Starting phenix.real_space_refine on Fri Mar 6 19:01:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pnm_13549/03_2026/7pnm_13549.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pnm_13549/03_2026/7pnm_13549.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pnm_13549/03_2026/7pnm_13549.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pnm_13549/03_2026/7pnm_13549.map" model { file = "/net/cci-nas-00/data/ceres_data/7pnm_13549/03_2026/7pnm_13549.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pnm_13549/03_2026/7pnm_13549.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.035 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 207 5.16 5 C 21303 2.51 5 N 5487 2.21 5 O 6543 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33540 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 9150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1175, 9150 Classifications: {'peptide': 1175} Link IDs: {'PCIS': 4, 'PTRANS': 46, 'TRANS': 1124} Chain breaks: 5 Chain: "L" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 847 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 104} Chain: "H" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 959 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "B" Number of atoms: 9150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1175, 9150 Classifications: {'peptide': 1175} Link IDs: {'PCIS': 4, 'PTRANS': 46, 'TRANS': 1124} Chain breaks: 5 Chain: "D" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 847 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 104} Chain: "G" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 959 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "C" Number of atoms: 9150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1175, 9150 Classifications: {'peptide': 1175} Link IDs: {'PCIS': 4, 'PTRANS': 46, 'TRANS': 1124} Chain breaks: 5 Chain: "E" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 847 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 104} Chain: "I" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 959 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} 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: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" 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: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" 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: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 7.98, per 1000 atoms: 0.24 Number of scatterers: 33540 At special positions: 0 Unit cell: (191.7, 207.675, 161.88, 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 207 16.00 O 6543 8.00 N 5487 7.00 C 21303 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=69, symmetry=0 Simple disulfide: pdb=" SG CYS A 21 " - pdb=" SG CYS A 169 " distance=2.03 Simple disulfide: pdb=" SG CYS A 164 " - pdb=" SG CYS A 197 " distance=2.04 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 256 " distance=2.03 Simple disulfide: pdb=" SG CYS A 290 " - pdb=" SG CYS A 300 " distance=2.03 Simple disulfide: pdb=" SG CYS A 335 " - pdb=" SG CYS A 360 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 431 " distance=2.03 Simple disulfide: pdb=" SG CYS A 390 " - pdb=" SG CYS A 606 " distance=2.05 Simple disulfide: pdb=" SG CYS A 483 " - pdb=" SG CYS A 553 " distance=2.03 Simple disulfide: pdb=" SG CYS A 491 " - pdb=" SG CYS A 514 " distance=2.03 Simple disulfide: pdb=" SG CYS A 493 " - pdb=" SG CYS A 568 " distance=2.03 Simple disulfide: pdb=" SG CYS A 527 " - pdb=" SG CYS A 540 " distance=2.03 Simple disulfide: pdb=" SG CYS A 563 " - pdb=" SG CYS A 570 " distance=2.03 Simple disulfide: pdb=" SG CYS A 583 " - pdb=" SG CYS A 589 " distance=2.04 Simple disulfide: pdb=" SG CYS A 622 " - pdb=" SG CYS A 675 " distance=2.04 Simple disulfide: pdb=" SG CYS A 700 " - pdb=" SG CYS A 725 " distance=2.03 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 818 " - pdb=" SG CYS A 840 " distance=2.03 Simple disulfide: pdb=" SG CYS A 823 " - pdb=" SG CYS A 829 " distance=2.03 Simple disulfide: pdb=" SG CYS A 930 " - pdb=" SG CYS A 941 " distance=2.03 Simple disulfide: pdb=" SG CYS A1118 " - pdb=" SG CYS A1129 " distance=2.04 Simple disulfide: pdb=" SG CYS A1168 " - pdb=" SG CYS A1213 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 169 " distance=2.03 Simple disulfide: pdb=" SG CYS B 164 " - pdb=" SG CYS B 197 " distance=2.04 Simple disulfide: pdb=" SG CYS B 176 " - pdb=" SG CYS B 256 " distance=2.03 Simple disulfide: pdb=" SG CYS B 290 " - pdb=" SG CYS B 300 " distance=2.03 Simple disulfide: pdb=" SG CYS B 335 " - pdb=" SG CYS B 360 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 431 " distance=2.03 Simple disulfide: pdb=" SG CYS B 390 " - pdb=" SG CYS B 606 " distance=2.05 Simple disulfide: pdb=" SG CYS B 483 " - pdb=" SG CYS B 553 " distance=2.03 Simple disulfide: pdb=" SG CYS B 491 " - pdb=" SG CYS B 514 " distance=2.03 Simple disulfide: pdb=" SG CYS B 493 " - pdb=" SG CYS B 568 " distance=2.03 Simple disulfide: pdb=" SG CYS B 527 " - pdb=" SG CYS B 540 " distance=2.03 Simple disulfide: pdb=" SG CYS B 563 " - pdb=" SG CYS B 570 " distance=2.03 Simple disulfide: pdb=" SG CYS B 583 " - pdb=" SG CYS B 589 " distance=2.04 Simple disulfide: pdb=" SG CYS B 622 " - pdb=" SG CYS B 675 " distance=2.04 Simple disulfide: pdb=" SG CYS B 700 " - pdb=" SG CYS B 725 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 818 " - pdb=" SG CYS B 840 " distance=2.03 Simple disulfide: pdb=" SG CYS B 823 " - pdb=" SG CYS B 829 " distance=2.03 Simple disulfide: pdb=" SG CYS B 930 " - pdb=" SG CYS B 941 " distance=2.03 Simple disulfide: pdb=" SG CYS B1118 " - pdb=" SG CYS B1129 " distance=2.04 Simple disulfide: pdb=" SG CYS B1168 " - pdb=" SG CYS B1213 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 93 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 21 " - pdb=" SG CYS C 169 " distance=2.03 Simple disulfide: pdb=" SG CYS C 164 " - pdb=" SG CYS C 197 " distance=2.04 Simple disulfide: pdb=" SG CYS C 176 " - pdb=" SG CYS C 256 " distance=2.03 Simple disulfide: pdb=" SG CYS C 290 " - pdb=" SG CYS C 300 " distance=2.03 Simple disulfide: pdb=" SG CYS C 335 " - pdb=" SG CYS C 360 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 431 " distance=2.03 Simple disulfide: pdb=" SG CYS C 390 " - pdb=" SG CYS C 606 " distance=2.04 Simple disulfide: pdb=" SG CYS C 483 " - pdb=" SG CYS C 553 " distance=2.03 Simple disulfide: pdb=" SG CYS C 491 " - pdb=" SG CYS C 514 " distance=2.03 Simple disulfide: pdb=" SG CYS C 493 " - pdb=" SG CYS C 568 " distance=2.03 Simple disulfide: pdb=" SG CYS C 527 " - pdb=" SG CYS C 540 " distance=2.03 Simple disulfide: pdb=" SG CYS C 563 " - pdb=" SG CYS C 570 " distance=2.03 Simple disulfide: pdb=" SG CYS C 583 " - pdb=" SG CYS C 589 " distance=2.04 Simple disulfide: pdb=" SG CYS C 622 " - pdb=" SG CYS C 675 " distance=2.04 Simple disulfide: pdb=" SG CYS C 700 " - pdb=" SG CYS C 725 " distance=2.03 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 818 " - pdb=" SG CYS C 840 " distance=2.03 Simple disulfide: pdb=" SG CYS C 823 " - pdb=" SG CYS C 829 " distance=2.03 Simple disulfide: pdb=" SG CYS C 930 " - pdb=" SG CYS C 941 " distance=2.03 Simple disulfide: pdb=" SG CYS C1118 " - pdb=" SG CYS C1129 " distance=2.04 Simple disulfide: pdb=" SG CYS C1168 " - pdb=" SG CYS C1213 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 93 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A1401 " - " ASN A 441 " " NAG A1402 " - " ASN A 640 " " NAG A1403 " - " ASN A 731 " " NAG A1404 " - " ASN A 59 " " NAG A1405 " - " ASN A 146 " " NAG A1406 " - " ASN A 667 " " NAG A1407 " - " ASN A 687 " " NAG A1408 " - " ASN A 706 " " NAG B1401 " - " ASN B 441 " " NAG B1402 " - " ASN B 640 " " NAG B1403 " - " ASN B 731 " " NAG B1404 " - " ASN B 59 " " NAG B1405 " - " ASN B 146 " " NAG B1406 " - " ASN B 667 " " NAG B1407 " - " ASN B 687 " " NAG B1408 " - " ASN B 706 " " NAG C1401 " - " ASN C 441 " " NAG C1402 " - " ASN C 640 " " NAG C1403 " - " ASN C 731 " " NAG C1404 " - " ASN C 59 " " NAG C1405 " - " ASN C 146 " " NAG C1406 " - " ASN C 667 " " NAG C1407 " - " ASN C 687 " " NAG C1408 " - " ASN C 706 " " NAG F 1 " - " ASN A 133 " " NAG J 1 " - " ASN A 202 " " NAG K 1 " - " ASN A 363 " " NAG M 1 " - " ASN A 929 " " NAG N 1 " - " ASN B 133 " " NAG O 1 " - " ASN B 202 " " NAG P 1 " - " ASN B 363 " " NAG Q 1 " - " ASN B 929 " " NAG R 1 " - " ASN C 133 " " NAG S 1 " - " ASN C 202 " " NAG T 1 " - " ASN C 363 " " NAG U 1 " - " ASN C 929 " Time building additional restraints: 2.95 Conformation dependent library (CDL) restraints added in 1.5 seconds 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7854 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 84 sheets defined 21.8% alpha, 31.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.76 Creating SS restraints... Processing helix chain 'A' and resid 89 through 91 No H-bonds generated for 'chain 'A' and resid 89 through 91' Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 336 through 342 removed outlier: 3.563A pdb=" N TRP A 340 " --> pdb=" O ASN A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 371 removed outlier: 3.765A pdb=" N LEU A 367 " --> pdb=" O ASN A 363 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N SER A 369 " --> pdb=" O SER A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.598A pdb=" N LEU A 409 " --> pdb=" O LYS A 406 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 421 Processing helix chain 'A' and resid 450 through 456 removed outlier: 3.507A pdb=" N LYS A 454 " --> pdb=" O SER A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 464 removed outlier: 3.718A pdb=" N VAL A 463 " --> pdb=" O ILE A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 573 No H-bonds generated for 'chain 'A' and resid 571 through 573' Processing helix chain 'A' and resid 700 through 708 removed outlier: 3.627A pdb=" N PHE A 705 " --> pdb=" O CYS A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 823 Processing helix chain 'A' and resid 826 through 834 removed outlier: 3.990A pdb=" N VAL A 834 " --> pdb=" O LYS A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 836 through 866 removed outlier: 3.717A pdb=" N CYS A 840 " --> pdb=" O TYR A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 878 removed outlier: 3.676A pdb=" N GLY A 878 " --> pdb=" O LEU A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 906 through 915 removed outlier: 3.626A pdb=" N LYS A 915 " --> pdb=" O LEU A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 930 removed outlier: 4.095A pdb=" N CYS A 930 " --> pdb=" O ALA A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 946 removed outlier: 3.500A pdb=" N LYS A 946 " --> pdb=" O VAL A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 956 through 973 Processing helix chain 'A' and resid 983 through 994 Processing helix chain 'A' and resid 1000 through 1004 removed outlier: 3.793A pdb=" N SER A1003 " --> pdb=" O ASP A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1023 Processing helix chain 'A' and resid 1028 through 1050 Processing helix chain 'A' and resid 1051 through 1053 No H-bonds generated for 'chain 'A' and resid 1051 through 1053' Processing helix chain 'A' and resid 1062 through 1070 Processing helix chain 'A' and resid 1071 through 1118 Processing helix chain 'L' and resid 84 through 88 removed outlier: 3.875A pdb=" N VAL L 88 " --> pdb=" O ALA L 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.700A pdb=" N SER H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.909A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 105 removed outlier: 3.529A pdb=" N ASP H 104 " --> pdb=" O GLN H 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 91 No H-bonds generated for 'chain 'B' and resid 89 through 91' Processing helix chain 'B' and resid 293 through 302 Processing helix chain 'B' and resid 336 through 342 removed outlier: 3.591A pdb=" N TRP B 340 " --> pdb=" O ASN B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 371 removed outlier: 3.769A pdb=" N LEU B 367 " --> pdb=" O ASN B 363 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N SER B 369 " --> pdb=" O SER B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.600A pdb=" N LEU B 409 " --> pdb=" O LYS B 406 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLN B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 421 Processing helix chain 'B' and resid 450 through 456 removed outlier: 3.506A pdb=" N LYS B 454 " --> pdb=" O SER B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 464 removed outlier: 3.747A pdb=" N VAL B 463 " --> pdb=" O ILE B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 573 No H-bonds generated for 'chain 'B' and resid 571 through 573' Processing helix chain 'B' and resid 700 through 708 removed outlier: 3.605A pdb=" N PHE B 705 " --> pdb=" O CYS B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 823 Processing helix chain 'B' and resid 826 through 834 removed outlier: 3.977A pdb=" N VAL B 834 " --> pdb=" O LYS B 830 " (cutoff:3.500A) Processing helix chain 'B' and resid 836 through 866 removed outlier: 3.737A pdb=" N CYS B 840 " --> pdb=" O TYR B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 874 through 878 removed outlier: 3.667A pdb=" N GLY B 878 " --> pdb=" O LEU B 875 " (cutoff:3.500A) Processing helix chain 'B' and resid 906 through 915 removed outlier: 3.570A pdb=" N LYS B 915 " --> pdb=" O LEU B 911 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 930 removed outlier: 4.116A pdb=" N CYS B 930 " --> pdb=" O ALA B 926 " (cutoff:3.500A) Processing helix chain 'B' and resid 938 through 946 removed outlier: 3.506A pdb=" N LYS B 946 " --> pdb=" O VAL B 942 " (cutoff:3.500A) Processing helix chain 'B' and resid 956 through 973 Processing helix chain 'B' and resid 983 through 994 Processing helix chain 'B' and resid 1000 through 1004 removed outlier: 3.834A pdb=" N SER B1003 " --> pdb=" O ASP B1000 " (cutoff:3.500A) Processing helix chain 'B' and resid 1005 through 1023 Processing helix chain 'B' and resid 1028 through 1050 Processing helix chain 'B' and resid 1051 through 1053 No H-bonds generated for 'chain 'B' and resid 1051 through 1053' Processing helix chain 'B' and resid 1062 through 1070 Processing helix chain 'B' and resid 1071 through 1118 Processing helix chain 'D' and resid 84 through 88 removed outlier: 3.892A pdb=" N VAL D 88 " --> pdb=" O ALA D 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.718A pdb=" N SER G 31 " --> pdb=" O THR G 28 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N TYR G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 28 through 32' Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.877A pdb=" N THR G 91 " --> pdb=" O ALA G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 105 removed outlier: 3.532A pdb=" N ASP G 104 " --> pdb=" O GLN G 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 91 No H-bonds generated for 'chain 'C' and resid 89 through 91' Processing helix chain 'C' and resid 293 through 302 Processing helix chain 'C' and resid 336 through 342 removed outlier: 3.587A pdb=" N TRP C 340 " --> pdb=" O ASN C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 371 removed outlier: 3.768A pdb=" N LEU C 367 " --> pdb=" O ASN C 363 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N SER C 369 " --> pdb=" O SER C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.586A pdb=" N LEU C 409 " --> pdb=" O LYS C 406 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 421 Processing helix chain 'C' and resid 450 through 456 removed outlier: 3.548A pdb=" N LYS C 454 " --> pdb=" O SER C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 464 removed outlier: 3.733A pdb=" N VAL C 463 " --> pdb=" O ILE C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 573 No H-bonds generated for 'chain 'C' and resid 571 through 573' Processing helix chain 'C' and resid 700 through 708 removed outlier: 3.613A pdb=" N PHE C 705 " --> pdb=" O CYS C 700 " (cutoff:3.500A) Processing helix chain 'C' and resid 817 through 823 Processing helix chain 'C' and resid 826 through 834 removed outlier: 3.988A pdb=" N VAL C 834 " --> pdb=" O LYS C 830 " (cutoff:3.500A) Processing helix chain 'C' and resid 836 through 866 removed outlier: 3.740A pdb=" N CYS C 840 " --> pdb=" O TYR C 836 " (cutoff:3.500A) Processing helix chain 'C' and resid 874 through 878 removed outlier: 3.669A pdb=" N GLY C 878 " --> pdb=" O LEU C 875 " (cutoff:3.500A) Processing helix chain 'C' and resid 906 through 915 removed outlier: 3.561A pdb=" N LYS C 915 " --> pdb=" O LEU C 911 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 930 removed outlier: 4.071A pdb=" N CYS C 930 " --> pdb=" O ALA C 926 " (cutoff:3.500A) Processing helix chain 'C' and resid 938 through 946 removed outlier: 3.510A pdb=" N LYS C 946 " --> pdb=" O VAL C 942 " (cutoff:3.500A) Processing helix chain 'C' and resid 956 through 973 Processing helix chain 'C' and resid 983 through 994 Processing helix chain 'C' and resid 1000 through 1004 removed outlier: 3.799A pdb=" N SER C1003 " --> pdb=" O ASP C1000 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1023 Processing helix chain 'C' and resid 1028 through 1050 Processing helix chain 'C' and resid 1051 through 1053 No H-bonds generated for 'chain 'C' and resid 1051 through 1053' Processing helix chain 'C' and resid 1062 through 1070 Processing helix chain 'C' and resid 1071 through 1118 Processing helix chain 'E' and resid 84 through 88 removed outlier: 3.882A pdb=" N VAL E 88 " --> pdb=" O ALA E 85 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.720A pdb=" N SER I 31 " --> pdb=" O THR I 28 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N TYR I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 28 through 32' Processing helix chain 'I' and resid 87 through 91 removed outlier: 3.867A pdb=" N THR I 91 " --> pdb=" O ALA I 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 101 through 105 removed outlier: 3.525A pdb=" N ASP I 104 " --> pdb=" O GLN I 101 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 27 Processing sheet with id=AA2, first strand: chain 'A' and resid 61 through 69 removed outlier: 4.604A pdb=" N GLU A 263 " --> pdb=" O LYS A 108 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS A 108 " --> pdb=" O GLU A 263 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLY A 102 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR A 213 " --> pdb=" O THR A 228 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR A 217 " --> pdb=" O TYR A 224 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR A 222 " --> pdb=" O GLU A 219 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N PHE A 223 " --> pdb=" O ASN A 239 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ASN A 239 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ALA A 225 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU A 237 " --> pdb=" O ALA A 225 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 61 through 69 removed outlier: 3.845A pdb=" N ASN A 286 " --> pdb=" O ALA A 277 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 81 through 82 removed outlier: 7.195A pdb=" N THR A 174 " --> pdb=" O THR A 255 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 96 through 98 removed outlier: 3.761A pdb=" N VAL A 139 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN A 141 " --> pdb=" O GLU A 160 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL A 161 " --> pdb=" O ARG A 201 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR A 199 " --> pdb=" O VAL A 163 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 96 through 98 removed outlier: 3.761A pdb=" N VAL A 139 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN A 141 " --> pdb=" O GLU A 160 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY A 157 " --> pdb=" O TYR A 205 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N TYR A 205 " --> pdb=" O GLY A 157 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 110 through 114 Processing sheet with id=AA8, first strand: chain 'A' and resid 310 through 313 removed outlier: 3.901A pdb=" N PHE A 684 " --> pdb=" O GLY A 310 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 317 through 318 Processing sheet with id=AB1, first strand: chain 'A' and resid 323 through 327 removed outlier: 3.677A pdb=" N GLY A 632 " --> pdb=" O TYR A 625 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N TYR A 659 " --> pdb=" O ILE A 672 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLY A 660 " --> pdb=" O LEU A 651 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 353 through 358 removed outlier: 3.784A pdb=" N GLU A 353 " --> pdb=" O LYS A 398 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS A 398 " --> pdb=" O GLU A 353 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS A 355 " --> pdb=" O ILE A 396 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ILE A 396 " --> pdb=" O LYS A 355 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N SER A 393 " --> pdb=" O HIS A 598 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER A 375 " --> pdb=" O TYR A 434 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N ASN A 436 " --> pdb=" O ALA A 373 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ALA A 373 " --> pdb=" O ASN A 436 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 353 through 358 removed outlier: 3.784A pdb=" N GLU A 353 " --> pdb=" O LYS A 398 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS A 398 " --> pdb=" O GLU A 353 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS A 355 " --> pdb=" O ILE A 396 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ILE A 396 " --> pdb=" O LYS A 355 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N SER A 393 " --> pdb=" O HIS A 598 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 361 through 362 Processing sheet with id=AB5, first strand: chain 'A' and resid 476 through 480 Processing sheet with id=AB6, first strand: chain 'A' and resid 483 through 485 removed outlier: 4.327A pdb=" N CYS A 483 " --> pdb=" O SER A 545 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR A 543 " --> pdb=" O LYS A 485 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 557 through 558 Processing sheet with id=AB8, first strand: chain 'A' and resid 730 through 737 removed outlier: 7.373A pdb=" N TYR A 730 " --> pdb=" O PHE A 768 " (cutoff:3.500A) removed outlier: 9.020A pdb=" N ASN A 770 " --> pdb=" O TYR A 730 " (cutoff:3.500A) removed outlier: 9.921A pdb=" N SER A 732 " --> pdb=" O ASN A 770 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TYR A 748 " --> pdb=" O VAL A 744 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU A 742 " --> pdb=" O VAL A 750 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 777 through 779 removed outlier: 5.819A pdb=" N ASN A 777 " --> pdb=" O LEU B 871 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 790 through 800 removed outlier: 3.698A pdb=" N ILE A 792 " --> pdb=" O ALA A1161 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA A1161 " --> pdb=" O ILE A 792 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LYS A1157 " --> pdb=" O SER A 796 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N PHE A 798 " --> pdb=" O PRO A1155 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ILE A 800 " --> pdb=" O TYR A1153 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N TYR A1153 " --> pdb=" O ILE A 800 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 790 through 800 removed outlier: 3.698A pdb=" N ILE A 792 " --> pdb=" O ALA A1161 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA A1161 " --> pdb=" O ILE A 792 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LYS A1157 " --> pdb=" O SER A 796 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N PHE A 798 " --> pdb=" O PRO A1155 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ILE A 800 " --> pdb=" O TYR A1153 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N TYR A1153 " --> pdb=" O ILE A 800 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY A1145 " --> pdb=" O ALA A1142 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA A1142 " --> pdb=" O GLY A1145 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ILE A1136 " --> pdb=" O PHE A1151 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N TYR A1153 " --> pdb=" O HIS A1134 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N HIS A1134 " --> pdb=" O TYR A1153 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 814 through 816 Processing sheet with id=AC4, first strand: chain 'A' and resid 870 through 872 Processing sheet with id=AC5, first strand: chain 'A' and resid 882 through 883 removed outlier: 3.544A pdb=" N VAL A 883 " --> pdb=" O ILE A 886 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 1207 through 1210 removed outlier: 3.698A pdb=" N ALA A1176 " --> pdb=" O VAL A1208 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU A1167 " --> pdb=" O ILE A1175 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 1181 through 1185 Processing sheet with id=AC8, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.625A pdb=" N VAL L 13 " --> pdb=" O GLU L 110 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL L 90 " --> pdb=" O GLN L 43 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN L 43 " --> pdb=" O VAL L 90 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N MET L 94 " --> pdb=" O ASP L 39 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASP L 39 " --> pdb=" O MET L 94 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N TRP L 40 " --> pdb=" O LEU L 52 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AD1, first strand: chain 'H' and resid 3 through 7 removed outlier: 4.268A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU H 20 " --> pdb=" O LEU H 81 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 10 through 12 removed outlier: 7.253A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL H 50 " --> pdb=" O TYR H 59 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N TYR H 59 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 26 through 27 Processing sheet with id=AD4, first strand: chain 'B' and resid 61 through 69 removed outlier: 4.585A pdb=" N GLU B 263 " --> pdb=" O LYS B 108 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS B 108 " --> pdb=" O GLU B 263 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLY B 102 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR B 213 " --> pdb=" O THR B 228 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR B 217 " --> pdb=" O TYR B 224 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR B 222 " --> pdb=" O GLU B 219 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N PHE B 238 " --> pdb=" O ALA B 225 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N PHE B 227 " --> pdb=" O PHE B 236 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N PHE B 236 " --> pdb=" O PHE B 227 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 61 through 69 removed outlier: 3.783A pdb=" N ASN B 286 " --> pdb=" O ALA B 277 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 81 through 82 removed outlier: 8.372A pdb=" N THR B 255 " --> pdb=" O PRO B 172 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N THR B 174 " --> pdb=" O THR B 255 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N TRP B 188 " --> pdb=" O CYS B 169 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.764A pdb=" N VAL B 139 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN B 141 " --> pdb=" O GLU B 160 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL B 161 " --> pdb=" O ARG B 201 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR B 199 " --> pdb=" O VAL B 163 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.764A pdb=" N VAL B 139 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN B 141 " --> pdb=" O GLU B 160 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLY B 157 " --> pdb=" O TYR B 205 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TYR B 205 " --> pdb=" O GLY B 157 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 110 through 114 Processing sheet with id=AE1, first strand: chain 'B' and resid 310 through 313 removed outlier: 3.862A pdb=" N PHE B 684 " --> pdb=" O GLY B 310 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER B 681 " --> pdb=" O LEU B 694 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 323 through 327 removed outlier: 3.732A pdb=" N GLY B 632 " --> pdb=" O TYR B 625 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N TYR B 659 " --> pdb=" O ILE B 672 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLY B 660 " --> pdb=" O LEU B 651 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 355 through 358 removed outlier: 3.837A pdb=" N LYS B 355 " --> pdb=" O ILE B 396 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE B 396 " --> pdb=" O LYS B 355 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N SER B 393 " --> pdb=" O HIS B 598 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER B 430 " --> pdb=" O ASN B 379 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER B 375 " --> pdb=" O TYR B 434 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ASN B 436 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N ALA B 373 " --> pdb=" O ASN B 436 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 355 through 358 removed outlier: 3.837A pdb=" N LYS B 355 " --> pdb=" O ILE B 396 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE B 396 " --> pdb=" O LYS B 355 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N SER B 393 " --> pdb=" O HIS B 598 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 361 through 362 Processing sheet with id=AE6, first strand: chain 'B' and resid 476 through 480 Processing sheet with id=AE7, first strand: chain 'B' and resid 483 through 485 removed outlier: 4.272A pdb=" N CYS B 483 " --> pdb=" O SER B 545 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR B 543 " --> pdb=" O LYS B 485 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 557 through 558 Processing sheet with id=AE9, first strand: chain 'B' and resid 730 through 737 removed outlier: 7.322A pdb=" N TYR B 730 " --> pdb=" O PHE B 768 " (cutoff:3.500A) removed outlier: 8.998A pdb=" N ASN B 770 " --> pdb=" O TYR B 730 " (cutoff:3.500A) removed outlier: 9.961A pdb=" N SER B 732 " --> pdb=" O ASN B 770 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N TYR B 748 " --> pdb=" O VAL B 744 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LEU B 742 " --> pdb=" O VAL B 750 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 777 through 779 removed outlier: 5.825A pdb=" N ASN B 777 " --> pdb=" O LEU C 871 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'B' and resid 790 through 800 removed outlier: 3.718A pdb=" N ILE B 792 " --> pdb=" O ALA B1161 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA B1161 " --> pdb=" O ILE B 792 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LYS B1157 " --> pdb=" O SER B 796 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N PHE B 798 " --> pdb=" O PRO B1155 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N ILE B 800 " --> pdb=" O TYR B1153 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N TYR B1153 " --> pdb=" O ILE B 800 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 790 through 800 removed outlier: 3.718A pdb=" N ILE B 792 " --> pdb=" O ALA B1161 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA B1161 " --> pdb=" O ILE B 792 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LYS B1157 " --> pdb=" O SER B 796 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N PHE B 798 " --> pdb=" O PRO B1155 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N ILE B 800 " --> pdb=" O TYR B1153 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N TYR B1153 " --> pdb=" O ILE B 800 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY B1145 " --> pdb=" O ALA B1142 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA B1142 " --> pdb=" O GLY B1145 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE B1136 " --> pdb=" O PHE B1151 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N TYR B1153 " --> pdb=" O HIS B1134 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N HIS B1134 " --> pdb=" O TYR B1153 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 814 through 816 Processing sheet with id=AF5, first strand: chain 'B' and resid 882 through 883 removed outlier: 3.550A pdb=" N VAL B 883 " --> pdb=" O ILE B 886 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'B' and resid 1207 through 1210 removed outlier: 3.679A pdb=" N ALA B1176 " --> pdb=" O VAL B1208 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU B1167 " --> pdb=" O ILE B1175 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'B' and resid 1181 through 1185 Processing sheet with id=AF8, first strand: chain 'D' and resid 10 through 13 removed outlier: 3.641A pdb=" N VAL D 13 " --> pdb=" O GLU D 110 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL D 90 " --> pdb=" O GLN D 43 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLN D 43 " --> pdb=" O VAL D 90 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N MET D 94 " --> pdb=" O ASP D 39 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASP D 39 " --> pdb=" O MET D 94 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N TRP D 40 " --> pdb=" O LEU D 52 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 19 through 24 Processing sheet with id=AG1, first strand: chain 'G' and resid 3 through 7 removed outlier: 4.287A pdb=" N GLN G 3 " --> pdb=" O SER G 25 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N SER G 25 " --> pdb=" O GLN G 3 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU G 20 " --> pdb=" O LEU G 81 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.516A pdb=" N THR G 118 " --> pdb=" O GLY G 10 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL G 117 " --> pdb=" O ALA G 92 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N MET G 34 " --> pdb=" O VAL G 50 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N VAL G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL G 50 " --> pdb=" O TYR G 59 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N TYR G 59 " --> pdb=" O VAL G 50 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 26 through 27 Processing sheet with id=AG4, first strand: chain 'C' and resid 61 through 69 removed outlier: 4.642A pdb=" N GLU C 263 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS C 108 " --> pdb=" O GLU C 263 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLY C 102 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR C 213 " --> pdb=" O THR C 228 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR C 217 " --> pdb=" O TYR C 224 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR C 222 " --> pdb=" O GLU C 219 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N PHE C 238 " --> pdb=" O ALA C 225 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N PHE C 227 " --> pdb=" O PHE C 236 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N PHE C 236 " --> pdb=" O PHE C 227 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 61 through 69 removed outlier: 3.753A pdb=" N ASN C 286 " --> pdb=" O ALA C 277 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'C' and resid 81 through 82 removed outlier: 8.374A pdb=" N THR C 255 " --> pdb=" O PRO C 172 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N THR C 174 " --> pdb=" O THR C 255 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N TRP C 188 " --> pdb=" O CYS C 169 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.755A pdb=" N VAL C 139 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN C 141 " --> pdb=" O GLU C 160 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL C 161 " --> pdb=" O ARG C 201 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR C 199 " --> pdb=" O VAL C 163 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.755A pdb=" N VAL C 139 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN C 141 " --> pdb=" O GLU C 160 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY C 157 " --> pdb=" O TYR C 205 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TYR C 205 " --> pdb=" O GLY C 157 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'C' and resid 110 through 114 Processing sheet with id=AH1, first strand: chain 'C' and resid 310 through 313 removed outlier: 3.883A pdb=" N PHE C 684 " --> pdb=" O GLY C 310 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'C' and resid 317 through 318 removed outlier: 3.550A pdb=" N TYR C 317 " --> pdb=" O GLY C 678 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY C 678 " --> pdb=" O TYR C 317 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH2 Processing sheet with id=AH3, first strand: chain 'C' and resid 323 through 327 removed outlier: 3.720A pdb=" N GLY C 632 " --> pdb=" O TYR C 625 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N TYR C 659 " --> pdb=" O ILE C 672 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLY C 660 " --> pdb=" O LEU C 651 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'C' and resid 353 through 354 removed outlier: 3.776A pdb=" N GLU C 353 " --> pdb=" O LYS C 398 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS C 398 " --> pdb=" O GLU C 353 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N SER C 393 " --> pdb=" O HIS C 598 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER C 430 " --> pdb=" O ASN C 379 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER C 375 " --> pdb=" O TYR C 434 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ASN C 436 " --> pdb=" O ALA C 373 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N ALA C 373 " --> pdb=" O ASN C 436 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'C' and resid 357 through 358 removed outlier: 4.170A pdb=" N SER C 393 " --> pdb=" O HIS C 598 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'C' and resid 361 through 362 Processing sheet with id=AH7, first strand: chain 'C' and resid 476 through 480 Processing sheet with id=AH8, first strand: chain 'C' and resid 483 through 485 removed outlier: 4.325A pdb=" N CYS C 483 " --> pdb=" O SER C 545 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR C 543 " --> pdb=" O LYS C 485 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'C' and resid 557 through 558 Processing sheet with id=AI1, first strand: chain 'C' and resid 730 through 737 removed outlier: 7.307A pdb=" N TYR C 730 " --> pdb=" O PHE C 768 " (cutoff:3.500A) removed outlier: 8.999A pdb=" N ASN C 770 " --> pdb=" O TYR C 730 " (cutoff:3.500A) removed outlier: 9.931A pdb=" N SER C 732 " --> pdb=" O ASN C 770 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N TYR C 748 " --> pdb=" O VAL C 744 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU C 742 " --> pdb=" O VAL C 750 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'C' and resid 790 through 800 removed outlier: 3.728A pdb=" N ILE C 792 " --> pdb=" O ALA C1161 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA C1161 " --> pdb=" O ILE C 792 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LYS C1157 " --> pdb=" O SER C 796 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N PHE C 798 " --> pdb=" O PRO C1155 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ILE C 800 " --> pdb=" O TYR C1153 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N TYR C1153 " --> pdb=" O ILE C 800 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'C' and resid 790 through 800 removed outlier: 3.728A pdb=" N ILE C 792 " --> pdb=" O ALA C1161 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA C1161 " --> pdb=" O ILE C 792 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LYS C1157 " --> pdb=" O SER C 796 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N PHE C 798 " --> pdb=" O PRO C1155 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ILE C 800 " --> pdb=" O TYR C1153 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N TYR C1153 " --> pdb=" O ILE C 800 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY C1145 " --> pdb=" O ALA C1142 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA C1142 " --> pdb=" O GLY C1145 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ILE C1136 " --> pdb=" O PHE C1151 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N TYR C1153 " --> pdb=" O HIS C1134 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N HIS C1134 " --> pdb=" O TYR C1153 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'C' and resid 814 through 816 Processing sheet with id=AI5, first strand: chain 'C' and resid 882 through 883 removed outlier: 3.544A pdb=" N VAL C 883 " --> pdb=" O ILE C 886 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'C' and resid 1167 through 1168 Processing sheet with id=AI7, first strand: chain 'C' and resid 1174 through 1177 removed outlier: 3.647A pdb=" N ALA C1176 " --> pdb=" O VAL C1208 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'C' and resid 1181 through 1185 Processing sheet with id=AI9, first strand: chain 'E' and resid 10 through 13 removed outlier: 3.652A pdb=" N VAL E 13 " --> pdb=" O GLU E 110 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL E 90 " --> pdb=" O GLN E 43 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN E 43 " --> pdb=" O VAL E 90 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N MET E 94 " --> pdb=" O ASP E 39 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASP E 39 " --> pdb=" O MET E 94 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N TRP E 40 " --> pdb=" O LEU E 52 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'E' and resid 19 through 24 Processing sheet with id=AJ2, first strand: chain 'I' and resid 3 through 7 removed outlier: 4.279A pdb=" N GLN I 3 " --> pdb=" O SER I 25 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N SER I 25 " --> pdb=" O GLN I 3 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU I 20 " --> pdb=" O LEU I 81 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.534A pdb=" N THR I 118 " --> pdb=" O GLY I 10 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N MET I 34 " --> pdb=" O VAL I 50 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N VAL I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL I 50 " --> pdb=" O TYR I 59 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N TYR I 59 " --> pdb=" O VAL I 50 " (cutoff:3.500A) 1246 hydrogen bonds defined for protein. 3411 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: 9.60 Time building geometry restraints manager: 4.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10653 1.34 - 1.47: 8740 1.47 - 1.59: 14630 1.59 - 1.72: 0 1.72 - 1.84: 273 Bond restraints: 34296 Sorted by residual: bond pdb=" C1 NAG C1404 " pdb=" O5 NAG C1404 " ideal model delta sigma weight residual 1.406 1.501 -0.095 2.00e-02 2.50e+03 2.26e+01 bond pdb=" C1 NAG A1404 " pdb=" O5 NAG A1404 " ideal model delta sigma weight residual 1.406 1.501 -0.095 2.00e-02 2.50e+03 2.26e+01 bond pdb=" C1 NAG B1404 " pdb=" O5 NAG B1404 " ideal model delta sigma weight residual 1.406 1.501 -0.095 2.00e-02 2.50e+03 2.24e+01 bond pdb=" C1 NAG A1405 " pdb=" O5 NAG A1405 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.69e+00 bond pdb=" C1 NAG C1405 " pdb=" O5 NAG C1405 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.62e+00 ... (remaining 34291 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 45864 2.50 - 5.01: 708 5.01 - 7.51: 76 7.51 - 10.02: 26 10.02 - 12.52: 3 Bond angle restraints: 46677 Sorted by residual: angle pdb=" N GLN B 860 " pdb=" CA GLN B 860 " pdb=" CB GLN B 860 " ideal model delta sigma weight residual 110.16 116.23 -6.07 1.48e+00 4.57e-01 1.68e+01 angle pdb=" N GLN A 860 " pdb=" CA GLN A 860 " pdb=" CB GLN A 860 " ideal model delta sigma weight residual 110.16 116.17 -6.01 1.48e+00 4.57e-01 1.65e+01 angle pdb=" C ASN B1186 " pdb=" N ASN B1187 " pdb=" CA ASN B1187 " ideal model delta sigma weight residual 121.54 129.22 -7.68 1.91e+00 2.74e-01 1.62e+01 angle pdb=" N VAL G 64 " pdb=" CA VAL G 64 " pdb=" C VAL G 64 " ideal model delta sigma weight residual 112.96 108.95 4.01 1.00e+00 1.00e+00 1.61e+01 angle pdb=" C ASN C1186 " pdb=" N ASN C1187 " pdb=" CA ASN C1187 " ideal model delta sigma weight residual 121.54 129.17 -7.63 1.91e+00 2.74e-01 1.60e+01 ... (remaining 46672 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.53: 19813 23.53 - 47.05: 1049 47.05 - 70.58: 102 70.58 - 94.11: 33 94.11 - 117.63: 9 Dihedral angle restraints: 21006 sinusoidal: 8703 harmonic: 12303 Sorted by residual: dihedral pdb=" CB CYS A 164 " pdb=" SG CYS A 164 " pdb=" SG CYS A 197 " pdb=" CB CYS A 197 " ideal model delta sinusoidal sigma weight residual 93.00 33.11 59.89 1 1.00e+01 1.00e-02 4.78e+01 dihedral pdb=" CB CYS B 164 " pdb=" SG CYS B 164 " pdb=" SG CYS B 197 " pdb=" CB CYS B 197 " ideal model delta sinusoidal sigma weight residual 93.00 33.14 59.86 1 1.00e+01 1.00e-02 4.78e+01 dihedral pdb=" CB CYS C 164 " pdb=" SG CYS C 164 " pdb=" SG CYS C 197 " pdb=" CB CYS C 197 " ideal model delta sinusoidal sigma weight residual 93.00 33.75 59.25 1 1.00e+01 1.00e-02 4.69e+01 ... (remaining 21003 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 4574 0.074 - 0.149: 738 0.149 - 0.223: 58 0.223 - 0.297: 3 0.297 - 0.371: 3 Chirality restraints: 5376 Sorted by residual: chirality pdb=" C1 NAG B1405 " pdb=" ND2 ASN B 146 " pdb=" C2 NAG B1405 " pdb=" O5 NAG B1405 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.45e+00 chirality pdb=" C1 NAG C1405 " pdb=" ND2 ASN C 146 " pdb=" C2 NAG C1405 " pdb=" O5 NAG C1405 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.43e+00 chirality pdb=" C1 NAG A1405 " pdb=" ND2 ASN A 146 " pdb=" C2 NAG A1405 " pdb=" O5 NAG A1405 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.40e+00 ... (remaining 5373 not shown) Planarity restraints: 5988 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU C 772 " 0.031 5.00e-02 4.00e+02 4.78e-02 3.66e+00 pdb=" N PRO C 773 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO C 773 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 773 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 92 " -0.032 5.00e-02 4.00e+02 4.78e-02 3.65e+00 pdb=" N PRO B 93 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 93 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 93 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 92 " 0.031 5.00e-02 4.00e+02 4.69e-02 3.52e+00 pdb=" N PRO A 93 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 93 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 93 " 0.026 5.00e-02 4.00e+02 ... (remaining 5985 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 8672 2.80 - 3.32: 27854 3.32 - 3.85: 55776 3.85 - 4.37: 62158 4.37 - 4.90: 109433 Nonbonded interactions: 263893 Sorted by model distance: nonbonded pdb=" O GLU C 852 " pdb=" OG1 THR C 856 " model vdw 2.275 3.040 nonbonded pdb=" O GLU B 852 " pdb=" OG1 THR B 856 " model vdw 2.278 3.040 nonbonded pdb=" O GLU A 852 " pdb=" OG1 THR A 856 " model vdw 2.287 3.040 nonbonded pdb=" OD2 ASP A 397 " pdb=" OH TYR A 422 " model vdw 2.291 3.040 nonbonded pdb=" OD2 ASP B 397 " pdb=" OH TYR B 422 " model vdw 2.296 3.040 ... (remaining 263888 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'L' } ncs_group { reference = chain 'F' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.540 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 34.870 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6774 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 0.095 34413 Z= 0.197 Angle : 0.768 12.896 46959 Z= 0.397 Chirality : 0.053 0.371 5376 Planarity : 0.005 0.048 5952 Dihedral : 13.599 117.634 12945 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.14 % Allowed : 0.41 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.11 (0.12), residues: 4176 helix: -1.65 (0.16), residues: 750 sheet: -0.88 (0.16), residues: 981 loop : -1.54 (0.11), residues: 2445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 19 TYR 0.028 0.002 TYR B 317 PHE 0.018 0.001 PHE A 122 TRP 0.014 0.001 TRP E 40 HIS 0.006 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00393 (34296) covalent geometry : angle 0.75232 (46677) SS BOND : bond 0.00465 ( 69) SS BOND : angle 1.62332 ( 138) hydrogen bonds : bond 0.22987 ( 1134) hydrogen bonds : angle 9.55135 ( 3411) link_BETA1-4 : bond 0.00555 ( 12) link_BETA1-4 : angle 1.47402 ( 36) link_NAG-ASN : bond 0.00745 ( 36) link_NAG-ASN : angle 2.77708 ( 108) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 949 residues out of total 3660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 944 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.7116 (mmm) cc_final: 0.6843 (tpt) REVERT: A 180 LEU cc_start: 0.8557 (mt) cc_final: 0.8246 (mt) REVERT: A 259 LYS cc_start: 0.7852 (ptmt) cc_final: 0.7435 (ptmt) REVERT: A 315 ASN cc_start: 0.7542 (p0) cc_final: 0.7304 (p0) REVERT: A 329 LYS cc_start: 0.7537 (mmmm) cc_final: 0.7328 (ttmm) REVERT: A 425 ASP cc_start: 0.7202 (t70) cc_final: 0.6924 (t0) REVERT: A 437 LEU cc_start: 0.8001 (mt) cc_final: 0.7513 (mt) REVERT: A 626 ASP cc_start: 0.6826 (t0) cc_final: 0.6348 (t0) REVERT: A 1000 ASP cc_start: 0.7427 (t0) cc_final: 0.6994 (t0) REVERT: A 1005 ASN cc_start: 0.7344 (t0) cc_final: 0.7022 (t0) REVERT: A 1035 GLN cc_start: 0.7499 (tp40) cc_final: 0.7243 (tp40) REVERT: A 1060 SER cc_start: 0.7642 (t) cc_final: 0.7421 (t) REVERT: A 1079 ILE cc_start: 0.7571 (mt) cc_final: 0.7043 (mt) REVERT: A 1087 LEU cc_start: 0.7616 (mt) cc_final: 0.7192 (mt) REVERT: A 1182 PHE cc_start: 0.7508 (m-80) cc_final: 0.7206 (m-80) REVERT: A 1187 ASN cc_start: 0.8835 (p0) cc_final: 0.8630 (p0) REVERT: L 75 ASP cc_start: 0.7330 (p0) cc_final: 0.6712 (m-30) REVERT: H 103 LEU cc_start: 0.8925 (tp) cc_final: 0.8207 (tt) REVERT: B 29 LYS cc_start: 0.7540 (tptt) cc_final: 0.7118 (ttpp) REVERT: B 78 MET cc_start: 0.7007 (mmm) cc_final: 0.6699 (tpt) REVERT: B 106 LYS cc_start: 0.6938 (tptp) cc_final: 0.6607 (ttmm) REVERT: B 180 LEU cc_start: 0.8530 (mt) cc_final: 0.8238 (mt) REVERT: B 235 LYS cc_start: 0.7624 (mtmm) cc_final: 0.7412 (mtmm) REVERT: B 259 LYS cc_start: 0.7648 (ptmt) cc_final: 0.7300 (ptmt) REVERT: B 423 ARG cc_start: 0.7825 (mmm-85) cc_final: 0.7424 (mmm-85) REVERT: B 437 LEU cc_start: 0.7816 (mt) cc_final: 0.7500 (mt) REVERT: B 478 VAL cc_start: 0.8205 (p) cc_final: 0.7853 (m) REVERT: B 596 ILE cc_start: 0.8737 (mm) cc_final: 0.8205 (mm) REVERT: B 597 LEU cc_start: 0.8472 (mt) cc_final: 0.8238 (mt) REVERT: B 626 ASP cc_start: 0.7021 (t0) cc_final: 0.6473 (t0) REVERT: B 662 ARG cc_start: 0.7270 (mtp-110) cc_final: 0.7041 (mtp-110) REVERT: B 668 ARG cc_start: 0.7499 (mtp85) cc_final: 0.7287 (mtm-85) REVERT: B 697 ASN cc_start: 0.7013 (m-40) cc_final: 0.6695 (m-40) REVERT: B 720 ASP cc_start: 0.7295 (m-30) cc_final: 0.6661 (m-30) REVERT: B 808 GLN cc_start: 0.6900 (pt0) cc_final: 0.6582 (pt0) REVERT: B 923 PHE cc_start: 0.7519 (m-80) cc_final: 0.6991 (m-80) REVERT: B 958 ASN cc_start: 0.7404 (m110) cc_final: 0.7023 (m-40) REVERT: B 963 TYR cc_start: 0.7486 (m-10) cc_final: 0.7161 (m-80) REVERT: B 1035 GLN cc_start: 0.7704 (tp40) cc_final: 0.7499 (tp40) REVERT: B 1039 ASN cc_start: 0.7666 (t0) cc_final: 0.7399 (t0) REVERT: B 1079 ILE cc_start: 0.7544 (mt) cc_final: 0.7288 (mt) REVERT: B 1087 LEU cc_start: 0.7457 (mt) cc_final: 0.6937 (mt) REVERT: B 1126 ILE cc_start: 0.8188 (mm) cc_final: 0.7944 (mm) REVERT: B 1139 VAL cc_start: 0.8449 (t) cc_final: 0.8016 (p) REVERT: B 1141 ASN cc_start: 0.8094 (t0) cc_final: 0.7792 (t0) REVERT: B 1182 PHE cc_start: 0.7531 (m-80) cc_final: 0.7144 (m-80) REVERT: B 1198 TYR cc_start: 0.7070 (t80) cc_final: 0.6860 (t80) REVERT: D 75 ASP cc_start: 0.7267 (p0) cc_final: 0.6877 (m-30) REVERT: G 103 LEU cc_start: 0.8938 (tp) cc_final: 0.8422 (tt) REVERT: G 105 TYR cc_start: 0.5107 (t80) cc_final: 0.4853 (t80) REVERT: C 29 LYS cc_start: 0.7446 (tptt) cc_final: 0.7082 (ttpp) REVERT: C 78 MET cc_start: 0.6854 (mmm) cc_final: 0.6517 (tpp) REVERT: C 180 LEU cc_start: 0.8471 (mt) cc_final: 0.8174 (mp) REVERT: C 237 LEU cc_start: 0.7747 (tp) cc_final: 0.7506 (tp) REVERT: C 259 LYS cc_start: 0.7625 (ptmt) cc_final: 0.7310 (ptmt) REVERT: C 344 LYS cc_start: 0.7878 (ttpp) cc_final: 0.7630 (ttmm) REVERT: C 382 ASP cc_start: 0.7507 (p0) cc_final: 0.7220 (p0) REVERT: C 422 TYR cc_start: 0.7138 (t80) cc_final: 0.6774 (t80) REVERT: C 425 ASP cc_start: 0.7126 (t70) cc_final: 0.6898 (t0) REVERT: C 461 ASP cc_start: 0.7154 (p0) cc_final: 0.6921 (p0) REVERT: C 478 VAL cc_start: 0.8435 (p) cc_final: 0.8111 (m) REVERT: C 596 ILE cc_start: 0.8820 (mm) cc_final: 0.8536 (mm) REVERT: C 689 SER cc_start: 0.7227 (t) cc_final: 0.7004 (t) REVERT: C 799 THR cc_start: 0.7556 (t) cc_final: 0.7346 (t) REVERT: C 855 ASP cc_start: 0.6530 (p0) cc_final: 0.6224 (p0) REVERT: C 1000 ASP cc_start: 0.7408 (t0) cc_final: 0.7177 (t0) REVERT: C 1039 ASN cc_start: 0.7579 (t0) cc_final: 0.7195 (t0) REVERT: C 1073 LEU cc_start: 0.6491 (pt) cc_final: 0.6170 (pt) REVERT: C 1079 ILE cc_start: 0.7612 (mt) cc_final: 0.7406 (mt) REVERT: C 1106 PHE cc_start: 0.6753 (t80) cc_final: 0.6409 (t80) REVERT: C 1154 VAL cc_start: 0.7880 (t) cc_final: 0.7670 (p) REVERT: C 1182 PHE cc_start: 0.7426 (m-80) cc_final: 0.7165 (m-80) REVERT: E 21 ILE cc_start: 0.8619 (mt) cc_final: 0.8414 (tp) REVERT: I 103 LEU cc_start: 0.8745 (tp) cc_final: 0.8449 (tt) outliers start: 5 outliers final: 0 residues processed: 949 average time/residue: 0.1948 time to fit residues: 305.0537 Evaluate side-chains 830 residues out of total 3660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 830 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 4.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 6.9990 chunk 401 optimal weight: 6.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 GLN A 697 ASN A1064 GLN A1097 GLN A1110 GLN ** L 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 GLN B 697 ASN B 777 ASN B 844 ASN B 928 ASN B1096 GLN B1150 HIS G 13 GLN ** C 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 315 ASN C 379 ASN C 410 GLN C 657 ASN C 844 ASN ** C 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1064 GLN C1096 GLN ** I 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.139556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.112870 restraints weight = 57197.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.117373 restraints weight = 29026.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.120496 restraints weight = 17806.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.122607 restraints weight = 12356.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.124035 restraints weight = 9402.852| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.122 34413 Z= 0.314 Angle : 0.752 9.039 46959 Z= 0.399 Chirality : 0.051 0.394 5376 Planarity : 0.005 0.042 5952 Dihedral : 7.842 101.961 5592 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.02 % Allowed : 9.97 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.12), residues: 4176 helix: -0.52 (0.18), residues: 735 sheet: -0.89 (0.16), residues: 1020 loop : -1.30 (0.12), residues: 2421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 87 TYR 0.026 0.003 TYR C1198 PHE 0.033 0.003 PHE C 399 TRP 0.028 0.003 TRP G 102 HIS 0.009 0.002 HIS B 215 Details of bonding type rmsd covalent geometry : bond 0.00677 (34296) covalent geometry : angle 0.74033 (46677) SS BOND : bond 0.00506 ( 69) SS BOND : angle 1.43525 ( 138) hydrogen bonds : bond 0.05264 ( 1134) hydrogen bonds : angle 6.76104 ( 3411) link_BETA1-4 : bond 0.00657 ( 12) link_BETA1-4 : angle 1.54131 ( 36) link_NAG-ASN : bond 0.00715 ( 36) link_NAG-ASN : angle 2.41052 ( 108) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 974 residues out of total 3660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 900 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 LEU cc_start: 0.8580 (mt) cc_final: 0.8269 (mp) REVERT: A 208 ASN cc_start: 0.8117 (m-40) cc_final: 0.7906 (m-40) REVERT: A 235 LYS cc_start: 0.7832 (mtmm) cc_final: 0.7298 (mtmm) REVERT: A 259 LYS cc_start: 0.7902 (ptmt) cc_final: 0.7452 (ptmt) REVERT: A 280 GLN cc_start: 0.7159 (mm110) cc_final: 0.6598 (mm-40) REVERT: A 312 TYR cc_start: 0.7801 (m-10) cc_final: 0.7494 (m-10) REVERT: A 315 ASN cc_start: 0.7873 (p0) cc_final: 0.7501 (p0) REVERT: A 328 ARG cc_start: 0.6968 (mpt180) cc_final: 0.6368 (mpt180) REVERT: A 342 ASN cc_start: 0.8170 (t0) cc_final: 0.7799 (t0) REVERT: A 343 ASP cc_start: 0.7550 (t0) cc_final: 0.7271 (t0) REVERT: A 344 LYS cc_start: 0.8083 (ttpp) cc_final: 0.7878 (ttpp) REVERT: A 345 SER cc_start: 0.8105 (p) cc_final: 0.7601 (m) REVERT: A 375 SER cc_start: 0.7950 (t) cc_final: 0.7327 (m) REVERT: A 425 ASP cc_start: 0.7828 (t70) cc_final: 0.7273 (t0) REVERT: A 437 LEU cc_start: 0.7997 (mt) cc_final: 0.7772 (mt) REVERT: A 478 VAL cc_start: 0.8234 (p) cc_final: 0.7941 (m) REVERT: A 491 CYS cc_start: 0.5528 (t) cc_final: 0.5302 (t) REVERT: A 551 GLU cc_start: 0.6998 (tp30) cc_final: 0.6789 (tp30) REVERT: A 573 GLN cc_start: 0.7869 (mp10) cc_final: 0.7653 (mp10) REVERT: A 596 ILE cc_start: 0.8547 (mm) cc_final: 0.8311 (mm) REVERT: A 626 ASP cc_start: 0.6840 (t0) cc_final: 0.6233 (t0) REVERT: A 663 ASP cc_start: 0.7680 (t70) cc_final: 0.7369 (t70) REVERT: A 731 ASN cc_start: 0.7615 (t0) cc_final: 0.7247 (t0) REVERT: A 832 GLN cc_start: 0.7823 (mm110) cc_final: 0.7460 (mm110) REVERT: A 858 GLN cc_start: 0.7775 (mm110) cc_final: 0.7517 (mm110) REVERT: A 958 ASN cc_start: 0.8343 (m-40) cc_final: 0.8081 (m-40) REVERT: A 960 PHE cc_start: 0.8353 (OUTLIER) cc_final: 0.8150 (m-80) REVERT: A 1000 ASP cc_start: 0.7628 (t0) cc_final: 0.7303 (t0) REVERT: A 1035 GLN cc_start: 0.8292 (tp40) cc_final: 0.8079 (tp40) REVERT: A 1039 ASN cc_start: 0.8534 (t0) cc_final: 0.8118 (t0) REVERT: A 1051 GLN cc_start: 0.7521 (mp10) cc_final: 0.7071 (mp10) REVERT: A 1060 SER cc_start: 0.8314 (t) cc_final: 0.7913 (t) REVERT: A 1065 GLU cc_start: 0.7028 (mt-10) cc_final: 0.6140 (mt-10) REVERT: A 1076 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7189 (tt0) REVERT: A 1080 ASP cc_start: 0.7662 (t0) cc_final: 0.7130 (t0) REVERT: A 1112 MET cc_start: 0.7517 (mmm) cc_final: 0.7221 (mmm) REVERT: A 1113 GLU cc_start: 0.7886 (tt0) cc_final: 0.7634 (tt0) REVERT: A 1141 ASN cc_start: 0.8457 (t0) cc_final: 0.8034 (t0) REVERT: A 1177 PRO cc_start: 0.8169 (Cg_endo) cc_final: 0.7737 (Cg_exo) REVERT: A 1182 PHE cc_start: 0.7476 (m-80) cc_final: 0.6649 (m-80) REVERT: A 1187 ASN cc_start: 0.8819 (p0) cc_final: 0.8614 (p0) REVERT: A 1190 MET cc_start: 0.7196 (ttt) cc_final: 0.6494 (ttt) REVERT: A 1198 TYR cc_start: 0.7413 (t80) cc_final: 0.7045 (t80) REVERT: A 1200 GLU cc_start: 0.7408 (mt-10) cc_final: 0.7197 (tt0) REVERT: L 31 HIS cc_start: 0.7633 (t-170) cc_final: 0.6980 (t-170) REVERT: H 52 TRP cc_start: 0.7040 (OUTLIER) cc_final: 0.6103 (t-100) REVERT: H 80 TYR cc_start: 0.6693 (m-10) cc_final: 0.6458 (m-10) REVERT: H 103 LEU cc_start: 0.8928 (tp) cc_final: 0.8184 (tt) REVERT: B 29 LYS cc_start: 0.7866 (tptt) cc_final: 0.7659 (tptt) REVERT: B 201 ARG cc_start: 0.7591 (ptm-80) cc_final: 0.7000 (ptm-80) REVERT: B 235 LYS cc_start: 0.8183 (mtmm) cc_final: 0.7726 (mtmm) REVERT: B 259 LYS cc_start: 0.7818 (ptmt) cc_final: 0.7361 (ptmt) REVERT: B 312 TYR cc_start: 0.7981 (m-10) cc_final: 0.7640 (m-10) REVERT: B 344 LYS cc_start: 0.8135 (ttmm) cc_final: 0.7762 (ttmm) REVERT: B 416 TYR cc_start: 0.7496 (m-10) cc_final: 0.7243 (m-10) REVERT: B 478 VAL cc_start: 0.8210 (p) cc_final: 0.7840 (m) REVERT: B 627 LEU cc_start: 0.8571 (mt) cc_final: 0.8351 (mt) REVERT: B 662 ARG cc_start: 0.8084 (mtp-110) cc_final: 0.7854 (mtp-110) REVERT: B 670 PHE cc_start: 0.7591 (m-80) cc_final: 0.7213 (m-80) REVERT: B 689 SER cc_start: 0.7616 (t) cc_final: 0.7266 (t) REVERT: B 697 ASN cc_start: 0.8116 (m110) cc_final: 0.7788 (m-40) REVERT: B 772 GLU cc_start: 0.7508 (tp30) cc_final: 0.7118 (tp30) REVERT: B 852 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7789 (mt-10) REVERT: B 860 GLN cc_start: 0.7607 (mp10) cc_final: 0.7381 (mp10) REVERT: B 874 LYS cc_start: 0.6240 (OUTLIER) cc_final: 0.5746 (pttp) REVERT: B 923 PHE cc_start: 0.8067 (m-80) cc_final: 0.7780 (m-80) REVERT: B 951 LEU cc_start: 0.8989 (mm) cc_final: 0.8758 (mt) REVERT: B 957 GLU cc_start: 0.6896 (mm-30) cc_final: 0.6553 (mm-30) REVERT: B 958 ASN cc_start: 0.8300 (m110) cc_final: 0.7812 (m-40) REVERT: B 963 TYR cc_start: 0.8476 (m-10) cc_final: 0.7921 (m-80) REVERT: B 999 MET cc_start: 0.6732 (ttp) cc_final: 0.6479 (ttp) REVERT: B 1000 ASP cc_start: 0.7620 (t0) cc_final: 0.7216 (t70) REVERT: B 1017 LEU cc_start: 0.8576 (mm) cc_final: 0.8314 (mp) REVERT: B 1051 GLN cc_start: 0.7602 (mp10) cc_final: 0.7147 (mp10) REVERT: B 1112 MET cc_start: 0.7758 (OUTLIER) cc_final: 0.7133 (mpp) REVERT: B 1113 GLU cc_start: 0.7845 (tt0) cc_final: 0.7067 (tt0) REVERT: B 1139 VAL cc_start: 0.8680 (t) cc_final: 0.8295 (p) REVERT: B 1141 ASN cc_start: 0.8526 (t0) cc_final: 0.7996 (t0) REVERT: B 1182 PHE cc_start: 0.7591 (m-80) cc_final: 0.7150 (m-80) REVERT: B 1190 MET cc_start: 0.7193 (ttm) cc_final: 0.6668 (ttt) REVERT: D 75 ASP cc_start: 0.7588 (p0) cc_final: 0.7024 (m-30) REVERT: G 52 TRP cc_start: 0.6687 (OUTLIER) cc_final: 0.5695 (t-100) REVERT: G 103 LEU cc_start: 0.9101 (tp) cc_final: 0.8371 (tt) REVERT: C 55 ARG cc_start: 0.7583 (mtt-85) cc_final: 0.7337 (mmm-85) REVERT: C 180 LEU cc_start: 0.8670 (mt) cc_final: 0.8296 (mp) REVERT: C 227 PHE cc_start: 0.7197 (t80) cc_final: 0.6981 (t80) REVERT: C 235 LYS cc_start: 0.8025 (mtmm) cc_final: 0.7550 (mtmm) REVERT: C 237 LEU cc_start: 0.8498 (tp) cc_final: 0.8109 (tp) REVERT: C 259 LYS cc_start: 0.7748 (ptmt) cc_final: 0.7406 (ptmt) REVERT: C 314 LEU cc_start: 0.8729 (mm) cc_final: 0.8500 (mp) REVERT: C 325 VAL cc_start: 0.7362 (p) cc_final: 0.7076 (m) REVERT: C 328 ARG cc_start: 0.6907 (mpt180) cc_final: 0.6597 (mpt180) REVERT: C 342 ASN cc_start: 0.8497 (t0) cc_final: 0.8261 (t0) REVERT: C 344 LYS cc_start: 0.8013 (ttpp) cc_final: 0.7656 (ttmm) REVERT: C 403 ASN cc_start: 0.7839 (m-40) cc_final: 0.7617 (m-40) REVERT: C 425 ASP cc_start: 0.7689 (t70) cc_final: 0.7245 (t0) REVERT: C 478 VAL cc_start: 0.8191 (p) cc_final: 0.7957 (m) REVERT: C 494 LYS cc_start: 0.7905 (mmmt) cc_final: 0.7520 (mmmt) REVERT: C 587 ASP cc_start: 0.7192 (p0) cc_final: 0.6984 (p0) REVERT: C 604 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7697 (mm) REVERT: C 612 LYS cc_start: 0.7502 (mmmm) cc_final: 0.7202 (mmmm) REVERT: C 626 ASP cc_start: 0.6719 (t0) cc_final: 0.6192 (t0) REVERT: C 662 ARG cc_start: 0.7935 (mtp-110) cc_final: 0.7471 (mtm110) REVERT: C 663 ASP cc_start: 0.7547 (t70) cc_final: 0.7241 (t0) REVERT: C 689 SER cc_start: 0.7476 (t) cc_final: 0.7231 (t) REVERT: C 699 LYS cc_start: 0.8232 (mmmm) cc_final: 0.7705 (mtmm) REVERT: C 730 TYR cc_start: 0.6944 (p90) cc_final: 0.6503 (p90) REVERT: C 832 GLN cc_start: 0.8108 (mm110) cc_final: 0.7240 (mp10) REVERT: C 858 GLN cc_start: 0.7633 (mm110) cc_final: 0.7432 (mm110) REVERT: C 925 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7275 (mt-10) REVERT: C 999 MET cc_start: 0.6576 (ttp) cc_final: 0.5984 (mtp) REVERT: C 1001 VAL cc_start: 0.8222 (m) cc_final: 0.8018 (p) REVERT: C 1005 ASN cc_start: 0.7563 (t0) cc_final: 0.7103 (t0) REVERT: C 1039 ASN cc_start: 0.8438 (t0) cc_final: 0.8060 (t0) REVERT: C 1080 ASP cc_start: 0.7462 (t0) cc_final: 0.7219 (t0) REVERT: C 1083 ILE cc_start: 0.8773 (mt) cc_final: 0.8480 (mm) REVERT: C 1106 PHE cc_start: 0.8212 (t80) cc_final: 0.8012 (t80) REVERT: C 1113 GLU cc_start: 0.7987 (tt0) cc_final: 0.7712 (tt0) REVERT: C 1141 ASN cc_start: 0.8562 (t0) cc_final: 0.8362 (t0) REVERT: C 1177 PRO cc_start: 0.8196 (Cg_endo) cc_final: 0.7765 (Cg_exo) REVERT: C 1182 PHE cc_start: 0.7423 (m-80) cc_final: 0.6735 (m-80) REVERT: C 1190 MET cc_start: 0.6874 (ttt) cc_final: 0.6094 (ttt) REVERT: C 1191 TYR cc_start: 0.7437 (t80) cc_final: 0.7125 (t80) REVERT: E 54 TYR cc_start: 0.7284 (p90) cc_final: 0.7033 (p90) REVERT: I 103 LEU cc_start: 0.8919 (tp) cc_final: 0.8467 (tt) outliers start: 74 outliers final: 37 residues processed: 926 average time/residue: 0.1960 time to fit residues: 300.6440 Evaluate side-chains 879 residues out of total 3660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 835 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 379 ASN Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 792 ILE Chi-restraints excluded: chain A residue 919 SER Chi-restraints excluded: chain A residue 960 PHE Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 1076 GLU Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1192 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain H residue 52 TRP Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 730 TYR Chi-restraints excluded: chain B residue 874 LYS Chi-restraints excluded: chain B residue 919 SER Chi-restraints excluded: chain B residue 992 ILE Chi-restraints excluded: chain B residue 1043 GLU Chi-restraints excluded: chain B residue 1112 MET Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain D residue 54 TYR Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain G residue 52 TRP Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 614 ASN Chi-restraints excluded: chain C residue 675 CYS Chi-restraints excluded: chain C residue 732 SER Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 988 VAL Chi-restraints excluded: chain C residue 992 ILE Chi-restraints excluded: chain C residue 1082 LEU Chi-restraints excluded: chain I residue 52 TRP Chi-restraints excluded: chain I residue 87 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 126 optimal weight: 5.9990 chunk 306 optimal weight: 2.9990 chunk 375 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 395 optimal weight: 4.9990 chunk 169 optimal weight: 1.9990 chunk 104 optimal weight: 0.5980 chunk 127 optimal weight: 4.9990 chunk 202 optimal weight: 0.0970 chunk 173 optimal weight: 0.5980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 GLN A 624 ASN A 657 ASN A 697 ASN A1064 GLN A1150 HIS L 31 HIS B 248 HIS B 315 ASN B 380 ASN B 410 GLN B 844 ASN B 928 ASN B1091 ASN B1134 HIS B1150 HIS ** D 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 GLN C 844 ASN C1064 GLN C1096 GLN E 27 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.140888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.114886 restraints weight = 56819.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.119328 restraints weight = 29330.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.122376 restraints weight = 18006.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.124432 restraints weight = 12523.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.125717 restraints weight = 9514.073| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 34413 Z= 0.162 Angle : 0.638 9.072 46959 Z= 0.331 Chirality : 0.047 0.351 5376 Planarity : 0.004 0.045 5952 Dihedral : 7.313 101.390 5592 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.24 % Allowed : 12.87 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.12), residues: 4176 helix: -0.11 (0.18), residues: 750 sheet: -0.81 (0.16), residues: 1038 loop : -1.18 (0.12), residues: 2388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 19 TYR 0.023 0.002 TYR B 67 PHE 0.025 0.002 PHE B 420 TRP 0.029 0.002 TRP D 40 HIS 0.005 0.001 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00362 (34296) covalent geometry : angle 0.62527 (46677) SS BOND : bond 0.00610 ( 69) SS BOND : angle 1.50345 ( 138) hydrogen bonds : bond 0.04422 ( 1134) hydrogen bonds : angle 6.25577 ( 3411) link_BETA1-4 : bond 0.00289 ( 12) link_BETA1-4 : angle 1.12860 ( 36) link_NAG-ASN : bond 0.00472 ( 36) link_NAG-ASN : angle 2.12431 ( 108) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 953 residues out of total 3660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 871 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8111 (tptt) cc_final: 0.7637 (tppt) REVERT: A 180 LEU cc_start: 0.8594 (mt) cc_final: 0.8304 (mt) REVERT: A 260 LEU cc_start: 0.7992 (pt) cc_final: 0.7753 (pt) REVERT: A 280 GLN cc_start: 0.7219 (mm110) cc_final: 0.6693 (mm-40) REVERT: A 312 TYR cc_start: 0.7786 (m-10) cc_final: 0.7462 (m-10) REVERT: A 315 ASN cc_start: 0.7825 (p0) cc_final: 0.7345 (p0) REVERT: A 328 ARG cc_start: 0.7028 (mpt180) cc_final: 0.6543 (mpt180) REVERT: A 329 LYS cc_start: 0.8140 (ttmm) cc_final: 0.7929 (ttmm) REVERT: A 342 ASN cc_start: 0.8109 (t0) cc_final: 0.7663 (t0) REVERT: A 344 LYS cc_start: 0.8086 (ttpp) cc_final: 0.7869 (ttpp) REVERT: A 345 SER cc_start: 0.8251 (p) cc_final: 0.8047 (m) REVERT: A 375 SER cc_start: 0.7895 (t) cc_final: 0.7276 (m) REVERT: A 385 LYS cc_start: 0.7500 (ptpp) cc_final: 0.7283 (ptpp) REVERT: A 425 ASP cc_start: 0.7775 (t70) cc_final: 0.7282 (t0) REVERT: A 437 LEU cc_start: 0.7973 (mt) cc_final: 0.7442 (mt) REVERT: A 478 VAL cc_start: 0.8195 (p) cc_final: 0.7959 (m) REVERT: A 551 GLU cc_start: 0.6994 (tp30) cc_final: 0.6776 (tp30) REVERT: A 596 ILE cc_start: 0.8453 (mm) cc_final: 0.8182 (mt) REVERT: A 598 HIS cc_start: 0.8089 (m90) cc_final: 0.7471 (m90) REVERT: A 626 ASP cc_start: 0.6863 (t0) cc_final: 0.6302 (t0) REVERT: A 663 ASP cc_start: 0.7644 (t70) cc_final: 0.6774 (t70) REVERT: A 699 LYS cc_start: 0.8216 (mmmm) cc_final: 0.7917 (mtmm) REVERT: A 731 ASN cc_start: 0.7596 (t0) cc_final: 0.7195 (t0) REVERT: A 772 GLU cc_start: 0.7581 (tp30) cc_final: 0.7361 (tp30) REVERT: A 832 GLN cc_start: 0.7817 (mm110) cc_final: 0.7608 (mm110) REVERT: A 858 GLN cc_start: 0.7679 (mm110) cc_final: 0.7394 (mm110) REVERT: A 860 GLN cc_start: 0.7427 (mt0) cc_final: 0.7186 (mp10) REVERT: A 1000 ASP cc_start: 0.7499 (t0) cc_final: 0.7255 (t0) REVERT: A 1039 ASN cc_start: 0.8471 (t0) cc_final: 0.8197 (t0) REVERT: A 1051 GLN cc_start: 0.7463 (mp10) cc_final: 0.7095 (mp10) REVERT: A 1060 SER cc_start: 0.8356 (t) cc_final: 0.8085 (t) REVERT: A 1065 GLU cc_start: 0.6990 (mt-10) cc_final: 0.6080 (mt-10) REVERT: A 1076 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7134 (tt0) REVERT: A 1112 MET cc_start: 0.7428 (mmm) cc_final: 0.7104 (mmm) REVERT: A 1141 ASN cc_start: 0.8463 (t0) cc_final: 0.7891 (t0) REVERT: A 1177 PRO cc_start: 0.8228 (Cg_endo) cc_final: 0.7704 (Cg_exo) REVERT: A 1182 PHE cc_start: 0.7379 (m-80) cc_final: 0.6513 (m-80) REVERT: A 1187 ASN cc_start: 0.8789 (p0) cc_final: 0.8589 (p0) REVERT: A 1190 MET cc_start: 0.7143 (ttt) cc_final: 0.6479 (ttt) REVERT: L 4 MET cc_start: 0.4947 (mpp) cc_final: 0.4647 (mpp) REVERT: L 31 HIS cc_start: 0.7529 (t70) cc_final: 0.7311 (t-170) REVERT: H 52 TRP cc_start: 0.6952 (OUTLIER) cc_final: 0.6119 (t-100) REVERT: H 80 TYR cc_start: 0.6662 (m-10) cc_final: 0.6423 (m-10) REVERT: H 103 LEU cc_start: 0.8954 (tp) cc_final: 0.8327 (tt) REVERT: B 122 PHE cc_start: 0.8104 (p90) cc_final: 0.7880 (p90) REVERT: B 201 ARG cc_start: 0.7550 (ptm-80) cc_final: 0.6891 (ptm-80) REVERT: B 235 LYS cc_start: 0.8050 (mtmm) cc_final: 0.7650 (mtmm) REVERT: B 259 LYS cc_start: 0.7773 (ptmt) cc_final: 0.7290 (ptmt) REVERT: B 312 TYR cc_start: 0.8029 (m-10) cc_final: 0.7723 (m-10) REVERT: B 329 LYS cc_start: 0.8222 (mttt) cc_final: 0.7945 (mmtt) REVERT: B 344 LYS cc_start: 0.8120 (ttmm) cc_final: 0.7752 (ttmm) REVERT: B 405 ARG cc_start: 0.8143 (mmm160) cc_final: 0.7478 (tpp-160) REVERT: B 416 TYR cc_start: 0.7415 (m-10) cc_final: 0.7139 (m-10) REVERT: B 478 VAL cc_start: 0.8185 (p) cc_final: 0.7845 (m) REVERT: B 627 LEU cc_start: 0.8462 (mt) cc_final: 0.8195 (mt) REVERT: B 662 ARG cc_start: 0.8004 (mtp-110) cc_final: 0.7766 (mtp-110) REVERT: B 663 ASP cc_start: 0.7809 (t0) cc_final: 0.7485 (t0) REVERT: B 689 SER cc_start: 0.7429 (t) cc_final: 0.7082 (t) REVERT: B 697 ASN cc_start: 0.7915 (m110) cc_final: 0.7576 (m-40) REVERT: B 726 VAL cc_start: 0.6688 (OUTLIER) cc_final: 0.5602 (p) REVERT: B 749 CYS cc_start: 0.5567 (OUTLIER) cc_final: 0.5078 (t) REVERT: B 768 PHE cc_start: 0.6462 (t80) cc_final: 0.6050 (t80) REVERT: B 772 GLU cc_start: 0.7594 (tp30) cc_final: 0.7157 (tp30) REVERT: B 858 GLN cc_start: 0.7710 (mm110) cc_final: 0.7454 (mm110) REVERT: B 860 GLN cc_start: 0.7585 (OUTLIER) cc_final: 0.7218 (mp10) REVERT: B 874 LYS cc_start: 0.6303 (OUTLIER) cc_final: 0.5906 (pttp) REVERT: B 923 PHE cc_start: 0.7856 (m-80) cc_final: 0.7626 (m-80) REVERT: B 951 LEU cc_start: 0.8999 (mm) cc_final: 0.8765 (mt) REVERT: B 958 ASN cc_start: 0.8247 (m110) cc_final: 0.7715 (m-40) REVERT: B 999 MET cc_start: 0.6726 (ttp) cc_final: 0.6080 (ttp) REVERT: B 1051 GLN cc_start: 0.7517 (OUTLIER) cc_final: 0.7060 (mp10) REVERT: B 1076 GLU cc_start: 0.7674 (mt-10) cc_final: 0.7408 (tt0) REVERT: B 1080 ASP cc_start: 0.7494 (t0) cc_final: 0.7033 (t0) REVERT: B 1091 ASN cc_start: 0.8203 (m-40) cc_final: 0.7947 (m110) REVERT: B 1112 MET cc_start: 0.7688 (OUTLIER) cc_final: 0.6775 (mpp) REVERT: B 1139 VAL cc_start: 0.8630 (t) cc_final: 0.8229 (p) REVERT: B 1141 ASN cc_start: 0.8589 (t0) cc_final: 0.8161 (t0) REVERT: B 1182 PHE cc_start: 0.7575 (m-80) cc_final: 0.7086 (m-80) REVERT: B 1190 MET cc_start: 0.7166 (ttm) cc_final: 0.6638 (ttt) REVERT: G 52 TRP cc_start: 0.6683 (OUTLIER) cc_final: 0.5668 (t-100) REVERT: G 103 LEU cc_start: 0.9061 (tp) cc_final: 0.8710 (tp) REVERT: C 55 ARG cc_start: 0.7544 (mtt-85) cc_final: 0.7324 (mmm-85) REVERT: C 180 LEU cc_start: 0.8679 (mt) cc_final: 0.8298 (mp) REVERT: C 227 PHE cc_start: 0.7100 (t80) cc_final: 0.6893 (t80) REVERT: C 235 LYS cc_start: 0.7973 (mtmm) cc_final: 0.7505 (mtmm) REVERT: C 237 LEU cc_start: 0.8450 (tp) cc_final: 0.8070 (tp) REVERT: C 259 LYS cc_start: 0.7713 (ptmt) cc_final: 0.7375 (ptmt) REVERT: C 314 LEU cc_start: 0.8729 (mm) cc_final: 0.8446 (mp) REVERT: C 325 VAL cc_start: 0.7450 (p) cc_final: 0.7180 (m) REVERT: C 326 TYR cc_start: 0.7375 (t80) cc_final: 0.7140 (t80) REVERT: C 342 ASN cc_start: 0.8381 (t0) cc_final: 0.8065 (t0) REVERT: C 344 LYS cc_start: 0.7956 (ttpp) cc_final: 0.7624 (ttmm) REVERT: C 385 LYS cc_start: 0.7558 (OUTLIER) cc_final: 0.7341 (mtpt) REVERT: C 425 ASP cc_start: 0.7671 (t70) cc_final: 0.7226 (t0) REVERT: C 478 VAL cc_start: 0.8187 (p) cc_final: 0.7977 (m) REVERT: C 662 ARG cc_start: 0.7834 (mtp-110) cc_final: 0.7372 (mtm110) REVERT: C 663 ASP cc_start: 0.7438 (t70) cc_final: 0.6896 (t0) REVERT: C 680 VAL cc_start: 0.8177 (t) cc_final: 0.7945 (m) REVERT: C 689 SER cc_start: 0.7391 (t) cc_final: 0.7139 (t) REVERT: C 699 LYS cc_start: 0.8253 (mmmm) cc_final: 0.7732 (mtmm) REVERT: C 730 TYR cc_start: 0.6900 (p90) cc_final: 0.6463 (p90) REVERT: C 817 ASP cc_start: 0.6869 (t70) cc_final: 0.6564 (p0) REVERT: C 832 GLN cc_start: 0.8041 (mm110) cc_final: 0.7236 (mp10) REVERT: C 925 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7243 (mt-10) REVERT: C 1005 ASN cc_start: 0.7565 (t0) cc_final: 0.7098 (t0) REVERT: C 1039 ASN cc_start: 0.8377 (t0) cc_final: 0.7958 (t0) REVERT: C 1113 GLU cc_start: 0.7898 (tt0) cc_final: 0.7576 (tt0) REVERT: C 1182 PHE cc_start: 0.7397 (m-80) cc_final: 0.6979 (m-80) REVERT: C 1190 MET cc_start: 0.6950 (ttt) cc_final: 0.6219 (ttt) REVERT: C 1191 TYR cc_start: 0.7363 (t80) cc_final: 0.7082 (t80) REVERT: E 21 ILE cc_start: 0.8717 (mt) cc_final: 0.8366 (tp) REVERT: E 84 GLU cc_start: 0.6763 (pp20) cc_final: 0.6123 (pp20) REVERT: I 103 LEU cc_start: 0.8941 (tp) cc_final: 0.8403 (tt) outliers start: 82 outliers final: 45 residues processed: 901 average time/residue: 0.1922 time to fit residues: 285.9782 Evaluate side-chains 886 residues out of total 3660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 831 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 614 ASN Chi-restraints excluded: chain A residue 807 ILE Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 919 SER Chi-restraints excluded: chain A residue 941 CYS Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 1076 GLU Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 44 LYS Chi-restraints excluded: chain H residue 52 TRP Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 614 ASN Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 730 TYR Chi-restraints excluded: chain B residue 732 SER Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 860 GLN Chi-restraints excluded: chain B residue 874 LYS Chi-restraints excluded: chain B residue 919 SER Chi-restraints excluded: chain B residue 992 ILE Chi-restraints excluded: chain B residue 1043 GLU Chi-restraints excluded: chain B residue 1051 GLN Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain B residue 1112 MET Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain G residue 52 TRP Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 385 LYS Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 430 SER Chi-restraints excluded: chain C residue 614 ASN Chi-restraints excluded: chain C residue 638 GLU Chi-restraints excluded: chain C residue 732 SER Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 990 TYR Chi-restraints excluded: chain C residue 992 ILE Chi-restraints excluded: chain C residue 1082 LEU Chi-restraints excluded: chain C residue 1084 ASN Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain I residue 52 TRP Chi-restraints excluded: chain I residue 87 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 393 optimal weight: 4.9990 chunk 325 optimal weight: 0.9980 chunk 131 optimal weight: 0.9990 chunk 228 optimal weight: 5.9990 chunk 178 optimal weight: 2.9990 chunk 118 optimal weight: 20.0000 chunk 168 optimal weight: 0.1980 chunk 283 optimal weight: 2.9990 chunk 386 optimal weight: 0.7980 chunk 327 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 GLN ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 697 ASN A1064 GLN A1097 GLN B 844 ASN ** B1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 GLN C 315 ASN C 844 ASN C 867 ASN C1014 ASN C1064 GLN I 13 GLN I 106 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.141364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.115401 restraints weight = 56398.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.119886 restraints weight = 29070.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.122940 restraints weight = 17807.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.124562 restraints weight = 12374.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.126177 restraints weight = 9879.702| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 34413 Z= 0.137 Angle : 0.618 11.143 46959 Z= 0.316 Chirality : 0.046 0.345 5376 Planarity : 0.004 0.044 5952 Dihedral : 6.850 99.736 5592 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.49 % Allowed : 14.62 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.12), residues: 4176 helix: 0.10 (0.18), residues: 747 sheet: -0.69 (0.16), residues: 1038 loop : -1.16 (0.12), residues: 2391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 668 TYR 0.023 0.002 TYR B1093 PHE 0.027 0.001 PHE A 420 TRP 0.033 0.002 TRP H 102 HIS 0.005 0.001 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00309 (34296) covalent geometry : angle 0.60666 (46677) SS BOND : bond 0.00367 ( 69) SS BOND : angle 1.31332 ( 138) hydrogen bonds : bond 0.04027 ( 1134) hydrogen bonds : angle 5.94347 ( 3411) link_BETA1-4 : bond 0.00256 ( 12) link_BETA1-4 : angle 1.01147 ( 36) link_NAG-ASN : bond 0.00457 ( 36) link_NAG-ASN : angle 2.06124 ( 108) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 964 residues out of total 3660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 873 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 TYR cc_start: 0.8334 (m-80) cc_final: 0.7878 (m-10) REVERT: A 180 LEU cc_start: 0.8610 (mt) cc_final: 0.8326 (mt) REVERT: A 260 LEU cc_start: 0.7992 (pt) cc_final: 0.7769 (pt) REVERT: A 280 GLN cc_start: 0.7245 (mm110) cc_final: 0.6704 (mm-40) REVERT: A 312 TYR cc_start: 0.7797 (m-10) cc_final: 0.7441 (m-10) REVERT: A 315 ASN cc_start: 0.7770 (p0) cc_final: 0.7289 (p0) REVERT: A 328 ARG cc_start: 0.7251 (mpt180) cc_final: 0.6643 (mpt180) REVERT: A 329 LYS cc_start: 0.8170 (ttmm) cc_final: 0.7945 (ttmm) REVERT: A 342 ASN cc_start: 0.8082 (t0) cc_final: 0.7636 (t0) REVERT: A 344 LYS cc_start: 0.8118 (ttpp) cc_final: 0.7914 (ttpp) REVERT: A 375 SER cc_start: 0.7858 (t) cc_final: 0.7273 (m) REVERT: A 425 ASP cc_start: 0.7766 (t70) cc_final: 0.7265 (t0) REVERT: A 437 LEU cc_start: 0.7972 (mt) cc_final: 0.7663 (mt) REVERT: A 448 ASN cc_start: 0.8712 (t0) cc_final: 0.8412 (t0) REVERT: A 478 VAL cc_start: 0.8159 (p) cc_final: 0.7926 (m) REVERT: A 551 GLU cc_start: 0.6992 (tp30) cc_final: 0.6791 (tp30) REVERT: A 573 GLN cc_start: 0.7836 (mp10) cc_final: 0.7574 (mp10) REVERT: A 596 ILE cc_start: 0.8464 (mm) cc_final: 0.8194 (mt) REVERT: A 598 HIS cc_start: 0.8017 (m90) cc_final: 0.7405 (m90) REVERT: A 626 ASP cc_start: 0.6855 (t0) cc_final: 0.6263 (t0) REVERT: A 663 ASP cc_start: 0.7455 (t70) cc_final: 0.6963 (t70) REVERT: A 699 LYS cc_start: 0.8258 (mmmm) cc_final: 0.7979 (mtmm) REVERT: A 731 ASN cc_start: 0.7589 (t0) cc_final: 0.7175 (t0) REVERT: A 858 GLN cc_start: 0.7733 (mm110) cc_final: 0.7386 (mm110) REVERT: A 860 GLN cc_start: 0.7570 (mt0) cc_final: 0.7286 (mp10) REVERT: A 1000 ASP cc_start: 0.7492 (t0) cc_final: 0.7212 (t0) REVERT: A 1039 ASN cc_start: 0.8513 (t0) cc_final: 0.8216 (t0) REVERT: A 1051 GLN cc_start: 0.7467 (mp10) cc_final: 0.7075 (mp10) REVERT: A 1060 SER cc_start: 0.8238 (t) cc_final: 0.7972 (t) REVERT: A 1065 GLU cc_start: 0.6971 (mt-10) cc_final: 0.6127 (mt-10) REVERT: A 1076 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7225 (tt0) REVERT: A 1112 MET cc_start: 0.7507 (mmm) cc_final: 0.7167 (mmm) REVERT: A 1113 GLU cc_start: 0.7778 (tt0) cc_final: 0.7525 (mt-10) REVERT: A 1119 VAL cc_start: 0.7185 (p) cc_final: 0.6896 (m) REVERT: A 1141 ASN cc_start: 0.8478 (t0) cc_final: 0.7894 (t0) REVERT: A 1147 TYR cc_start: 0.7960 (t80) cc_final: 0.7603 (t80) REVERT: A 1177 PRO cc_start: 0.8207 (Cg_endo) cc_final: 0.7768 (Cg_exo) REVERT: A 1182 PHE cc_start: 0.7374 (m-80) cc_final: 0.6946 (m-80) REVERT: A 1190 MET cc_start: 0.7123 (ttt) cc_final: 0.6492 (ttt) REVERT: L 4 MET cc_start: 0.5194 (mpp) cc_final: 0.4903 (mpp) REVERT: L 31 HIS cc_start: 0.7592 (t70) cc_final: 0.6945 (t-170) REVERT: L 44 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.8413 (mttt) REVERT: L 78 LEU cc_start: 0.7932 (tp) cc_final: 0.7560 (tp) REVERT: H 52 TRP cc_start: 0.6921 (OUTLIER) cc_final: 0.6141 (t-100) REVERT: H 103 LEU cc_start: 0.8980 (tp) cc_final: 0.8320 (tt) REVERT: B 122 PHE cc_start: 0.8079 (p90) cc_final: 0.7871 (p90) REVERT: B 201 ARG cc_start: 0.7541 (ptm-80) cc_final: 0.6904 (ptm-80) REVERT: B 235 LYS cc_start: 0.8072 (mtmm) cc_final: 0.7651 (mtmm) REVERT: B 237 LEU cc_start: 0.8633 (tp) cc_final: 0.8401 (tp) REVERT: B 259 LYS cc_start: 0.7727 (ptmt) cc_final: 0.7257 (ptmt) REVERT: B 312 TYR cc_start: 0.7994 (m-10) cc_final: 0.7708 (m-10) REVERT: B 343 ASP cc_start: 0.7380 (t0) cc_final: 0.7006 (t0) REVERT: B 344 LYS cc_start: 0.8127 (ttmm) cc_final: 0.7886 (ttmm) REVERT: B 395 THR cc_start: 0.8244 (m) cc_final: 0.7778 (p) REVERT: B 405 ARG cc_start: 0.8150 (mmm160) cc_final: 0.7552 (tpp-160) REVERT: B 416 TYR cc_start: 0.7423 (m-10) cc_final: 0.7154 (m-10) REVERT: B 478 VAL cc_start: 0.8182 (p) cc_final: 0.7937 (m) REVERT: B 596 ILE cc_start: 0.8389 (mm) cc_final: 0.7965 (mp) REVERT: B 662 ARG cc_start: 0.7965 (mtp-110) cc_final: 0.7609 (mtp-110) REVERT: B 663 ASP cc_start: 0.7779 (t0) cc_final: 0.7524 (t0) REVERT: B 689 SER cc_start: 0.7484 (t) cc_final: 0.7164 (t) REVERT: B 697 ASN cc_start: 0.7853 (m110) cc_final: 0.7556 (m-40) REVERT: B 772 GLU cc_start: 0.7697 (tp30) cc_final: 0.7199 (tp30) REVERT: B 860 GLN cc_start: 0.7410 (OUTLIER) cc_final: 0.6987 (mp10) REVERT: B 874 LYS cc_start: 0.6242 (OUTLIER) cc_final: 0.5845 (pttp) REVERT: B 923 PHE cc_start: 0.7835 (m-80) cc_final: 0.7601 (m-80) REVERT: B 951 LEU cc_start: 0.8961 (mm) cc_final: 0.8741 (mt) REVERT: B 958 ASN cc_start: 0.8246 (m110) cc_final: 0.7733 (m-40) REVERT: B 999 MET cc_start: 0.6741 (ttp) cc_final: 0.6087 (ttp) REVERT: B 1048 LEU cc_start: 0.8429 (tp) cc_final: 0.8042 (tp) REVERT: B 1051 GLN cc_start: 0.7498 (OUTLIER) cc_final: 0.6904 (mp10) REVERT: B 1080 ASP cc_start: 0.7466 (t0) cc_final: 0.6985 (t0) REVERT: B 1091 ASN cc_start: 0.8198 (m-40) cc_final: 0.7997 (m110) REVERT: B 1112 MET cc_start: 0.7730 (OUTLIER) cc_final: 0.6792 (mpp) REVERT: B 1139 VAL cc_start: 0.8605 (t) cc_final: 0.8205 (p) REVERT: B 1141 ASN cc_start: 0.8595 (t0) cc_final: 0.8142 (t0) REVERT: B 1182 PHE cc_start: 0.7538 (m-80) cc_final: 0.7071 (m-80) REVERT: B 1190 MET cc_start: 0.7160 (ttm) cc_final: 0.6588 (ttt) REVERT: D 75 ASP cc_start: 0.7812 (p0) cc_final: 0.6859 (m-30) REVERT: G 52 TRP cc_start: 0.6700 (OUTLIER) cc_final: 0.5703 (t-100) REVERT: G 103 LEU cc_start: 0.9050 (tp) cc_final: 0.8700 (tp) REVERT: C 180 LEU cc_start: 0.8690 (mt) cc_final: 0.8327 (mp) REVERT: C 235 LYS cc_start: 0.7966 (mtmm) cc_final: 0.7496 (mtmm) REVERT: C 237 LEU cc_start: 0.8432 (tp) cc_final: 0.8063 (tp) REVERT: C 259 LYS cc_start: 0.7708 (ptmt) cc_final: 0.7371 (ptmt) REVERT: C 312 TYR cc_start: 0.7772 (m-10) cc_final: 0.7481 (m-10) REVERT: C 325 VAL cc_start: 0.7491 (p) cc_final: 0.7236 (m) REVERT: C 342 ASN cc_start: 0.8363 (t0) cc_final: 0.8005 (t0) REVERT: C 344 LYS cc_start: 0.7945 (ttpp) cc_final: 0.7602 (ttmm) REVERT: C 375 SER cc_start: 0.7562 (t) cc_final: 0.7262 (m) REVERT: C 385 LYS cc_start: 0.7439 (OUTLIER) cc_final: 0.7161 (mtpt) REVERT: C 425 ASP cc_start: 0.7660 (t70) cc_final: 0.7167 (t0) REVERT: C 460 GLU cc_start: 0.8232 (mp0) cc_final: 0.7951 (mp0) REVERT: C 478 VAL cc_start: 0.8143 (p) cc_final: 0.7905 (m) REVERT: C 662 ARG cc_start: 0.7843 (mtp-110) cc_final: 0.7347 (mtm110) REVERT: C 663 ASP cc_start: 0.7467 (t70) cc_final: 0.6850 (t0) REVERT: C 680 VAL cc_start: 0.8310 (t) cc_final: 0.8097 (m) REVERT: C 689 SER cc_start: 0.7340 (t) cc_final: 0.7071 (t) REVERT: C 699 LYS cc_start: 0.8249 (mmmm) cc_final: 0.7801 (mtmm) REVERT: C 730 TYR cc_start: 0.6879 (p90) cc_final: 0.6438 (p90) REVERT: C 817 ASP cc_start: 0.6890 (t70) cc_final: 0.6590 (p0) REVERT: C 832 GLN cc_start: 0.7975 (mm110) cc_final: 0.7188 (mp10) REVERT: C 925 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7276 (mt-10) REVERT: C 959 GLN cc_start: 0.8456 (mt0) cc_final: 0.8155 (mt0) REVERT: C 1005 ASN cc_start: 0.7623 (t0) cc_final: 0.7170 (t0) REVERT: C 1039 ASN cc_start: 0.8383 (t0) cc_final: 0.7946 (t0) REVERT: C 1065 GLU cc_start: 0.7168 (mt-10) cc_final: 0.6910 (mt-10) REVERT: C 1113 GLU cc_start: 0.7952 (tt0) cc_final: 0.7579 (tt0) REVERT: C 1182 PHE cc_start: 0.7398 (m-80) cc_final: 0.6956 (m-80) REVERT: C 1190 MET cc_start: 0.6957 (ttt) cc_final: 0.6615 (ttt) REVERT: C 1191 TYR cc_start: 0.7325 (t80) cc_final: 0.7124 (t80) REVERT: E 21 ILE cc_start: 0.8706 (mt) cc_final: 0.8373 (tp) REVERT: I 103 LEU cc_start: 0.8919 (tp) cc_final: 0.8331 (tt) outliers start: 91 outliers final: 49 residues processed: 906 average time/residue: 0.1941 time to fit residues: 291.8727 Evaluate side-chains 901 residues out of total 3660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 843 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 614 ASN Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 807 ILE Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 839 PHE Chi-restraints excluded: chain A residue 919 SER Chi-restraints excluded: chain A residue 941 CYS Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 1076 GLU Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain L residue 44 LYS Chi-restraints excluded: chain H residue 52 TRP Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 197 CYS Chi-restraints excluded: chain B residue 607 SER Chi-restraints excluded: chain B residue 614 ASN Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 860 GLN Chi-restraints excluded: chain B residue 874 LYS Chi-restraints excluded: chain B residue 919 SER Chi-restraints excluded: chain B residue 941 CYS Chi-restraints excluded: chain B residue 992 ILE Chi-restraints excluded: chain B residue 1043 GLU Chi-restraints excluded: chain B residue 1051 GLN Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain B residue 1112 MET Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain G residue 52 TRP Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 385 LYS Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 430 SER Chi-restraints excluded: chain C residue 614 ASN Chi-restraints excluded: chain C residue 732 SER Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 942 VAL Chi-restraints excluded: chain C residue 990 TYR Chi-restraints excluded: chain C residue 1082 LEU Chi-restraints excluded: chain C residue 1112 MET Chi-restraints excluded: chain C residue 1185 VAL Chi-restraints excluded: chain I residue 52 TRP Chi-restraints excluded: chain I residue 87 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 372 optimal weight: 0.0070 chunk 161 optimal weight: 0.0000 chunk 186 optimal weight: 0.6980 chunk 192 optimal weight: 3.9990 chunk 290 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 16 optimal weight: 8.9990 chunk 148 optimal weight: 3.9990 chunk 291 optimal weight: 2.9990 chunk 285 optimal weight: 2.9990 chunk 227 optimal weight: 0.9980 overall best weight: 0.4602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 GLN ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 624 ASN A 867 ASN A1064 GLN A1187 ASN B 182 ASN B 410 GLN B 844 ASN B1014 ASN ** B1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 GLN C 182 ASN C 844 ASN C1064 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.145376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.118655 restraints weight = 56261.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.123509 restraints weight = 28538.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.126818 restraints weight = 17332.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.128639 restraints weight = 11938.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.130349 restraints weight = 9387.494| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6882 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 34413 Z= 0.112 Angle : 0.606 9.417 46959 Z= 0.308 Chirality : 0.046 0.337 5376 Planarity : 0.003 0.043 5952 Dihedral : 6.447 97.607 5592 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.16 % Allowed : 16.20 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.13), residues: 4176 helix: 0.16 (0.18), residues: 756 sheet: -0.60 (0.16), residues: 1014 loop : -1.09 (0.12), residues: 2406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 16 TYR 0.024 0.001 TYR C 435 PHE 0.036 0.001 PHE C 122 TRP 0.035 0.002 TRP H 102 HIS 0.004 0.001 HIS I 35 Details of bonding type rmsd covalent geometry : bond 0.00255 (34296) covalent geometry : angle 0.59606 (46677) SS BOND : bond 0.00363 ( 69) SS BOND : angle 1.15820 ( 138) hydrogen bonds : bond 0.03810 ( 1134) hydrogen bonds : angle 5.68829 ( 3411) link_BETA1-4 : bond 0.00282 ( 12) link_BETA1-4 : angle 0.96081 ( 36) link_NAG-ASN : bond 0.00455 ( 36) link_NAG-ASN : angle 2.00129 ( 108) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 954 residues out of total 3660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 875 time to evaluate : 1.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8139 (tptt) cc_final: 0.7664 (tppt) REVERT: A 136 TYR cc_start: 0.8329 (m-80) cc_final: 0.7890 (m-10) REVERT: A 180 LEU cc_start: 0.8622 (mt) cc_final: 0.8337 (mp) REVERT: A 260 LEU cc_start: 0.7968 (pt) cc_final: 0.7750 (pt) REVERT: A 280 GLN cc_start: 0.7249 (mm110) cc_final: 0.6733 (mm-40) REVERT: A 312 TYR cc_start: 0.7779 (m-10) cc_final: 0.7470 (m-10) REVERT: A 315 ASN cc_start: 0.7727 (p0) cc_final: 0.7226 (p0) REVERT: A 328 ARG cc_start: 0.7231 (mpt180) cc_final: 0.6601 (mpt180) REVERT: A 329 LYS cc_start: 0.8131 (ttmm) cc_final: 0.7893 (ttmm) REVERT: A 335 CYS cc_start: 0.5474 (m) cc_final: 0.5250 (m) REVERT: A 342 ASN cc_start: 0.8052 (t0) cc_final: 0.7597 (t0) REVERT: A 375 SER cc_start: 0.7762 (t) cc_final: 0.7189 (m) REVERT: A 425 ASP cc_start: 0.7753 (t70) cc_final: 0.7247 (t0) REVERT: A 437 LEU cc_start: 0.7883 (mt) cc_final: 0.7517 (mt) REVERT: A 573 GLN cc_start: 0.7805 (mp10) cc_final: 0.7508 (mp10) REVERT: A 596 ILE cc_start: 0.8389 (mm) cc_final: 0.8123 (mt) REVERT: A 598 HIS cc_start: 0.7924 (m90) cc_final: 0.7334 (m90) REVERT: A 626 ASP cc_start: 0.6759 (t0) cc_final: 0.6198 (t0) REVERT: A 663 ASP cc_start: 0.7404 (t70) cc_final: 0.6766 (t70) REVERT: A 699 LYS cc_start: 0.8268 (mmmm) cc_final: 0.7979 (mtmm) REVERT: A 731 ASN cc_start: 0.7621 (t0) cc_final: 0.7275 (t0) REVERT: A 766 TYR cc_start: 0.6941 (m-80) cc_final: 0.6535 (m-10) REVERT: A 774 PHE cc_start: 0.7470 (m-80) cc_final: 0.7171 (m-80) REVERT: A 833 LEU cc_start: 0.7271 (tp) cc_final: 0.7060 (tt) REVERT: A 858 GLN cc_start: 0.7796 (mm110) cc_final: 0.7413 (mm110) REVERT: A 976 TRP cc_start: 0.6211 (m-90) cc_final: 0.5713 (m-90) REVERT: A 1000 ASP cc_start: 0.7443 (t0) cc_final: 0.7232 (t0) REVERT: A 1033 LYS cc_start: 0.8626 (tppt) cc_final: 0.8232 (ttmm) REVERT: A 1051 GLN cc_start: 0.7493 (mp10) cc_final: 0.7068 (mp10) REVERT: A 1065 GLU cc_start: 0.7091 (mt-10) cc_final: 0.6287 (mt-10) REVERT: A 1076 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7627 (tt0) REVERT: A 1112 MET cc_start: 0.7573 (mmm) cc_final: 0.7199 (mmm) REVERT: A 1113 GLU cc_start: 0.7822 (tt0) cc_final: 0.7547 (mt-10) REVERT: A 1141 ASN cc_start: 0.8456 (t0) cc_final: 0.8033 (t0) REVERT: A 1147 TYR cc_start: 0.7924 (t80) cc_final: 0.7630 (t80) REVERT: A 1177 PRO cc_start: 0.8100 (Cg_endo) cc_final: 0.7609 (Cg_exo) REVERT: A 1182 PHE cc_start: 0.7357 (m-80) cc_final: 0.6929 (m-80) REVERT: A 1190 MET cc_start: 0.7123 (ttt) cc_final: 0.6585 (ttt) REVERT: L 31 HIS cc_start: 0.7574 (t70) cc_final: 0.6942 (t-170) REVERT: L 78 LEU cc_start: 0.7862 (tp) cc_final: 0.7520 (tp) REVERT: H 52 TRP cc_start: 0.6942 (OUTLIER) cc_final: 0.6135 (t-100) REVERT: H 103 LEU cc_start: 0.8973 (tp) cc_final: 0.8260 (tt) REVERT: B 64 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7810 (tt) REVERT: B 201 ARG cc_start: 0.7500 (ptm-80) cc_final: 0.6884 (ptm-80) REVERT: B 235 LYS cc_start: 0.8055 (mtmm) cc_final: 0.7487 (mtmm) REVERT: B 237 LEU cc_start: 0.8633 (tp) cc_final: 0.8389 (tp) REVERT: B 259 LYS cc_start: 0.7737 (ptmt) cc_final: 0.7251 (ptmt) REVERT: B 312 TYR cc_start: 0.7964 (m-10) cc_final: 0.7651 (m-10) REVERT: B 325 VAL cc_start: 0.7478 (OUTLIER) cc_final: 0.7166 (m) REVERT: B 329 LYS cc_start: 0.8310 (mttt) cc_final: 0.8106 (mmtt) REVERT: B 343 ASP cc_start: 0.7368 (t0) cc_final: 0.7111 (t0) REVERT: B 344 LYS cc_start: 0.8109 (ttmm) cc_final: 0.7849 (ttmm) REVERT: B 395 THR cc_start: 0.8172 (m) cc_final: 0.7762 (p) REVERT: B 405 ARG cc_start: 0.8197 (mmm160) cc_final: 0.7557 (tpp-160) REVERT: B 416 TYR cc_start: 0.7357 (m-10) cc_final: 0.7032 (m-10) REVERT: B 478 VAL cc_start: 0.8148 (p) cc_final: 0.7921 (m) REVERT: B 596 ILE cc_start: 0.8338 (mm) cc_final: 0.7917 (mp) REVERT: B 626 ASP cc_start: 0.7053 (t0) cc_final: 0.6098 (t0) REVERT: B 662 ARG cc_start: 0.7934 (mtp-110) cc_final: 0.7586 (mtp-110) REVERT: B 689 SER cc_start: 0.7523 (t) cc_final: 0.7234 (t) REVERT: B 697 ASN cc_start: 0.7834 (m110) cc_final: 0.7585 (m-40) REVERT: B 772 GLU cc_start: 0.7704 (tp30) cc_final: 0.7152 (tp30) REVERT: B 832 GLN cc_start: 0.7772 (mm110) cc_final: 0.7468 (mp10) REVERT: B 860 GLN cc_start: 0.7401 (OUTLIER) cc_final: 0.6958 (mp10) REVERT: B 874 LYS cc_start: 0.6215 (OUTLIER) cc_final: 0.5839 (pttp) REVERT: B 923 PHE cc_start: 0.7837 (m-80) cc_final: 0.7628 (m-80) REVERT: B 951 LEU cc_start: 0.8915 (mm) cc_final: 0.8714 (mt) REVERT: B 958 ASN cc_start: 0.8114 (m110) cc_final: 0.7587 (m-40) REVERT: B 1048 LEU cc_start: 0.8380 (tp) cc_final: 0.7967 (tp) REVERT: B 1051 GLN cc_start: 0.7501 (OUTLIER) cc_final: 0.6933 (mp10) REVERT: B 1073 LEU cc_start: 0.8120 (pt) cc_final: 0.7804 (pp) REVERT: B 1076 GLU cc_start: 0.7859 (tt0) cc_final: 0.7576 (tt0) REVERT: B 1080 ASP cc_start: 0.7508 (t0) cc_final: 0.6842 (t0) REVERT: B 1091 ASN cc_start: 0.8208 (m-40) cc_final: 0.7987 (m110) REVERT: B 1112 MET cc_start: 0.7723 (OUTLIER) cc_final: 0.6768 (mpp) REVERT: B 1139 VAL cc_start: 0.8574 (t) cc_final: 0.8140 (p) REVERT: B 1141 ASN cc_start: 0.8588 (t0) cc_final: 0.8107 (t0) REVERT: B 1182 PHE cc_start: 0.7554 (m-80) cc_final: 0.7070 (m-80) REVERT: B 1190 MET cc_start: 0.7136 (ttm) cc_final: 0.6533 (ttt) REVERT: D 47 GLN cc_start: 0.6097 (mm-40) cc_final: 0.5882 (mm-40) REVERT: D 75 ASP cc_start: 0.7818 (p0) cc_final: 0.6879 (m-30) REVERT: G 52 TRP cc_start: 0.6707 (OUTLIER) cc_final: 0.5816 (t-100) REVERT: G 102 TRP cc_start: 0.7726 (p-90) cc_final: 0.7131 (p-90) REVERT: G 103 LEU cc_start: 0.9048 (tp) cc_final: 0.8698 (tp) REVERT: C 111 LYS cc_start: 0.7954 (mtmm) cc_final: 0.7701 (mtmm) REVERT: C 180 LEU cc_start: 0.8723 (mt) cc_final: 0.8362 (mp) REVERT: C 235 LYS cc_start: 0.7961 (mtmm) cc_final: 0.7474 (mtmm) REVERT: C 237 LEU cc_start: 0.8434 (tp) cc_final: 0.8070 (tp) REVERT: C 259 LYS cc_start: 0.7698 (ptmt) cc_final: 0.7411 (ptmt) REVERT: C 312 TYR cc_start: 0.7732 (m-10) cc_final: 0.7377 (m-10) REVERT: C 325 VAL cc_start: 0.7488 (p) cc_final: 0.7166 (m) REVERT: C 328 ARG cc_start: 0.7209 (mpt180) cc_final: 0.6876 (mpt180) REVERT: C 342 ASN cc_start: 0.8336 (t0) cc_final: 0.7951 (t0) REVERT: C 344 LYS cc_start: 0.7892 (ttpp) cc_final: 0.7564 (ttmm) REVERT: C 375 SER cc_start: 0.7458 (t) cc_final: 0.7206 (m) REVERT: C 378 CYS cc_start: 0.5011 (m) cc_final: 0.4636 (m) REVERT: C 385 LYS cc_start: 0.7433 (mtpt) cc_final: 0.7149 (mtpt) REVERT: C 425 ASP cc_start: 0.7631 (t70) cc_final: 0.7078 (t0) REVERT: C 460 GLU cc_start: 0.8218 (mp0) cc_final: 0.7923 (mp0) REVERT: C 662 ARG cc_start: 0.7874 (mtp-110) cc_final: 0.7517 (mtm110) REVERT: C 663 ASP cc_start: 0.7366 (t70) cc_final: 0.6672 (t0) REVERT: C 689 SER cc_start: 0.7291 (t) cc_final: 0.7044 (t) REVERT: C 699 LYS cc_start: 0.8249 (mmmm) cc_final: 0.7757 (mtmm) REVERT: C 702 TYR cc_start: 0.7835 (t80) cc_final: 0.7532 (t80) REVERT: C 730 TYR cc_start: 0.6829 (p90) cc_final: 0.6380 (p90) REVERT: C 832 GLN cc_start: 0.7980 (mm110) cc_final: 0.7226 (mp10) REVERT: C 921 VAL cc_start: 0.7969 (m) cc_final: 0.7377 (m) REVERT: C 925 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7275 (mt-10) REVERT: C 959 GLN cc_start: 0.8551 (mt0) cc_final: 0.8096 (mt0) REVERT: C 1005 ASN cc_start: 0.7729 (t0) cc_final: 0.7254 (t0) REVERT: C 1039 ASN cc_start: 0.8351 (t0) cc_final: 0.7924 (t0) REVERT: C 1074 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7339 (mm-30) REVERT: C 1113 GLU cc_start: 0.7980 (tt0) cc_final: 0.7588 (tt0) REVERT: C 1119 VAL cc_start: 0.7117 (p) cc_final: 0.6908 (m) REVERT: C 1148 PHE cc_start: 0.8013 (m-80) cc_final: 0.7726 (m-80) REVERT: C 1182 PHE cc_start: 0.7384 (m-80) cc_final: 0.6902 (m-80) REVERT: C 1190 MET cc_start: 0.6951 (ttt) cc_final: 0.6479 (ttt) REVERT: C 1191 TYR cc_start: 0.7316 (t80) cc_final: 0.7103 (t80) REVERT: E 21 ILE cc_start: 0.8678 (mt) cc_final: 0.8394 (tp) REVERT: E 84 GLU cc_start: 0.6739 (pp20) cc_final: 0.6133 (pp20) REVERT: I 103 LEU cc_start: 0.8909 (tp) cc_final: 0.8290 (tt) outliers start: 79 outliers final: 44 residues processed: 905 average time/residue: 0.1934 time to fit residues: 290.6281 Evaluate side-chains 889 residues out of total 3660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 836 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 416 TYR Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 807 ILE Chi-restraints excluded: chain A residue 839 PHE Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 1076 GLU Chi-restraints excluded: chain A residue 1224 MET Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 39 ASP Chi-restraints excluded: chain H residue 52 TRP Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 607 SER Chi-restraints excluded: chain B residue 614 ASN Chi-restraints excluded: chain B residue 807 ILE Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 860 GLN Chi-restraints excluded: chain B residue 874 LYS Chi-restraints excluded: chain B residue 941 CYS Chi-restraints excluded: chain B residue 960 PHE Chi-restraints excluded: chain B residue 988 VAL Chi-restraints excluded: chain B residue 992 ILE Chi-restraints excluded: chain B residue 1051 GLN Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1112 MET Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain G residue 52 TRP Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 614 ASN Chi-restraints excluded: chain C residue 732 SER Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 941 CYS Chi-restraints excluded: chain C residue 990 TYR Chi-restraints excluded: chain C residue 992 ILE Chi-restraints excluded: chain C residue 1082 LEU Chi-restraints excluded: chain C residue 1167 LEU Chi-restraints excluded: chain C residue 1185 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 326 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 chunk 240 optimal weight: 0.9980 chunk 365 optimal weight: 7.9990 chunk 193 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 305 optimal weight: 1.9990 chunk 150 optimal weight: 0.1980 chunk 217 optimal weight: 0.3980 chunk 371 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 GLN ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1064 GLN B 858 GLN B1150 HIS G 13 GLN G 106 HIS C 315 ASN C 844 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.142679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.116140 restraints weight = 56270.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.120778 restraints weight = 28918.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.123946 restraints weight = 17731.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.126064 restraints weight = 12294.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.127583 restraints weight = 9353.407| |-----------------------------------------------------------------------------| r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 34413 Z= 0.121 Angle : 0.613 11.144 46959 Z= 0.310 Chirality : 0.046 0.336 5376 Planarity : 0.003 0.044 5952 Dihedral : 6.165 95.551 5592 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.81 % Allowed : 16.83 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.13), residues: 4176 helix: 0.25 (0.18), residues: 756 sheet: -0.58 (0.16), residues: 1014 loop : -1.06 (0.12), residues: 2406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 991 TYR 0.028 0.001 TYR A 50 PHE 0.027 0.001 PHE C 771 TRP 0.039 0.002 TRP H 102 HIS 0.004 0.001 HIS B1150 Details of bonding type rmsd covalent geometry : bond 0.00274 (34296) covalent geometry : angle 0.60240 (46677) SS BOND : bond 0.00577 ( 69) SS BOND : angle 1.35785 ( 138) hydrogen bonds : bond 0.03765 ( 1134) hydrogen bonds : angle 5.57431 ( 3411) link_BETA1-4 : bond 0.00269 ( 12) link_BETA1-4 : angle 0.97069 ( 36) link_NAG-ASN : bond 0.00450 ( 36) link_NAG-ASN : angle 2.02252 ( 108) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 968 residues out of total 3660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 865 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8103 (tptt) cc_final: 0.7872 (tppt) REVERT: A 78 MET cc_start: 0.7688 (mmm) cc_final: 0.7272 (ttm) REVERT: A 136 TYR cc_start: 0.8330 (m-80) cc_final: 0.7893 (m-10) REVERT: A 180 LEU cc_start: 0.8641 (mt) cc_final: 0.8350 (mt) REVERT: A 260 LEU cc_start: 0.8003 (pt) cc_final: 0.7771 (pt) REVERT: A 280 GLN cc_start: 0.7268 (mm110) cc_final: 0.6736 (mm-40) REVERT: A 293 ASP cc_start: 0.7244 (m-30) cc_final: 0.6958 (m-30) REVERT: A 312 TYR cc_start: 0.7804 (m-10) cc_final: 0.7499 (m-10) REVERT: A 315 ASN cc_start: 0.7700 (p0) cc_final: 0.7190 (p0) REVERT: A 328 ARG cc_start: 0.7195 (mpt180) cc_final: 0.6593 (mpt180) REVERT: A 329 LYS cc_start: 0.8126 (ttmm) cc_final: 0.7891 (ttmm) REVERT: A 335 CYS cc_start: 0.5498 (m) cc_final: 0.5268 (m) REVERT: A 342 ASN cc_start: 0.8057 (t0) cc_final: 0.7612 (t0) REVERT: A 375 SER cc_start: 0.7799 (t) cc_final: 0.7233 (m) REVERT: A 418 GLN cc_start: 0.8117 (tt0) cc_final: 0.7833 (tt0) REVERT: A 425 ASP cc_start: 0.7749 (t70) cc_final: 0.7245 (t0) REVERT: A 437 LEU cc_start: 0.7900 (mt) cc_final: 0.7522 (mt) REVERT: A 573 GLN cc_start: 0.7801 (mp10) cc_final: 0.7488 (mp10) REVERT: A 596 ILE cc_start: 0.8392 (mm) cc_final: 0.8149 (mt) REVERT: A 598 HIS cc_start: 0.7948 (m90) cc_final: 0.7375 (m90) REVERT: A 626 ASP cc_start: 0.6766 (t0) cc_final: 0.6239 (t0) REVERT: A 663 ASP cc_start: 0.7412 (t70) cc_final: 0.6945 (t70) REVERT: A 699 LYS cc_start: 0.8287 (mmmm) cc_final: 0.8004 (mtmm) REVERT: A 766 TYR cc_start: 0.6970 (m-80) cc_final: 0.6566 (m-10) REVERT: A 817 ASP cc_start: 0.7172 (t0) cc_final: 0.6769 (p0) REVERT: A 833 LEU cc_start: 0.7396 (tp) cc_final: 0.7191 (tt) REVERT: A 858 GLN cc_start: 0.7758 (mm110) cc_final: 0.7405 (mm110) REVERT: A 976 TRP cc_start: 0.6208 (m-90) cc_final: 0.5728 (m-90) REVERT: A 991 ARG cc_start: 0.6449 (mmm-85) cc_final: 0.6238 (mmm-85) REVERT: A 1000 ASP cc_start: 0.7593 (t0) cc_final: 0.7316 (t0) REVERT: A 1033 LYS cc_start: 0.8634 (tppt) cc_final: 0.8235 (ttmm) REVERT: A 1051 GLN cc_start: 0.7490 (mp10) cc_final: 0.7077 (mp10) REVERT: A 1065 GLU cc_start: 0.6946 (mt-10) cc_final: 0.6329 (mt-10) REVERT: A 1076 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7429 (tt0) REVERT: A 1112 MET cc_start: 0.7561 (mmm) cc_final: 0.7197 (mmm) REVERT: A 1113 GLU cc_start: 0.7753 (tt0) cc_final: 0.7499 (mt-10) REVERT: A 1119 VAL cc_start: 0.7073 (OUTLIER) cc_final: 0.6777 (m) REVERT: A 1141 ASN cc_start: 0.8419 (t0) cc_final: 0.8006 (t0) REVERT: A 1147 TYR cc_start: 0.7964 (t80) cc_final: 0.7711 (t80) REVERT: A 1177 PRO cc_start: 0.8048 (Cg_endo) cc_final: 0.7539 (Cg_exo) REVERT: A 1182 PHE cc_start: 0.7374 (m-80) cc_final: 0.6927 (m-80) REVERT: A 1190 MET cc_start: 0.7160 (ttt) cc_final: 0.6501 (ttt) REVERT: L 31 HIS cc_start: 0.7600 (t70) cc_final: 0.6938 (t-170) REVERT: L 78 LEU cc_start: 0.7857 (tp) cc_final: 0.7539 (tp) REVERT: H 52 TRP cc_start: 0.6878 (OUTLIER) cc_final: 0.6174 (t-100) REVERT: H 103 LEU cc_start: 0.8954 (tp) cc_final: 0.8227 (tt) REVERT: B 29 LYS cc_start: 0.7752 (tptt) cc_final: 0.7229 (tppt) REVERT: B 64 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7933 (tt) REVERT: B 176 CYS cc_start: 0.4717 (t) cc_final: 0.4516 (t) REVERT: B 235 LYS cc_start: 0.8066 (mtmm) cc_final: 0.7504 (mtmm) REVERT: B 237 LEU cc_start: 0.8637 (tp) cc_final: 0.8423 (tp) REVERT: B 259 LYS cc_start: 0.7753 (ptmt) cc_final: 0.7284 (ptmt) REVERT: B 312 TYR cc_start: 0.7953 (m-10) cc_final: 0.7651 (m-10) REVERT: B 328 ARG cc_start: 0.7447 (mpt180) cc_final: 0.6854 (mpt180) REVERT: B 329 LYS cc_start: 0.8313 (mttt) cc_final: 0.8087 (mmtt) REVERT: B 344 LYS cc_start: 0.8119 (ttmm) cc_final: 0.7770 (ttmm) REVERT: B 395 THR cc_start: 0.8182 (m) cc_final: 0.7763 (p) REVERT: B 405 ARG cc_start: 0.8237 (mmm160) cc_final: 0.7637 (tpp-160) REVERT: B 431 CYS cc_start: 0.5566 (m) cc_final: 0.5174 (m) REVERT: B 596 ILE cc_start: 0.8420 (mm) cc_final: 0.8064 (mp) REVERT: B 617 ILE cc_start: 0.8447 (mm) cc_final: 0.8011 (mm) REVERT: B 626 ASP cc_start: 0.7064 (t0) cc_final: 0.6542 (t0) REVERT: B 662 ARG cc_start: 0.7940 (mtp-110) cc_final: 0.7604 (mtp-110) REVERT: B 663 ASP cc_start: 0.7666 (t0) cc_final: 0.7294 (t0) REVERT: B 689 SER cc_start: 0.7544 (t) cc_final: 0.7239 (t) REVERT: B 697 ASN cc_start: 0.7821 (m110) cc_final: 0.7491 (m-40) REVERT: B 719 PHE cc_start: 0.8099 (p90) cc_final: 0.7374 (p90) REVERT: B 720 ASP cc_start: 0.7099 (m-30) cc_final: 0.6624 (m-30) REVERT: B 772 GLU cc_start: 0.7719 (tp30) cc_final: 0.7193 (tp30) REVERT: B 832 GLN cc_start: 0.7759 (mm110) cc_final: 0.7551 (mp10) REVERT: B 860 GLN cc_start: 0.7391 (OUTLIER) cc_final: 0.6953 (mp10) REVERT: B 874 LYS cc_start: 0.6187 (OUTLIER) cc_final: 0.5760 (pttp) REVERT: B 923 PHE cc_start: 0.7759 (m-80) cc_final: 0.7513 (m-80) REVERT: B 951 LEU cc_start: 0.8919 (mm) cc_final: 0.8706 (mt) REVERT: B 958 ASN cc_start: 0.8099 (m110) cc_final: 0.7567 (m-40) REVERT: B 1000 ASP cc_start: 0.7340 (t0) cc_final: 0.7130 (t0) REVERT: B 1048 LEU cc_start: 0.8411 (tp) cc_final: 0.7971 (tp) REVERT: B 1051 GLN cc_start: 0.7490 (OUTLIER) cc_final: 0.6888 (mp10) REVERT: B 1073 LEU cc_start: 0.8108 (pt) cc_final: 0.7793 (pp) REVERT: B 1076 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7554 (tt0) REVERT: B 1080 ASP cc_start: 0.7503 (t0) cc_final: 0.7022 (t0) REVERT: B 1112 MET cc_start: 0.7709 (OUTLIER) cc_final: 0.6771 (mpp) REVERT: B 1139 VAL cc_start: 0.8562 (t) cc_final: 0.8162 (p) REVERT: B 1182 PHE cc_start: 0.7545 (m-80) cc_final: 0.7207 (m-80) REVERT: B 1190 MET cc_start: 0.7124 (ttm) cc_final: 0.6584 (ttt) REVERT: B 1198 TYR cc_start: 0.7239 (t80) cc_final: 0.6861 (t80) REVERT: D 4 MET cc_start: 0.4291 (mpp) cc_final: 0.4084 (mpp) REVERT: G 52 TRP cc_start: 0.6697 (OUTLIER) cc_final: 0.5797 (t-100) REVERT: G 102 TRP cc_start: 0.7731 (p-90) cc_final: 0.7141 (p-90) REVERT: G 103 LEU cc_start: 0.9035 (tp) cc_final: 0.8696 (tp) REVERT: C 111 LYS cc_start: 0.7943 (mtmm) cc_final: 0.7690 (mtmm) REVERT: C 180 LEU cc_start: 0.8722 (mt) cc_final: 0.8336 (mp) REVERT: C 235 LYS cc_start: 0.7960 (mtmm) cc_final: 0.7465 (mtmm) REVERT: C 237 LEU cc_start: 0.8469 (tp) cc_final: 0.8094 (tp) REVERT: C 259 LYS cc_start: 0.7705 (ptmt) cc_final: 0.7417 (ptmt) REVERT: C 312 TYR cc_start: 0.7708 (m-10) cc_final: 0.7369 (m-10) REVERT: C 325 VAL cc_start: 0.7528 (p) cc_final: 0.7223 (m) REVERT: C 328 ARG cc_start: 0.7243 (mpt180) cc_final: 0.6942 (mpt180) REVERT: C 342 ASN cc_start: 0.8341 (t0) cc_final: 0.7922 (t0) REVERT: C 344 LYS cc_start: 0.7896 (ttpp) cc_final: 0.7576 (ttmm) REVERT: C 375 SER cc_start: 0.7473 (t) cc_final: 0.7210 (m) REVERT: C 376 PHE cc_start: 0.7991 (t80) cc_final: 0.7637 (t80) REVERT: C 385 LYS cc_start: 0.7496 (OUTLIER) cc_final: 0.7214 (mtpt) REVERT: C 425 ASP cc_start: 0.7597 (t70) cc_final: 0.7045 (t0) REVERT: C 460 GLU cc_start: 0.8212 (mp0) cc_final: 0.7903 (mp0) REVERT: C 662 ARG cc_start: 0.7855 (mtp-110) cc_final: 0.7487 (mtm110) REVERT: C 663 ASP cc_start: 0.7400 (t70) cc_final: 0.6867 (t0) REVERT: C 689 SER cc_start: 0.7306 (t) cc_final: 0.7054 (t) REVERT: C 699 LYS cc_start: 0.8240 (mmmm) cc_final: 0.7765 (mtmm) REVERT: C 702 TYR cc_start: 0.7806 (t80) cc_final: 0.7521 (t80) REVERT: C 730 TYR cc_start: 0.6824 (p90) cc_final: 0.6371 (p90) REVERT: C 774 PHE cc_start: 0.7311 (m-80) cc_final: 0.7048 (m-80) REVERT: C 817 ASP cc_start: 0.6877 (t70) cc_final: 0.6627 (p0) REVERT: C 832 GLN cc_start: 0.7996 (mm110) cc_final: 0.7233 (mp10) REVERT: C 860 GLN cc_start: 0.7580 (mp10) cc_final: 0.7234 (mp10) REVERT: C 921 VAL cc_start: 0.7997 (m) cc_final: 0.7379 (m) REVERT: C 925 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7179 (mt-10) REVERT: C 959 GLN cc_start: 0.8469 (mt0) cc_final: 0.8065 (mt0) REVERT: C 991 ARG cc_start: 0.6493 (mmm-85) cc_final: 0.6095 (mtp85) REVERT: C 1005 ASN cc_start: 0.7743 (t0) cc_final: 0.7272 (t0) REVERT: C 1039 ASN cc_start: 0.8270 (t0) cc_final: 0.7831 (t0) REVERT: C 1065 GLU cc_start: 0.7122 (mt-10) cc_final: 0.6769 (mt-10) REVERT: C 1074 GLU cc_start: 0.7690 (mm-30) cc_final: 0.7271 (mm-30) REVERT: C 1113 GLU cc_start: 0.7952 (tt0) cc_final: 0.7549 (tt0) REVERT: C 1148 PHE cc_start: 0.7993 (m-80) cc_final: 0.7757 (m-80) REVERT: C 1182 PHE cc_start: 0.7397 (m-80) cc_final: 0.6866 (m-80) REVERT: C 1190 MET cc_start: 0.7078 (ttt) cc_final: 0.6599 (ttt) REVERT: E 21 ILE cc_start: 0.8666 (mt) cc_final: 0.8373 (tp) REVERT: I 52 TRP cc_start: 0.6549 (OUTLIER) cc_final: 0.5698 (t-100) REVERT: I 103 LEU cc_start: 0.8905 (tp) cc_final: 0.8261 (tt) outliers start: 103 outliers final: 62 residues processed: 905 average time/residue: 0.1882 time to fit residues: 283.8697 Evaluate side-chains 915 residues out of total 3660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 841 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 416 TYR Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 807 ILE Chi-restraints excluded: chain A residue 839 PHE Chi-restraints excluded: chain A residue 919 SER Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 960 PHE Chi-restraints excluded: chain A residue 1076 GLU Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1224 MET Chi-restraints excluded: chain L residue 39 ASP Chi-restraints excluded: chain H residue 52 TRP Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 197 CYS Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 607 SER Chi-restraints excluded: chain B residue 614 ASN Chi-restraints excluded: chain B residue 638 GLU Chi-restraints excluded: chain B residue 730 TYR Chi-restraints excluded: chain B residue 807 ILE Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 858 GLN Chi-restraints excluded: chain B residue 860 GLN Chi-restraints excluded: chain B residue 874 LYS Chi-restraints excluded: chain B residue 919 SER Chi-restraints excluded: chain B residue 941 CYS Chi-restraints excluded: chain B residue 960 PHE Chi-restraints excluded: chain B residue 988 VAL Chi-restraints excluded: chain B residue 1051 GLN Chi-restraints excluded: chain B residue 1076 GLU Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain B residue 1112 MET Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain G residue 13 GLN Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 52 TRP Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 385 LYS Chi-restraints excluded: chain C residue 614 ASN Chi-restraints excluded: chain C residue 732 SER Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 941 CYS Chi-restraints excluded: chain C residue 990 TYR Chi-restraints excluded: chain C residue 1082 LEU Chi-restraints excluded: chain C residue 1112 MET Chi-restraints excluded: chain C residue 1167 LEU Chi-restraints excluded: chain C residue 1185 VAL Chi-restraints excluded: chain I residue 52 TRP Chi-restraints excluded: chain I residue 91 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 285 optimal weight: 2.9990 chunk 196 optimal weight: 6.9990 chunk 173 optimal weight: 0.7980 chunk 86 optimal weight: 9.9990 chunk 367 optimal weight: 0.7980 chunk 166 optimal weight: 1.9990 chunk 273 optimal weight: 0.2980 chunk 48 optimal weight: 6.9990 chunk 194 optimal weight: 0.8980 chunk 56 optimal weight: 6.9990 chunk 418 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 ASN A 410 GLN ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 860 GLN A1014 ASN A1064 GLN A1187 ASN H 13 GLN ** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1091 ASN ** B1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 315 ASN C 844 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.143886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.117124 restraints weight = 56404.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.121919 restraints weight = 28684.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.125211 restraints weight = 17471.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.127400 restraints weight = 12037.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.128843 restraints weight = 9101.091| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 34413 Z= 0.148 Angle : 0.635 10.077 46959 Z= 0.322 Chirality : 0.046 0.337 5376 Planarity : 0.004 0.045 5952 Dihedral : 5.985 93.306 5592 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.62 % Allowed : 17.68 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.13), residues: 4176 helix: 0.22 (0.18), residues: 756 sheet: -0.62 (0.16), residues: 1005 loop : -1.05 (0.12), residues: 2415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 991 TYR 0.025 0.001 TYR C 435 PHE 0.033 0.001 PHE B 122 TRP 0.040 0.002 TRP H 102 HIS 0.005 0.001 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00334 (34296) covalent geometry : angle 0.62373 (46677) SS BOND : bond 0.00413 ( 69) SS BOND : angle 1.40009 ( 138) hydrogen bonds : bond 0.03832 ( 1134) hydrogen bonds : angle 5.55107 ( 3411) link_BETA1-4 : bond 0.00273 ( 12) link_BETA1-4 : angle 1.00841 ( 36) link_NAG-ASN : bond 0.00461 ( 36) link_NAG-ASN : angle 2.07173 ( 108) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 964 residues out of total 3660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 868 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8173 (tptt) cc_final: 0.7716 (tppt) REVERT: A 136 TYR cc_start: 0.8333 (m-80) cc_final: 0.7894 (m-10) REVERT: A 180 LEU cc_start: 0.8663 (mt) cc_final: 0.8394 (mt) REVERT: A 280 GLN cc_start: 0.7280 (mm110) cc_final: 0.6888 (mm110) REVERT: A 293 ASP cc_start: 0.7273 (m-30) cc_final: 0.6965 (m-30) REVERT: A 312 TYR cc_start: 0.7810 (m-10) cc_final: 0.7455 (m-10) REVERT: A 315 ASN cc_start: 0.7707 (p0) cc_final: 0.7201 (p0) REVERT: A 328 ARG cc_start: 0.7194 (mpt180) cc_final: 0.6563 (mpt180) REVERT: A 329 LYS cc_start: 0.8168 (ttmm) cc_final: 0.7882 (ttmm) REVERT: A 335 CYS cc_start: 0.5518 (m) cc_final: 0.5303 (m) REVERT: A 342 ASN cc_start: 0.8083 (t0) cc_final: 0.7622 (t0) REVERT: A 375 SER cc_start: 0.7808 (t) cc_final: 0.7220 (m) REVERT: A 425 ASP cc_start: 0.7757 (t70) cc_final: 0.7232 (t0) REVERT: A 437 LEU cc_start: 0.7898 (mt) cc_final: 0.7506 (mt) REVERT: A 448 ASN cc_start: 0.8675 (t0) cc_final: 0.8334 (t0) REVERT: A 573 GLN cc_start: 0.7836 (mp10) cc_final: 0.7492 (mp10) REVERT: A 596 ILE cc_start: 0.8338 (mm) cc_final: 0.8136 (mt) REVERT: A 626 ASP cc_start: 0.6737 (t0) cc_final: 0.6189 (t0) REVERT: A 663 ASP cc_start: 0.7436 (t70) cc_final: 0.7183 (t0) REVERT: A 699 LYS cc_start: 0.8276 (mmmm) cc_final: 0.7975 (mtmm) REVERT: A 731 ASN cc_start: 0.7625 (t0) cc_final: 0.7285 (t0) REVERT: A 766 TYR cc_start: 0.6986 (m-80) cc_final: 0.6640 (m-10) REVERT: A 772 GLU cc_start: 0.7632 (tp30) cc_final: 0.7242 (tp30) REVERT: A 858 GLN cc_start: 0.7765 (mm110) cc_final: 0.7444 (mm110) REVERT: A 860 GLN cc_start: 0.8086 (mt0) cc_final: 0.7453 (mp10) REVERT: A 976 TRP cc_start: 0.6233 (m-90) cc_final: 0.5685 (m-90) REVERT: A 1000 ASP cc_start: 0.7607 (t0) cc_final: 0.7034 (t0) REVERT: A 1033 LYS cc_start: 0.8629 (tppt) cc_final: 0.8254 (ttmm) REVERT: A 1051 GLN cc_start: 0.7538 (mp10) cc_final: 0.7066 (mp10) REVERT: A 1065 GLU cc_start: 0.7031 (mt-10) cc_final: 0.6369 (mt-10) REVERT: A 1076 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7588 (tt0) REVERT: A 1112 MET cc_start: 0.7585 (mmm) cc_final: 0.7218 (mmm) REVERT: A 1113 GLU cc_start: 0.7782 (tt0) cc_final: 0.7545 (mt-10) REVERT: A 1119 VAL cc_start: 0.7106 (OUTLIER) cc_final: 0.6785 (m) REVERT: A 1141 ASN cc_start: 0.8445 (t0) cc_final: 0.8121 (t0) REVERT: A 1147 TYR cc_start: 0.7940 (t80) cc_final: 0.7708 (t80) REVERT: A 1190 MET cc_start: 0.7230 (ttt) cc_final: 0.6508 (ttt) REVERT: A 1198 TYR cc_start: 0.7385 (t80) cc_final: 0.6547 (t80) REVERT: L 31 HIS cc_start: 0.7668 (t70) cc_final: 0.6962 (t-170) REVERT: L 78 LEU cc_start: 0.7822 (tp) cc_final: 0.7561 (tp) REVERT: H 52 TRP cc_start: 0.6854 (OUTLIER) cc_final: 0.6153 (t-100) REVERT: H 103 LEU cc_start: 0.8919 (tp) cc_final: 0.7995 (tt) REVERT: B 136 TYR cc_start: 0.8284 (m-80) cc_final: 0.8059 (m-80) REVERT: B 168 MET cc_start: 0.5542 (mmm) cc_final: 0.4950 (mmm) REVERT: B 235 LYS cc_start: 0.8056 (mtmm) cc_final: 0.7503 (mtmm) REVERT: B 237 LEU cc_start: 0.8661 (tp) cc_final: 0.8310 (tt) REVERT: B 259 LYS cc_start: 0.7746 (ptmt) cc_final: 0.7283 (ptmt) REVERT: B 328 ARG cc_start: 0.7496 (mpt180) cc_final: 0.7020 (mmt180) REVERT: B 344 LYS cc_start: 0.8227 (ttmm) cc_final: 0.7861 (ttmm) REVERT: B 395 THR cc_start: 0.8197 (m) cc_final: 0.7765 (p) REVERT: B 405 ARG cc_start: 0.8339 (mmm160) cc_final: 0.7743 (tpp-160) REVERT: B 596 ILE cc_start: 0.8384 (mm) cc_final: 0.8054 (mp) REVERT: B 662 ARG cc_start: 0.7970 (mtp-110) cc_final: 0.7637 (mtp-110) REVERT: B 663 ASP cc_start: 0.7759 (t0) cc_final: 0.7332 (t0) REVERT: B 689 SER cc_start: 0.7505 (t) cc_final: 0.7235 (t) REVERT: B 697 ASN cc_start: 0.7863 (m110) cc_final: 0.7567 (m-40) REVERT: B 719 PHE cc_start: 0.8154 (p90) cc_final: 0.7377 (p90) REVERT: B 772 GLU cc_start: 0.7741 (tp30) cc_final: 0.7204 (tp30) REVERT: B 798 PHE cc_start: 0.7815 (p90) cc_final: 0.7427 (p90) REVERT: B 858 GLN cc_start: 0.7835 (mm110) cc_final: 0.7592 (mm110) REVERT: B 860 GLN cc_start: 0.7470 (OUTLIER) cc_final: 0.6947 (mp10) REVERT: B 874 LYS cc_start: 0.6212 (OUTLIER) cc_final: 0.5759 (pttm) REVERT: B 923 PHE cc_start: 0.7781 (m-80) cc_final: 0.7554 (m-80) REVERT: B 958 ASN cc_start: 0.8136 (m110) cc_final: 0.7702 (m-40) REVERT: B 959 GLN cc_start: 0.8239 (mt0) cc_final: 0.7892 (mt0) REVERT: B 960 PHE cc_start: 0.7998 (OUTLIER) cc_final: 0.7527 (m-80) REVERT: B 1000 ASP cc_start: 0.7350 (t0) cc_final: 0.7102 (t0) REVERT: B 1051 GLN cc_start: 0.7552 (OUTLIER) cc_final: 0.7233 (mp10) REVERT: B 1073 LEU cc_start: 0.8173 (pt) cc_final: 0.7885 (pp) REVERT: B 1076 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7584 (tt0) REVERT: B 1080 ASP cc_start: 0.7562 (t0) cc_final: 0.7050 (t0) REVERT: B 1112 MET cc_start: 0.7783 (OUTLIER) cc_final: 0.6817 (mpp) REVERT: B 1139 VAL cc_start: 0.8590 (t) cc_final: 0.8209 (p) REVERT: B 1182 PHE cc_start: 0.7556 (m-80) cc_final: 0.7217 (m-80) REVERT: B 1190 MET cc_start: 0.7047 (ttm) cc_final: 0.6522 (ttt) REVERT: B 1198 TYR cc_start: 0.7296 (t80) cc_final: 0.7019 (t80) REVERT: D 4 MET cc_start: 0.4337 (mpp) cc_final: 0.4129 (mpp) REVERT: D 75 ASP cc_start: 0.7784 (p0) cc_final: 0.6806 (m-30) REVERT: G 52 TRP cc_start: 0.6712 (OUTLIER) cc_final: 0.5831 (t-100) REVERT: G 103 LEU cc_start: 0.9014 (tp) cc_final: 0.8670 (tp) REVERT: C 111 LYS cc_start: 0.7981 (mtmm) cc_final: 0.7721 (mtmm) REVERT: C 180 LEU cc_start: 0.8724 (mt) cc_final: 0.8361 (mp) REVERT: C 235 LYS cc_start: 0.7925 (mtmm) cc_final: 0.7434 (mtmm) REVERT: C 237 LEU cc_start: 0.8513 (tp) cc_final: 0.8125 (tp) REVERT: C 259 LYS cc_start: 0.7720 (ptmt) cc_final: 0.7421 (ptmt) REVERT: C 312 TYR cc_start: 0.7712 (m-10) cc_final: 0.7342 (m-10) REVERT: C 325 VAL cc_start: 0.7516 (p) cc_final: 0.7218 (m) REVERT: C 328 ARG cc_start: 0.7246 (mpt180) cc_final: 0.6912 (mpt180) REVERT: C 342 ASN cc_start: 0.8350 (t0) cc_final: 0.7955 (t0) REVERT: C 375 SER cc_start: 0.7434 (t) cc_final: 0.7187 (m) REVERT: C 376 PHE cc_start: 0.7988 (t80) cc_final: 0.7673 (t80) REVERT: C 385 LYS cc_start: 0.7576 (OUTLIER) cc_final: 0.7290 (mtpt) REVERT: C 425 ASP cc_start: 0.7606 (t70) cc_final: 0.7044 (t0) REVERT: C 460 GLU cc_start: 0.8251 (mp0) cc_final: 0.7972 (mp0) REVERT: C 662 ARG cc_start: 0.7900 (mtp-110) cc_final: 0.7523 (mtm110) REVERT: C 663 ASP cc_start: 0.7441 (t70) cc_final: 0.6756 (t0) REVERT: C 689 SER cc_start: 0.7317 (t) cc_final: 0.7080 (t) REVERT: C 699 LYS cc_start: 0.8275 (mmmm) cc_final: 0.7821 (mtmm) REVERT: C 702 TYR cc_start: 0.7796 (t80) cc_final: 0.7509 (t80) REVERT: C 730 TYR cc_start: 0.6838 (p90) cc_final: 0.6358 (p90) REVERT: C 774 PHE cc_start: 0.7340 (m-80) cc_final: 0.7061 (m-80) REVERT: C 817 ASP cc_start: 0.6929 (t70) cc_final: 0.6597 (p0) REVERT: C 832 GLN cc_start: 0.7952 (mm110) cc_final: 0.7233 (mp10) REVERT: C 921 VAL cc_start: 0.8035 (m) cc_final: 0.7440 (m) REVERT: C 925 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7204 (mt-10) REVERT: C 959 GLN cc_start: 0.8500 (mt0) cc_final: 0.8092 (mt0) REVERT: C 1005 ASN cc_start: 0.7822 (t0) cc_final: 0.7341 (t0) REVERT: C 1039 ASN cc_start: 0.8292 (t0) cc_final: 0.7870 (t0) REVERT: C 1065 GLU cc_start: 0.7183 (mt-10) cc_final: 0.6824 (mt-10) REVERT: C 1074 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7291 (mm-30) REVERT: C 1080 ASP cc_start: 0.7498 (t0) cc_final: 0.7065 (t0) REVERT: C 1113 GLU cc_start: 0.8028 (tt0) cc_final: 0.7584 (tt0) REVERT: C 1141 ASN cc_start: 0.8659 (t0) cc_final: 0.8304 (m-40) REVERT: C 1182 PHE cc_start: 0.7439 (m-80) cc_final: 0.6925 (m-80) REVERT: C 1190 MET cc_start: 0.7081 (ttt) cc_final: 0.6695 (ttt) REVERT: E 21 ILE cc_start: 0.8644 (mt) cc_final: 0.8372 (tp) REVERT: I 33 VAL cc_start: 0.5767 (OUTLIER) cc_final: 0.5360 (p) REVERT: I 103 LEU cc_start: 0.8864 (tp) cc_final: 0.8166 (tt) outliers start: 96 outliers final: 65 residues processed: 902 average time/residue: 0.1876 time to fit residues: 281.5295 Evaluate side-chains 927 residues out of total 3660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 850 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 416 TYR Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 614 ASN Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 807 ILE Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 839 PHE Chi-restraints excluded: chain A residue 866 MET Chi-restraints excluded: chain A residue 919 SER Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 960 PHE Chi-restraints excluded: chain A residue 1076 GLU Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1224 MET Chi-restraints excluded: chain L residue 39 ASP Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain H residue 52 TRP Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 197 CYS Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 607 SER Chi-restraints excluded: chain B residue 614 ASN Chi-restraints excluded: chain B residue 638 GLU Chi-restraints excluded: chain B residue 730 TYR Chi-restraints excluded: chain B residue 807 ILE Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 860 GLN Chi-restraints excluded: chain B residue 874 LYS Chi-restraints excluded: chain B residue 919 SER Chi-restraints excluded: chain B residue 941 CYS Chi-restraints excluded: chain B residue 960 PHE Chi-restraints excluded: chain B residue 988 VAL Chi-restraints excluded: chain B residue 1051 GLN Chi-restraints excluded: chain B residue 1076 GLU Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain B residue 1112 MET Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 52 TRP Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 315 ASN Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 385 LYS Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 614 ASN Chi-restraints excluded: chain C residue 732 SER Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 840 CYS Chi-restraints excluded: chain C residue 941 CYS Chi-restraints excluded: chain C residue 990 TYR Chi-restraints excluded: chain C residue 1082 LEU Chi-restraints excluded: chain C residue 1084 ASN Chi-restraints excluded: chain C residue 1112 MET Chi-restraints excluded: chain C residue 1167 LEU Chi-restraints excluded: chain C residue 1185 VAL Chi-restraints excluded: chain I residue 33 VAL Chi-restraints excluded: chain I residue 52 TRP Chi-restraints excluded: chain I residue 91 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 67 optimal weight: 3.9990 chunk 367 optimal weight: 0.6980 chunk 64 optimal weight: 5.9990 chunk 231 optimal weight: 0.7980 chunk 392 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 chunk 251 optimal weight: 6.9990 chunk 43 optimal weight: 0.4980 chunk 342 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 265 optimal weight: 9.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 GLN C 844 ASN C 860 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.143063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.116395 restraints weight = 56368.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.121130 restraints weight = 28723.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.124364 restraints weight = 17543.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.126544 restraints weight = 12148.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.127939 restraints weight = 9199.612| |-----------------------------------------------------------------------------| r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 34413 Z= 0.169 Angle : 0.653 12.122 46959 Z= 0.332 Chirality : 0.047 0.410 5376 Planarity : 0.004 0.047 5952 Dihedral : 5.829 90.440 5592 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.76 % Allowed : 18.36 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.13), residues: 4176 helix: 0.33 (0.18), residues: 732 sheet: -0.72 (0.16), residues: 1044 loop : -1.07 (0.12), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 991 TYR 0.026 0.002 TYR C 435 PHE 0.049 0.002 PHE C 122 TRP 0.041 0.002 TRP H 102 HIS 0.006 0.001 HIS B 215 Details of bonding type rmsd covalent geometry : bond 0.00378 (34296) covalent geometry : angle 0.64085 (46677) SS BOND : bond 0.00443 ( 69) SS BOND : angle 1.47669 ( 138) hydrogen bonds : bond 0.03931 ( 1134) hydrogen bonds : angle 5.55258 ( 3411) link_BETA1-4 : bond 0.00259 ( 12) link_BETA1-4 : angle 1.07074 ( 36) link_NAG-ASN : bond 0.00475 ( 36) link_NAG-ASN : angle 2.13486 ( 108) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 970 residues out of total 3660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 869 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.8185 (tptt) cc_final: 0.7938 (tppt) REVERT: A 127 ILE cc_start: 0.7892 (OUTLIER) cc_final: 0.7652 (mm) REVERT: A 136 TYR cc_start: 0.8347 (m-80) cc_final: 0.7881 (m-10) REVERT: A 174 THR cc_start: 0.7467 (p) cc_final: 0.7242 (t) REVERT: A 280 GLN cc_start: 0.7271 (mm110) cc_final: 0.6882 (mm110) REVERT: A 293 ASP cc_start: 0.7324 (m-30) cc_final: 0.7085 (m-30) REVERT: A 312 TYR cc_start: 0.7826 (m-10) cc_final: 0.7491 (m-10) REVERT: A 315 ASN cc_start: 0.7708 (p0) cc_final: 0.7160 (p0) REVERT: A 328 ARG cc_start: 0.7212 (mpt180) cc_final: 0.6570 (mpt180) REVERT: A 329 LYS cc_start: 0.8150 (ttmm) cc_final: 0.7778 (ttmm) REVERT: A 335 CYS cc_start: 0.5479 (m) cc_final: 0.5274 (m) REVERT: A 342 ASN cc_start: 0.8077 (t0) cc_final: 0.7626 (t0) REVERT: A 375 SER cc_start: 0.7820 (t) cc_final: 0.7244 (m) REVERT: A 425 ASP cc_start: 0.7752 (t70) cc_final: 0.7232 (t0) REVERT: A 437 LEU cc_start: 0.7935 (mt) cc_final: 0.7589 (mt) REVERT: A 448 ASN cc_start: 0.8688 (t0) cc_final: 0.8347 (t0) REVERT: A 612 LYS cc_start: 0.7496 (mmtp) cc_final: 0.7284 (mmtm) REVERT: A 626 ASP cc_start: 0.6739 (t0) cc_final: 0.6148 (t0) REVERT: A 663 ASP cc_start: 0.7518 (t70) cc_final: 0.7286 (t0) REVERT: A 694 LEU cc_start: 0.7199 (OUTLIER) cc_final: 0.6900 (tp) REVERT: A 699 LYS cc_start: 0.8273 (mmmm) cc_final: 0.8011 (mtmm) REVERT: A 731 ASN cc_start: 0.7652 (t0) cc_final: 0.7291 (t0) REVERT: A 772 GLU cc_start: 0.7580 (tp30) cc_final: 0.7145 (tp30) REVERT: A 833 LEU cc_start: 0.7489 (tp) cc_final: 0.7155 (tt) REVERT: A 858 GLN cc_start: 0.7732 (mm110) cc_final: 0.7399 (mm110) REVERT: A 860 GLN cc_start: 0.8101 (mt0) cc_final: 0.7410 (mp10) REVERT: A 976 TRP cc_start: 0.6293 (m-90) cc_final: 0.5720 (m-90) REVERT: A 1000 ASP cc_start: 0.7604 (t0) cc_final: 0.7117 (t0) REVERT: A 1033 LYS cc_start: 0.8639 (tppt) cc_final: 0.8211 (ttmm) REVERT: A 1051 GLN cc_start: 0.7542 (mp10) cc_final: 0.7060 (mp10) REVERT: A 1055 ARG cc_start: 0.8138 (ttm110) cc_final: 0.7912 (ttp-110) REVERT: A 1065 GLU cc_start: 0.7018 (mt-10) cc_final: 0.6473 (mt-10) REVERT: A 1076 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7713 (tt0) REVERT: A 1112 MET cc_start: 0.7608 (mmm) cc_final: 0.7246 (mmm) REVERT: A 1113 GLU cc_start: 0.7775 (tt0) cc_final: 0.7554 (mt-10) REVERT: A 1147 TYR cc_start: 0.7939 (t80) cc_final: 0.7708 (t80) REVERT: A 1177 PRO cc_start: 0.8027 (Cg_endo) cc_final: 0.7411 (Cg_exo) REVERT: A 1182 PHE cc_start: 0.7481 (m-80) cc_final: 0.6680 (m-80) REVERT: A 1190 MET cc_start: 0.7257 (ttt) cc_final: 0.6523 (ttt) REVERT: A 1198 TYR cc_start: 0.7381 (t80) cc_final: 0.6565 (t80) REVERT: L 79 LYS cc_start: 0.7891 (OUTLIER) cc_final: 0.7584 (tptt) REVERT: H 52 TRP cc_start: 0.6875 (OUTLIER) cc_final: 0.6268 (t-100) REVERT: H 103 LEU cc_start: 0.8894 (tp) cc_final: 0.8446 (tp) REVERT: B 136 TYR cc_start: 0.8340 (m-80) cc_final: 0.8134 (m-80) REVERT: B 168 MET cc_start: 0.5486 (mmm) cc_final: 0.4897 (mmm) REVERT: B 235 LYS cc_start: 0.8069 (mtmm) cc_final: 0.7512 (mtmm) REVERT: B 237 LEU cc_start: 0.8669 (tp) cc_final: 0.8305 (tt) REVERT: B 259 LYS cc_start: 0.7752 (ptmt) cc_final: 0.7329 (ptmt) REVERT: B 325 VAL cc_start: 0.7509 (OUTLIER) cc_final: 0.7190 (m) REVERT: B 329 LYS cc_start: 0.8331 (mttt) cc_final: 0.8053 (mmtt) REVERT: B 395 THR cc_start: 0.8191 (m) cc_final: 0.7734 (p) REVERT: B 405 ARG cc_start: 0.8399 (mmm160) cc_final: 0.7830 (tpp-160) REVERT: B 544 LYS cc_start: 0.6537 (mmmm) cc_final: 0.6035 (mmtp) REVERT: B 596 ILE cc_start: 0.8415 (mm) cc_final: 0.8062 (mp) REVERT: B 662 ARG cc_start: 0.7976 (mtp-110) cc_final: 0.7605 (mtp-110) REVERT: B 663 ASP cc_start: 0.7805 (t0) cc_final: 0.7405 (t0) REVERT: B 689 SER cc_start: 0.7491 (t) cc_final: 0.7219 (t) REVERT: B 697 ASN cc_start: 0.7900 (m110) cc_final: 0.7595 (m-40) REVERT: B 719 PHE cc_start: 0.8142 (p90) cc_final: 0.7330 (p90) REVERT: B 772 GLU cc_start: 0.7735 (tp30) cc_final: 0.7491 (tp30) REVERT: B 798 PHE cc_start: 0.7850 (p90) cc_final: 0.7462 (p90) REVERT: B 860 GLN cc_start: 0.7449 (OUTLIER) cc_final: 0.6964 (mp10) REVERT: B 874 LYS cc_start: 0.6215 (OUTLIER) cc_final: 0.5927 (pttp) REVERT: B 923 PHE cc_start: 0.7786 (m-80) cc_final: 0.7530 (m-80) REVERT: B 958 ASN cc_start: 0.8177 (m110) cc_final: 0.7735 (m-40) REVERT: B 959 GLN cc_start: 0.8225 (mt0) cc_final: 0.7842 (mt0) REVERT: B 1000 ASP cc_start: 0.7327 (t0) cc_final: 0.6791 (t0) REVERT: B 1064 GLN cc_start: 0.7915 (tp40) cc_final: 0.7706 (mm-40) REVERT: B 1073 LEU cc_start: 0.8221 (pt) cc_final: 0.7910 (pp) REVERT: B 1080 ASP cc_start: 0.7564 (t0) cc_final: 0.7000 (t0) REVERT: B 1112 MET cc_start: 0.7784 (OUTLIER) cc_final: 0.6791 (mpp) REVERT: B 1139 VAL cc_start: 0.8582 (t) cc_final: 0.8191 (p) REVERT: B 1147 TYR cc_start: 0.7920 (t80) cc_final: 0.7542 (t80) REVERT: B 1182 PHE cc_start: 0.7591 (m-80) cc_final: 0.7256 (m-80) REVERT: B 1190 MET cc_start: 0.7024 (ttm) cc_final: 0.6518 (ttt) REVERT: B 1198 TYR cc_start: 0.7309 (t80) cc_final: 0.6380 (t80) REVERT: D 4 MET cc_start: 0.4579 (mpp) cc_final: 0.4371 (mpp) REVERT: D 75 ASP cc_start: 0.7744 (p0) cc_final: 0.6814 (m-30) REVERT: G 45 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7401 (mm) REVERT: G 52 TRP cc_start: 0.6731 (OUTLIER) cc_final: 0.5837 (t-100) REVERT: G 103 LEU cc_start: 0.8967 (tp) cc_final: 0.8639 (tp) REVERT: C 111 LYS cc_start: 0.7974 (mtmm) cc_final: 0.7752 (mtmm) REVERT: C 180 LEU cc_start: 0.8737 (mt) cc_final: 0.8374 (mp) REVERT: C 235 LYS cc_start: 0.7910 (mtmm) cc_final: 0.7418 (mtmm) REVERT: C 237 LEU cc_start: 0.8529 (tp) cc_final: 0.8125 (tp) REVERT: C 259 LYS cc_start: 0.7752 (ptmt) cc_final: 0.7436 (ptmt) REVERT: C 312 TYR cc_start: 0.7777 (m-10) cc_final: 0.7393 (m-10) REVERT: C 315 ASN cc_start: 0.7693 (p0) cc_final: 0.7423 (p0) REVERT: C 317 TYR cc_start: 0.6255 (t80) cc_final: 0.6054 (t80) REVERT: C 325 VAL cc_start: 0.7546 (p) cc_final: 0.7252 (m) REVERT: C 329 LYS cc_start: 0.8419 (mttt) cc_final: 0.7686 (ttmm) REVERT: C 342 ASN cc_start: 0.8381 (t0) cc_final: 0.7969 (t0) REVERT: C 375 SER cc_start: 0.7439 (t) cc_final: 0.7176 (m) REVERT: C 376 PHE cc_start: 0.7953 (t80) cc_final: 0.7657 (t80) REVERT: C 385 LYS cc_start: 0.7630 (OUTLIER) cc_final: 0.7357 (mtpt) REVERT: C 389 MET cc_start: 0.7202 (tpp) cc_final: 0.6965 (tpp) REVERT: C 425 ASP cc_start: 0.7596 (t70) cc_final: 0.7056 (t0) REVERT: C 460 GLU cc_start: 0.8264 (mp0) cc_final: 0.7896 (mp0) REVERT: C 662 ARG cc_start: 0.7944 (mtp-110) cc_final: 0.7617 (mtm110) REVERT: C 663 ASP cc_start: 0.7499 (t70) cc_final: 0.6928 (t0) REVERT: C 675 CYS cc_start: 0.4824 (p) cc_final: 0.4382 (p) REVERT: C 699 LYS cc_start: 0.8275 (mmmm) cc_final: 0.7847 (mtmm) REVERT: C 702 TYR cc_start: 0.7815 (t80) cc_final: 0.7514 (t80) REVERT: C 730 TYR cc_start: 0.6852 (p90) cc_final: 0.6359 (p90) REVERT: C 774 PHE cc_start: 0.7458 (m-80) cc_final: 0.7183 (m-80) REVERT: C 817 ASP cc_start: 0.6890 (t70) cc_final: 0.6570 (p0) REVERT: C 832 GLN cc_start: 0.7960 (mm110) cc_final: 0.7235 (mp10) REVERT: C 860 GLN cc_start: 0.8088 (mt0) cc_final: 0.7566 (mp10) REVERT: C 921 VAL cc_start: 0.8069 (m) cc_final: 0.7463 (m) REVERT: C 925 GLU cc_start: 0.7707 (mt-10) cc_final: 0.7230 (mt-10) REVERT: C 959 GLN cc_start: 0.8458 (mt0) cc_final: 0.7960 (mt0) REVERT: C 991 ARG cc_start: 0.6506 (mmm-85) cc_final: 0.6096 (mtp85) REVERT: C 1005 ASN cc_start: 0.7834 (t0) cc_final: 0.7417 (t0) REVERT: C 1039 ASN cc_start: 0.8359 (t0) cc_final: 0.7958 (t0) REVERT: C 1065 GLU cc_start: 0.7236 (mt-10) cc_final: 0.6814 (mt-10) REVERT: C 1074 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7290 (mm-30) REVERT: C 1113 GLU cc_start: 0.8013 (tt0) cc_final: 0.7579 (tt0) REVERT: C 1141 ASN cc_start: 0.8653 (t0) cc_final: 0.8325 (m-40) REVERT: C 1182 PHE cc_start: 0.7459 (m-80) cc_final: 0.6925 (m-80) REVERT: C 1190 MET cc_start: 0.7079 (ttt) cc_final: 0.6682 (ttt) REVERT: E 21 ILE cc_start: 0.8634 (mt) cc_final: 0.8375 (tp) REVERT: E 54 TYR cc_start: 0.7299 (p90) cc_final: 0.6987 (p90) REVERT: E 84 GLU cc_start: 0.6610 (pp20) cc_final: 0.6019 (pp20) REVERT: I 103 LEU cc_start: 0.8973 (tp) cc_final: 0.8247 (tt) outliers start: 101 outliers final: 70 residues processed: 908 average time/residue: 0.1924 time to fit residues: 289.2913 Evaluate side-chains 935 residues out of total 3660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 853 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 416 TYR Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 807 ILE Chi-restraints excluded: chain A residue 839 PHE Chi-restraints excluded: chain A residue 866 MET Chi-restraints excluded: chain A residue 919 SER Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 960 PHE Chi-restraints excluded: chain A residue 1076 GLU Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1224 MET Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 39 ASP Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 51 LEU Chi-restraints excluded: chain L residue 79 LYS Chi-restraints excluded: chain H residue 52 TRP Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 197 CYS Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 589 CYS Chi-restraints excluded: chain B residue 607 SER Chi-restraints excluded: chain B residue 614 ASN Chi-restraints excluded: chain B residue 730 TYR Chi-restraints excluded: chain B residue 807 ILE Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 860 GLN Chi-restraints excluded: chain B residue 874 LYS Chi-restraints excluded: chain B residue 919 SER Chi-restraints excluded: chain B residue 941 CYS Chi-restraints excluded: chain B residue 960 PHE Chi-restraints excluded: chain B residue 988 VAL Chi-restraints excluded: chain B residue 1076 GLU Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain B residue 1112 MET Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain G residue 13 GLN Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 52 TRP Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 385 LYS Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 614 ASN Chi-restraints excluded: chain C residue 732 SER Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 840 CYS Chi-restraints excluded: chain C residue 941 CYS Chi-restraints excluded: chain C residue 990 TYR Chi-restraints excluded: chain C residue 1082 LEU Chi-restraints excluded: chain C residue 1084 ASN Chi-restraints excluded: chain C residue 1112 MET Chi-restraints excluded: chain C residue 1167 LEU Chi-restraints excluded: chain C residue 1185 VAL Chi-restraints excluded: chain I residue 52 TRP Chi-restraints excluded: chain I residue 91 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 355 optimal weight: 3.9990 chunk 90 optimal weight: 0.4980 chunk 306 optimal weight: 0.7980 chunk 80 optimal weight: 0.7980 chunk 207 optimal weight: 5.9990 chunk 186 optimal weight: 0.8980 chunk 413 optimal weight: 0.0020 chunk 240 optimal weight: 0.9980 chunk 124 optimal weight: 6.9990 chunk 286 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1064 GLN ** L 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 286 ASN B 320 GLN ** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 858 GLN ** B1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 844 ASN C 867 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.144408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.117923 restraints weight = 55770.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.122698 restraints weight = 28373.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.125957 restraints weight = 17272.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.128169 restraints weight = 11912.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.129356 restraints weight = 9002.961| |-----------------------------------------------------------------------------| r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 34413 Z= 0.125 Angle : 0.650 13.781 46959 Z= 0.328 Chirality : 0.046 0.383 5376 Planarity : 0.004 0.047 5952 Dihedral : 5.633 87.309 5592 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.27 % Allowed : 19.37 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.13), residues: 4176 helix: 0.34 (0.18), residues: 735 sheet: -0.58 (0.17), residues: 963 loop : -1.11 (0.12), residues: 2478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 991 TYR 0.035 0.001 TYR B 68 PHE 0.046 0.001 PHE B 771 TRP 0.045 0.002 TRP H 102 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00286 (34296) covalent geometry : angle 0.63749 (46677) SS BOND : bond 0.00402 ( 69) SS BOND : angle 1.55302 ( 138) hydrogen bonds : bond 0.03767 ( 1134) hydrogen bonds : angle 5.48352 ( 3411) link_BETA1-4 : bond 0.00249 ( 12) link_BETA1-4 : angle 0.99227 ( 36) link_NAG-ASN : bond 0.00453 ( 36) link_NAG-ASN : angle 2.09475 ( 108) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 939 residues out of total 3660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 856 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 ILE cc_start: 0.7924 (OUTLIER) cc_final: 0.7714 (mm) REVERT: A 136 TYR cc_start: 0.8350 (m-80) cc_final: 0.7877 (m-10) REVERT: A 280 GLN cc_start: 0.7289 (mm110) cc_final: 0.6892 (mm110) REVERT: A 312 TYR cc_start: 0.7821 (m-10) cc_final: 0.7460 (m-10) REVERT: A 315 ASN cc_start: 0.7633 (p0) cc_final: 0.7089 (p0) REVERT: A 328 ARG cc_start: 0.7204 (mpt180) cc_final: 0.6572 (mpt180) REVERT: A 375 SER cc_start: 0.7791 (t) cc_final: 0.7234 (m) REVERT: A 389 MET cc_start: 0.6552 (tpt) cc_final: 0.6189 (tpt) REVERT: A 425 ASP cc_start: 0.7744 (t70) cc_final: 0.7232 (t0) REVERT: A 437 LEU cc_start: 0.7895 (mt) cc_final: 0.7680 (mt) REVERT: A 448 ASN cc_start: 0.8662 (t0) cc_final: 0.8302 (t0) REVERT: A 573 GLN cc_start: 0.7808 (mp10) cc_final: 0.7522 (mp10) REVERT: A 626 ASP cc_start: 0.6703 (t0) cc_final: 0.6155 (t0) REVERT: A 663 ASP cc_start: 0.7468 (t70) cc_final: 0.7184 (t70) REVERT: A 679 ARG cc_start: 0.7384 (mtp85) cc_final: 0.6998 (ptm160) REVERT: A 694 LEU cc_start: 0.7152 (OUTLIER) cc_final: 0.6870 (tp) REVERT: A 699 LYS cc_start: 0.8199 (mmmm) cc_final: 0.7895 (mtmm) REVERT: A 731 ASN cc_start: 0.7616 (t0) cc_final: 0.7250 (t0) REVERT: A 832 GLN cc_start: 0.7714 (mm110) cc_final: 0.7427 (mt0) REVERT: A 858 GLN cc_start: 0.7712 (mm110) cc_final: 0.7385 (mm110) REVERT: A 860 GLN cc_start: 0.8090 (mt0) cc_final: 0.7389 (mp10) REVERT: A 913 PHE cc_start: 0.7728 (m-10) cc_final: 0.7364 (m-80) REVERT: A 976 TRP cc_start: 0.6192 (m-90) cc_final: 0.5691 (m-90) REVERT: A 1000 ASP cc_start: 0.7531 (t0) cc_final: 0.7013 (t0) REVERT: A 1033 LYS cc_start: 0.8634 (tppt) cc_final: 0.8205 (ttmm) REVERT: A 1051 GLN cc_start: 0.7519 (mp10) cc_final: 0.7045 (mp10) REVERT: A 1065 GLU cc_start: 0.6988 (mt-10) cc_final: 0.6462 (mt-10) REVERT: A 1112 MET cc_start: 0.7593 (mmm) cc_final: 0.7228 (mmm) REVERT: A 1113 GLU cc_start: 0.7745 (tt0) cc_final: 0.7517 (mt-10) REVERT: A 1119 VAL cc_start: 0.7141 (OUTLIER) cc_final: 0.6883 (m) REVERT: A 1182 PHE cc_start: 0.7437 (m-80) cc_final: 0.6993 (m-80) REVERT: A 1190 MET cc_start: 0.7247 (ttt) cc_final: 0.6508 (ttt) REVERT: A 1198 TYR cc_start: 0.7347 (t80) cc_final: 0.6533 (t80) REVERT: L 31 HIS cc_start: 0.7704 (t-170) cc_final: 0.7118 (t-170) REVERT: L 79 LYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7645 (tptt) REVERT: H 52 TRP cc_start: 0.6806 (OUTLIER) cc_final: 0.6265 (t-100) REVERT: H 58 LYS cc_start: 0.8239 (mttt) cc_final: 0.7898 (mptt) REVERT: H 103 LEU cc_start: 0.8884 (tp) cc_final: 0.8672 (tp) REVERT: B 29 LYS cc_start: 0.7811 (tptt) cc_final: 0.7359 (tppt) REVERT: B 136 TYR cc_start: 0.8346 (m-80) cc_final: 0.8140 (m-80) REVERT: B 168 MET cc_start: 0.5578 (mmm) cc_final: 0.4987 (mmm) REVERT: B 235 LYS cc_start: 0.8059 (mtmm) cc_final: 0.7495 (mtmm) REVERT: B 237 LEU cc_start: 0.8648 (tp) cc_final: 0.8279 (tt) REVERT: B 259 LYS cc_start: 0.7750 (ptmt) cc_final: 0.7331 (ptmt) REVERT: B 325 VAL cc_start: 0.7501 (OUTLIER) cc_final: 0.7090 (m) REVERT: B 329 LYS cc_start: 0.8386 (mttt) cc_final: 0.8110 (mmtt) REVERT: B 395 THR cc_start: 0.8169 (m) cc_final: 0.7716 (p) REVERT: B 405 ARG cc_start: 0.8403 (mmm160) cc_final: 0.7786 (tpp-160) REVERT: B 544 LYS cc_start: 0.6541 (mmmm) cc_final: 0.6064 (mmtp) REVERT: B 596 ILE cc_start: 0.8378 (mm) cc_final: 0.8017 (mp) REVERT: B 662 ARG cc_start: 0.7941 (mtp-110) cc_final: 0.7618 (mtp-110) REVERT: B 663 ASP cc_start: 0.7708 (t0) cc_final: 0.7305 (t0) REVERT: B 689 SER cc_start: 0.7422 (t) cc_final: 0.7161 (t) REVERT: B 697 ASN cc_start: 0.7781 (m110) cc_final: 0.7473 (m-40) REVERT: B 720 ASP cc_start: 0.6916 (m-30) cc_final: 0.6119 (t0) REVERT: B 772 GLU cc_start: 0.7752 (tp30) cc_final: 0.7196 (tp30) REVERT: B 798 PHE cc_start: 0.7806 (p90) cc_final: 0.7455 (p90) REVERT: B 860 GLN cc_start: 0.7371 (OUTLIER) cc_final: 0.6868 (mp10) REVERT: B 874 LYS cc_start: 0.6194 (OUTLIER) cc_final: 0.5747 (pttm) REVERT: B 923 PHE cc_start: 0.7747 (m-80) cc_final: 0.7502 (m-80) REVERT: B 959 GLN cc_start: 0.8194 (mt0) cc_final: 0.7899 (mt0) REVERT: B 1000 ASP cc_start: 0.7269 (t0) cc_final: 0.6858 (t0) REVERT: B 1052 LEU cc_start: 0.8202 (mt) cc_final: 0.7990 (mm) REVERT: B 1073 LEU cc_start: 0.8195 (pt) cc_final: 0.7882 (pp) REVERT: B 1080 ASP cc_start: 0.7546 (t0) cc_final: 0.7014 (t0) REVERT: B 1112 MET cc_start: 0.7734 (OUTLIER) cc_final: 0.6753 (mpp) REVERT: B 1114 LYS cc_start: 0.8274 (mttm) cc_final: 0.7987 (mttt) REVERT: B 1139 VAL cc_start: 0.8569 (t) cc_final: 0.8172 (p) REVERT: B 1147 TYR cc_start: 0.7880 (t80) cc_final: 0.7472 (t80) REVERT: B 1182 PHE cc_start: 0.7558 (m-80) cc_final: 0.7219 (m-80) REVERT: B 1190 MET cc_start: 0.7014 (ttm) cc_final: 0.6505 (ttt) REVERT: B 1198 TYR cc_start: 0.7256 (t80) cc_final: 0.6331 (t80) REVERT: D 75 ASP cc_start: 0.7682 (p0) cc_final: 0.6778 (m-30) REVERT: G 52 TRP cc_start: 0.6699 (OUTLIER) cc_final: 0.5847 (t-100) REVERT: G 102 TRP cc_start: 0.7802 (p-90) cc_final: 0.7257 (p-90) REVERT: G 103 LEU cc_start: 0.8954 (tp) cc_final: 0.8633 (tp) REVERT: C 111 LYS cc_start: 0.7983 (mtmm) cc_final: 0.7758 (mtmm) REVERT: C 180 LEU cc_start: 0.8730 (mt) cc_final: 0.8359 (mp) REVERT: C 235 LYS cc_start: 0.7918 (mtmm) cc_final: 0.7437 (mtmm) REVERT: C 237 LEU cc_start: 0.8470 (tp) cc_final: 0.7877 (tp) REVERT: C 259 LYS cc_start: 0.7748 (ptmt) cc_final: 0.7430 (ptmt) REVERT: C 312 TYR cc_start: 0.7737 (m-10) cc_final: 0.7340 (m-10) REVERT: C 315 ASN cc_start: 0.7704 (p0) cc_final: 0.7429 (p0) REVERT: C 317 TYR cc_start: 0.6189 (t80) cc_final: 0.5970 (t80) REVERT: C 325 VAL cc_start: 0.7529 (p) cc_final: 0.7253 (m) REVERT: C 328 ARG cc_start: 0.7257 (mpt180) cc_final: 0.6643 (mpt180) REVERT: C 329 LYS cc_start: 0.8461 (mttt) cc_final: 0.7712 (ttmm) REVERT: C 342 ASN cc_start: 0.8342 (t0) cc_final: 0.7928 (t0) REVERT: C 375 SER cc_start: 0.7402 (t) cc_final: 0.7159 (m) REVERT: C 385 LYS cc_start: 0.7619 (OUTLIER) cc_final: 0.7367 (mtpt) REVERT: C 425 ASP cc_start: 0.7580 (t70) cc_final: 0.7031 (t0) REVERT: C 460 GLU cc_start: 0.8256 (mp0) cc_final: 0.7917 (mp0) REVERT: C 626 ASP cc_start: 0.6626 (t0) cc_final: 0.5690 (t0) REVERT: C 662 ARG cc_start: 0.7926 (mtp-110) cc_final: 0.7536 (mtm110) REVERT: C 663 ASP cc_start: 0.7460 (t70) cc_final: 0.6798 (t0) REVERT: C 689 SER cc_start: 0.7266 (t) cc_final: 0.7059 (t) REVERT: C 699 LYS cc_start: 0.8259 (mmmm) cc_final: 0.7832 (mtmm) REVERT: C 702 TYR cc_start: 0.7741 (t80) cc_final: 0.7448 (t80) REVERT: C 730 TYR cc_start: 0.6825 (p90) cc_final: 0.6341 (p90) REVERT: C 774 PHE cc_start: 0.7288 (m-80) cc_final: 0.6988 (m-80) REVERT: C 817 ASP cc_start: 0.6838 (t70) cc_final: 0.6576 (p0) REVERT: C 832 GLN cc_start: 0.7943 (mm110) cc_final: 0.7222 (mp10) REVERT: C 921 VAL cc_start: 0.8043 (m) cc_final: 0.7444 (m) REVERT: C 925 GLU cc_start: 0.7700 (mt-10) cc_final: 0.7207 (mt-10) REVERT: C 959 GLN cc_start: 0.8379 (mt0) cc_final: 0.7912 (mt0) REVERT: C 991 ARG cc_start: 0.6491 (mmm-85) cc_final: 0.6063 (mtp85) REVERT: C 1005 ASN cc_start: 0.7917 (t0) cc_final: 0.7398 (t0) REVERT: C 1039 ASN cc_start: 0.8273 (t0) cc_final: 0.7849 (t0) REVERT: C 1065 GLU cc_start: 0.7209 (mt-10) cc_final: 0.6893 (mt-10) REVERT: C 1074 GLU cc_start: 0.7696 (mm-30) cc_final: 0.7260 (mm-30) REVERT: C 1080 ASP cc_start: 0.7494 (t0) cc_final: 0.7034 (t0) REVERT: C 1113 GLU cc_start: 0.7971 (tt0) cc_final: 0.7546 (tt0) REVERT: C 1141 ASN cc_start: 0.8648 (t0) cc_final: 0.8290 (m-40) REVERT: C 1182 PHE cc_start: 0.7445 (m-80) cc_final: 0.6892 (m-80) REVERT: C 1190 MET cc_start: 0.7015 (ttt) cc_final: 0.6671 (ttt) REVERT: C 1205 ASN cc_start: 0.8388 (m110) cc_final: 0.8077 (m110) REVERT: E 21 ILE cc_start: 0.8598 (mt) cc_final: 0.8346 (tp) REVERT: E 84 GLU cc_start: 0.6650 (pp20) cc_final: 0.6081 (pp20) outliers start: 83 outliers final: 60 residues processed: 883 average time/residue: 0.1929 time to fit residues: 281.6279 Evaluate side-chains 913 residues out of total 3660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 842 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 416 TYR Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 807 ILE Chi-restraints excluded: chain A residue 839 PHE Chi-restraints excluded: chain A residue 866 MET Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 960 PHE Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1224 MET Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 39 ASP Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 79 LYS Chi-restraints excluded: chain L residue 84 GLU Chi-restraints excluded: chain H residue 52 TRP Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 197 CYS Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 607 SER Chi-restraints excluded: chain B residue 614 ASN Chi-restraints excluded: chain B residue 807 ILE Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 858 GLN Chi-restraints excluded: chain B residue 860 GLN Chi-restraints excluded: chain B residue 874 LYS Chi-restraints excluded: chain B residue 919 SER Chi-restraints excluded: chain B residue 941 CYS Chi-restraints excluded: chain B residue 960 PHE Chi-restraints excluded: chain B residue 988 VAL Chi-restraints excluded: chain B residue 1076 GLU Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain B residue 1112 MET Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain G residue 52 TRP Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 385 LYS Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 614 ASN Chi-restraints excluded: chain C residue 732 SER Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 941 CYS Chi-restraints excluded: chain C residue 990 TYR Chi-restraints excluded: chain C residue 1082 LEU Chi-restraints excluded: chain C residue 1112 MET Chi-restraints excluded: chain C residue 1167 LEU Chi-restraints excluded: chain C residue 1185 VAL Chi-restraints excluded: chain I residue 52 TRP Chi-restraints excluded: chain I residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 127 optimal weight: 0.7980 chunk 168 optimal weight: 0.0050 chunk 301 optimal weight: 0.6980 chunk 273 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 161 optimal weight: 0.8980 chunk 275 optimal weight: 6.9990 chunk 84 optimal weight: 6.9990 chunk 378 optimal weight: 5.9990 chunk 174 optimal weight: 0.7980 chunk 367 optimal weight: 0.6980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 697 ASN A1005 ASN ** L 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 286 ASN ** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 844 ASN ** C 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.144314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.117812 restraints weight = 56290.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.122608 restraints weight = 28539.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.125751 restraints weight = 17331.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.127920 restraints weight = 12063.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.129308 restraints weight = 9206.752| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.158 34413 Z= 0.164 Angle : 0.838 59.179 46959 Z= 0.460 Chirality : 0.047 0.426 5376 Planarity : 0.004 0.067 5952 Dihedral : 5.633 87.285 5592 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.21 % Allowed : 19.45 % Favored : 78.33 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.13), residues: 4176 helix: 0.32 (0.18), residues: 735 sheet: -0.57 (0.17), residues: 963 loop : -1.11 (0.12), residues: 2478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 991 TYR 0.038 0.002 TYR B 68 PHE 0.038 0.001 PHE C 122 TRP 0.041 0.002 TRP H 102 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00368 (34296) covalent geometry : angle 0.81655 (46677) SS BOND : bond 0.00558 ( 69) SS BOND : angle 3.12296 ( 138) hydrogen bonds : bond 0.03780 ( 1134) hydrogen bonds : angle 5.48891 ( 3411) link_BETA1-4 : bond 0.00331 ( 12) link_BETA1-4 : angle 1.02975 ( 36) link_NAG-ASN : bond 0.00454 ( 36) link_NAG-ASN : angle 2.09550 ( 108) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8352 Ramachandran restraints generated. 4176 Oldfield, 0 Emsley, 4176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 924 residues out of total 3660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 843 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 ILE cc_start: 0.7919 (OUTLIER) cc_final: 0.7709 (mm) REVERT: A 136 TYR cc_start: 0.8343 (m-80) cc_final: 0.7873 (m-10) REVERT: A 280 GLN cc_start: 0.7286 (mm110) cc_final: 0.6887 (mm110) REVERT: A 293 ASP cc_start: 0.7252 (m-30) cc_final: 0.6991 (m-30) REVERT: A 312 TYR cc_start: 0.7810 (m-10) cc_final: 0.7456 (m-10) REVERT: A 315 ASN cc_start: 0.7629 (p0) cc_final: 0.7093 (p0) REVERT: A 328 ARG cc_start: 0.7209 (mpt180) cc_final: 0.6544 (mpt180) REVERT: A 329 LYS cc_start: 0.8226 (tttt) cc_final: 0.7715 (ttmm) REVERT: A 375 SER cc_start: 0.7792 (t) cc_final: 0.7225 (m) REVERT: A 389 MET cc_start: 0.6570 (tpt) cc_final: 0.6213 (tpt) REVERT: A 425 ASP cc_start: 0.7745 (t70) cc_final: 0.7236 (t0) REVERT: A 437 LEU cc_start: 0.7926 (mt) cc_final: 0.7671 (mt) REVERT: A 448 ASN cc_start: 0.8661 (t0) cc_final: 0.8301 (t0) REVERT: A 573 GLN cc_start: 0.7806 (mp10) cc_final: 0.7515 (mp10) REVERT: A 626 ASP cc_start: 0.6712 (t0) cc_final: 0.6148 (t0) REVERT: A 679 ARG cc_start: 0.7368 (mtp85) cc_final: 0.6988 (ptm160) REVERT: A 694 LEU cc_start: 0.7146 (OUTLIER) cc_final: 0.6859 (tp) REVERT: A 699 LYS cc_start: 0.8198 (mmmm) cc_final: 0.7896 (mtmm) REVERT: A 731 ASN cc_start: 0.7616 (t0) cc_final: 0.7251 (t0) REVERT: A 772 GLU cc_start: 0.7536 (tp30) cc_final: 0.7079 (tp30) REVERT: A 858 GLN cc_start: 0.7719 (mm110) cc_final: 0.7390 (mm110) REVERT: A 860 GLN cc_start: 0.8090 (mt0) cc_final: 0.7387 (mp10) REVERT: A 913 PHE cc_start: 0.7748 (m-10) cc_final: 0.7381 (m-80) REVERT: A 976 TRP cc_start: 0.6184 (m-90) cc_final: 0.5691 (m-90) REVERT: A 1000 ASP cc_start: 0.7527 (t0) cc_final: 0.7011 (t0) REVERT: A 1033 LYS cc_start: 0.8635 (tppt) cc_final: 0.8208 (ttmm) REVERT: A 1051 GLN cc_start: 0.7523 (mp10) cc_final: 0.7044 (mp10) REVERT: A 1065 GLU cc_start: 0.6975 (mt-10) cc_final: 0.6466 (mt-10) REVERT: A 1112 MET cc_start: 0.7586 (mmm) cc_final: 0.7227 (mmm) REVERT: A 1113 GLU cc_start: 0.7749 (tt0) cc_final: 0.7529 (mt-10) REVERT: A 1119 VAL cc_start: 0.7148 (OUTLIER) cc_final: 0.6877 (m) REVERT: A 1182 PHE cc_start: 0.7405 (m-80) cc_final: 0.6990 (m-80) REVERT: A 1190 MET cc_start: 0.7253 (ttt) cc_final: 0.6527 (ttt) REVERT: A 1198 TYR cc_start: 0.7350 (t80) cc_final: 0.6531 (t80) REVERT: L 31 HIS cc_start: 0.7698 (t-170) cc_final: 0.7101 (t-170) REVERT: L 79 LYS cc_start: 0.7946 (OUTLIER) cc_final: 0.7644 (tptt) REVERT: H 52 TRP cc_start: 0.6839 (OUTLIER) cc_final: 0.6262 (t-100) REVERT: H 58 LYS cc_start: 0.8241 (mttt) cc_final: 0.7894 (mptt) REVERT: H 103 LEU cc_start: 0.8885 (tp) cc_final: 0.8671 (tp) REVERT: B 29 LYS cc_start: 0.7813 (tptt) cc_final: 0.7314 (tppt) REVERT: B 136 TYR cc_start: 0.8347 (m-80) cc_final: 0.8135 (m-80) REVERT: B 168 MET cc_start: 0.5586 (mmm) cc_final: 0.4987 (mmm) REVERT: B 235 LYS cc_start: 0.8058 (mtmm) cc_final: 0.7493 (mtmm) REVERT: B 237 LEU cc_start: 0.8649 (tp) cc_final: 0.8280 (tt) REVERT: B 259 LYS cc_start: 0.7738 (ptmt) cc_final: 0.7328 (ptmt) REVERT: B 325 VAL cc_start: 0.7462 (OUTLIER) cc_final: 0.7105 (m) REVERT: B 329 LYS cc_start: 0.8385 (mttt) cc_final: 0.8069 (mmtt) REVERT: B 332 LEU cc_start: 0.8244 (mm) cc_final: 0.7880 (mm) REVERT: B 395 THR cc_start: 0.8169 (m) cc_final: 0.7716 (p) REVERT: B 405 ARG cc_start: 0.8404 (mmm160) cc_final: 0.7783 (tpp-160) REVERT: B 544 LYS cc_start: 0.6531 (mmmm) cc_final: 0.6048 (mmtp) REVERT: B 596 ILE cc_start: 0.8368 (mm) cc_final: 0.8009 (mp) REVERT: B 662 ARG cc_start: 0.7942 (mtp-110) cc_final: 0.7606 (mtp-110) REVERT: B 663 ASP cc_start: 0.7694 (t0) cc_final: 0.7307 (t0) REVERT: B 689 SER cc_start: 0.7413 (t) cc_final: 0.7125 (t) REVERT: B 697 ASN cc_start: 0.7780 (m110) cc_final: 0.7474 (m-40) REVERT: B 720 ASP cc_start: 0.6939 (m-30) cc_final: 0.6130 (t0) REVERT: B 772 GLU cc_start: 0.7757 (tp30) cc_final: 0.7193 (tp30) REVERT: B 798 PHE cc_start: 0.7795 (p90) cc_final: 0.7457 (p90) REVERT: B 833 LEU cc_start: 0.7245 (tt) cc_final: 0.7029 (tp) REVERT: B 858 GLN cc_start: 0.7521 (OUTLIER) cc_final: 0.6894 (tp-100) REVERT: B 860 GLN cc_start: 0.7373 (OUTLIER) cc_final: 0.6922 (mp10) REVERT: B 874 LYS cc_start: 0.6195 (OUTLIER) cc_final: 0.5745 (pttm) REVERT: B 923 PHE cc_start: 0.7759 (m-80) cc_final: 0.7504 (m-80) REVERT: B 959 GLN cc_start: 0.8198 (mt0) cc_final: 0.7864 (mt0) REVERT: B 1000 ASP cc_start: 0.7298 (t0) cc_final: 0.6862 (t0) REVERT: B 1052 LEU cc_start: 0.8264 (mt) cc_final: 0.8008 (mm) REVERT: B 1073 LEU cc_start: 0.8187 (pt) cc_final: 0.7889 (pp) REVERT: B 1080 ASP cc_start: 0.7584 (t0) cc_final: 0.7022 (t0) REVERT: B 1112 MET cc_start: 0.7730 (OUTLIER) cc_final: 0.6757 (mpp) REVERT: B 1114 LYS cc_start: 0.8273 (mttm) cc_final: 0.8002 (mttt) REVERT: B 1139 VAL cc_start: 0.8564 (t) cc_final: 0.8169 (p) REVERT: B 1147 TYR cc_start: 0.7882 (t80) cc_final: 0.7483 (t80) REVERT: B 1182 PHE cc_start: 0.7542 (m-80) cc_final: 0.7214 (m-80) REVERT: B 1190 MET cc_start: 0.7014 (ttm) cc_final: 0.6498 (ttt) REVERT: B 1198 TYR cc_start: 0.7258 (t80) cc_final: 0.6330 (t80) REVERT: D 75 ASP cc_start: 0.7681 (p0) cc_final: 0.6775 (m-30) REVERT: G 52 TRP cc_start: 0.6692 (OUTLIER) cc_final: 0.5844 (t-100) REVERT: G 103 LEU cc_start: 0.8949 (tp) cc_final: 0.8606 (tp) REVERT: C 111 LYS cc_start: 0.7984 (mtmm) cc_final: 0.7760 (mtmm) REVERT: C 180 LEU cc_start: 0.8731 (mt) cc_final: 0.8360 (mp) REVERT: C 235 LYS cc_start: 0.7932 (mtmm) cc_final: 0.7425 (mtmm) REVERT: C 259 LYS cc_start: 0.7754 (ptmt) cc_final: 0.7435 (ptmt) REVERT: C 312 TYR cc_start: 0.7731 (m-10) cc_final: 0.7330 (m-10) REVERT: C 315 ASN cc_start: 0.7690 (p0) cc_final: 0.7432 (p0) REVERT: C 317 TYR cc_start: 0.6181 (t80) cc_final: 0.5968 (t80) REVERT: C 325 VAL cc_start: 0.7538 (p) cc_final: 0.7249 (m) REVERT: C 328 ARG cc_start: 0.7246 (mpt180) cc_final: 0.6540 (mpt180) REVERT: C 329 LYS cc_start: 0.8466 (mttt) cc_final: 0.7712 (ttmm) REVERT: C 342 ASN cc_start: 0.8345 (t0) cc_final: 0.7929 (t0) REVERT: C 375 SER cc_start: 0.7394 (t) cc_final: 0.7148 (m) REVERT: C 385 LYS cc_start: 0.7621 (OUTLIER) cc_final: 0.7367 (mtpt) REVERT: C 425 ASP cc_start: 0.7589 (t70) cc_final: 0.7034 (t0) REVERT: C 460 GLU cc_start: 0.8250 (mp0) cc_final: 0.7918 (mp0) REVERT: C 626 ASP cc_start: 0.6630 (t0) cc_final: 0.5597 (t0) REVERT: C 662 ARG cc_start: 0.7929 (mtp-110) cc_final: 0.7533 (mtm110) REVERT: C 663 ASP cc_start: 0.7461 (t70) cc_final: 0.6801 (t0) REVERT: C 699 LYS cc_start: 0.8262 (mmmm) cc_final: 0.7831 (mtmm) REVERT: C 702 TYR cc_start: 0.7736 (t80) cc_final: 0.7445 (t80) REVERT: C 730 TYR cc_start: 0.6829 (p90) cc_final: 0.6342 (p90) REVERT: C 774 PHE cc_start: 0.7289 (m-80) cc_final: 0.6993 (m-80) REVERT: C 817 ASP cc_start: 0.6839 (t70) cc_final: 0.6581 (p0) REVERT: C 832 GLN cc_start: 0.7946 (mm110) cc_final: 0.7229 (mp10) REVERT: C 860 GLN cc_start: 0.7985 (mt0) cc_final: 0.7299 (mp10) REVERT: C 921 VAL cc_start: 0.8041 (m) cc_final: 0.7445 (m) REVERT: C 925 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7208 (mt-10) REVERT: C 959 GLN cc_start: 0.8370 (mt0) cc_final: 0.7921 (mt0) REVERT: C 991 ARG cc_start: 0.6490 (mmm-85) cc_final: 0.6065 (mtp85) REVERT: C 1005 ASN cc_start: 0.7925 (t0) cc_final: 0.7405 (t0) REVERT: C 1039 ASN cc_start: 0.8285 (t0) cc_final: 0.7852 (t0) REVERT: C 1074 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7260 (mm-30) REVERT: C 1080 ASP cc_start: 0.7500 (t0) cc_final: 0.7051 (t0) REVERT: C 1113 GLU cc_start: 0.7969 (tt0) cc_final: 0.7553 (tt0) REVERT: C 1141 ASN cc_start: 0.8643 (t0) cc_final: 0.8294 (m-40) REVERT: C 1182 PHE cc_start: 0.7445 (m-80) cc_final: 0.6892 (m-80) REVERT: C 1190 MET cc_start: 0.7017 (ttt) cc_final: 0.6668 (ttt) REVERT: C 1205 ASN cc_start: 0.8383 (m110) cc_final: 0.8077 (m110) REVERT: E 21 ILE cc_start: 0.8599 (mt) cc_final: 0.8345 (tp) REVERT: E 84 GLU cc_start: 0.6657 (pp20) cc_final: 0.6072 (pp20) outliers start: 81 outliers final: 65 residues processed: 869 average time/residue: 0.1910 time to fit residues: 275.0278 Evaluate side-chains 917 residues out of total 3660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 840 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain A residue 416 TYR Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 807 ILE Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 839 PHE Chi-restraints excluded: chain A residue 866 MET Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 960 PHE Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1224 MET Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 39 ASP Chi-restraints excluded: chain L residue 42 LEU Chi-restraints excluded: chain L residue 79 LYS Chi-restraints excluded: chain L residue 84 GLU Chi-restraints excluded: chain H residue 52 TRP Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 185 LYS Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 197 CYS Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 401 ILE Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 607 SER Chi-restraints excluded: chain B residue 614 ASN Chi-restraints excluded: chain B residue 807 ILE Chi-restraints excluded: chain B residue 822 VAL Chi-restraints excluded: chain B residue 858 GLN Chi-restraints excluded: chain B residue 860 GLN Chi-restraints excluded: chain B residue 874 LYS Chi-restraints excluded: chain B residue 916 VAL Chi-restraints excluded: chain B residue 919 SER Chi-restraints excluded: chain B residue 941 CYS Chi-restraints excluded: chain B residue 960 PHE Chi-restraints excluded: chain B residue 988 VAL Chi-restraints excluded: chain B residue 1076 GLU Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain B residue 1112 MET Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain G residue 52 TRP Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 118 MET Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 385 LYS Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain C residue 614 ASN Chi-restraints excluded: chain C residue 732 SER Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 822 VAL Chi-restraints excluded: chain C residue 874 LYS Chi-restraints excluded: chain C residue 941 CYS Chi-restraints excluded: chain C residue 990 TYR Chi-restraints excluded: chain C residue 1017 LEU Chi-restraints excluded: chain C residue 1082 LEU Chi-restraints excluded: chain C residue 1112 MET Chi-restraints excluded: chain C residue 1167 LEU Chi-restraints excluded: chain C residue 1185 VAL Chi-restraints excluded: chain I residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 363 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 307 optimal weight: 0.9980 chunk 351 optimal weight: 0.6980 chunk 187 optimal weight: 0.2980 chunk 75 optimal weight: 1.9990 chunk 186 optimal weight: 0.0370 chunk 164 optimal weight: 3.9990 chunk 382 optimal weight: 5.9990 chunk 371 optimal weight: 5.9990 chunk 221 optimal weight: 0.6980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 697 ASN ** A 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1064 GLN ** L 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 286 ASN ** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 844 ASN ** C 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.144396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.117771 restraints weight = 56152.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.122554 restraints weight = 28564.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.125833 restraints weight = 17398.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.128036 restraints weight = 12002.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.129594 restraints weight = 9079.266| |-----------------------------------------------------------------------------| r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.504 34413 Z= 0.255 Angle : 0.841 59.178 46959 Z= 0.461 Chirality : 0.047 0.426 5376 Planarity : 0.004 0.067 5952 Dihedral : 5.633 87.285 5592 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.10 % Allowed : 19.62 % Favored : 78.28 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.13), residues: 4176 helix: 0.32 (0.18), residues: 735 sheet: -0.57 (0.17), residues: 963 loop : -1.11 (0.12), residues: 2478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 991 TYR 0.038 0.002 TYR B 68 PHE 0.038 0.001 PHE C 122 TRP 0.041 0.002 TRP H 102 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00368 (34296) covalent geometry : angle 0.81655 (46677) SS BOND : bond 0.08720 ( 69) SS BOND : angle 3.38076 ( 138) hydrogen bonds : bond 0.03780 ( 1134) hydrogen bonds : angle 5.48891 ( 3411) link_BETA1-4 : bond 0.00331 ( 12) link_BETA1-4 : angle 1.02975 ( 36) link_NAG-ASN : bond 0.00454 ( 36) link_NAG-ASN : angle 2.09550 ( 108) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7208.21 seconds wall clock time: 124 minutes 26.35 seconds (7466.35 seconds total)