedral : 7.787 102.079 5045 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.35 % Favored : 97.63 % Rotamer: Outliers : 3.74 % Allowed : 20.56 % Favored : 75.70 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 3.28 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.14), residues: 3538 helix: 1.50 (0.19), residues: 730 sheet: 0.22 (0.18), residues: 829 loop : -0.58 (0.13), residues: 1979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 47 HIS 0.006 0.001 HIS B 691 PHE 0.020 0.001 PHE C 243 TYR 0.022 0.001 TYR L 89 ARG 0.005 0.000 ARG B 547 Details of bonding type rmsd link_NAG-ASN : bond 0.00512 ( 34) link_NAG-ASN : angle 3.76724 ( 102) link_ALPHA1-6 : bond 0.00535 ( 1) link_ALPHA1-6 : angle 1.29479 ( 3) link_BETA1-4 : bond 0.00663 ( 17) link_BETA1-4 : angle 2.40072 ( 51) link_ALPHA1-3 : bond 0.01304 ( 1) link_ALPHA1-3 : angle 2.89766 ( 3) hydrogen bonds : bond 0.04506 ( 1122) hydrogen bonds : angle 5.16733 ( 3231) link_BETA1-6 : bond 0.00840 ( 3) link_BETA1-6 : angle 1.68855 ( 9) SS BOND : bond 0.00806 ( 51) SS BOND : angle 3.31748 ( 102) covalent geometry : bond 0.00462 (29174) covalent geometry : angle 0.73272 (39667) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25300.46 seconds wall clock time: 434 minutes 45.50 seconds (26085.50 seconds total)