Starting phenix.real_space_refine on Fri Mar 6 17:29:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7po5_13563/03_2026/7po5_13563.cif Found real_map, /net/cci-nas-00/data/ceres_data/7po5_13563/03_2026/7po5_13563.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7po5_13563/03_2026/7po5_13563.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7po5_13563/03_2026/7po5_13563.map" model { file = "/net/cci-nas-00/data/ceres_data/7po5_13563/03_2026/7po5_13563.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7po5_13563/03_2026/7po5_13563.cif" } resolution = 3.9 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= 0.036 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 201 5.16 5 C 20940 2.51 5 N 5421 2.21 5 O 6372 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s 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: 32934 Number of models: 1 Model: "" Number of chains: 12 Chain: "Z" Number of atoms: 954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 954 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "D" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 804 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} 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: "X" Number of atoms: 954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 954 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "F" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 804 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} 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: "H" Number of atoms: 954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 954 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "L" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 804 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} 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: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 7.04, per 1000 atoms: 0.21 Number of scatterers: 32934 At special positions: 0 Unit cell: (153.36, 150.165, 198.09, 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 201 16.00 O 6372 8.00 N 5421 7.00 C 20940 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=69, symmetry=0 Simple disulfide: pdb=" SG CYS Z 22 " - pdb=" SG CYS Z 95 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " 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=2.03 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=2.03 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 X 22 " - pdb=" SG CYS X 95 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " 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=2.03 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=2.03 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 H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 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=2.03 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A1168 " - pdb=" SG CYS A1213 " 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 NAG-ASN " NAG A1401 " - " ASN A 59 " " NAG A1402 " - " ASN A 146 " " NAG A1403 " - " ASN A 667 " " NAG A1404 " - " ASN A 687 " " NAG A1405 " - " ASN A 706 " " NAG B1401 " - " ASN B 59 " " NAG B1402 " - " ASN B 146 " " NAG B1403 " - " ASN B 667 " " NAG B1404 " - " ASN B 687 " " NAG B1405 " - " ASN B 706 " " NAG C1401 " - " ASN C 59 " " NAG C1402 " - " ASN C 146 " " NAG C1403 " - " ASN C 667 " " NAG C1404 " - " ASN C 687 " " NAG C1405 " - " ASN C 706 " Time building additional restraints: 2.63 Conformation dependent library (CDL) restraints added in 1.2 seconds 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7824 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 75 sheets defined 22.0% alpha, 27.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'Z' and resid 60 through 64 removed outlier: 3.702A pdb=" N LYS Z 64 " --> pdb=" O PRO Z 61 " (cutoff:3.500A) Processing helix chain 'Z' and resid 86 through 90 removed outlier: 3.671A pdb=" N THR Z 90 " --> pdb=" O ALA Z 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 83 removed outlier: 4.094A pdb=" N PHE D 83 " --> pdb=" O SER D 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 92 removed outlier: 3.583A pdb=" N LYS B 92 " --> pdb=" O LEU B 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 89 through 92' Processing helix chain 'B' and resid 293 through 302 removed outlier: 3.603A pdb=" N THR B 302 " --> pdb=" O ILE B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 342 Processing helix chain 'B' and resid 363 through 371 removed outlier: 3.526A pdb=" N LEU B 367 " --> pdb=" O ASN B 363 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER B 369 " --> pdb=" O SER B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 388 removed outlier: 3.958A pdb=" N GLY B 388 " --> pdb=" O LYS B 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 385 through 388' Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.829A pdb=" N GLN B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 421 removed outlier: 3.613A pdb=" N SER B 419 " --> pdb=" O GLY B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 456 Processing helix chain 'B' and resid 565 through 568 Processing helix chain 'B' and resid 699 through 708 Processing helix chain 'B' and resid 817 through 823 removed outlier: 3.598A pdb=" N CYS B 823 " --> pdb=" O ALA B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 826 through 833 Processing helix chain 'B' and resid 836 through 866 removed outlier: 3.581A pdb=" N CYS B 840 " --> pdb=" O TYR B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 874 through 877 Processing helix chain 'B' and resid 906 through 916 removed outlier: 4.007A pdb=" N LYS B 915 " --> pdb=" O LEU B 911 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL B 916 " --> pdb=" O LEU B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 929 Processing helix chain 'B' and resid 938 through 946 Processing helix chain 'B' and resid 956 through 970 Processing helix chain 'B' and resid 976 through 980 removed outlier: 3.829A pdb=" N ALA B 980 " --> pdb=" O THR B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 994 Processing helix chain 'B' and resid 999 through 1004 removed outlier: 4.121A pdb=" N GLN B1004 " --> pdb=" O ASP B1000 " (cutoff:3.500A) Processing helix chain 'B' and resid 1005 through 1023 Processing helix chain 'B' and resid 1028 through 1051 Processing helix chain 'B' and resid 1052 through 1054 No H-bonds generated for 'chain 'B' and resid 1052 through 1054' Processing helix chain 'B' and resid 1062 through 1070 Processing helix chain 'B' and resid 1071 through 1119 removed outlier: 3.634A pdb=" N ALA B1077 " --> pdb=" O LEU B1073 " (cutoff:3.500A) Processing helix chain 'B' and resid 1203 through 1207 removed outlier: 3.617A pdb=" N ASN B1206 " --> pdb=" O THR B1203 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL B1207 " --> pdb=" O GLU B1204 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1203 through 1207' Processing helix chain 'X' and resid 60 through 64 removed outlier: 3.703A pdb=" N LYS X 64 " --> pdb=" O PRO X 61 " (cutoff:3.500A) Processing helix chain 'X' and resid 86 through 90 removed outlier: 3.670A pdb=" N THR X 90 " --> pdb=" O ALA X 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 83 removed outlier: 4.093A pdb=" N PHE F 83 " --> pdb=" O SER F 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 92 removed outlier: 3.613A pdb=" N LYS C 92 " --> pdb=" O LEU C 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 89 through 92' Processing helix chain 'C' and resid 293 through 302 removed outlier: 3.605A pdb=" N THR C 302 " --> pdb=" O ILE C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 342 Processing helix chain 'C' and resid 363 through 371 removed outlier: 4.037A pdb=" N SER C 369 " --> pdb=" O SER C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 388 removed outlier: 3.995A pdb=" N GLY C 388 " --> pdb=" O LYS C 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 385 through 388' Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.799A pdb=" N GLN C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 421 removed outlier: 3.665A pdb=" N SER C 419 " --> pdb=" O GLY C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 456 Processing helix chain 'C' and resid 565 through 568 Processing helix chain 'C' and resid 699 through 708 Processing helix chain 'C' and resid 817 through 823 removed outlier: 3.543A pdb=" N CYS C 823 " --> pdb=" O ALA C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 826 through 833 Processing helix chain 'C' and resid 836 through 866 removed outlier: 3.588A pdb=" N CYS C 840 " --> pdb=" O TYR C 836 " (cutoff:3.500A) Processing helix chain 'C' and resid 874 through 877 Processing helix chain 'C' and resid 906 through 916 removed outlier: 3.991A pdb=" N LYS C 915 " --> pdb=" O LEU C 911 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL C 916 " --> pdb=" O LEU C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 929 Processing helix chain 'C' and resid 938 through 946 Processing helix chain 'C' and resid 956 through 970 Processing helix chain 'C' and resid 976 through 980 removed outlier: 3.512A pdb=" N ALA C 979 " --> pdb=" O TRP C 976 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA C 980 " --> pdb=" O THR C 977 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 976 through 980' Processing helix chain 'C' and resid 983 through 994 Processing helix chain 'C' and resid 999 through 1004 removed outlier: 4.046A pdb=" N GLN C1004 " --> pdb=" O ASP C1000 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1023 Processing helix chain 'C' and resid 1028 through 1051 Processing helix chain 'C' and resid 1052 through 1054 No H-bonds generated for 'chain 'C' and resid 1052 through 1054' Processing helix chain 'C' and resid 1062 through 1070 Processing helix chain 'C' and resid 1071 through 1119 removed outlier: 3.605A pdb=" N ALA C1077 " --> pdb=" O LEU C1073 " (cutoff:3.500A) Processing helix chain 'C' and resid 1203 through 1207 removed outlier: 3.617A pdb=" N ASN C1206 " --> pdb=" O THR C1203 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL C1207 " --> pdb=" O GLU C1204 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1203 through 1207' Processing helix chain 'H' and resid 60 through 64 removed outlier: 3.706A pdb=" N LYS H 64 " --> pdb=" O PRO H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 90 removed outlier: 3.673A pdb=" N THR H 90 " --> pdb=" O ALA H 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.087A pdb=" N PHE L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 92 removed outlier: 3.587A pdb=" N LYS A 92 " --> pdb=" O LEU A 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 89 through 92' Processing helix chain 'A' and resid 293 through 302 removed outlier: 3.635A pdb=" N THR A 302 " --> pdb=" O ILE A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 342 Processing helix chain 'A' and resid 363 through 371 removed outlier: 3.516A pdb=" N LEU A 367 " --> pdb=" O ASN A 363 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N SER A 369 " --> pdb=" O SER A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 388 removed outlier: 3.911A pdb=" N GLY A 388 " --> pdb=" O LYS A 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 385 through 388' Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.893A pdb=" N GLN A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 421 removed outlier: 3.620A pdb=" N SER A 419 " --> pdb=" O GLY A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 456 Processing helix chain 'A' and resid 565 through 568 removed outlier: 3.502A pdb=" N CYS A 568 " --> pdb=" O GLY A 565 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 565 through 568' Processing helix chain 'A' and resid 699 through 708 Processing helix chain 'A' and resid 817 through 823 removed outlier: 3.575A pdb=" N CYS A 823 " --> pdb=" O ALA A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 833 Processing helix chain 'A' and resid 836 through 866 removed outlier: 3.612A pdb=" N CYS A 840 " --> pdb=" O TYR A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 877 Processing helix chain 'A' and resid 906 through 916 removed outlier: 4.010A pdb=" N LYS A 915 " --> pdb=" O LEU A 911 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL A 916 " --> pdb=" O LEU A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 929 Processing helix chain 'A' and resid 938 through 946 Processing helix chain 'A' and resid 956 through 970 Processing helix chain 'A' and resid 976 through 980 removed outlier: 3.518A pdb=" N ALA A 979 " --> pdb=" O TRP A 976 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA A 980 " --> pdb=" O THR A 977 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 976 through 980' Processing helix chain 'A' and resid 983 through 994 Processing helix chain 'A' and resid 999 through 1004 removed outlier: 4.060A pdb=" N GLN A1004 " --> pdb=" O ASP A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1023 Processing helix chain 'A' and resid 1028 through 1051 Processing helix chain 'A' and resid 1052 through 1054 No H-bonds generated for 'chain 'A' and resid 1052 through 1054' Processing helix chain 'A' and resid 1062 through 1070 Processing helix chain 'A' and resid 1071 through 1119 removed outlier: 3.558A pdb=" N ALA A1077 " --> pdb=" O LEU A1073 " (cutoff:3.500A) Processing helix chain 'A' and resid 1203 through 1207 removed outlier: 3.604A pdb=" N ASN A1206 " --> pdb=" O THR A1203 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL A1207 " --> pdb=" O GLU A1204 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1203 through 1207' Processing sheet with id=AA1, first strand: chain 'Z' and resid 4 through 7 removed outlier: 3.775A pdb=" N THR Z 21 " --> pdb=" O TRP Z 7 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'Z' and resid 51 through 52 removed outlier: 3.687A pdb=" N TYR Z 33 " --> pdb=" O GLY Z 98 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'Z' and resid 100 through 101 Processing sheet with id=AA4, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.775A pdb=" N SER D 7 " --> pdb=" O SER D 22 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER D 22 " --> pdb=" O SER D 7 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA D 19 " --> pdb=" O ILE D 75 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE D 71 " --> pdb=" O CYS D 23 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU D 70 " --> pdb=" O SER D 67 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.292A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE D 48 " --> pdb=" O TRP D 35 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N GLN D 37 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N LEU D 46 " --> pdb=" O GLN D 37 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR D 53 " --> pdb=" O TYR D 49 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 26 through 27 Processing sheet with id=AA7, first strand: chain 'B' and resid 36 through 40 removed outlier: 3.537A pdb=" N SER B 37 " --> pdb=" O TYR B 75 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N TYR B 75 " --> pdb=" O SER B 37 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N THR B 74 " --> pdb=" O PRO B 268 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLY B 102 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TYR B 213 " --> pdb=" O THR B 228 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR B 222 " --> pdb=" O GLU B 219 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE B 238 " --> pdb=" O ALA B 225 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N PHE B 227 " --> pdb=" O PHE B 236 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N PHE B 236 " --> pdb=" O PHE B 227 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 61 through 69 removed outlier: 3.635A pdb=" N GLY B 66 " --> pdb=" O ARG B 272 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASN B 286 " --> pdb=" O ALA B 277 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 55 through 56 removed outlier: 3.845A pdb=" N GLY A 660 " --> pdb=" O LEU A 651 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N THR A 669 " --> pdb=" O VAL A 639 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY A 632 " --> pdb=" O TYR A 625 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY A 634 " --> pdb=" O VAL A 623 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 97 through 98 removed outlier: 3.735A pdb=" N TYR B 249 " --> pdb=" O SER B 97 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN B 141 " --> pdb=" O GLU B 160 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLY B 157 " --> pdb=" O TYR B 205 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TYR B 205 " --> pdb=" O GLY B 157 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 110 through 114 Processing sheet with id=AB3, first strand: chain 'B' and resid 187 through 189 removed outlier: 7.719A pdb=" N TRP B 188 " --> pdb=" O CYS B 169 " (cutoff:3.500A) removed outlier: 9.232A pdb=" N THR B 255 " --> pdb=" O PRO B 172 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N THR B 174 " --> pdb=" O THR B 255 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 310 through 311 removed outlier: 3.795A pdb=" N SER B 681 " --> pdb=" O LEU B 694 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE B 719 " --> pdb=" O VAL B 726 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 324 through 327 removed outlier: 3.680A pdb=" N GLY B 634 " --> pdb=" O VAL B 623 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY B 632 " --> pdb=" O TYR B 625 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N THR B 669 " --> pdb=" O VAL B 639 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY B 660 " --> pdb=" O LEU B 651 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU B 650 " --> pdb=" O VAL C 56 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 353 through 357 removed outlier: 3.770A pdb=" N GLU B 353 " --> pdb=" O LYS B 398 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS B 355 " --> pdb=" O ILE B 396 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE B 362 " --> pdb=" O CYS B 606 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 353 through 357 removed outlier: 3.770A pdb=" N GLU B 353 " --> pdb=" O LYS B 398 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS B 355 " --> pdb=" O ILE B 396 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N PHE B 391 " --> pdb=" O VAL B 600 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N VAL B 600 " --> pdb=" O PHE B 391 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER B 393 " --> pdb=" O HIS B 598 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N ASN B 436 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ALA B 373 " --> pdb=" O ASN B 436 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 476 through 480 Processing sheet with id=AB9, first strand: chain 'B' and resid 484 through 485 removed outlier: 3.756A pdb=" N THR B 543 " --> pdb=" O LYS B 485 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 557 through 558 Processing sheet with id=AC2, first strand: chain 'B' and resid 563 through 564 removed outlier: 3.505A pdb=" N GLY B 564 " --> pdb=" O THR B 569 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 730 through 737 removed outlier: 6.839A pdb=" N TYR B 730 " --> pdb=" O PHE B 768 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N ASN B 770 " --> pdb=" O TYR B 730 " (cutoff:3.500A) removed outlier: 9.396A pdb=" N SER B 732 " --> pdb=" O ASN B 770 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N TYR B 748 " --> pdb=" O VAL B 744 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU B 742 " --> pdb=" O VAL B 750 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 777 through 779 removed outlier: 6.006A pdb=" N ASN B 777 " --> pdb=" O LEU C 871 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 790 through 807 removed outlier: 6.381A pdb=" N GLU B 791 " --> pdb=" O ARG B1162 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ARG B1162 " --> pdb=" O GLU B 791 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N GLN B 793 " --> pdb=" O THR B1160 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N THR B1160 " --> pdb=" O GLN B 793 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N TYR B1158 " --> pdb=" O PRO B 795 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLU B 797 " --> pdb=" O THR B1156 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER B1152 " --> pdb=" O GLY B 801 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU B 805 " --> pdb=" O PHE B1148 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY B1145 " --> pdb=" O ALA B1142 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA B1142 " --> pdb=" O GLY B1145 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE B1136 " --> pdb=" O PHE B1151 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N TYR B1153 " --> pdb=" O HIS B1134 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N HIS B1134 " --> pdb=" O TYR B1153 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 813 through 815 removed outlier: 4.218A pdb=" N LYS B 813 " --> pdb=" O LEU B 951 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS B 949 " --> pdb=" O THR B 815 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 870 through 872 Processing sheet with id=AC8, first strand: chain 'B' and resid 1167 through 1168 Processing sheet with id=AC9, first strand: chain 'B' and resid 1180 through 1185 removed outlier: 3.564A pdb=" N THR B1192 " --> pdb=" O TYR B1181 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'X' and resid 4 through 7 removed outlier: 3.754A pdb=" N THR X 21 " --> pdb=" O TRP X 7 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'X' and resid 51 through 52 removed outlier: 3.700A pdb=" N TYR X 33 " --> pdb=" O GLY X 98 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'X' and resid 100 through 101 Processing sheet with id=AD4, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.734A pdb=" N SER F 7 " --> pdb=" O SER F 22 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER F 22 " --> pdb=" O SER F 7 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA F 19 " --> pdb=" O ILE F 75 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE F 71 " --> pdb=" O CYS F 23 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU F 70 " --> pdb=" O SER F 67 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.316A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR F 53 " --> pdb=" O TYR F 49 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 26 through 27 Processing sheet with id=AD7, first strand: chain 'C' and resid 36 through 40 removed outlier: 3.528A pdb=" N SER C 37 " --> pdb=" O TYR C 75 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N TYR C 75 " --> pdb=" O SER C 37 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N THR C 74 " --> pdb=" O PRO C 268 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLY C 102 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR C 213 " --> pdb=" O THR C 228 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR C 222 " --> pdb=" O GLU C 219 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE C 238 " --> pdb=" O ALA C 225 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N PHE C 227 " --> pdb=" O PHE C 236 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N PHE C 236 " --> pdb=" O PHE C 227 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 61 through 69 removed outlier: 3.642A pdb=" N GLY C 66 " --> pdb=" O ARG C 272 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASN C 286 " --> pdb=" O ALA C 277 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 97 through 98 removed outlier: 3.515A pdb=" N SER C 97 " --> pdb=" O TYR C 249 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR C 249 " --> pdb=" O SER C 97 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN C 141 " --> pdb=" O GLU C 160 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLY C 157 " --> pdb=" O TYR C 205 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR C 205 " --> pdb=" O GLY C 157 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 110 through 114 Processing sheet with id=AE2, first strand: chain 'C' and resid 187 through 189 removed outlier: 7.737A pdb=" N TRP C 188 " --> pdb=" O CYS C 169 " (cutoff:3.500A) removed outlier: 9.234A pdb=" N THR C 255 " --> pdb=" O PRO C 172 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N THR C 174 " --> pdb=" O THR C 255 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 310 through 311 removed outlier: 3.650A pdb=" N PHE C 719 " --> pdb=" O VAL C 726 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 324 through 327 removed outlier: 3.686A pdb=" N GLY C 634 " --> pdb=" O VAL C 623 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY C 632 " --> pdb=" O TYR C 625 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N THR C 669 " --> pdb=" O VAL C 639 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY C 660 " --> pdb=" O LEU C 651 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LEU C 650 " --> pdb=" O VAL A 56 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 353 through 357 removed outlier: 3.778A pdb=" N GLU C 353 " --> pdb=" O LYS C 398 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS C 355 " --> pdb=" O ILE C 396 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE C 362 " --> pdb=" O CYS C 606 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 353 through 357 removed outlier: 3.778A pdb=" N GLU C 353 " --> pdb=" O LYS C 398 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS C 355 " --> pdb=" O ILE C 396 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N PHE C 391 " --> pdb=" O VAL C 600 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N VAL C 600 " --> pdb=" O PHE C 391 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER C 393 " --> pdb=" O HIS C 598 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N ASN C 436 " --> pdb=" O ALA C 373 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N ALA C 373 " --> pdb=" O ASN C 436 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 476 through 480 Processing sheet with id=AE8, first strand: chain 'C' and resid 484 through 485 removed outlier: 3.779A pdb=" N THR C 543 " --> pdb=" O LYS C 485 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 557 through 558 Processing sheet with id=AF1, first strand: chain 'C' and resid 563 through 564 Processing sheet with id=AF2, first strand: chain 'C' and resid 730 through 737 removed outlier: 10.283A pdb=" N TYR C 766 " --> pdb=" O ASN C 731 " (cutoff:3.500A) removed outlier: 9.545A pdb=" N THR C 733 " --> pdb=" O TYR C 766 " (cutoff:3.500A) removed outlier: 9.005A pdb=" N PHE C 768 " --> pdb=" O THR C 733 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE C 735 " --> pdb=" O PHE C 768 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N TYR C 748 " --> pdb=" O VAL C 744 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU C 742 " --> pdb=" O VAL C 750 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 777 through 779 removed outlier: 5.994A pdb=" N ASN C 777 " --> pdb=" O LEU A 871 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'C' and resid 790 through 807 removed outlier: 6.384A pdb=" N GLU C 791 " --> pdb=" O ARG C1162 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ARG C1162 " --> pdb=" O GLU C 791 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N GLN C 793 " --> pdb=" O THR C1160 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N THR C1160 " --> pdb=" O GLN C 793 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N TYR C1158 " --> pdb=" O PRO C 795 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLU C 797 " --> pdb=" O THR C1156 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU C 805 " --> pdb=" O PHE C1148 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY C1145 " --> pdb=" O ALA C1142 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA C1142 " --> pdb=" O GLY C1145 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE C1136 " --> pdb=" O PHE C1151 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N TYR C1153 " --> pdb=" O HIS C1134 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N HIS C1134 " --> pdb=" O TYR C1153 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 813 through 816 removed outlier: 4.210A pdb=" N LYS C 813 " --> pdb=" O LEU C 951 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1167 through 1168 removed outlier: 3.508A pdb=" N LEU C1167 " --> pdb=" O ILE C1175 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 1180 through 1185 removed outlier: 3.560A pdb=" N THR C1192 " --> pdb=" O TYR C1181 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 4 through 7 removed outlier: 3.794A pdb=" N THR H 21 " --> pdb=" O TRP H 7 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 51 through 52 removed outlier: 3.690A pdb=" N TYR H 33 " --> pdb=" O GLY H 98 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 100 through 101 Processing sheet with id=AG2, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.786A pdb=" N SER L 7 " --> pdb=" O SER L 22 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER L 22 " --> pdb=" O SER L 7 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.298A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'A' and resid 26 through 27 Processing sheet with id=AG5, first strand: chain 'A' and resid 36 through 40 removed outlier: 3.544A pdb=" N SER A 37 " --> pdb=" O TYR A 75 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N TYR A 75 " --> pdb=" O SER A 37 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N THR A 74 " --> pdb=" O PRO A 268 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLY A 102 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N TYR A 213 " --> pdb=" O THR A 228 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR A 222 " --> pdb=" O GLU A 219 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE A 238 " --> pdb=" O ALA A 225 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N PHE A 227 " --> pdb=" O PHE A 236 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N PHE A 236 " --> pdb=" O PHE A 227 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'A' and resid 61 through 69 removed outlier: 3.623A pdb=" N GLY A 66 " --> pdb=" O ARG A 272 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASN A 286 " --> pdb=" O ALA A 277 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'A' and resid 97 through 98 removed outlier: 3.507A pdb=" N SER A 97 " --> pdb=" O TYR A 249 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR A 249 " --> pdb=" O SER A 97 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN A 141 " --> pdb=" O GLU A 160 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLY A 157 " --> pdb=" O TYR A 205 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR A 205 " --> pdb=" O GLY A 157 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'A' and resid 110 through 114 Processing sheet with id=AG9, first strand: chain 'A' and resid 187 through 189 removed outlier: 7.678A pdb=" N TRP A 188 " --> pdb=" O CYS A 169 " (cutoff:3.500A) removed outlier: 9.214A pdb=" N THR A 255 " --> pdb=" O PRO A 172 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N THR A 174 " --> pdb=" O THR A 255 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'A' and resid 310 through 311 removed outlier: 3.690A pdb=" N PHE A 719 " --> pdb=" O VAL A 726 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'A' and resid 353 through 357 removed outlier: 3.790A pdb=" N GLU A 353 " --> pdb=" O LYS A 398 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS A 355 " --> pdb=" O ILE A 396 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE A 362 " --> pdb=" O CYS A 606 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'A' and resid 353 through 357 removed outlier: 3.790A pdb=" N GLU A 353 " --> pdb=" O LYS A 398 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS A 355 " --> pdb=" O ILE A 396 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N PHE A 391 " --> pdb=" O VAL A 600 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N VAL A 600 " --> pdb=" O PHE A 391 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER A 393 " --> pdb=" O HIS A 598 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU A 437 " --> pdb=" O CYS A 589 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N ASN A 436 " --> pdb=" O ALA A 373 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ALA A 373 " --> pdb=" O ASN A 436 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'A' and resid 476 through 480 Processing sheet with id=AH5, first strand: chain 'A' and resid 484 through 485 removed outlier: 3.782A pdb=" N THR A 543 " --> pdb=" O LYS A 485 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'A' and resid 557 through 558 Processing sheet with id=AH7, first strand: chain 'A' and resid 563 through 564 removed outlier: 3.514A pdb=" N GLY A 564 " --> pdb=" O THR A 569 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'A' and resid 730 through 737 removed outlier: 6.923A pdb=" N TYR A 730 " --> pdb=" O PHE A 768 " (cutoff:3.500A) removed outlier: 8.872A pdb=" N ASN A 770 " --> pdb=" O TYR A 730 " (cutoff:3.500A) removed outlier: 9.470A pdb=" N SER A 732 " --> pdb=" O ASN A 770 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N TYR A 748 " --> pdb=" O VAL A 744 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU A 742 " --> pdb=" O VAL A 750 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'A' and resid 790 through 807 removed outlier: 6.391A pdb=" N GLU A 791 " --> pdb=" O ARG A1162 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ARG A1162 " --> pdb=" O GLU A 791 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N GLN A 793 " --> pdb=" O THR A1160 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N THR A1160 " --> pdb=" O GLN A 793 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N TYR A1158 " --> pdb=" O PRO A 795 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLU A 797 " --> pdb=" O THR A1156 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU A 805 " --> pdb=" O PHE A1148 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY A1145 " --> pdb=" O ALA A1142 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA A1142 " --> pdb=" O GLY A1145 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE A1136 " --> pdb=" O PHE A1151 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N TYR A1153 " --> pdb=" O HIS A1134 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N HIS A1134 " --> pdb=" O TYR A1153 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'A' and resid 813 through 815 removed outlier: 4.218A pdb=" N LYS A 813 " --> pdb=" O LEU A 951 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS A 949 " --> pdb=" O THR A 815 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'A' and resid 1167 through 1168 removed outlier: 3.591A pdb=" N LEU A1167 " --> pdb=" O ILE A1175 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'A' and resid 1180 through 1185 removed outlier: 3.531A pdb=" N THR A1192 " --> pdb=" O TYR A1181 " (cutoff:3.500A) 1140 hydrogen bonds defined for protein. 3162 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: 8.55 Time building geometry restraints manager: 3.55 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: 10515 1.34 - 1.47: 8542 1.47 - 1.59: 14372 1.59 - 1.71: 0 1.71 - 1.83: 261 Bond restraints: 33690 Sorted by residual: bond pdb=" C1 NAG B1405 " pdb=" O5 NAG B1405 " ideal model delta sigma weight residual 1.406 1.507 -0.101 2.00e-02 2.50e+03 2.56e+01 bond pdb=" C1 NAG A1405 " pdb=" O5 NAG A1405 " ideal model delta sigma weight residual 1.406 1.507 -0.101 2.00e-02 2.50e+03 2.56e+01 bond pdb=" C1 NAG C1405 " pdb=" O5 NAG C1405 " ideal model delta sigma weight residual 1.406 1.507 -0.101 2.00e-02 2.50e+03 2.55e+01 bond pdb=" C1 NAG B1401 " pdb=" O5 NAG B1401 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.35e+00 bond pdb=" C1 NAG A1401 " pdb=" O5 NAG A1401 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 6.03e+00 ... (remaining 33685 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 44699 1.87 - 3.73: 1042 3.73 - 5.60: 98 5.60 - 7.47: 25 7.47 - 9.34: 6 Bond angle restraints: 45870 Sorted by residual: angle pdb=" C GLY C1130 " pdb=" N ASN C1131 " pdb=" CA ASN C1131 " ideal model delta sigma weight residual 121.54 130.88 -9.34 1.91e+00 2.74e-01 2.39e+01 angle pdb=" C GLY B1130 " pdb=" N ASN B1131 " pdb=" CA ASN B1131 " ideal model delta sigma weight residual 121.54 130.81 -9.27 1.91e+00 2.74e-01 2.35e+01 angle pdb=" C GLY A1130 " pdb=" N ASN A1131 " pdb=" CA ASN A1131 " ideal model delta sigma weight residual 121.54 130.79 -9.25 1.91e+00 2.74e-01 2.34e+01 angle pdb=" C ASN C 379 " pdb=" N ASN C 380 " pdb=" CA ASN C 380 " ideal model delta sigma weight residual 121.54 128.82 -7.28 1.91e+00 2.74e-01 1.45e+01 angle pdb=" C ASN A 379 " pdb=" N ASN A 380 " pdb=" CA ASN A 380 " ideal model delta sigma weight residual 121.54 128.82 -7.28 1.91e+00 2.74e-01 1.45e+01 ... (remaining 45865 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.36: 18953 22.36 - 44.73: 1089 44.73 - 67.09: 121 67.09 - 89.46: 18 89.46 - 111.82: 9 Dihedral angle restraints: 20190 sinusoidal: 7920 harmonic: 12270 Sorted by residual: dihedral pdb=" CB CYS B 21 " pdb=" SG CYS B 21 " pdb=" SG CYS B 169 " pdb=" CB CYS B 169 " ideal model delta sinusoidal sigma weight residual 93.00 154.77 -61.77 1 1.00e+01 1.00e-02 5.06e+01 dihedral pdb=" CB CYS C 21 " pdb=" SG CYS C 21 " pdb=" SG CYS C 169 " pdb=" CB CYS C 169 " ideal model delta sinusoidal sigma weight residual 93.00 154.38 -61.38 1 1.00e+01 1.00e-02 5.00e+01 dihedral pdb=" CB CYS A 21 " pdb=" SG CYS A 21 " pdb=" SG CYS A 169 " pdb=" CB CYS A 169 " ideal model delta sinusoidal sigma weight residual 93.00 153.98 -60.98 1 1.00e+01 1.00e-02 4.94e+01 ... (remaining 20187 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 5016 0.112 - 0.223: 174 0.223 - 0.335: 3 0.335 - 0.446: 0 0.446 - 0.558: 3 Chirality restraints: 5196 Sorted by residual: chirality pdb=" C1 NAG C1402 " pdb=" ND2 ASN C 146 " pdb=" C2 NAG C1402 " pdb=" O5 NAG C1402 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-01 2.50e+01 7.77e+00 chirality pdb=" C1 NAG B1402 " pdb=" ND2 ASN B 146 " pdb=" C2 NAG B1402 " pdb=" O5 NAG B1402 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-01 2.50e+01 7.76e+00 chirality pdb=" C1 NAG A1402 " pdb=" ND2 ASN A 146 " pdb=" C2 NAG A1402 " pdb=" O5 NAG A1402 " both_signs ideal model delta sigma weight residual False -2.40 -1.85 -0.55 2.00e-01 2.50e+01 7.64e+00 ... (remaining 5193 not shown) Planarity restraints: 5904 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 889 " 0.048 5.00e-02 4.00e+02 7.24e-02 8.38e+00 pdb=" N PRO A 890 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO A 890 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 890 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 889 " 0.048 5.00e-02 4.00e+02 7.16e-02 8.20e+00 pdb=" N PRO C 890 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO C 890 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 890 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 889 " -0.047 5.00e-02 4.00e+02 7.09e-02 8.04e+00 pdb=" N PRO B 890 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO B 890 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 890 " -0.040 5.00e-02 4.00e+02 ... (remaining 5901 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 8695 2.80 - 3.33: 26609 3.33 - 3.85: 54551 3.85 - 4.38: 60558 4.38 - 4.90: 107492 Nonbonded interactions: 257905 Sorted by model distance: nonbonded pdb=" OG SER A 348 " pdb=" OD1 ASN A 351 " model vdw 2.277 3.040 nonbonded pdb=" OG SER B 348 " pdb=" OD1 ASN B 351 " model vdw 2.281 3.040 nonbonded pdb=" OG SER C 348 " pdb=" OD1 ASN C 351 " model vdw 2.282 3.040 nonbonded pdb=" OH TYR B 990 " pdb=" O PRO A1177 " model vdw 2.288 3.040 nonbonded pdb=" O VAL B 639 " pdb=" OG1 THR B 669 " model vdw 2.303 3.040 ... (remaining 257900 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: 0.07 Found NCS groups: ncs_group { reference = chain 'Z' selection = chain 'X' selection = chain 'H' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'L' } ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'A' } 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: 2.480 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: 0.040 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 30.560 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.060 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6715 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 : 0.003 0.101 33774 Z= 0.171 Angle : 0.679 16.095 46053 Z= 0.362 Chirality : 0.049 0.558 5196 Planarity : 0.006 0.072 5889 Dihedral : 13.442 111.819 12159 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.03 % Allowed : 0.47 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.12), residues: 4170 helix: -1.28 (0.15), residues: 816 sheet: -0.43 (0.17), residues: 990 loop : -1.34 (0.12), residues: 2364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 696 TYR 0.022 0.001 TYR C 317 PHE 0.016 0.002 PHE A 399 TRP 0.011 0.001 TRP B 452 HIS 0.004 0.001 HIS B 215 Details of bonding type rmsd covalent geometry : bond 0.00339 (33690) covalent geometry : angle 0.65036 (45870) SS BOND : bond 0.00272 ( 69) SS BOND : angle 1.00304 ( 138) hydrogen bonds : bond 0.23618 ( 1128) hydrogen bonds : angle 8.63334 ( 3162) link_NAG-ASN : bond 0.01488 ( 15) link_NAG-ASN : angle 6.07669 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1177 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1176 time to evaluate : 1.160 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: 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: B 16 ILE cc_start: 0.7935 (mm) cc_final: 0.7716 (mt) REVERT: B 75 TYR cc_start: 0.7791 (m-10) cc_final: 0.7581 (m-80) REVERT: B 88 ARG cc_start: 0.7314 (mtt90) cc_final: 0.7006 (mtt90) REVERT: B 213 TYR cc_start: 0.7854 (m-80) cc_final: 0.7571 (m-10) REVERT: B 261 THR cc_start: 0.7366 (m) cc_final: 0.6582 (p) REVERT: B 279 ASN cc_start: 0.7171 (p0) cc_final: 0.6738 (p0) REVERT: B 299 LYS cc_start: 0.7340 (mttt) cc_final: 0.6918 (mttt) REVERT: B 301 LYS cc_start: 0.7889 (tptp) cc_final: 0.7578 (tptm) REVERT: B 318 THR cc_start: 0.7075 (m) cc_final: 0.6741 (t) REVERT: B 359 ASN cc_start: 0.7990 (m-40) cc_final: 0.7785 (m-40) REVERT: B 368 MET cc_start: 0.6265 (mtm) cc_final: 0.5794 (mtm) REVERT: B 379 ASN cc_start: 0.6958 (t0) cc_final: 0.6729 (t0) REVERT: B 382 ASP cc_start: 0.7620 (p0) cc_final: 0.7330 (p0) REVERT: B 389 MET cc_start: 0.3579 (ptp) cc_final: 0.3213 (ptp) REVERT: B 398 LYS cc_start: 0.7989 (ttpt) cc_final: 0.7733 (ttpp) REVERT: B 471 VAL cc_start: 0.8170 (m) cc_final: 0.7692 (p) REVERT: B 559 LYS cc_start: 0.7658 (pttt) cc_final: 0.7392 (pttt) REVERT: B 590 ASN cc_start: 0.7632 (m-40) cc_final: 0.6921 (m-40) REVERT: B 626 ASP cc_start: 0.6671 (t0) cc_final: 0.6435 (t0) REVERT: B 673 ARG cc_start: 0.6876 (mtp85) cc_final: 0.6320 (ttm110) REVERT: B 731 ASN cc_start: 0.6499 (t0) cc_final: 0.6285 (t0) REVERT: B 768 PHE cc_start: 0.7644 (t80) cc_final: 0.7437 (t80) REVERT: B 802 ASN cc_start: 0.6692 (p0) cc_final: 0.6430 (p0) REVERT: B 906 SER cc_start: 0.7614 (p) cc_final: 0.7166 (t) REVERT: B 925 GLU cc_start: 0.6482 (tt0) cc_final: 0.6094 (tt0) REVERT: B 928 ASN cc_start: 0.7873 (m-40) cc_final: 0.7670 (m110) REVERT: B 946 LYS cc_start: 0.7950 (mmtp) cc_final: 0.7596 (mmtm) REVERT: B 1033 LYS cc_start: 0.7280 (mtpp) cc_final: 0.6969 (mtpp) REVERT: B 1035 GLN cc_start: 0.6967 (mm-40) cc_final: 0.6575 (mm-40) REVERT: B 1046 ASN cc_start: 0.6107 (t0) cc_final: 0.5818 (t0) REVERT: B 1049 LEU cc_start: 0.7830 (tp) cc_final: 0.6862 (tt) REVERT: B 1069 ARG cc_start: 0.6909 (mtp180) cc_final: 0.6695 (ttm170) REVERT: B 1073 LEU cc_start: 0.7304 (tt) cc_final: 0.7064 (pt) REVERT: B 1106 PHE cc_start: 0.6387 (t80) cc_final: 0.6110 (t80) REVERT: B 1112 MET cc_start: 0.6174 (mtp) cc_final: 0.5739 (mtp) REVERT: B 1113 GLU cc_start: 0.6174 (tt0) cc_final: 0.5889 (tt0) REVERT: B 1118 CYS cc_start: 0.5281 (m) cc_final: 0.4715 (m) REVERT: B 1187 ASN cc_start: 0.7674 (m-40) cc_final: 0.7134 (t0) REVERT: C 24 ASP cc_start: 0.7298 (t0) cc_final: 0.7088 (t0) REVERT: C 88 ARG cc_start: 0.7071 (mtt90) cc_final: 0.6840 (mtt90) REVERT: C 98 ASP cc_start: 0.7165 (p0) cc_final: 0.6875 (p0) REVERT: C 114 LYS cc_start: 0.7510 (tttm) cc_final: 0.7292 (tttm) REVERT: C 136 TYR cc_start: 0.7074 (m-80) cc_final: 0.6598 (m-80) REVERT: C 206 ASP cc_start: 0.6529 (t70) cc_final: 0.6321 (p0) REVERT: C 275 LEU cc_start: 0.7869 (tp) cc_final: 0.7625 (tt) REVERT: C 279 ASN cc_start: 0.7200 (p0) cc_final: 0.6498 (p0) REVERT: C 280 GLN cc_start: 0.6436 (mm-40) cc_final: 0.6196 (mm110) REVERT: C 285 PHE cc_start: 0.8215 (p90) cc_final: 0.7976 (p90) REVERT: C 301 LYS cc_start: 0.8027 (tptp) cc_final: 0.7675 (tppt) REVERT: C 313 GLU cc_start: 0.6500 (mm-30) cc_final: 0.6257 (mm-30) REVERT: C 314 LEU cc_start: 0.7344 (mt) cc_final: 0.6954 (mt) REVERT: C 318 THR cc_start: 0.7200 (m) cc_final: 0.6970 (t) REVERT: C 477 VAL cc_start: 0.8109 (t) cc_final: 0.7859 (p) REVERT: C 590 ASN cc_start: 0.7617 (m-40) cc_final: 0.7111 (m-40) REVERT: C 602 SER cc_start: 0.7347 (t) cc_final: 0.6882 (t) REVERT: C 619 LEU cc_start: 0.7907 (tt) cc_final: 0.7703 (tt) REVERT: C 624 ASN cc_start: 0.7457 (m-40) cc_final: 0.6838 (m-40) REVERT: C 645 ASN cc_start: 0.5603 (m-40) cc_final: 0.5382 (m-40) REVERT: C 679 ARG cc_start: 0.6618 (ttt180) cc_final: 0.6233 (ttt180) REVERT: C 684 PHE cc_start: 0.7627 (t80) cc_final: 0.7349 (t80) REVERT: C 888 PHE cc_start: 0.7182 (m-10) cc_final: 0.6867 (m-80) REVERT: C 913 PHE cc_start: 0.6645 (m-80) cc_final: 0.6433 (m-80) REVERT: C 923 PHE cc_start: 0.6877 (m-10) cc_final: 0.6483 (m-80) REVERT: C 927 TYR cc_start: 0.6885 (m-10) cc_final: 0.6415 (m-80) REVERT: C 928 ASN cc_start: 0.7828 (m-40) cc_final: 0.7445 (m110) REVERT: C 946 LYS cc_start: 0.8111 (mmtp) cc_final: 0.7719 (mmtm) REVERT: C 948 ILE cc_start: 0.6930 (mm) cc_final: 0.6410 (mm) REVERT: C 969 SER cc_start: 0.7839 (m) cc_final: 0.7543 (p) REVERT: C 1009 ILE cc_start: 0.7714 (tp) cc_final: 0.6922 (tp) REVERT: C 1013 PHE cc_start: 0.6487 (m-80) cc_final: 0.6157 (m-80) REVERT: C 1035 GLN cc_start: 0.7243 (mm-40) cc_final: 0.6983 (mm-40) REVERT: C 1049 LEU cc_start: 0.8023 (tp) cc_final: 0.7781 (tt) REVERT: C 1052 LEU cc_start: 0.8110 (mt) cc_final: 0.7869 (mt) REVERT: C 1069 ARG cc_start: 0.7105 (mtp180) cc_final: 0.6853 (ttp-110) REVERT: C 1082 LEU cc_start: 0.7972 (mt) cc_final: 0.7685 (mm) REVERT: C 1113 GLU cc_start: 0.6249 (tt0) cc_final: 0.5820 (tt0) REVERT: C 1114 LYS cc_start: 0.6472 (mttm) cc_final: 0.6176 (mttm) REVERT: C 1124 SER cc_start: 0.7567 (p) cc_final: 0.6911 (p) REVERT: C 1135 ILE cc_start: 0.8216 (mt) cc_final: 0.7915 (mp) REVERT: C 1150 HIS cc_start: 0.6562 (m-70) cc_final: 0.6263 (m-70) REVERT: A 119 TYR cc_start: 0.6402 (m-80) cc_final: 0.6061 (m-80) REVERT: A 274 TYR cc_start: 0.7630 (m-10) cc_final: 0.7264 (m-10) REVERT: A 279 ASN cc_start: 0.7126 (p0) cc_final: 0.6687 (p0) REVERT: A 313 GLU cc_start: 0.6613 (mm-30) cc_final: 0.6200 (mm-30) REVERT: A 346 VAL cc_start: 0.8169 (p) cc_final: 0.7799 (m) REVERT: A 359 ASN cc_start: 0.7669 (m-40) cc_final: 0.7274 (m-40) REVERT: A 378 CYS cc_start: 0.4931 (m) cc_final: 0.4569 (m) REVERT: A 379 ASN cc_start: 0.6954 (t0) cc_final: 0.6748 (t0) REVERT: A 543 THR cc_start: 0.8120 (m) cc_final: 0.7807 (p) REVERT: A 559 LYS cc_start: 0.7438 (pttt) cc_final: 0.7155 (pttt) REVERT: A 590 ASN cc_start: 0.7773 (m-40) cc_final: 0.6387 (m-40) REVERT: A 602 SER cc_start: 0.7565 (t) cc_final: 0.7226 (p) REVERT: A 610 LEU cc_start: 0.7734 (mm) cc_final: 0.7515 (mt) REVERT: A 624 ASN cc_start: 0.7598 (m-40) cc_final: 0.6170 (m-40) REVERT: A 631 LEU cc_start: 0.8510 (mt) cc_final: 0.8062 (mt) REVERT: A 720 ASP cc_start: 0.6956 (m-30) cc_final: 0.6571 (m-30) REVERT: A 774 PHE cc_start: 0.7943 (m-80) cc_final: 0.7455 (m-80) REVERT: A 838 SER cc_start: 0.7888 (t) cc_final: 0.7605 (t) REVERT: A 906 SER cc_start: 0.7945 (p) cc_final: 0.7563 (t) REVERT: A 923 PHE cc_start: 0.6704 (m-10) cc_final: 0.6490 (m-80) REVERT: A 927 TYR cc_start: 0.6966 (m-10) cc_final: 0.6271 (m-80) REVERT: A 942 VAL cc_start: 0.8124 (t) cc_final: 0.7922 (t) REVERT: A 946 LYS cc_start: 0.8236 (mmtp) cc_final: 0.7916 (mmtm) REVERT: A 1035 GLN cc_start: 0.7030 (mm-40) cc_final: 0.6667 (mm-40) REVERT: A 1052 LEU cc_start: 0.8042 (mt) cc_final: 0.7816 (mt) REVERT: A 1082 LEU cc_start: 0.7880 (mt) cc_final: 0.7601 (mp) REVERT: A 1106 PHE cc_start: 0.6496 (t80) cc_final: 0.6246 (t80) REVERT: A 1198 TYR cc_start: 0.7737 (t80) cc_final: 0.7428 (t80) outliers start: 1 outliers final: 1 residues processed: 1176 average time/residue: 0.2123 time to fit residues: 399.0426 Evaluate side-chains 999 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 998 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 802 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 0.1980 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.9980 chunk 401 optimal weight: 0.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 9.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 6 GLN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 GLN B 380 ASN B 481 GLN B 573 GLN B 590 ASN B 648 GLN B 649 ASN B 707 ASN ** B 943 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1050 GLN B1096 GLN F 6 GLN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 655 ASN ** C 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 802 ASN ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 880 ASN C1127 ASN ** C1140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN A 248 HIS A 280 GLN A 573 GLN A 585 GLN A 590 ASN A 649 ASN A 655 ASN A 731 ASN A 802 ASN A 858 GLN A1050 GLN A1127 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.145360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.117083 restraints weight = 56736.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.121467 restraints weight = 28119.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.124403 restraints weight = 16772.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.126277 restraints weight = 11393.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.127586 restraints weight = 8662.922| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 33774 Z= 0.139 Angle : 0.633 10.959 46053 Z= 0.332 Chirality : 0.047 0.481 5196 Planarity : 0.005 0.054 5889 Dihedral : 6.369 99.493 4889 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.87 % Allowed : 10.85 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.13), residues: 4170 helix: 0.27 (0.18), residues: 738 sheet: -0.37 (0.16), residues: 1014 loop : -0.95 (0.12), residues: 2418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 467 TYR 0.024 0.001 TYR B 676 PHE 0.026 0.001 PHE B 595 TRP 0.022 0.002 TRP A 452 HIS 0.004 0.001 HIS B1150 Details of bonding type rmsd covalent geometry : bond 0.00307 (33690) covalent geometry : angle 0.60928 (45870) SS BOND : bond 0.00534 ( 69) SS BOND : angle 2.08547 ( 138) hydrogen bonds : bond 0.04396 ( 1128) hydrogen bonds : angle 6.13621 ( 3162) link_NAG-ASN : bond 0.00816 ( 15) link_NAG-ASN : angle 4.30967 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1087 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 1019 time to evaluate : 1.146 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: symmetry clash revert: symmetry clash REVERT: B 16 ILE cc_start: 0.8364 (mm) cc_final: 0.8103 (mt) REVERT: B 28 ASP cc_start: 0.7453 (t0) cc_final: 0.7161 (t0) REVERT: B 43 VAL cc_start: 0.7124 (m) cc_final: 0.6734 (t) REVERT: B 75 TYR cc_start: 0.8374 (m-80) cc_final: 0.7598 (m-80) REVERT: B 106 LYS cc_start: 0.7871 (ttpp) cc_final: 0.7604 (ttpp) REVERT: B 119 TYR cc_start: 0.6731 (m-80) cc_final: 0.6405 (m-80) REVERT: B 138 VAL cc_start: 0.7897 (t) cc_final: 0.7588 (p) REVERT: B 200 LYS cc_start: 0.7873 (tptp) cc_final: 0.7490 (mptt) REVERT: B 213 TYR cc_start: 0.8067 (m-80) cc_final: 0.7734 (m-10) REVERT: B 244 MET cc_start: 0.6474 (mmm) cc_final: 0.6249 (mmp) REVERT: B 279 ASN cc_start: 0.7594 (p0) cc_final: 0.7361 (p0) REVERT: B 301 LYS cc_start: 0.8137 (tptp) cc_final: 0.7815 (tppt) REVERT: B 318 THR cc_start: 0.7200 (m) cc_final: 0.6770 (t) REVERT: B 329 LYS cc_start: 0.8774 (tttt) cc_final: 0.8351 (tttt) REVERT: B 368 MET cc_start: 0.7852 (mtm) cc_final: 0.7562 (mtm) REVERT: B 379 ASN cc_start: 0.7798 (t0) cc_final: 0.7384 (t0) REVERT: B 380 ASN cc_start: 0.8075 (m110) cc_final: 0.7592 (m-40) REVERT: B 398 LYS cc_start: 0.8453 (ttpt) cc_final: 0.8203 (ttpp) REVERT: B 405 ARG cc_start: 0.8196 (tpp-160) cc_final: 0.7768 (tpp-160) REVERT: B 571 ARG cc_start: 0.8309 (mtp85) cc_final: 0.8050 (mtp85) REVERT: B 585 GLN cc_start: 0.7482 (mt0) cc_final: 0.7182 (mt0) REVERT: B 590 ASN cc_start: 0.7731 (m110) cc_final: 0.7389 (m-40) REVERT: B 635 ILE cc_start: 0.8089 (mp) cc_final: 0.7806 (pt) REVERT: B 644 TYR cc_start: 0.7615 (m-80) cc_final: 0.7384 (m-80) REVERT: B 670 PHE cc_start: 0.8105 (m-80) cc_final: 0.7692 (m-80) REVERT: B 671 MET cc_start: 0.7305 (mmm) cc_final: 0.7049 (mmm) REVERT: B 673 ARG cc_start: 0.7685 (mtp85) cc_final: 0.6982 (ttm110) REVERT: B 690 GLU cc_start: 0.7184 (pt0) cc_final: 0.6726 (pt0) REVERT: B 714 GLN cc_start: 0.7734 (tp40) cc_final: 0.7233 (tm-30) REVERT: B 750 VAL cc_start: 0.8393 (OUTLIER) cc_final: 0.8175 (m) REVERT: B 768 PHE cc_start: 0.7941 (t80) cc_final: 0.7666 (t80) REVERT: B 817 ASP cc_start: 0.7713 (t0) cc_final: 0.7452 (t0) REVERT: B 822 VAL cc_start: 0.8390 (t) cc_final: 0.8171 (m) REVERT: B 835 GLU cc_start: 0.6853 (mt-10) cc_final: 0.6636 (mm-30) REVERT: B 866 MET cc_start: 0.7390 (mmm) cc_final: 0.7186 (tpp) REVERT: B 906 SER cc_start: 0.7665 (p) cc_final: 0.6814 (m) REVERT: B 915 LYS cc_start: 0.8180 (mmmt) cc_final: 0.7783 (mmmt) REVERT: B 918 LEU cc_start: 0.7723 (mt) cc_final: 0.7462 (mm) REVERT: B 925 GLU cc_start: 0.7775 (tt0) cc_final: 0.7496 (tt0) REVERT: B 928 ASN cc_start: 0.8509 (m-40) cc_final: 0.8094 (m110) REVERT: B 939 LEU cc_start: 0.8293 (mm) cc_final: 0.7869 (mt) REVERT: B 957 GLU cc_start: 0.7055 (mm-30) cc_final: 0.6844 (mm-30) REVERT: B 963 TYR cc_start: 0.7996 (m-10) cc_final: 0.7792 (m-80) REVERT: B 1035 GLN cc_start: 0.7974 (mm-40) cc_final: 0.6901 (mm-40) REVERT: B 1039 ASN cc_start: 0.7731 (m-40) cc_final: 0.6162 (m-40) REVERT: B 1043 GLU cc_start: 0.7779 (mt-10) cc_final: 0.6650 (mt-10) REVERT: B 1055 ARG cc_start: 0.7732 (ptp-170) cc_final: 0.7331 (mtm110) REVERT: B 1076 GLU cc_start: 0.7092 (mt-10) cc_final: 0.6771 (mt-10) REVERT: B 1096 GLN cc_start: 0.7828 (OUTLIER) cc_final: 0.7058 (mm110) REVERT: B 1106 PHE cc_start: 0.7990 (t80) cc_final: 0.7770 (t80) REVERT: B 1110 GLN cc_start: 0.8350 (tp-100) cc_final: 0.7835 (tp40) REVERT: B 1114 LYS cc_start: 0.8458 (mttm) cc_final: 0.8104 (tttm) REVERT: B 1120 LYS cc_start: 0.8250 (mmmm) cc_final: 0.7946 (mttt) REVERT: B 1125 ARG cc_start: 0.7262 (mtp180) cc_final: 0.6235 (mtp180) REVERT: B 1128 PHE cc_start: 0.7230 (t80) cc_final: 0.6603 (t80) REVERT: B 1147 TYR cc_start: 0.7656 (t80) cc_final: 0.7427 (t80) REVERT: B 1150 HIS cc_start: 0.7523 (m-70) cc_final: 0.7265 (m-70) REVERT: B 1182 PHE cc_start: 0.7417 (m-10) cc_final: 0.7102 (m-10) REVERT: B 1187 ASN cc_start: 0.8376 (m-40) cc_final: 0.7543 (t0) REVERT: F 87 TYR cc_start: 0.4389 (m-80) cc_final: 0.4181 (m-80) REVERT: F 89 GLN cc_start: 0.6719 (pp30) cc_final: 0.6514 (pp30) REVERT: C 24 ASP cc_start: 0.7571 (t0) cc_final: 0.7224 (t0) REVERT: C 88 ARG cc_start: 0.7626 (mtt90) cc_final: 0.6771 (mtt90) REVERT: C 98 ASP cc_start: 0.7600 (p0) cc_final: 0.7379 (p0) REVERT: C 106 LYS cc_start: 0.7793 (tttt) cc_final: 0.7581 (ttpt) REVERT: C 119 TYR cc_start: 0.6579 (m-80) cc_final: 0.6296 (m-80) REVERT: C 200 LYS cc_start: 0.7755 (tptp) cc_final: 0.7314 (mptt) REVERT: C 206 ASP cc_start: 0.7296 (t70) cc_final: 0.6658 (p0) REVERT: C 250 TYR cc_start: 0.7576 (t80) cc_final: 0.7332 (t80) REVERT: C 301 LYS cc_start: 0.8352 (tptp) cc_final: 0.8092 (tppt) REVERT: C 313 GLU cc_start: 0.7322 (mm-30) cc_final: 0.6868 (mm-30) REVERT: C 318 THR cc_start: 0.7418 (m) cc_final: 0.6943 (t) REVERT: C 329 LYS cc_start: 0.8770 (tttt) cc_final: 0.8326 (tttt) REVERT: C 405 ARG cc_start: 0.8117 (tpp-160) cc_final: 0.7670 (tpp80) REVERT: C 451 THR cc_start: 0.7962 (p) cc_final: 0.7605 (t) REVERT: C 456 PHE cc_start: 0.7078 (m-80) cc_final: 0.6712 (m-80) REVERT: C 543 THR cc_start: 0.7895 (m) cc_final: 0.7677 (p) REVERT: C 581 ASP cc_start: 0.6430 (m-30) cc_final: 0.6087 (m-30) REVERT: C 663 ASP cc_start: 0.7483 (t0) cc_final: 0.6779 (t0) REVERT: C 698 ILE cc_start: 0.8726 (mt) cc_final: 0.8341 (mm) REVERT: C 702 TYR cc_start: 0.8554 (t80) cc_final: 0.8229 (t80) REVERT: C 707 ASN cc_start: 0.7784 (m-40) cc_final: 0.7504 (m110) REVERT: C 738 GLN cc_start: 0.7545 (OUTLIER) cc_final: 0.7330 (mm110) REVERT: C 772 GLU cc_start: 0.7621 (tp30) cc_final: 0.6970 (tp30) REVERT: C 774 PHE cc_start: 0.8512 (m-80) cc_final: 0.7667 (m-80) REVERT: C 791 GLU cc_start: 0.7836 (pt0) cc_final: 0.7618 (pt0) REVERT: C 817 ASP cc_start: 0.7578 (t0) cc_final: 0.7304 (t0) REVERT: C 860 GLN cc_start: 0.8063 (mt0) cc_final: 0.7590 (mt0) REVERT: C 915 LYS cc_start: 0.8196 (mmmt) cc_final: 0.7887 (mmmt) REVERT: C 918 LEU cc_start: 0.7926 (mt) cc_final: 0.7490 (mm) REVERT: C 923 PHE cc_start: 0.7843 (m-10) cc_final: 0.7333 (m-80) REVERT: C 927 TYR cc_start: 0.7974 (m-10) cc_final: 0.7088 (m-80) REVERT: C 928 ASN cc_start: 0.8416 (m-40) cc_final: 0.8177 (m110) REVERT: C 948 ILE cc_start: 0.7596 (mm) cc_final: 0.7228 (mm) REVERT: C 973 PHE cc_start: 0.7785 (m-10) cc_final: 0.7529 (m-10) REVERT: C 989 GLN cc_start: 0.8303 (tt0) cc_final: 0.7784 (tt0) REVERT: C 1009 ILE cc_start: 0.8468 (tp) cc_final: 0.7801 (tp) REVERT: C 1013 PHE cc_start: 0.8084 (m-80) cc_final: 0.7278 (m-80) REVERT: C 1047 ASN cc_start: 0.7732 (m-40) cc_final: 0.7414 (m-40) REVERT: C 1049 LEU cc_start: 0.8681 (tp) cc_final: 0.8406 (tt) REVERT: C 1052 LEU cc_start: 0.8797 (mt) cc_final: 0.8537 (mt) REVERT: C 1055 ARG cc_start: 0.7604 (ptp-170) cc_final: 0.7125 (mtm110) REVERT: C 1069 ARG cc_start: 0.8185 (mtp180) cc_final: 0.7817 (ttm170) REVERT: C 1082 LEU cc_start: 0.8738 (mt) cc_final: 0.8462 (mm) REVERT: C 1083 ILE cc_start: 0.8303 (mt) cc_final: 0.7941 (mm) REVERT: C 1124 SER cc_start: 0.7843 (p) cc_final: 0.7573 (p) REVERT: C 1135 ILE cc_start: 0.8363 (mt) cc_final: 0.8140 (mp) REVERT: C 1144 TYR cc_start: 0.7110 (m-80) cc_final: 0.6866 (m-80) REVERT: C 1190 MET cc_start: 0.6047 (mmm) cc_final: 0.5827 (mmm) REVERT: H 33 TYR cc_start: 0.6113 (m-10) cc_final: 0.5814 (m-80) REVERT: A 28 ASP cc_start: 0.7846 (t0) cc_final: 0.7595 (t0) REVERT: A 108 LYS cc_start: 0.8156 (tmtt) cc_final: 0.7296 (tmtt) REVERT: A 138 VAL cc_start: 0.7987 (t) cc_final: 0.7637 (p) REVERT: A 200 LYS cc_start: 0.7767 (tptp) cc_final: 0.7420 (mptt) REVERT: A 250 TYR cc_start: 0.7411 (t80) cc_final: 0.7056 (t80) REVERT: A 262 LEU cc_start: 0.8103 (tp) cc_final: 0.7877 (tp) REVERT: A 274 TYR cc_start: 0.7997 (m-10) cc_final: 0.7683 (m-10) REVERT: A 313 GLU cc_start: 0.7229 (mm-30) cc_final: 0.6863 (mm-30) REVERT: A 336 ASN cc_start: 0.8479 (m-40) cc_final: 0.8208 (m-40) REVERT: A 346 VAL cc_start: 0.8536 (p) cc_final: 0.8310 (m) REVERT: A 359 ASN cc_start: 0.8270 (m-40) cc_final: 0.7882 (m-40) REVERT: A 364 MET cc_start: 0.7056 (mmm) cc_final: 0.6222 (tmm) REVERT: A 368 MET cc_start: 0.7706 (mtm) cc_final: 0.7132 (mtm) REVERT: A 378 CYS cc_start: 0.4862 (m) cc_final: 0.4568 (m) REVERT: A 379 ASN cc_start: 0.7773 (t0) cc_final: 0.7474 (t0) REVERT: A 385 LYS cc_start: 0.7996 (mmtm) cc_final: 0.7786 (mttm) REVERT: A 416 TYR cc_start: 0.7629 (m-10) cc_final: 0.7183 (m-10) REVERT: A 481 GLN cc_start: 0.7506 (mt0) cc_final: 0.7302 (mt0) REVERT: A 484 PHE cc_start: 0.6601 (m-80) cc_final: 0.6368 (m-80) REVERT: A 543 THR cc_start: 0.7866 (m) cc_final: 0.7580 (p) REVERT: A 559 LYS cc_start: 0.8045 (pttt) cc_final: 0.7668 (pttt) REVERT: A 581 ASP cc_start: 0.5841 (m-30) cc_final: 0.5606 (m-30) REVERT: A 610 LEU cc_start: 0.8337 (mm) cc_final: 0.8036 (mt) REVERT: A 631 LEU cc_start: 0.8431 (mt) cc_final: 0.8188 (mt) REVERT: A 644 TYR cc_start: 0.7787 (m-80) cc_final: 0.6767 (m-80) REVERT: A 649 ASN cc_start: 0.7945 (m-40) cc_final: 0.7476 (m-40) REVERT: A 663 ASP cc_start: 0.7384 (t0) cc_final: 0.7013 (t0) REVERT: A 674 SER cc_start: 0.7075 (m) cc_final: 0.6802 (p) REVERT: A 707 ASN cc_start: 0.7990 (m110) cc_final: 0.7588 (m110) REVERT: A 720 ASP cc_start: 0.8047 (m-30) cc_final: 0.7808 (m-30) REVERT: A 767 ARG cc_start: 0.7240 (mtm180) cc_final: 0.6937 (mtm-85) REVERT: A 772 GLU cc_start: 0.7033 (tp30) cc_final: 0.6777 (tp30) REVERT: A 838 SER cc_start: 0.8432 (t) cc_final: 0.7998 (t) REVERT: A 891 VAL cc_start: 0.8630 (m) cc_final: 0.8317 (p) REVERT: A 906 SER cc_start: 0.8342 (p) cc_final: 0.7868 (t) REVERT: A 909 GLU cc_start: 0.7238 (mt-10) cc_final: 0.6983 (mt-10) REVERT: A 1035 GLN cc_start: 0.8083 (mm-40) cc_final: 0.7161 (tp40) REVERT: A 1039 ASN cc_start: 0.7897 (m-40) cc_final: 0.7597 (m-40) REVERT: A 1069 ARG cc_start: 0.8283 (ttp-110) cc_final: 0.7989 (ttm110) REVERT: A 1084 ASN cc_start: 0.7925 (t0) cc_final: 0.7654 (t0) REVERT: A 1106 PHE cc_start: 0.8102 (t80) cc_final: 0.7859 (t80) REVERT: A 1224 MET cc_start: 0.5360 (mpp) cc_final: 0.4972 (tpp) outliers start: 68 outliers final: 39 residues processed: 1048 average time/residue: 0.2129 time to fit residues: 357.1923 Evaluate side-chains 1008 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 966 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 792 ILE Chi-restraints excluded: chain B residue 838 SER Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1096 GLN Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 551 GLU Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain C residue 665 ILE Chi-restraints excluded: chain C residue 738 GLN Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain C residue 838 SER Chi-restraints excluded: chain C residue 843 ILE Chi-restraints excluded: chain C residue 912 LEU Chi-restraints excluded: chain C residue 921 VAL Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 606 CYS Chi-restraints excluded: chain A residue 665 ILE Chi-restraints excluded: chain A residue 706 ASN Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 849 GLU Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 1060 SER Chi-restraints excluded: chain A residue 1066 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 339 optimal weight: 0.9990 chunk 256 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 370 optimal weight: 0.5980 chunk 87 optimal weight: 0.7980 chunk 200 optimal weight: 0.8980 chunk 90 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 377 optimal weight: 3.9990 chunk 245 optimal weight: 0.1980 chunk 255 optimal weight: 0.1980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 HIS B 851 ASN ** B1004 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1041 ASN B1096 GLN ** B1141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 89 GLN C 248 HIS ** C 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 851 ASN ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 GLN A 475 HIS A 585 GLN ** A 633 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 ASN A 738 GLN A 858 GLN A1116 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.147683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.119566 restraints weight = 56541.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.123954 restraints weight = 27884.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.126853 restraints weight = 16575.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.128768 restraints weight = 11258.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.130040 restraints weight = 8502.349| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 33774 Z= 0.121 Angle : 0.586 11.249 46053 Z= 0.307 Chirality : 0.045 0.426 5196 Planarity : 0.004 0.048 5889 Dihedral : 5.918 94.125 4887 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.90 % Allowed : 14.62 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.13), residues: 4170 helix: 0.56 (0.19), residues: 780 sheet: -0.25 (0.16), residues: 1053 loop : -1.00 (0.13), residues: 2337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 571 TYR 0.024 0.001 TYR C 68 PHE 0.017 0.001 PHE B 888 TRP 0.031 0.002 TRP X 7 HIS 0.006 0.001 HIS A 552 Details of bonding type rmsd covalent geometry : bond 0.00268 (33690) covalent geometry : angle 0.56280 (45870) SS BOND : bond 0.00418 ( 69) SS BOND : angle 2.08246 ( 138) hydrogen bonds : bond 0.03895 ( 1128) hydrogen bonds : angle 5.73576 ( 3162) link_NAG-ASN : bond 0.00908 ( 15) link_NAG-ASN : angle 3.84651 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1051 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 982 time to evaluate : 1.122 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: D 87 TYR cc_start: 0.4859 (m-80) cc_final: 0.4656 (m-80) REVERT: D 89 GLN cc_start: 0.6877 (pp30) cc_final: 0.6515 (pp30) REVERT: B 16 ILE cc_start: 0.8404 (mm) cc_final: 0.8154 (mt) REVERT: B 43 VAL cc_start: 0.7066 (m) cc_final: 0.6713 (t) REVERT: B 75 TYR cc_start: 0.8357 (m-80) cc_final: 0.7694 (m-80) REVERT: B 81 LYS cc_start: 0.7544 (tptp) cc_final: 0.7305 (tptp) REVERT: B 106 LYS cc_start: 0.7942 (ttpp) cc_final: 0.7626 (ttpp) REVERT: B 138 VAL cc_start: 0.7858 (t) cc_final: 0.7569 (p) REVERT: B 200 LYS cc_start: 0.7827 (tptp) cc_final: 0.7482 (mptt) REVERT: B 206 ASP cc_start: 0.7337 (t0) cc_final: 0.7128 (t0) REVERT: B 213 TYR cc_start: 0.8032 (m-80) cc_final: 0.7665 (m-10) REVERT: B 244 MET cc_start: 0.6480 (mmm) cc_final: 0.6277 (mmp) REVERT: B 280 GLN cc_start: 0.7659 (pm20) cc_final: 0.7290 (pm20) REVERT: B 299 LYS cc_start: 0.7934 (mttt) cc_final: 0.7676 (mttt) REVERT: B 301 LYS cc_start: 0.8132 (tptp) cc_final: 0.7737 (tppt) REVERT: B 329 LYS cc_start: 0.8751 (tttt) cc_final: 0.8334 (tttt) REVERT: B 368 MET cc_start: 0.7877 (mtm) cc_final: 0.7627 (mtm) REVERT: B 379 ASN cc_start: 0.7777 (t0) cc_final: 0.7343 (t0) REVERT: B 398 LYS cc_start: 0.8483 (ttpt) cc_final: 0.8186 (ttpp) REVERT: B 410 GLN cc_start: 0.7865 (mm-40) cc_final: 0.7584 (mm-40) REVERT: B 559 LYS cc_start: 0.8152 (pttt) cc_final: 0.7839 (pttm) REVERT: B 571 ARG cc_start: 0.8209 (mtp85) cc_final: 0.7967 (mtp85) REVERT: B 585 GLN cc_start: 0.7546 (mt0) cc_final: 0.7254 (mt0) REVERT: B 590 ASN cc_start: 0.7723 (m110) cc_final: 0.7352 (m-40) REVERT: B 624 ASN cc_start: 0.8248 (OUTLIER) cc_final: 0.7979 (p0) REVERT: B 635 ILE cc_start: 0.8063 (mp) cc_final: 0.7760 (pt) REVERT: B 671 MET cc_start: 0.7236 (mmm) cc_final: 0.6885 (mmm) REVERT: B 673 ARG cc_start: 0.7654 (mtp85) cc_final: 0.6924 (ttm110) REVERT: B 690 GLU cc_start: 0.7174 (pt0) cc_final: 0.6768 (pt0) REVERT: B 714 GLN cc_start: 0.7755 (tp40) cc_final: 0.7329 (tm-30) REVERT: B 717 ASN cc_start: 0.7824 (m110) cc_final: 0.7616 (m-40) REVERT: B 750 VAL cc_start: 0.8360 (t) cc_final: 0.8159 (m) REVERT: B 803 MET cc_start: 0.6883 (mmm) cc_final: 0.6610 (tmm) REVERT: B 817 ASP cc_start: 0.7673 (t0) cc_final: 0.7282 (t0) REVERT: B 835 GLU cc_start: 0.6714 (mt-10) cc_final: 0.6504 (mt-10) REVERT: B 860 GLN cc_start: 0.8096 (mt0) cc_final: 0.7759 (mt0) REVERT: B 906 SER cc_start: 0.7653 (p) cc_final: 0.6663 (m) REVERT: B 917 LYS cc_start: 0.7927 (ttpp) cc_final: 0.7645 (ttpp) REVERT: B 928 ASN cc_start: 0.8567 (m-40) cc_final: 0.8172 (m110) REVERT: B 957 GLU cc_start: 0.7118 (mm-30) cc_final: 0.6828 (mm-30) REVERT: B 999 MET cc_start: 0.7819 (mmm) cc_final: 0.7498 (mmm) REVERT: B 1035 GLN cc_start: 0.7893 (mm-40) cc_final: 0.6782 (mm-40) REVERT: B 1039 ASN cc_start: 0.7770 (m-40) cc_final: 0.6324 (m-40) REVERT: B 1043 GLU cc_start: 0.7724 (mt-10) cc_final: 0.6964 (mt-10) REVERT: B 1049 LEU cc_start: 0.8728 (tp) cc_final: 0.8502 (tt) REVERT: B 1076 GLU cc_start: 0.7163 (mt-10) cc_final: 0.6691 (mt-10) REVERT: B 1096 GLN cc_start: 0.7781 (mm-40) cc_final: 0.7446 (mm110) REVERT: B 1110 GLN cc_start: 0.8365 (tp-100) cc_final: 0.7765 (tp40) REVERT: B 1114 LYS cc_start: 0.8501 (mttm) cc_final: 0.8282 (tttm) REVERT: B 1116 ASN cc_start: 0.7764 (m-40) cc_final: 0.7459 (m-40) REVERT: B 1120 LYS cc_start: 0.8171 (mmmm) cc_final: 0.7812 (mttt) REVERT: B 1125 ARG cc_start: 0.7314 (mtp180) cc_final: 0.6496 (mtp180) REVERT: B 1128 PHE cc_start: 0.7422 (t80) cc_final: 0.6733 (t80) REVERT: B 1147 TYR cc_start: 0.7683 (t80) cc_final: 0.7453 (t80) REVERT: B 1182 PHE cc_start: 0.7520 (m-10) cc_final: 0.6975 (m-10) REVERT: B 1187 ASN cc_start: 0.8328 (m-40) cc_final: 0.7506 (t0) REVERT: F 87 TYR cc_start: 0.4484 (m-80) cc_final: 0.4268 (m-80) REVERT: F 89 GLN cc_start: 0.6833 (OUTLIER) cc_final: 0.6476 (pp30) REVERT: C 24 ASP cc_start: 0.7577 (t0) cc_final: 0.7234 (t0) REVERT: C 88 ARG cc_start: 0.7635 (mtt90) cc_final: 0.6938 (mtt90) REVERT: C 108 LYS cc_start: 0.7963 (tmtt) cc_final: 0.7172 (tmtt) REVERT: C 136 TYR cc_start: 0.7809 (m-80) cc_final: 0.7298 (m-80) REVERT: C 200 LYS cc_start: 0.7793 (tptp) cc_final: 0.7353 (mptt) REVERT: C 206 ASP cc_start: 0.7283 (t70) cc_final: 0.6672 (p0) REVERT: C 234 THR cc_start: 0.7543 (p) cc_final: 0.7024 (t) REVERT: C 250 TYR cc_start: 0.7582 (t80) cc_final: 0.7263 (t80) REVERT: C 313 GLU cc_start: 0.7319 (mm-30) cc_final: 0.6986 (mm-30) REVERT: C 318 THR cc_start: 0.7158 (m) cc_final: 0.6714 (t) REVERT: C 329 LYS cc_start: 0.8748 (tttt) cc_final: 0.8307 (tttt) REVERT: C 379 ASN cc_start: 0.8071 (t0) cc_final: 0.7815 (t0) REVERT: C 405 ARG cc_start: 0.8098 (tpp-160) cc_final: 0.7690 (tpp80) REVERT: C 414 LEU cc_start: 0.7735 (OUTLIER) cc_final: 0.7462 (mp) REVERT: C 437 LEU cc_start: 0.8278 (mt) cc_final: 0.7758 (mp) REVERT: C 456 PHE cc_start: 0.7113 (m-80) cc_final: 0.6778 (m-80) REVERT: C 543 THR cc_start: 0.7817 (m) cc_final: 0.7592 (p) REVERT: C 581 ASP cc_start: 0.6427 (m-30) cc_final: 0.6157 (m-30) REVERT: C 612 LYS cc_start: 0.8038 (ptpp) cc_final: 0.7456 (mtmm) REVERT: C 663 ASP cc_start: 0.7434 (t0) cc_final: 0.7071 (t0) REVERT: C 698 ILE cc_start: 0.8635 (mt) cc_final: 0.8403 (mm) REVERT: C 699 LYS cc_start: 0.8110 (mmtp) cc_final: 0.7884 (mmmm) REVERT: C 707 ASN cc_start: 0.7935 (m-40) cc_final: 0.7573 (m110) REVERT: C 731 ASN cc_start: 0.6630 (t0) cc_final: 0.6380 (t0) REVERT: C 738 GLN cc_start: 0.7557 (OUTLIER) cc_final: 0.6997 (mm110) REVERT: C 772 GLU cc_start: 0.7651 (tp30) cc_final: 0.6559 (tp30) REVERT: C 774 PHE cc_start: 0.8551 (m-80) cc_final: 0.7713 (m-80) REVERT: C 809 THR cc_start: 0.7908 (p) cc_final: 0.7536 (t) REVERT: C 860 GLN cc_start: 0.8131 (mt0) cc_final: 0.7676 (mt0) REVERT: C 874 LYS cc_start: 0.8217 (mmtt) cc_final: 0.7877 (mmtt) REVERT: C 915 LYS cc_start: 0.8234 (mmmt) cc_final: 0.7894 (mmmt) REVERT: C 918 LEU cc_start: 0.7925 (mt) cc_final: 0.7458 (mm) REVERT: C 923 PHE cc_start: 0.7859 (m-10) cc_final: 0.7286 (m-80) REVERT: C 927 TYR cc_start: 0.7894 (m-10) cc_final: 0.7088 (m-80) REVERT: C 928 ASN cc_start: 0.8404 (m-40) cc_final: 0.8192 (m110) REVERT: C 946 LYS cc_start: 0.8415 (mmtm) cc_final: 0.7754 (mmmm) REVERT: C 948 ILE cc_start: 0.7601 (mm) cc_final: 0.7334 (mm) REVERT: C 957 GLU cc_start: 0.7042 (mm-30) cc_final: 0.6763 (mm-30) REVERT: C 973 PHE cc_start: 0.7781 (m-10) cc_final: 0.7558 (m-10) REVERT: C 989 GLN cc_start: 0.8225 (tt0) cc_final: 0.7676 (tt0) REVERT: C 1009 ILE cc_start: 0.8466 (tp) cc_final: 0.7770 (tp) REVERT: C 1013 PHE cc_start: 0.8036 (m-80) cc_final: 0.7197 (m-80) REVERT: C 1039 ASN cc_start: 0.7671 (m-40) cc_final: 0.7300 (m-40) REVERT: C 1047 ASN cc_start: 0.7792 (m-40) cc_final: 0.7394 (m110) REVERT: C 1049 LEU cc_start: 0.8743 (tp) cc_final: 0.8453 (tt) REVERT: C 1055 ARG cc_start: 0.7576 (ptp-170) cc_final: 0.7113 (mtm110) REVERT: C 1069 ARG cc_start: 0.8159 (mtp180) cc_final: 0.7751 (ttm170) REVERT: C 1083 ILE cc_start: 0.8320 (mt) cc_final: 0.7929 (mm) REVERT: C 1096 GLN cc_start: 0.7738 (mt0) cc_final: 0.7061 (mm-40) REVERT: C 1124 SER cc_start: 0.7874 (p) cc_final: 0.7581 (p) REVERT: C 1135 ILE cc_start: 0.8378 (mt) cc_final: 0.8137 (mp) REVERT: C 1144 TYR cc_start: 0.7082 (m-80) cc_final: 0.6849 (m-80) REVERT: C 1190 MET cc_start: 0.6025 (mmm) cc_final: 0.5691 (mmm) REVERT: H 33 TYR cc_start: 0.6032 (m-10) cc_final: 0.5769 (m-80) REVERT: L 35 TRP cc_start: 0.7113 (m100) cc_final: 0.6911 (m100) REVERT: A 28 ASP cc_start: 0.7942 (t0) cc_final: 0.7672 (t0) REVERT: A 108 LYS cc_start: 0.8120 (tmtt) cc_final: 0.7617 (tttt) REVERT: A 138 VAL cc_start: 0.8040 (t) cc_final: 0.7693 (p) REVERT: A 200 LYS cc_start: 0.7818 (tptp) cc_final: 0.7495 (mptt) REVERT: A 250 TYR cc_start: 0.7442 (t80) cc_final: 0.7010 (t80) REVERT: A 263 GLU cc_start: 0.6926 (pt0) cc_final: 0.6449 (pt0) REVERT: A 274 TYR cc_start: 0.7997 (m-10) cc_final: 0.7653 (m-10) REVERT: A 297 GLU cc_start: 0.7086 (tt0) cc_final: 0.6823 (tt0) REVERT: A 313 GLU cc_start: 0.7276 (mm-30) cc_final: 0.6885 (mm-30) REVERT: A 346 VAL cc_start: 0.8499 (p) cc_final: 0.8296 (m) REVERT: A 364 MET cc_start: 0.6984 (mmm) cc_final: 0.5951 (mmm) REVERT: A 368 MET cc_start: 0.7761 (mtm) cc_final: 0.6685 (mtm) REVERT: A 379 ASN cc_start: 0.7813 (t0) cc_final: 0.7417 (t0) REVERT: A 385 LYS cc_start: 0.8064 (mmtm) cc_final: 0.7675 (mmtm) REVERT: A 398 LYS cc_start: 0.8206 (ttpt) cc_final: 0.7927 (ttpp) REVERT: A 414 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7653 (mp) REVERT: A 418 GLN cc_start: 0.7416 (tt0) cc_final: 0.7164 (tp40) REVERT: A 420 PHE cc_start: 0.7766 (m-10) cc_final: 0.7541 (m-10) REVERT: A 543 THR cc_start: 0.7851 (m) cc_final: 0.7635 (p) REVERT: A 571 ARG cc_start: 0.8027 (mtp85) cc_final: 0.7698 (mtm-85) REVERT: A 581 ASP cc_start: 0.5895 (m-30) cc_final: 0.5667 (m-30) REVERT: A 610 LEU cc_start: 0.8249 (mm) cc_final: 0.7985 (mt) REVERT: A 631 LEU cc_start: 0.8402 (mt) cc_final: 0.8143 (mt) REVERT: A 635 ILE cc_start: 0.8042 (mp) cc_final: 0.7797 (pt) REVERT: A 644 TYR cc_start: 0.7714 (m-80) cc_final: 0.6854 (m-80) REVERT: A 649 ASN cc_start: 0.7820 (m-40) cc_final: 0.7491 (m-40) REVERT: A 671 MET cc_start: 0.7263 (mmm) cc_final: 0.6707 (mmm) REVERT: A 699 LYS cc_start: 0.7816 (mmtp) cc_final: 0.7545 (mttp) REVERT: A 707 ASN cc_start: 0.7886 (m110) cc_final: 0.7492 (m110) REVERT: A 772 GLU cc_start: 0.7012 (tp30) cc_final: 0.6713 (tp30) REVERT: A 774 PHE cc_start: 0.8503 (m-80) cc_final: 0.8291 (m-80) REVERT: A 838 SER cc_start: 0.8395 (t) cc_final: 0.7965 (t) REVERT: A 860 GLN cc_start: 0.7914 (mt0) cc_final: 0.7553 (mt0) REVERT: A 866 MET cc_start: 0.7490 (mmm) cc_final: 0.7112 (tpp) REVERT: A 891 VAL cc_start: 0.8639 (OUTLIER) cc_final: 0.8329 (p) REVERT: A 906 SER cc_start: 0.8381 (p) cc_final: 0.7799 (t) REVERT: A 909 GLU cc_start: 0.7188 (mt-10) cc_final: 0.6924 (mt-10) REVERT: A 923 PHE cc_start: 0.7846 (m-80) cc_final: 0.7252 (m-80) REVERT: A 949 LYS cc_start: 0.8114 (tppp) cc_final: 0.7805 (ttmm) REVERT: A 1034 ILE cc_start: 0.8519 (tp) cc_final: 0.8277 (mt) REVERT: A 1035 GLN cc_start: 0.8013 (mm-40) cc_final: 0.7189 (tp40) REVERT: A 1039 ASN cc_start: 0.7867 (m-40) cc_final: 0.7662 (m-40) REVERT: A 1069 ARG cc_start: 0.8270 (ttp-110) cc_final: 0.7922 (ttm110) REVERT: A 1084 ASN cc_start: 0.7987 (t0) cc_final: 0.7709 (t0) REVERT: A 1118 CYS cc_start: 0.5436 (m) cc_final: 0.5174 (m) REVERT: A 1120 LYS cc_start: 0.8251 (mmmm) cc_final: 0.8043 (mmtm) REVERT: A 1224 MET cc_start: 0.5315 (mpp) cc_final: 0.4943 (tpp) outliers start: 69 outliers final: 37 residues processed: 1005 average time/residue: 0.2162 time to fit residues: 346.3423 Evaluate side-chains 970 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 927 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 615 THR Chi-restraints excluded: chain B residue 624 ASN Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 792 ILE Chi-restraints excluded: chain B residue 941 CYS Chi-restraints excluded: chain B residue 965 LEU Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain F residue 89 GLN Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain C residue 665 ILE Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 738 GLN Chi-restraints excluded: chain C residue 768 PHE Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain C residue 1067 LEU Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 483 CYS Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 665 ILE Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 778 SER Chi-restraints excluded: chain A residue 805 GLU Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain A residue 849 GLU Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 999 MET Chi-restraints excluded: chain A residue 1112 MET Chi-restraints excluded: chain A residue 1119 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 405 optimal weight: 3.9990 chunk 314 optimal weight: 9.9990 chunk 237 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 279 optimal weight: 2.9990 chunk 259 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 387 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 258 optimal weight: 0.8980 chunk 13 optimal weight: 20.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 89 GLN B 573 GLN B 858 GLN ** B1004 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1054 ASN ** B1064 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 248 HIS C 573 GLN ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 GLN A 475 HIS A 573 GLN A 731 ASN A 858 GLN A1096 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.147021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.119002 restraints weight = 55732.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.123336 restraints weight = 27446.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.126172 restraints weight = 16372.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.128016 restraints weight = 11181.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.129233 restraints weight = 8525.612| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.135 33774 Z= 0.235 Angle : 0.659 25.682 46053 Z= 0.346 Chirality : 0.049 0.862 5196 Planarity : 0.004 0.053 5889 Dihedral : 5.829 87.791 4887 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.69 % Allowed : 16.41 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.13), residues: 4170 helix: 0.59 (0.19), residues: 783 sheet: -0.22 (0.16), residues: 1065 loop : -0.96 (0.13), residues: 2322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 696 TYR 0.027 0.002 TYR C1147 PHE 0.023 0.002 PHE A 376 TRP 0.032 0.002 TRP D 35 HIS 0.008 0.001 HIS C1150 Details of bonding type rmsd covalent geometry : bond 0.00495 (33690) covalent geometry : angle 0.62418 (45870) SS BOND : bond 0.00572 ( 69) SS BOND : angle 2.19656 ( 138) hydrogen bonds : bond 0.04348 ( 1128) hydrogen bonds : angle 5.71686 ( 3162) link_NAG-ASN : bond 0.00749 ( 15) link_NAG-ASN : angle 5.75562 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1097 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 999 time to evaluate : 1.133 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: D 87 TYR cc_start: 0.4961 (m-80) cc_final: 0.4634 (m-80) REVERT: B 16 ILE cc_start: 0.8554 (mm) cc_final: 0.8315 (mt) REVERT: B 24 ASP cc_start: 0.7913 (t0) cc_final: 0.7656 (t70) REVERT: B 43 VAL cc_start: 0.7134 (m) cc_final: 0.6809 (t) REVERT: B 75 TYR cc_start: 0.8318 (m-80) cc_final: 0.7739 (m-80) REVERT: B 81 LYS cc_start: 0.7631 (tptp) cc_final: 0.7351 (tptp) REVERT: B 100 ILE cc_start: 0.8416 (mp) cc_final: 0.8136 (mm) REVERT: B 108 LYS cc_start: 0.8077 (tmtt) cc_final: 0.7414 (tttt) REVERT: B 138 VAL cc_start: 0.7919 (t) cc_final: 0.7646 (p) REVERT: B 206 ASP cc_start: 0.7455 (t0) cc_final: 0.7063 (t70) REVERT: B 229 ASP cc_start: 0.6589 (p0) cc_final: 0.6371 (p0) REVERT: B 234 THR cc_start: 0.7378 (p) cc_final: 0.6732 (t) REVERT: B 235 LYS cc_start: 0.7739 (mtmm) cc_final: 0.7195 (mtmm) REVERT: B 252 MET cc_start: 0.7152 (mpp) cc_final: 0.6736 (mpp) REVERT: B 297 GLU cc_start: 0.7601 (tt0) cc_final: 0.6995 (tt0) REVERT: B 299 LYS cc_start: 0.8087 (mttt) cc_final: 0.7855 (mttt) REVERT: B 301 LYS cc_start: 0.8183 (tptp) cc_final: 0.7982 (tppt) REVERT: B 329 LYS cc_start: 0.8735 (tttt) cc_final: 0.8365 (tttt) REVERT: B 368 MET cc_start: 0.7911 (mtm) cc_final: 0.7689 (mtm) REVERT: B 379 ASN cc_start: 0.7943 (t0) cc_final: 0.7563 (t0) REVERT: B 382 ASP cc_start: 0.7913 (p0) cc_final: 0.7418 (p0) REVERT: B 398 LYS cc_start: 0.8530 (ttpt) cc_final: 0.8298 (ttpp) REVERT: B 403 ASN cc_start: 0.8076 (t0) cc_final: 0.7647 (t0) REVERT: B 488 LYS cc_start: 0.8062 (ttpt) cc_final: 0.7840 (ttpt) REVERT: B 585 GLN cc_start: 0.7623 (mt0) cc_final: 0.7358 (mt0) REVERT: B 612 LYS cc_start: 0.8323 (ptpp) cc_final: 0.8059 (ptpp) REVERT: B 635 ILE cc_start: 0.8109 (mp) cc_final: 0.7768 (pt) REVERT: B 649 ASN cc_start: 0.8031 (m-40) cc_final: 0.7768 (m-40) REVERT: B 661 PHE cc_start: 0.8231 (p90) cc_final: 0.7766 (p90) REVERT: B 671 MET cc_start: 0.7141 (mmm) cc_final: 0.6854 (mmm) REVERT: B 673 ARG cc_start: 0.7675 (mtp85) cc_final: 0.6903 (ttm110) REVERT: B 680 VAL cc_start: 0.9061 (t) cc_final: 0.8857 (p) REVERT: B 690 GLU cc_start: 0.7336 (pt0) cc_final: 0.6747 (pt0) REVERT: B 714 GLN cc_start: 0.7817 (tp40) cc_final: 0.7455 (tm-30) REVERT: B 738 GLN cc_start: 0.7708 (mp10) cc_final: 0.7476 (mm110) REVERT: B 772 GLU cc_start: 0.7255 (tp30) cc_final: 0.6678 (tp30) REVERT: B 817 ASP cc_start: 0.7767 (t0) cc_final: 0.7398 (t0) REVERT: B 860 GLN cc_start: 0.8135 (mt0) cc_final: 0.7799 (mt0) REVERT: B 866 MET cc_start: 0.7118 (tpp) cc_final: 0.6776 (mpp) REVERT: B 917 LYS cc_start: 0.7876 (ttpp) cc_final: 0.7668 (ttpp) REVERT: B 939 LEU cc_start: 0.8145 (mm) cc_final: 0.7938 (mt) REVERT: B 957 GLU cc_start: 0.7311 (mm-30) cc_final: 0.6887 (mm-30) REVERT: B 995 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8092 (mm) REVERT: B 999 MET cc_start: 0.7868 (mmm) cc_final: 0.7561 (mmt) REVERT: B 1003 SER cc_start: 0.8518 (p) cc_final: 0.8286 (p) REVERT: B 1035 GLN cc_start: 0.8038 (mm-40) cc_final: 0.7096 (mm-40) REVERT: B 1039 ASN cc_start: 0.7877 (m-40) cc_final: 0.6366 (m-40) REVERT: B 1043 GLU cc_start: 0.7651 (mt-10) cc_final: 0.6819 (mt-10) REVERT: B 1049 LEU cc_start: 0.8801 (tp) cc_final: 0.8533 (tt) REVERT: B 1062 SER cc_start: 0.8573 (OUTLIER) cc_final: 0.7770 (p) REVERT: B 1076 GLU cc_start: 0.7289 (mt-10) cc_final: 0.6733 (mt-10) REVERT: B 1096 GLN cc_start: 0.7866 (mm-40) cc_final: 0.7133 (mm-40) REVERT: B 1110 GLN cc_start: 0.8362 (tp-100) cc_final: 0.7755 (tp40) REVERT: B 1112 MET cc_start: 0.7799 (mtp) cc_final: 0.7582 (mtp) REVERT: B 1114 LYS cc_start: 0.8557 (mttm) cc_final: 0.8330 (tttm) REVERT: B 1120 LYS cc_start: 0.8284 (mmmm) cc_final: 0.7838 (mttt) REVERT: B 1125 ARG cc_start: 0.7457 (mtp180) cc_final: 0.6549 (mtp180) REVERT: B 1128 PHE cc_start: 0.7599 (t80) cc_final: 0.6850 (t80) REVERT: B 1144 TYR cc_start: 0.7074 (m-80) cc_final: 0.6843 (m-80) REVERT: B 1147 TYR cc_start: 0.7739 (t80) cc_final: 0.7492 (t80) REVERT: B 1182 PHE cc_start: 0.7408 (m-10) cc_final: 0.7150 (m-10) REVERT: B 1187 ASN cc_start: 0.8320 (m-40) cc_final: 0.7515 (t0) REVERT: X 34 TRP cc_start: 0.7365 (m100) cc_final: 0.6484 (m-10) REVERT: X 66 ARG cc_start: 0.6739 (ptm-80) cc_final: 0.6250 (ptm-80) REVERT: F 87 TYR cc_start: 0.4596 (m-80) cc_final: 0.4323 (m-80) REVERT: C 24 ASP cc_start: 0.7494 (t0) cc_final: 0.7151 (t0) REVERT: C 55 ARG cc_start: 0.8419 (mtt180) cc_final: 0.7959 (mmm-85) REVERT: C 88 ARG cc_start: 0.7616 (mtt90) cc_final: 0.7010 (mtt90) REVERT: C 92 LYS cc_start: 0.7735 (mtpp) cc_final: 0.7336 (mtpp) REVERT: C 108 LYS cc_start: 0.8130 (tttt) cc_final: 0.7255 (tmtt) REVERT: C 136 TYR cc_start: 0.7777 (m-80) cc_final: 0.7152 (m-80) REVERT: C 206 ASP cc_start: 0.7434 (t70) cc_final: 0.6900 (p0) REVERT: C 234 THR cc_start: 0.7614 (p) cc_final: 0.7132 (t) REVERT: C 250 TYR cc_start: 0.7601 (t80) cc_final: 0.7226 (t80) REVERT: C 299 LYS cc_start: 0.8222 (mttt) cc_final: 0.7823 (mttt) REVERT: C 301 LYS cc_start: 0.8603 (tptp) cc_final: 0.8163 (tppt) REVERT: C 313 GLU cc_start: 0.7348 (mm-30) cc_final: 0.7084 (mm-30) REVERT: C 329 LYS cc_start: 0.8739 (tttt) cc_final: 0.8318 (tttt) REVERT: C 379 ASN cc_start: 0.8194 (t0) cc_final: 0.7751 (t0) REVERT: C 437 LEU cc_start: 0.8465 (mt) cc_final: 0.8249 (mt) REVERT: C 456 PHE cc_start: 0.7204 (m-80) cc_final: 0.6999 (m-10) REVERT: C 461 ASP cc_start: 0.7913 (m-30) cc_final: 0.7567 (p0) REVERT: C 543 THR cc_start: 0.8005 (m) cc_final: 0.7763 (p) REVERT: C 581 ASP cc_start: 0.6646 (m-30) cc_final: 0.6383 (m-30) REVERT: C 612 LYS cc_start: 0.8115 (ptpp) cc_final: 0.6374 (mtmm) REVERT: C 635 ILE cc_start: 0.7922 (mp) cc_final: 0.7556 (pt) REVERT: C 644 TYR cc_start: 0.7743 (m-80) cc_final: 0.7431 (m-80) REVERT: C 653 ASP cc_start: 0.7945 (t0) cc_final: 0.7177 (p0) REVERT: C 663 ASP cc_start: 0.7563 (t0) cc_final: 0.7209 (t0) REVERT: C 698 ILE cc_start: 0.8715 (mt) cc_final: 0.8439 (mt) REVERT: C 707 ASN cc_start: 0.8023 (m-40) cc_final: 0.7712 (m110) REVERT: C 731 ASN cc_start: 0.6381 (t0) cc_final: 0.6095 (t0) REVERT: C 738 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.7587 (mm110) REVERT: C 772 GLU cc_start: 0.7743 (tp30) cc_final: 0.6854 (tp30) REVERT: C 774 PHE cc_start: 0.8572 (m-80) cc_final: 0.7627 (m-80) REVERT: C 830 LYS cc_start: 0.8491 (mmmm) cc_final: 0.8257 (mmmm) REVERT: C 833 LEU cc_start: 0.8269 (tp) cc_final: 0.7946 (tp) REVERT: C 874 LYS cc_start: 0.8259 (mmtt) cc_final: 0.7906 (mmtt) REVERT: C 915 LYS cc_start: 0.8414 (mmmt) cc_final: 0.8101 (mmmt) REVERT: C 918 LEU cc_start: 0.7936 (mt) cc_final: 0.7732 (mm) REVERT: C 927 TYR cc_start: 0.8079 (m-80) cc_final: 0.7445 (m-80) REVERT: C 940 ILE cc_start: 0.8141 (mm) cc_final: 0.7896 (tt) REVERT: C 948 ILE cc_start: 0.7641 (mm) cc_final: 0.7254 (mm) REVERT: C 949 LYS cc_start: 0.8021 (tppp) cc_final: 0.7709 (ttmm) REVERT: C 989 GLN cc_start: 0.8251 (tt0) cc_final: 0.7660 (tt0) REVERT: C 1009 ILE cc_start: 0.8496 (tp) cc_final: 0.7791 (tp) REVERT: C 1013 PHE cc_start: 0.8045 (m-80) cc_final: 0.7212 (m-80) REVERT: C 1039 ASN cc_start: 0.7534 (m-40) cc_final: 0.7328 (m-40) REVERT: C 1047 ASN cc_start: 0.7763 (m-40) cc_final: 0.7447 (m110) REVERT: C 1049 LEU cc_start: 0.8828 (tp) cc_final: 0.8588 (tt) REVERT: C 1055 ARG cc_start: 0.7754 (ptp-170) cc_final: 0.7277 (mtm110) REVERT: C 1067 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8544 (mm) REVERT: C 1069 ARG cc_start: 0.8175 (mtp180) cc_final: 0.7899 (mtp180) REVERT: C 1083 ILE cc_start: 0.8486 (mt) cc_final: 0.8113 (mm) REVERT: C 1096 GLN cc_start: 0.7776 (mt0) cc_final: 0.7149 (mm-40) REVERT: C 1116 ASN cc_start: 0.7793 (m-40) cc_final: 0.7561 (m-40) REVERT: C 1124 SER cc_start: 0.7845 (p) cc_final: 0.7533 (p) REVERT: C 1135 ILE cc_start: 0.8362 (mt) cc_final: 0.8137 (mp) REVERT: C 1157 LYS cc_start: 0.7925 (mmmt) cc_final: 0.7035 (mmmt) REVERT: C 1165 PRO cc_start: 0.7406 (Cg_endo) cc_final: 0.7204 (Cg_exo) REVERT: H 33 TYR cc_start: 0.6228 (m-10) cc_final: 0.5976 (m-80) REVERT: H 111 MET cc_start: 0.5531 (tmm) cc_final: 0.5091 (tmm) REVERT: L 35 TRP cc_start: 0.7178 (m100) cc_final: 0.6855 (m100) REVERT: A 28 ASP cc_start: 0.7849 (t0) cc_final: 0.7621 (t0) REVERT: A 108 LYS cc_start: 0.8180 (tttt) cc_final: 0.7630 (tttt) REVERT: A 138 VAL cc_start: 0.8147 (t) cc_final: 0.7853 (p) REVERT: A 165 GLN cc_start: 0.7386 (mt0) cc_final: 0.7174 (mt0) REVERT: A 184 ARG cc_start: 0.6787 (mtt180) cc_final: 0.6575 (mtt180) REVERT: A 248 HIS cc_start: 0.7535 (m170) cc_final: 0.7309 (m170) REVERT: A 274 TYR cc_start: 0.7949 (m-10) cc_final: 0.7680 (m-10) REVERT: A 293 ASP cc_start: 0.8033 (p0) cc_final: 0.7707 (p0) REVERT: A 297 GLU cc_start: 0.7210 (tt0) cc_final: 0.6878 (tt0) REVERT: A 299 LYS cc_start: 0.8406 (mttt) cc_final: 0.8202 (mttp) REVERT: A 313 GLU cc_start: 0.7335 (mm-30) cc_final: 0.7064 (mm-30) REVERT: A 318 THR cc_start: 0.7708 (m) cc_final: 0.7092 (t) REVERT: A 359 ASN cc_start: 0.8319 (m-40) cc_final: 0.8059 (m-40) REVERT: A 364 MET cc_start: 0.6986 (mmm) cc_final: 0.6759 (mmm) REVERT: A 374 ASP cc_start: 0.7157 (t0) cc_final: 0.6925 (t70) REVERT: A 379 ASN cc_start: 0.7841 (t0) cc_final: 0.7535 (t160) REVERT: A 398 LYS cc_start: 0.8291 (ttpt) cc_final: 0.7955 (ttpp) REVERT: A 414 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7828 (mp) REVERT: A 418 GLN cc_start: 0.7573 (tt0) cc_final: 0.7175 (tt0) REVERT: A 420 PHE cc_start: 0.7937 (m-10) cc_final: 0.7534 (m-10) REVERT: A 476 ASP cc_start: 0.7209 (m-30) cc_final: 0.6870 (m-30) REVERT: A 543 THR cc_start: 0.7970 (m) cc_final: 0.7719 (p) REVERT: A 571 ARG cc_start: 0.8169 (mtp85) cc_final: 0.7800 (mtm-85) REVERT: A 599 ASP cc_start: 0.7443 (OUTLIER) cc_final: 0.6920 (t70) REVERT: A 610 LEU cc_start: 0.8199 (mm) cc_final: 0.7880 (mt) REVERT: A 631 LEU cc_start: 0.8535 (mt) cc_final: 0.8319 (mt) REVERT: A 635 ILE cc_start: 0.8148 (mp) cc_final: 0.7853 (pt) REVERT: A 644 TYR cc_start: 0.7814 (m-80) cc_final: 0.7013 (m-80) REVERT: A 649 ASN cc_start: 0.7763 (m-40) cc_final: 0.7259 (p0) REVERT: A 661 PHE cc_start: 0.8219 (p90) cc_final: 0.7814 (p90) REVERT: A 663 ASP cc_start: 0.7332 (t0) cc_final: 0.6859 (t0) REVERT: A 671 MET cc_start: 0.7246 (mmm) cc_final: 0.6720 (mmm) REVERT: A 707 ASN cc_start: 0.7994 (m110) cc_final: 0.7531 (m110) REVERT: A 772 GLU cc_start: 0.7170 (tp30) cc_final: 0.6679 (tp30) REVERT: A 774 PHE cc_start: 0.8528 (m-80) cc_final: 0.8303 (m-80) REVERT: A 835 GLU cc_start: 0.7110 (mt-10) cc_final: 0.6712 (mt-10) REVERT: A 860 GLN cc_start: 0.8006 (mt0) cc_final: 0.7623 (mt0) REVERT: A 906 SER cc_start: 0.8621 (p) cc_final: 0.7957 (m) REVERT: A 911 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8461 (tt) REVERT: A 923 PHE cc_start: 0.8125 (m-80) cc_final: 0.7702 (m-80) REVERT: A 938 ASP cc_start: 0.7432 (t0) cc_final: 0.7215 (t0) REVERT: A 940 ILE cc_start: 0.8158 (mm) cc_final: 0.7881 (tt) REVERT: A 949 LYS cc_start: 0.8172 (tppp) cc_final: 0.7943 (ttmm) REVERT: A 957 GLU cc_start: 0.6972 (mm-30) cc_final: 0.6496 (mm-30) REVERT: A 1003 SER cc_start: 0.8583 (p) cc_final: 0.8361 (p) REVERT: A 1035 GLN cc_start: 0.8069 (mm-40) cc_final: 0.7200 (tp40) REVERT: A 1039 ASN cc_start: 0.7980 (m-40) cc_final: 0.7741 (m-40) REVERT: A 1069 ARG cc_start: 0.8308 (ttp-110) cc_final: 0.7972 (ttm110) REVERT: A 1084 ASN cc_start: 0.8130 (t0) cc_final: 0.7870 (t0) REVERT: A 1098 LEU cc_start: 0.8667 (mp) cc_final: 0.8463 (tp) REVERT: A 1120 LYS cc_start: 0.8400 (mmmm) cc_final: 0.8196 (mmtm) REVERT: A 1177 PRO cc_start: 0.7882 (Cg_endo) cc_final: 0.7493 (Cg_exo) REVERT: A 1224 MET cc_start: 0.5327 (mpp) cc_final: 0.5006 (tpp) outliers start: 98 outliers final: 62 residues processed: 1038 average time/residue: 0.2146 time to fit residues: 354.7449 Evaluate side-chains 1018 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 949 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 615 THR Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 792 ILE Chi-restraints excluded: chain B residue 941 CYS Chi-restraints excluded: chain B residue 995 LEU Chi-restraints excluded: chain B residue 1062 SER Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1083 ILE Chi-restraints excluded: chain B residue 1124 SER Chi-restraints excluded: chain F residue 91 SER Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 369 SER Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 665 ILE Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 738 GLN Chi-restraints excluded: chain C residue 768 PHE Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain C residue 792 ILE Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 912 LEU Chi-restraints excluded: chain C residue 1067 LEU Chi-restraints excluded: chain C residue 1076 GLU Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 390 CYS Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 599 ASP Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 665 ILE Chi-restraints excluded: chain A residue 706 ASN Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 778 SER Chi-restraints excluded: chain A residue 849 GLU Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 999 MET Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1112 MET Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1124 SER Chi-restraints excluded: chain A residue 1137 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 193 optimal weight: 0.0370 chunk 298 optimal weight: 5.9990 chunk 333 optimal weight: 1.9990 chunk 214 optimal weight: 4.9990 chunk 398 optimal weight: 0.9990 chunk 321 optimal weight: 0.4980 chunk 364 optimal weight: 0.8980 chunk 183 optimal weight: 0.6980 chunk 196 optimal weight: 3.9990 chunk 303 optimal weight: 0.0270 chunk 50 optimal weight: 0.6980 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 379 ASN ** B1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1054 ASN C 453 ASN C 573 GLN C 844 ASN ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 GLN A 448 ASN A 475 HIS A 573 GLN A 585 GLN A 590 ASN A 731 ASN A 802 ASN ** A 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.149231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.121105 restraints weight = 56706.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.125662 restraints weight = 27910.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.128595 restraints weight = 16567.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.130559 restraints weight = 11265.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.131864 restraints weight = 8514.035| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 33774 Z= 0.118 Angle : 0.614 20.870 46053 Z= 0.317 Chirality : 0.047 0.978 5196 Planarity : 0.004 0.057 5889 Dihedral : 5.397 81.381 4887 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.25 % Allowed : 18.19 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.13), residues: 4170 helix: 0.94 (0.19), residues: 759 sheet: -0.13 (0.16), residues: 1053 loop : -0.94 (0.13), residues: 2358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 571 TYR 0.034 0.001 TYR C 68 PHE 0.031 0.001 PHE C 285 TRP 0.028 0.002 TRP F 94 HIS 0.006 0.001 HIS C1150 Details of bonding type rmsd covalent geometry : bond 0.00263 (33690) covalent geometry : angle 0.58308 (45870) SS BOND : bond 0.00648 ( 69) SS BOND : angle 2.16895 ( 138) hydrogen bonds : bond 0.03697 ( 1128) hydrogen bonds : angle 5.43767 ( 3162) link_NAG-ASN : bond 0.00722 ( 15) link_NAG-ASN : angle 5.01832 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1024 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 942 time to evaluate : 1.057 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 87 TYR cc_start: 0.4830 (m-80) cc_final: 0.4459 (m-80) REVERT: B 24 ASP cc_start: 0.7930 (t0) cc_final: 0.7697 (t70) REVERT: B 75 TYR cc_start: 0.8300 (m-80) cc_final: 0.7710 (m-80) REVERT: B 81 LYS cc_start: 0.7588 (tptp) cc_final: 0.7376 (tptp) REVERT: B 100 ILE cc_start: 0.8433 (mp) cc_final: 0.8154 (mm) REVERT: B 108 LYS cc_start: 0.8033 (tttt) cc_final: 0.7378 (tttt) REVERT: B 119 TYR cc_start: 0.6820 (m-80) cc_final: 0.6493 (m-80) REVERT: B 138 VAL cc_start: 0.7866 (t) cc_final: 0.7597 (p) REVERT: B 234 THR cc_start: 0.7405 (p) cc_final: 0.6781 (t) REVERT: B 235 LYS cc_start: 0.7663 (mtmm) cc_final: 0.7091 (mtmm) REVERT: B 252 MET cc_start: 0.7308 (mpp) cc_final: 0.6810 (mpp) REVERT: B 297 GLU cc_start: 0.7546 (tt0) cc_final: 0.6940 (tt0) REVERT: B 299 LYS cc_start: 0.7902 (mttt) cc_final: 0.7592 (mttt) REVERT: B 301 LYS cc_start: 0.8179 (tptp) cc_final: 0.7942 (tppt) REVERT: B 328 ARG cc_start: 0.6453 (mmt-90) cc_final: 0.6086 (mmt-90) REVERT: B 329 LYS cc_start: 0.8729 (tttt) cc_final: 0.8339 (tttt) REVERT: B 368 MET cc_start: 0.7859 (mtm) cc_final: 0.7615 (mtm) REVERT: B 379 ASN cc_start: 0.7908 (OUTLIER) cc_final: 0.7485 (t0) REVERT: B 398 LYS cc_start: 0.8528 (ttpt) cc_final: 0.8111 (ttpp) REVERT: B 488 LYS cc_start: 0.8129 (ttpt) cc_final: 0.7906 (ttpt) REVERT: B 551 GLU cc_start: 0.7005 (mm-30) cc_final: 0.6669 (mm-30) REVERT: B 635 ILE cc_start: 0.8059 (mp) cc_final: 0.7707 (pt) REVERT: B 649 ASN cc_start: 0.8044 (m-40) cc_final: 0.7811 (m-40) REVERT: B 653 ASP cc_start: 0.7789 (t0) cc_final: 0.7147 (p0) REVERT: B 661 PHE cc_start: 0.8205 (p90) cc_final: 0.7673 (p90) REVERT: B 662 ARG cc_start: 0.7656 (ptm-80) cc_final: 0.7373 (ptm-80) REVERT: B 671 MET cc_start: 0.7189 (mmm) cc_final: 0.6867 (mmm) REVERT: B 673 ARG cc_start: 0.7638 (mtp85) cc_final: 0.6875 (ttm110) REVERT: B 676 TYR cc_start: 0.7300 (t80) cc_final: 0.7081 (t80) REVERT: B 680 VAL cc_start: 0.9004 (t) cc_final: 0.8790 (p) REVERT: B 690 GLU cc_start: 0.7241 (pt0) cc_final: 0.6695 (pt0) REVERT: B 698 ILE cc_start: 0.8571 (mm) cc_final: 0.8287 (mm) REVERT: B 714 GLN cc_start: 0.7850 (tp40) cc_final: 0.7528 (tm-30) REVERT: B 731 ASN cc_start: 0.5971 (t0) cc_final: 0.5729 (t0) REVERT: B 738 GLN cc_start: 0.7638 (mp10) cc_final: 0.7369 (mm110) REVERT: B 772 GLU cc_start: 0.7246 (tp30) cc_final: 0.6601 (tp30) REVERT: B 803 MET cc_start: 0.6536 (tmm) cc_final: 0.6335 (tmm) REVERT: B 806 PHE cc_start: 0.8407 (t80) cc_final: 0.7994 (t80) REVERT: B 817 ASP cc_start: 0.7672 (t0) cc_final: 0.7281 (t0) REVERT: B 835 GLU cc_start: 0.6660 (mt-10) cc_final: 0.6297 (mm-30) REVERT: B 857 THR cc_start: 0.8292 (m) cc_final: 0.8019 (p) REVERT: B 860 GLN cc_start: 0.8091 (mt0) cc_final: 0.7759 (mt0) REVERT: B 866 MET cc_start: 0.7171 (tpp) cc_final: 0.6831 (mpp) REVERT: B 957 GLU cc_start: 0.7355 (mm-30) cc_final: 0.7071 (mm-30) REVERT: B 999 MET cc_start: 0.7829 (mmm) cc_final: 0.7448 (mmm) REVERT: B 1035 GLN cc_start: 0.7927 (mm-40) cc_final: 0.6975 (mm-40) REVERT: B 1039 ASN cc_start: 0.7765 (m-40) cc_final: 0.6413 (m-40) REVERT: B 1043 GLU cc_start: 0.7620 (mt-10) cc_final: 0.6811 (mt-10) REVERT: B 1049 LEU cc_start: 0.8770 (tp) cc_final: 0.8520 (tt) REVERT: B 1062 SER cc_start: 0.8490 (t) cc_final: 0.7654 (p) REVERT: B 1076 GLU cc_start: 0.7238 (mt-10) cc_final: 0.6646 (mt-10) REVERT: B 1079 ILE cc_start: 0.9023 (mt) cc_final: 0.8736 (mm) REVERT: B 1096 GLN cc_start: 0.7810 (mm-40) cc_final: 0.7169 (mm-40) REVERT: B 1110 GLN cc_start: 0.8270 (tp-100) cc_final: 0.7759 (tp40) REVERT: B 1114 LYS cc_start: 0.8459 (mttm) cc_final: 0.8144 (tttm) REVERT: B 1116 ASN cc_start: 0.7749 (m-40) cc_final: 0.7444 (m-40) REVERT: B 1120 LYS cc_start: 0.8228 (mmmm) cc_final: 0.7763 (mttt) REVERT: B 1128 PHE cc_start: 0.7694 (t80) cc_final: 0.7483 (t80) REVERT: B 1147 TYR cc_start: 0.7747 (t80) cc_final: 0.7457 (t80) REVERT: B 1150 HIS cc_start: 0.7780 (m90) cc_final: 0.7424 (m-70) REVERT: B 1182 PHE cc_start: 0.7448 (m-10) cc_final: 0.7230 (m-10) REVERT: B 1187 ASN cc_start: 0.8296 (m-40) cc_final: 0.7477 (t0) REVERT: B 1198 TYR cc_start: 0.8153 (t80) cc_final: 0.7831 (t80) REVERT: F 87 TYR cc_start: 0.4499 (m-80) cc_final: 0.4241 (m-80) REVERT: C 24 ASP cc_start: 0.7483 (t0) cc_final: 0.7148 (t0) REVERT: C 88 ARG cc_start: 0.7635 (mtt90) cc_final: 0.7004 (mtt90) REVERT: C 108 LYS cc_start: 0.8068 (tttt) cc_final: 0.7314 (tttt) REVERT: C 200 LYS cc_start: 0.7833 (tptp) cc_final: 0.7420 (mptt) REVERT: C 206 ASP cc_start: 0.7339 (t70) cc_final: 0.6752 (p0) REVERT: C 234 THR cc_start: 0.7591 (p) cc_final: 0.7091 (t) REVERT: C 250 TYR cc_start: 0.7500 (t80) cc_final: 0.7160 (t80) REVERT: C 295 MET cc_start: 0.6922 (tpt) cc_final: 0.6629 (tpt) REVERT: C 301 LYS cc_start: 0.8583 (tptp) cc_final: 0.8223 (tppt) REVERT: C 313 GLU cc_start: 0.7379 (mm-30) cc_final: 0.7139 (mm-30) REVERT: C 329 LYS cc_start: 0.8719 (tttt) cc_final: 0.8250 (tttt) REVERT: C 344 LYS cc_start: 0.8440 (ptpt) cc_final: 0.7948 (ptpp) REVERT: C 379 ASN cc_start: 0.8259 (t0) cc_final: 0.7777 (t0) REVERT: C 405 ARG cc_start: 0.8112 (tpp-160) cc_final: 0.7480 (tpp80) REVERT: C 408 ASP cc_start: 0.7384 (m-30) cc_final: 0.7135 (m-30) REVERT: C 437 LEU cc_start: 0.8474 (mt) cc_final: 0.8263 (mt) REVERT: C 456 PHE cc_start: 0.7173 (m-80) cc_final: 0.6896 (m-80) REVERT: C 476 ASP cc_start: 0.7301 (m-30) cc_final: 0.6944 (m-30) REVERT: C 543 THR cc_start: 0.7959 (m) cc_final: 0.7759 (p) REVERT: C 581 ASP cc_start: 0.6515 (m-30) cc_final: 0.6240 (m-30) REVERT: C 635 ILE cc_start: 0.7890 (mp) cc_final: 0.7550 (pt) REVERT: C 644 TYR cc_start: 0.7703 (m-80) cc_final: 0.7422 (m-80) REVERT: C 653 ASP cc_start: 0.7902 (t0) cc_final: 0.7151 (p0) REVERT: C 663 ASP cc_start: 0.7395 (t0) cc_final: 0.7011 (t0) REVERT: C 671 MET cc_start: 0.7192 (mmm) cc_final: 0.6889 (mmm) REVERT: C 711 ARG cc_start: 0.8279 (mtm180) cc_final: 0.8065 (mtm-85) REVERT: C 731 ASN cc_start: 0.6156 (t0) cc_final: 0.5859 (t0) REVERT: C 738 GLN cc_start: 0.7697 (OUTLIER) cc_final: 0.7236 (mm110) REVERT: C 772 GLU cc_start: 0.7732 (tp30) cc_final: 0.6451 (tp30) REVERT: C 774 PHE cc_start: 0.8560 (m-80) cc_final: 0.7625 (m-80) REVERT: C 830 LYS cc_start: 0.8474 (mmmm) cc_final: 0.8238 (mmmm) REVERT: C 860 GLN cc_start: 0.8143 (mt0) cc_final: 0.7924 (mt0) REVERT: C 874 LYS cc_start: 0.8183 (mmtt) cc_final: 0.7851 (mmtt) REVERT: C 915 LYS cc_start: 0.8381 (mmmt) cc_final: 0.8019 (mmmt) REVERT: C 918 LEU cc_start: 0.7853 (mt) cc_final: 0.7550 (mm) REVERT: C 948 ILE cc_start: 0.7546 (OUTLIER) cc_final: 0.7314 (mm) REVERT: C 1009 ILE cc_start: 0.8502 (tp) cc_final: 0.7851 (tp) REVERT: C 1013 PHE cc_start: 0.8004 (m-80) cc_final: 0.7152 (m-80) REVERT: C 1039 ASN cc_start: 0.7541 (m-40) cc_final: 0.7311 (m-40) REVERT: C 1049 LEU cc_start: 0.8817 (tp) cc_final: 0.8496 (tt) REVERT: C 1067 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8476 (mm) REVERT: C 1069 ARG cc_start: 0.8140 (mtp180) cc_final: 0.7765 (ttm170) REVERT: C 1083 ILE cc_start: 0.8454 (mt) cc_final: 0.8109 (mm) REVERT: C 1096 GLN cc_start: 0.7817 (mt0) cc_final: 0.7135 (mm-40) REVERT: C 1120 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.7786 (mmtt) REVERT: C 1124 SER cc_start: 0.7851 (p) cc_final: 0.7549 (p) REVERT: C 1135 ILE cc_start: 0.8331 (mt) cc_final: 0.8131 (mp) REVERT: C 1157 LYS cc_start: 0.7884 (mmmt) cc_final: 0.7023 (mmmt) REVERT: H 33 TYR cc_start: 0.6104 (m-10) cc_final: 0.5890 (m-80) REVERT: H 111 MET cc_start: 0.5373 (tmm) cc_final: 0.4845 (tmm) REVERT: L 35 TRP cc_start: 0.7122 (m100) cc_final: 0.6774 (m100) REVERT: A 108 LYS cc_start: 0.8149 (tttt) cc_final: 0.7683 (tttt) REVERT: A 138 VAL cc_start: 0.8107 (t) cc_final: 0.7764 (p) REVERT: A 263 GLU cc_start: 0.6979 (pt0) cc_final: 0.6475 (pt0) REVERT: A 293 ASP cc_start: 0.8012 (p0) cc_final: 0.7729 (p0) REVERT: A 297 GLU cc_start: 0.7167 (tt0) cc_final: 0.6887 (tt0) REVERT: A 299 LYS cc_start: 0.8267 (mttt) cc_final: 0.8027 (mttp) REVERT: A 312 TYR cc_start: 0.7639 (m-80) cc_final: 0.7428 (m-80) REVERT: A 313 GLU cc_start: 0.7275 (mm-30) cc_final: 0.7011 (mm-30) REVERT: A 324 ASP cc_start: 0.7779 (p0) cc_final: 0.7098 (t70) REVERT: A 364 MET cc_start: 0.6977 (mmm) cc_final: 0.6205 (mmm) REVERT: A 368 MET cc_start: 0.7812 (mtm) cc_final: 0.6723 (mtm) REVERT: A 379 ASN cc_start: 0.7961 (t0) cc_final: 0.7651 (t0) REVERT: A 398 LYS cc_start: 0.8221 (ttpt) cc_final: 0.7886 (ttpp) REVERT: A 414 LEU cc_start: 0.7970 (OUTLIER) cc_final: 0.7725 (mp) REVERT: A 418 GLN cc_start: 0.7487 (tt0) cc_final: 0.7164 (tt0) REVERT: A 420 PHE cc_start: 0.7865 (m-10) cc_final: 0.7469 (m-10) REVERT: A 437 LEU cc_start: 0.7675 (mt) cc_final: 0.7207 (mp) REVERT: A 488 LYS cc_start: 0.8227 (tttt) cc_final: 0.7852 (ttpt) REVERT: A 543 THR cc_start: 0.7796 (m) cc_final: 0.7593 (p) REVERT: A 571 ARG cc_start: 0.8006 (mtp85) cc_final: 0.7768 (mtm-85) REVERT: A 585 GLN cc_start: 0.7659 (pt0) cc_final: 0.7435 (pt0) REVERT: A 612 LYS cc_start: 0.8306 (ptpp) cc_final: 0.7994 (ptpp) REVERT: A 624 ASN cc_start: 0.7508 (m-40) cc_final: 0.7122 (m-40) REVERT: A 631 LEU cc_start: 0.8388 (mt) cc_final: 0.8103 (tp) REVERT: A 644 TYR cc_start: 0.7713 (m-80) cc_final: 0.6967 (m-80) REVERT: A 649 ASN cc_start: 0.7684 (m-40) cc_final: 0.7274 (p0) REVERT: A 653 ASP cc_start: 0.7547 (p0) cc_final: 0.7295 (p0) REVERT: A 661 PHE cc_start: 0.8166 (p90) cc_final: 0.7784 (p90) REVERT: A 671 MET cc_start: 0.7279 (mmm) cc_final: 0.6706 (mmm) REVERT: A 702 TYR cc_start: 0.8505 (t80) cc_final: 0.8259 (t80) REVERT: A 707 ASN cc_start: 0.8005 (m110) cc_final: 0.7477 (m110) REVERT: A 725 CYS cc_start: 0.5011 (OUTLIER) cc_final: 0.4789 (t) REVERT: A 772 GLU cc_start: 0.7121 (tp30) cc_final: 0.6657 (tp30) REVERT: A 774 PHE cc_start: 0.8487 (m-80) cc_final: 0.8254 (m-80) REVERT: A 803 MET cc_start: 0.6418 (tmm) cc_final: 0.6136 (tmm) REVERT: A 838 SER cc_start: 0.8321 (t) cc_final: 0.7860 (t) REVERT: A 857 THR cc_start: 0.8373 (m) cc_final: 0.7984 (p) REVERT: A 860 GLN cc_start: 0.7956 (mt0) cc_final: 0.7441 (mt0) REVERT: A 909 GLU cc_start: 0.7192 (mt-10) cc_final: 0.6591 (mt-10) REVERT: A 911 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8474 (tt) REVERT: A 918 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7511 (tp) REVERT: A 923 PHE cc_start: 0.7980 (m-80) cc_final: 0.7318 (m-80) REVERT: A 938 ASP cc_start: 0.7405 (t0) cc_final: 0.7139 (t0) REVERT: A 957 GLU cc_start: 0.7071 (mm-30) cc_final: 0.6779 (mm-30) REVERT: A 1035 GLN cc_start: 0.7974 (mm-40) cc_final: 0.7015 (tp40) REVERT: A 1039 ASN cc_start: 0.7902 (m-40) cc_final: 0.7656 (m110) REVERT: A 1055 ARG cc_start: 0.7444 (ptp-170) cc_final: 0.6386 (mtm110) REVERT: A 1084 ASN cc_start: 0.8138 (t0) cc_final: 0.7881 (t0) REVERT: A 1120 LYS cc_start: 0.8248 (mmmm) cc_final: 0.7706 (mttt) REVERT: A 1177 PRO cc_start: 0.7858 (Cg_endo) cc_final: 0.7472 (Cg_exo) REVERT: A 1224 MET cc_start: 0.5309 (mpp) cc_final: 0.4988 (tpp) outliers start: 82 outliers final: 52 residues processed: 976 average time/residue: 0.2123 time to fit residues: 330.8247 Evaluate side-chains 978 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 917 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 379 ASN Chi-restraints excluded: chain B residue 615 THR Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 792 ILE Chi-restraints excluded: chain B residue 842 ASN Chi-restraints excluded: chain B residue 941 CYS Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1083 ILE Chi-restraints excluded: chain X residue 80 LEU Chi-restraints excluded: chain C residue 114 LYS Chi-restraints excluded: chain C residue 176 CYS Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 551 GLU Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain C residue 590 ASN Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 665 ILE Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 725 CYS Chi-restraints excluded: chain C residue 738 GLN Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain C residue 792 ILE Chi-restraints excluded: chain C residue 948 ILE Chi-restraints excluded: chain C residue 1067 LEU Chi-restraints excluded: chain C residue 1119 VAL Chi-restraints excluded: chain C residue 1120 LYS Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 390 CYS Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 483 CYS Chi-restraints excluded: chain A residue 484 PHE Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 665 ILE Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 802 ASN Chi-restraints excluded: chain A residue 805 GLU Chi-restraints excluded: chain A residue 849 GLU Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 999 MET Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1112 MET Chi-restraints excluded: chain A residue 1119 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 405 optimal weight: 3.9990 chunk 336 optimal weight: 0.9980 chunk 189 optimal weight: 4.9990 chunk 312 optimal weight: 3.9990 chunk 149 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 278 optimal weight: 10.0000 chunk 291 optimal weight: 0.0970 chunk 157 optimal weight: 20.0000 chunk 10 optimal weight: 5.9990 overall best weight: 1.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 453 ASN B 802 ASN B1041 ASN B1054 ASN ** B1134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 208 ASN C 573 GLN C 649 ASN C 707 ASN C 738 GLN C 844 ASN ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 928 ASN ** C1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 208 ASN A 280 GLN A 303 GLN A 573 GLN A 585 GLN A 731 ASN A 851 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.145943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.118103 restraints weight = 55295.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.122428 restraints weight = 27346.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.125257 restraints weight = 16346.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.127093 restraints weight = 11186.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.128295 restraints weight = 8543.062| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 33774 Z= 0.264 Angle : 0.682 19.984 46053 Z= 0.360 Chirality : 0.049 0.758 5196 Planarity : 0.005 0.059 5889 Dihedral : 5.456 73.256 4887 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.97 % Allowed : 18.80 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.13), residues: 4170 helix: 0.49 (0.18), residues: 816 sheet: -0.16 (0.16), residues: 1047 loop : -1.02 (0.13), residues: 2307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C1125 TYR 0.032 0.002 TYR C 68 PHE 0.028 0.002 PHE C 285 TRP 0.044 0.003 TRP F 94 HIS 0.012 0.001 HIS B1134 Details of bonding type rmsd covalent geometry : bond 0.00548 (33690) covalent geometry : angle 0.65451 (45870) SS BOND : bond 0.00795 ( 69) SS BOND : angle 2.06395 ( 138) hydrogen bonds : bond 0.04490 ( 1128) hydrogen bonds : angle 5.68478 ( 3162) link_NAG-ASN : bond 0.00740 ( 15) link_NAG-ASN : angle 5.12105 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1082 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 974 time to evaluate : 1.189 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: symmetry clash REVERT: Z 58 ASN cc_start: 0.7037 (t0) cc_final: 0.6452 (m-40) REVERT: Z 66 ARG cc_start: 0.7048 (ptm-80) cc_final: 0.6784 (ptm-80) REVERT: D 87 TYR cc_start: 0.5051 (m-80) cc_final: 0.4688 (m-80) REVERT: B 28 ASP cc_start: 0.7564 (t0) cc_final: 0.7241 (t0) REVERT: B 75 TYR cc_start: 0.8247 (m-80) cc_final: 0.7690 (m-80) REVERT: B 81 LYS cc_start: 0.7660 (tptp) cc_final: 0.7428 (tptp) REVERT: B 100 ILE cc_start: 0.8464 (mp) cc_final: 0.8169 (mm) REVERT: B 108 LYS cc_start: 0.8094 (tttt) cc_final: 0.7592 (tttt) REVERT: B 119 TYR cc_start: 0.6941 (m-80) cc_final: 0.6621 (m-80) REVERT: B 138 VAL cc_start: 0.7907 (t) cc_final: 0.7639 (p) REVERT: B 141 GLN cc_start: 0.6984 (OUTLIER) cc_final: 0.6613 (pm20) REVERT: B 234 THR cc_start: 0.7374 (p) cc_final: 0.6930 (t) REVERT: B 280 GLN cc_start: 0.7450 (mm-40) cc_final: 0.6979 (mm-40) REVERT: B 297 GLU cc_start: 0.7588 (tt0) cc_final: 0.6981 (tt0) REVERT: B 299 LYS cc_start: 0.8128 (mttt) cc_final: 0.7473 (ttmm) REVERT: B 301 LYS cc_start: 0.8201 (tptp) cc_final: 0.7958 (tptt) REVERT: B 329 LYS cc_start: 0.8731 (tttt) cc_final: 0.8391 (tttt) REVERT: B 364 MET cc_start: 0.6960 (OUTLIER) cc_final: 0.6269 (mmm) REVERT: B 368 MET cc_start: 0.7990 (mtm) cc_final: 0.7611 (mtm) REVERT: B 398 LYS cc_start: 0.8318 (ttpt) cc_final: 0.8067 (ttpp) REVERT: B 403 ASN cc_start: 0.8105 (t0) cc_final: 0.7720 (t0) REVERT: B 447 PHE cc_start: 0.7494 (m-10) cc_final: 0.7199 (m-10) REVERT: B 478 VAL cc_start: 0.8247 (p) cc_final: 0.7821 (m) REVERT: B 488 LYS cc_start: 0.8115 (ttpt) cc_final: 0.7861 (ttpt) REVERT: B 619 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8065 (tt) REVERT: B 635 ILE cc_start: 0.8173 (mp) cc_final: 0.7814 (pt) REVERT: B 661 PHE cc_start: 0.8098 (p90) cc_final: 0.7481 (p90) REVERT: B 671 MET cc_start: 0.7156 (mmm) cc_final: 0.6878 (mmm) REVERT: B 673 ARG cc_start: 0.7615 (mtp85) cc_final: 0.6958 (ttm110) REVERT: B 680 VAL cc_start: 0.9076 (t) cc_final: 0.8868 (p) REVERT: B 709 LEU cc_start: 0.8365 (mt) cc_final: 0.7776 (tt) REVERT: B 714 GLN cc_start: 0.7931 (tp40) cc_final: 0.7626 (tm-30) REVERT: B 731 ASN cc_start: 0.6196 (t0) cc_final: 0.5744 (t0) REVERT: B 807 ILE cc_start: 0.7870 (mt) cc_final: 0.7667 (mp) REVERT: B 817 ASP cc_start: 0.7781 (t0) cc_final: 0.7406 (t0) REVERT: B 835 GLU cc_start: 0.6836 (mt-10) cc_final: 0.6603 (mt-10) REVERT: B 860 GLN cc_start: 0.8056 (mt0) cc_final: 0.7697 (mt0) REVERT: B 866 MET cc_start: 0.7060 (tpp) cc_final: 0.6753 (mpp) REVERT: B 918 LEU cc_start: 0.7749 (mt) cc_final: 0.7513 (mp) REVERT: B 957 GLU cc_start: 0.7415 (mm-30) cc_final: 0.7152 (mm-30) REVERT: B 960 PHE cc_start: 0.8176 (OUTLIER) cc_final: 0.7843 (m-80) REVERT: B 1003 SER cc_start: 0.8788 (p) cc_final: 0.8586 (p) REVERT: B 1035 GLN cc_start: 0.8027 (mm-40) cc_final: 0.7146 (mm-40) REVERT: B 1039 ASN cc_start: 0.7801 (m-40) cc_final: 0.6388 (m-40) REVERT: B 1043 GLU cc_start: 0.7658 (mt-10) cc_final: 0.6913 (mt-10) REVERT: B 1049 LEU cc_start: 0.8779 (tp) cc_final: 0.8569 (tt) REVERT: B 1062 SER cc_start: 0.8572 (t) cc_final: 0.7769 (p) REVERT: B 1064 GLN cc_start: 0.7981 (tt0) cc_final: 0.7359 (tt0) REVERT: B 1069 ARG cc_start: 0.8447 (ttp-170) cc_final: 0.8247 (ttm-80) REVERT: B 1076 GLU cc_start: 0.7415 (mt-10) cc_final: 0.6834 (mt-10) REVERT: B 1096 GLN cc_start: 0.7904 (mm-40) cc_final: 0.7319 (mm-40) REVERT: B 1110 GLN cc_start: 0.8287 (tp-100) cc_final: 0.7771 (tp40) REVERT: B 1114 LYS cc_start: 0.8578 (mttm) cc_final: 0.8204 (tttm) REVERT: B 1120 LYS cc_start: 0.8387 (mmmm) cc_final: 0.8164 (mmmm) REVERT: B 1147 TYR cc_start: 0.7738 (t80) cc_final: 0.7516 (t80) REVERT: B 1150 HIS cc_start: 0.7694 (m90) cc_final: 0.7341 (m-70) REVERT: B 1182 PHE cc_start: 0.7325 (m-10) cc_final: 0.7092 (m-10) REVERT: B 1187 ASN cc_start: 0.8269 (m-40) cc_final: 0.7456 (t0) REVERT: X 34 TRP cc_start: 0.7410 (m100) cc_final: 0.6500 (m-90) REVERT: F 35 TRP cc_start: 0.7144 (m100) cc_final: 0.6887 (m100) REVERT: F 87 TYR cc_start: 0.4743 (m-80) cc_final: 0.4528 (m-80) REVERT: C 24 ASP cc_start: 0.7463 (t0) cc_final: 0.7145 (t0) REVERT: C 88 ARG cc_start: 0.7601 (mtt90) cc_final: 0.7031 (mtt90) REVERT: C 108 LYS cc_start: 0.8161 (tttt) cc_final: 0.7512 (tttt) REVERT: C 187 LEU cc_start: 0.7771 (tp) cc_final: 0.7212 (tt) REVERT: C 240 VAL cc_start: 0.8345 (t) cc_final: 0.8127 (p) REVERT: C 248 HIS cc_start: 0.7388 (m170) cc_final: 0.6866 (m170) REVERT: C 250 TYR cc_start: 0.7534 (t80) cc_final: 0.7160 (t80) REVERT: C 279 ASN cc_start: 0.7688 (p0) cc_final: 0.7443 (p0) REVERT: C 289 ASP cc_start: 0.7087 (t0) cc_final: 0.6726 (t0) REVERT: C 295 MET cc_start: 0.6914 (tpt) cc_final: 0.6425 (tpt) REVERT: C 299 LYS cc_start: 0.8293 (mttt) cc_final: 0.7780 (mttt) REVERT: C 301 LYS cc_start: 0.8646 (tptp) cc_final: 0.8137 (ttmm) REVERT: C 313 GLU cc_start: 0.7307 (mm-30) cc_final: 0.7086 (mm-30) REVERT: C 329 LYS cc_start: 0.8737 (tttt) cc_final: 0.8295 (tttt) REVERT: C 379 ASN cc_start: 0.8251 (t0) cc_final: 0.7789 (t0) REVERT: C 403 ASN cc_start: 0.7990 (t0) cc_final: 0.7704 (t0) REVERT: C 405 ARG cc_start: 0.8186 (tpp-160) cc_final: 0.7424 (tpp80) REVERT: C 408 ASP cc_start: 0.7377 (m-30) cc_final: 0.7078 (m-30) REVERT: C 433 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7730 (tp) REVERT: C 437 LEU cc_start: 0.8570 (mt) cc_final: 0.8278 (mt) REVERT: C 456 PHE cc_start: 0.7349 (m-80) cc_final: 0.7131 (m-10) REVERT: C 476 ASP cc_start: 0.7341 (m-30) cc_final: 0.7003 (m-30) REVERT: C 485 LYS cc_start: 0.7571 (ttmm) cc_final: 0.7323 (ttmm) REVERT: C 543 THR cc_start: 0.8052 (m) cc_final: 0.7745 (p) REVERT: C 581 ASP cc_start: 0.6647 (m-30) cc_final: 0.6429 (m-30) REVERT: C 612 LYS cc_start: 0.8143 (ptpp) cc_final: 0.5870 (mtmm) REVERT: C 644 TYR cc_start: 0.7768 (m-80) cc_final: 0.7489 (m-80) REVERT: C 653 ASP cc_start: 0.7949 (t0) cc_final: 0.7254 (p0) REVERT: C 663 ASP cc_start: 0.7556 (t0) cc_final: 0.7199 (t0) REVERT: C 709 LEU cc_start: 0.8117 (mm) cc_final: 0.6801 (mm) REVERT: C 731 ASN cc_start: 0.6321 (t0) cc_final: 0.5948 (t0) REVERT: C 817 ASP cc_start: 0.7689 (t0) cc_final: 0.7442 (t0) REVERT: C 830 LYS cc_start: 0.8475 (mmmm) cc_final: 0.8208 (mmmm) REVERT: C 860 GLN cc_start: 0.8202 (mt0) cc_final: 0.7953 (mt0) REVERT: C 874 LYS cc_start: 0.8307 (mmtt) cc_final: 0.7965 (mmtt) REVERT: C 915 LYS cc_start: 0.8458 (mmmt) cc_final: 0.8098 (mmmt) REVERT: C 918 LEU cc_start: 0.7888 (mt) cc_final: 0.7649 (mm) REVERT: C 948 ILE cc_start: 0.7620 (OUTLIER) cc_final: 0.7334 (mm) REVERT: C 949 LYS cc_start: 0.8030 (tppp) cc_final: 0.7765 (ttmm) REVERT: C 1009 ILE cc_start: 0.8526 (tp) cc_final: 0.7846 (tp) REVERT: C 1013 PHE cc_start: 0.8037 (m-80) cc_final: 0.7155 (m-80) REVERT: C 1039 ASN cc_start: 0.7616 (m-40) cc_final: 0.7346 (m-40) REVERT: C 1046 ASN cc_start: 0.7882 (t0) cc_final: 0.7647 (m-40) REVERT: C 1049 LEU cc_start: 0.8825 (tp) cc_final: 0.8565 (tt) REVERT: C 1055 ARG cc_start: 0.7739 (ptp-170) cc_final: 0.7294 (mtm110) REVERT: C 1067 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8567 (mm) REVERT: C 1069 ARG cc_start: 0.8181 (mtp180) cc_final: 0.7916 (mtp180) REVERT: C 1083 ILE cc_start: 0.8585 (mt) cc_final: 0.8299 (mm) REVERT: C 1096 GLN cc_start: 0.7773 (mt0) cc_final: 0.7524 (mm-40) REVERT: C 1116 ASN cc_start: 0.7753 (m-40) cc_final: 0.7339 (t0) REVERT: C 1124 SER cc_start: 0.7781 (p) cc_final: 0.7478 (p) REVERT: C 1135 ILE cc_start: 0.8338 (mt) cc_final: 0.7946 (mm) REVERT: L 35 TRP cc_start: 0.7211 (m100) cc_final: 0.6792 (m100) REVERT: A 28 ASP cc_start: 0.7845 (t0) cc_final: 0.7598 (t0) REVERT: A 108 LYS cc_start: 0.8173 (tttt) cc_final: 0.7662 (tttt) REVERT: A 138 VAL cc_start: 0.8131 (t) cc_final: 0.7818 (p) REVERT: A 165 GLN cc_start: 0.7399 (mt0) cc_final: 0.7140 (mt0) REVERT: A 248 HIS cc_start: 0.7408 (m170) cc_final: 0.7147 (m170) REVERT: A 259 LYS cc_start: 0.8722 (tppt) cc_final: 0.8333 (tppt) REVERT: A 297 GLU cc_start: 0.7119 (tt0) cc_final: 0.6838 (tt0) REVERT: A 312 TYR cc_start: 0.7716 (m-80) cc_final: 0.7443 (m-80) REVERT: A 313 GLU cc_start: 0.7396 (mm-30) cc_final: 0.7057 (mm-30) REVERT: A 328 ARG cc_start: 0.7270 (mmt-90) cc_final: 0.6969 (mmt-90) REVERT: A 379 ASN cc_start: 0.8013 (t0) cc_final: 0.7627 (t0) REVERT: A 414 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7976 (mp) REVERT: A 418 GLN cc_start: 0.7665 (tt0) cc_final: 0.7329 (tt0) REVERT: A 420 PHE cc_start: 0.7993 (m-10) cc_final: 0.7751 (m-10) REVERT: A 448 ASN cc_start: 0.8430 (OUTLIER) cc_final: 0.7915 (m-40) REVERT: A 476 ASP cc_start: 0.7212 (m-30) cc_final: 0.6828 (m-30) REVERT: A 543 THR cc_start: 0.7904 (m) cc_final: 0.7653 (p) REVERT: A 585 GLN cc_start: 0.7872 (pt0) cc_final: 0.7552 (pt0) REVERT: A 599 ASP cc_start: 0.7499 (m-30) cc_final: 0.6855 (t0) REVERT: A 631 LEU cc_start: 0.8516 (mt) cc_final: 0.8191 (tp) REVERT: A 644 TYR cc_start: 0.7849 (m-80) cc_final: 0.7124 (m-80) REVERT: A 649 ASN cc_start: 0.7821 (m-40) cc_final: 0.7331 (p0) REVERT: A 653 ASP cc_start: 0.7530 (p0) cc_final: 0.7216 (p0) REVERT: A 663 ASP cc_start: 0.7324 (t0) cc_final: 0.6855 (t0) REVERT: A 671 MET cc_start: 0.7053 (mmm) cc_final: 0.6600 (mmm) REVERT: A 702 TYR cc_start: 0.8638 (t80) cc_final: 0.8431 (t80) REVERT: A 707 ASN cc_start: 0.7979 (m110) cc_final: 0.7470 (m110) REVERT: A 772 GLU cc_start: 0.7136 (tp30) cc_final: 0.6616 (tp30) REVERT: A 774 PHE cc_start: 0.8475 (m-80) cc_final: 0.8141 (m-80) REVERT: A 803 MET cc_start: 0.6592 (OUTLIER) cc_final: 0.6325 (tmm) REVERT: A 817 ASP cc_start: 0.7536 (t0) cc_final: 0.7185 (t0) REVERT: A 938 ASP cc_start: 0.7580 (t0) cc_final: 0.7175 (t70) REVERT: A 949 LYS cc_start: 0.8243 (tppp) cc_final: 0.8005 (ttmm) REVERT: A 957 GLU cc_start: 0.7405 (mm-30) cc_final: 0.7073 (mm-30) REVERT: A 1035 GLN cc_start: 0.8061 (mm-40) cc_final: 0.7699 (tp40) REVERT: A 1055 ARG cc_start: 0.7771 (ptp-170) cc_final: 0.7276 (mtm110) REVERT: A 1084 ASN cc_start: 0.8208 (t0) cc_final: 0.7948 (t0) REVERT: A 1177 PRO cc_start: 0.8040 (Cg_endo) cc_final: 0.7634 (Cg_exo) REVERT: A 1191 TYR cc_start: 0.7868 (t80) cc_final: 0.7612 (t80) REVERT: A 1224 MET cc_start: 0.5337 (mpp) cc_final: 0.5000 (tpp) outliers start: 108 outliers final: 66 residues processed: 1019 average time/residue: 0.2115 time to fit residues: 344.0727 Evaluate side-chains 1022 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 946 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 585 GLN Chi-restraints excluded: chain B residue 615 THR Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 697 ASN Chi-restraints excluded: chain B residue 792 ILE Chi-restraints excluded: chain B residue 802 ASN Chi-restraints excluded: chain B residue 912 LEU Chi-restraints excluded: chain B residue 925 GLU Chi-restraints excluded: chain B residue 941 CYS Chi-restraints excluded: chain B residue 960 PHE Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1083 ILE Chi-restraints excluded: chain B residue 1124 SER Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 389 MET Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 665 ILE Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 725 CYS Chi-restraints excluded: chain C residue 792 ILE Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 844 ASN Chi-restraints excluded: chain C residue 948 ILE Chi-restraints excluded: chain C residue 960 PHE Chi-restraints excluded: chain C residue 1047 ASN Chi-restraints excluded: chain C residue 1067 LEU Chi-restraints excluded: chain C residue 1076 GLU Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 483 CYS Chi-restraints excluded: chain A residue 484 PHE Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 665 ILE Chi-restraints excluded: chain A residue 698 ILE Chi-restraints excluded: chain A residue 706 ASN Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 803 MET Chi-restraints excluded: chain A residue 849 GLU Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 960 PHE Chi-restraints excluded: chain A residue 999 MET Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1112 MET Chi-restraints excluded: chain A residue 1124 SER Chi-restraints excluded: chain A residue 1137 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 297 optimal weight: 10.0000 chunk 300 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 385 optimal weight: 6.9990 chunk 222 optimal weight: 3.9990 chunk 116 optimal weight: 0.1980 chunk 162 optimal weight: 6.9990 chunk 296 optimal weight: 4.9990 chunk 239 optimal weight: 1.9990 chunk 410 optimal weight: 3.9990 chunk 233 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 802 ASN ** B1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1054 ASN ** B1134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 573 GLN ** C 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1140 GLN A 280 GLN A 303 GLN A 731 ASN A 867 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.147124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.119377 restraints weight = 55334.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.123734 restraints weight = 27338.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.126581 restraints weight = 16330.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.128445 restraints weight = 11163.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.129666 restraints weight = 8490.739| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 33774 Z= 0.191 Angle : 0.652 18.340 46053 Z= 0.340 Chirality : 0.048 0.742 5196 Planarity : 0.004 0.061 5889 Dihedral : 5.227 64.197 4887 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.97 % Allowed : 19.79 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.13), residues: 4170 helix: 0.68 (0.19), residues: 792 sheet: -0.13 (0.16), residues: 1014 loop : -1.02 (0.13), residues: 2364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG X 66 TYR 0.033 0.002 TYR A 274 PHE 0.033 0.002 PHE C 285 TRP 0.036 0.002 TRP F 94 HIS 0.012 0.001 HIS B1134 Details of bonding type rmsd covalent geometry : bond 0.00407 (33690) covalent geometry : angle 0.62561 (45870) SS BOND : bond 0.00665 ( 69) SS BOND : angle 1.94013 ( 138) hydrogen bonds : bond 0.04072 ( 1128) hydrogen bonds : angle 5.56547 ( 3162) link_NAG-ASN : bond 0.00701 ( 15) link_NAG-ASN : angle 4.88808 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1060 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 952 time to evaluate : 1.158 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: symmetry clash REVERT: Z 66 ARG cc_start: 0.6797 (ptm-80) cc_final: 0.6556 (ptm-80) REVERT: D 87 TYR cc_start: 0.5033 (m-80) cc_final: 0.4639 (m-80) REVERT: D 89 GLN cc_start: 0.6910 (tm-30) cc_final: 0.6466 (tm-30) REVERT: B 43 VAL cc_start: 0.7244 (m) cc_final: 0.6897 (t) REVERT: B 75 TYR cc_start: 0.8254 (m-80) cc_final: 0.7705 (m-80) REVERT: B 100 ILE cc_start: 0.8450 (mp) cc_final: 0.8173 (mm) REVERT: B 108 LYS cc_start: 0.8072 (tttt) cc_final: 0.7639 (tttt) REVERT: B 138 VAL cc_start: 0.7903 (t) cc_final: 0.7632 (p) REVERT: B 141 GLN cc_start: 0.6946 (OUTLIER) cc_final: 0.6625 (pm20) REVERT: B 234 THR cc_start: 0.7364 (p) cc_final: 0.6929 (t) REVERT: B 280 GLN cc_start: 0.7381 (mm-40) cc_final: 0.7009 (mm110) REVERT: B 297 GLU cc_start: 0.7591 (tt0) cc_final: 0.7079 (tt0) REVERT: B 299 LYS cc_start: 0.8018 (mttt) cc_final: 0.7351 (ttmm) REVERT: B 301 LYS cc_start: 0.8182 (tptp) cc_final: 0.7936 (tptt) REVERT: B 317 TYR cc_start: 0.5765 (t80) cc_final: 0.5495 (t80) REVERT: B 329 LYS cc_start: 0.8725 (tttt) cc_final: 0.8358 (tttt) REVERT: B 368 MET cc_start: 0.7953 (mtm) cc_final: 0.7732 (mtm) REVERT: B 379 ASN cc_start: 0.8002 (t0) cc_final: 0.7675 (t0) REVERT: B 403 ASN cc_start: 0.8098 (t0) cc_final: 0.7696 (t0) REVERT: B 418 GLN cc_start: 0.7670 (tt0) cc_final: 0.7318 (tt0) REVERT: B 488 LYS cc_start: 0.8106 (ttpt) cc_final: 0.7844 (ttpt) REVERT: B 635 ILE cc_start: 0.8150 (mp) cc_final: 0.7825 (pt) REVERT: B 652 TYR cc_start: 0.8166 (m-80) cc_final: 0.7914 (m-80) REVERT: B 661 PHE cc_start: 0.8123 (p90) cc_final: 0.7574 (p90) REVERT: B 671 MET cc_start: 0.7176 (mmm) cc_final: 0.6855 (mmm) REVERT: B 673 ARG cc_start: 0.7596 (mtp85) cc_final: 0.6945 (ttm110) REVERT: B 680 VAL cc_start: 0.9056 (t) cc_final: 0.8825 (p) REVERT: B 714 GLN cc_start: 0.7924 (tp40) cc_final: 0.7636 (tm-30) REVERT: B 731 ASN cc_start: 0.6068 (t0) cc_final: 0.5757 (t0) REVERT: B 806 PHE cc_start: 0.8351 (t80) cc_final: 0.8083 (t80) REVERT: B 817 ASP cc_start: 0.7761 (t0) cc_final: 0.7387 (t0) REVERT: B 857 THR cc_start: 0.8296 (m) cc_final: 0.8015 (p) REVERT: B 860 GLN cc_start: 0.8035 (mt0) cc_final: 0.7666 (mt0) REVERT: B 918 LEU cc_start: 0.7784 (mt) cc_final: 0.7183 (mm) REVERT: B 946 LYS cc_start: 0.8504 (mmtm) cc_final: 0.8276 (mmtm) REVERT: B 954 LEU cc_start: 0.7904 (mt) cc_final: 0.7539 (mp) REVERT: B 957 GLU cc_start: 0.7397 (mm-30) cc_final: 0.7136 (mm-30) REVERT: B 960 PHE cc_start: 0.8149 (OUTLIER) cc_final: 0.7698 (m-80) REVERT: B 1003 SER cc_start: 0.8755 (p) cc_final: 0.8542 (p) REVERT: B 1021 GLN cc_start: 0.7331 (tp40) cc_final: 0.6997 (tp40) REVERT: B 1035 GLN cc_start: 0.7969 (mm-40) cc_final: 0.7149 (mm-40) REVERT: B 1039 ASN cc_start: 0.7759 (m-40) cc_final: 0.7467 (m-40) REVERT: B 1049 LEU cc_start: 0.8775 (tp) cc_final: 0.8564 (tt) REVERT: B 1062 SER cc_start: 0.8539 (t) cc_final: 0.7694 (p) REVERT: B 1064 GLN cc_start: 0.7949 (tt0) cc_final: 0.7322 (tt0) REVERT: B 1076 GLU cc_start: 0.7398 (mt-10) cc_final: 0.6825 (mt-10) REVERT: B 1083 ILE cc_start: 0.8771 (OUTLIER) cc_final: 0.8449 (mt) REVERT: B 1096 GLN cc_start: 0.7916 (mm-40) cc_final: 0.7314 (mm-40) REVERT: B 1110 GLN cc_start: 0.8283 (tp-100) cc_final: 0.7773 (tp40) REVERT: B 1114 LYS cc_start: 0.8557 (mttm) cc_final: 0.8171 (tttm) REVERT: B 1120 LYS cc_start: 0.8332 (mmmm) cc_final: 0.8073 (mmmm) REVERT: B 1134 HIS cc_start: 0.6637 (t-170) cc_final: 0.6239 (t-170) REVERT: B 1144 TYR cc_start: 0.6985 (m-80) cc_final: 0.6618 (m-80) REVERT: B 1147 TYR cc_start: 0.7744 (t80) cc_final: 0.7443 (t80) REVERT: B 1150 HIS cc_start: 0.7785 (m90) cc_final: 0.7389 (m-70) REVERT: B 1187 ASN cc_start: 0.8258 (m-40) cc_final: 0.7436 (t0) REVERT: X 34 TRP cc_start: 0.7385 (m100) cc_final: 0.6502 (m-10) REVERT: C 24 ASP cc_start: 0.7495 (t0) cc_final: 0.7161 (t0) REVERT: C 88 ARG cc_start: 0.7616 (mtt90) cc_final: 0.7158 (mtt90) REVERT: C 108 LYS cc_start: 0.8190 (tttt) cc_final: 0.7567 (tttt) REVERT: C 119 TYR cc_start: 0.6793 (m-80) cc_final: 0.6517 (m-80) REVERT: C 200 LYS cc_start: 0.7905 (tptp) cc_final: 0.7539 (mppt) REVERT: C 206 ASP cc_start: 0.7334 (t70) cc_final: 0.6801 (p0) REVERT: C 229 ASP cc_start: 0.6768 (p0) cc_final: 0.6085 (p0) REVERT: C 248 HIS cc_start: 0.7364 (m170) cc_final: 0.6813 (m170) REVERT: C 250 TYR cc_start: 0.7501 (t80) cc_final: 0.7149 (t80) REVERT: C 301 LYS cc_start: 0.8644 (tptp) cc_final: 0.8295 (tppt) REVERT: C 329 LYS cc_start: 0.8739 (tttt) cc_final: 0.8269 (tttt) REVERT: C 344 LYS cc_start: 0.8487 (ptpt) cc_final: 0.8025 (ptpp) REVERT: C 379 ASN cc_start: 0.8321 (t0) cc_final: 0.7832 (t0) REVERT: C 403 ASN cc_start: 0.8009 (t0) cc_final: 0.7630 (t0) REVERT: C 405 ARG cc_start: 0.8177 (tpp-160) cc_final: 0.7485 (tpp80) REVERT: C 408 ASP cc_start: 0.7392 (m-30) cc_final: 0.7136 (m-30) REVERT: C 437 LEU cc_start: 0.8579 (mt) cc_final: 0.8264 (mt) REVERT: C 455 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.7714 (ptm-80) REVERT: C 456 PHE cc_start: 0.7337 (m-80) cc_final: 0.7105 (m-10) REVERT: C 476 ASP cc_start: 0.7303 (m-30) cc_final: 0.6947 (m-30) REVERT: C 543 THR cc_start: 0.8051 (m) cc_final: 0.7756 (p) REVERT: C 581 ASP cc_start: 0.6627 (m-30) cc_final: 0.6386 (m-30) REVERT: C 644 TYR cc_start: 0.7742 (m-80) cc_final: 0.7460 (m-80) REVERT: C 653 ASP cc_start: 0.7957 (t0) cc_final: 0.7240 (p0) REVERT: C 663 ASP cc_start: 0.7517 (t0) cc_final: 0.7151 (t0) REVERT: C 671 MET cc_start: 0.6999 (mmm) cc_final: 0.6504 (mmm) REVERT: C 731 ASN cc_start: 0.6233 (t0) cc_final: 0.5958 (t0) REVERT: C 738 GLN cc_start: 0.7832 (mm110) cc_final: 0.7343 (mm110) REVERT: C 803 MET cc_start: 0.6584 (OUTLIER) cc_final: 0.6190 (tmm) REVERT: C 806 PHE cc_start: 0.8251 (t80) cc_final: 0.7825 (t80) REVERT: C 830 LYS cc_start: 0.8457 (mmmm) cc_final: 0.8199 (mmmm) REVERT: C 860 GLN cc_start: 0.8191 (mt0) cc_final: 0.7931 (mt0) REVERT: C 874 LYS cc_start: 0.8277 (mmtt) cc_final: 0.7932 (mmtt) REVERT: C 915 LYS cc_start: 0.8447 (mmmt) cc_final: 0.8079 (mmmt) REVERT: C 948 ILE cc_start: 0.7659 (OUTLIER) cc_final: 0.7344 (mm) REVERT: C 1009 ILE cc_start: 0.8562 (tp) cc_final: 0.7865 (tp) REVERT: C 1013 PHE cc_start: 0.8044 (m-80) cc_final: 0.7165 (m-80) REVERT: C 1039 ASN cc_start: 0.7631 (m-40) cc_final: 0.7334 (m-40) REVERT: C 1049 LEU cc_start: 0.8824 (tp) cc_final: 0.8524 (tt) REVERT: C 1055 ARG cc_start: 0.7675 (ptp-170) cc_final: 0.7227 (mtm110) REVERT: C 1083 ILE cc_start: 0.8553 (mt) cc_final: 0.8153 (mm) REVERT: C 1096 GLN cc_start: 0.7937 (mt0) cc_final: 0.7483 (mm-40) REVERT: C 1116 ASN cc_start: 0.7709 (m-40) cc_final: 0.7283 (t0) REVERT: C 1120 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.7986 (mmtp) REVERT: C 1124 SER cc_start: 0.7824 (p) cc_final: 0.7531 (p) REVERT: C 1135 ILE cc_start: 0.8256 (mt) cc_final: 0.8048 (mp) REVERT: C 1138 LEU cc_start: 0.7870 (mt) cc_final: 0.7649 (mm) REVERT: C 1157 LYS cc_start: 0.7942 (mmmt) cc_final: 0.7075 (mmmt) REVERT: H 33 TYR cc_start: 0.6495 (m-10) cc_final: 0.6191 (m-10) REVERT: L 35 TRP cc_start: 0.7198 (m100) cc_final: 0.6778 (m100) REVERT: A 28 ASP cc_start: 0.7921 (t0) cc_final: 0.7664 (t0) REVERT: A 108 LYS cc_start: 0.8152 (tttt) cc_final: 0.7692 (tttt) REVERT: A 138 VAL cc_start: 0.8091 (t) cc_final: 0.7794 (p) REVERT: A 200 LYS cc_start: 0.7828 (tptp) cc_final: 0.7356 (mppt) REVERT: A 248 HIS cc_start: 0.7331 (m170) cc_final: 0.7086 (m170) REVERT: A 259 LYS cc_start: 0.8733 (tppt) cc_final: 0.8327 (tppt) REVERT: A 297 GLU cc_start: 0.7174 (tt0) cc_final: 0.6785 (tt0) REVERT: A 299 LYS cc_start: 0.8413 (mttp) cc_final: 0.8131 (mttp) REVERT: A 313 GLU cc_start: 0.7401 (mm-30) cc_final: 0.7121 (mm-30) REVERT: A 314 LEU cc_start: 0.8297 (mt) cc_final: 0.7500 (mt) REVERT: A 379 ASN cc_start: 0.8055 (t0) cc_final: 0.7715 (t0) REVERT: A 418 GLN cc_start: 0.7677 (tt0) cc_final: 0.7260 (tt0) REVERT: A 423 ARG cc_start: 0.7944 (tpp-160) cc_final: 0.7737 (tpp-160) REVERT: A 448 ASN cc_start: 0.8435 (OUTLIER) cc_final: 0.8043 (m-40) REVERT: A 476 ASP cc_start: 0.7131 (m-30) cc_final: 0.6780 (m-30) REVERT: A 543 THR cc_start: 0.7860 (m) cc_final: 0.7645 (p) REVERT: A 585 GLN cc_start: 0.7966 (pt0) cc_final: 0.7492 (pm20) REVERT: A 631 LEU cc_start: 0.8448 (mt) cc_final: 0.8136 (tp) REVERT: A 644 TYR cc_start: 0.7821 (m-80) cc_final: 0.7115 (m-80) REVERT: A 649 ASN cc_start: 0.7806 (m-40) cc_final: 0.7406 (p0) REVERT: A 652 TYR cc_start: 0.8080 (m-80) cc_final: 0.7816 (m-80) REVERT: A 653 ASP cc_start: 0.7550 (p0) cc_final: 0.7216 (p0) REVERT: A 663 ASP cc_start: 0.7358 (t0) cc_final: 0.6902 (t0) REVERT: A 671 MET cc_start: 0.7067 (mmm) cc_final: 0.6606 (mmm) REVERT: A 707 ASN cc_start: 0.7933 (m110) cc_final: 0.7387 (m110) REVERT: A 772 GLU cc_start: 0.7158 (tp30) cc_final: 0.6627 (tp30) REVERT: A 774 PHE cc_start: 0.8438 (m-80) cc_final: 0.8170 (m-80) REVERT: A 817 ASP cc_start: 0.7584 (t0) cc_final: 0.7268 (t0) REVERT: A 860 GLN cc_start: 0.8041 (mt0) cc_final: 0.7526 (mt0) REVERT: A 866 MET cc_start: 0.7166 (tpp) cc_final: 0.6712 (mpp) REVERT: A 909 GLU cc_start: 0.7181 (mt-10) cc_final: 0.6529 (mt-10) REVERT: A 938 ASP cc_start: 0.7587 (t0) cc_final: 0.7213 (t70) REVERT: A 949 LYS cc_start: 0.8273 (tppp) cc_final: 0.8026 (ttmm) REVERT: A 957 GLU cc_start: 0.7410 (mm-30) cc_final: 0.7088 (mm-30) REVERT: A 973 PHE cc_start: 0.7845 (m-80) cc_final: 0.7502 (m-80) REVERT: A 1035 GLN cc_start: 0.8052 (mm-40) cc_final: 0.7677 (tp40) REVERT: A 1055 ARG cc_start: 0.7752 (ptp-170) cc_final: 0.7246 (mtm110) REVERT: A 1084 ASN cc_start: 0.8224 (t0) cc_final: 0.7954 (t0) REVERT: A 1120 LYS cc_start: 0.8390 (mmmm) cc_final: 0.8062 (mmmm) REVERT: A 1128 PHE cc_start: 0.7634 (t80) cc_final: 0.7192 (t80) REVERT: A 1177 PRO cc_start: 0.8103 (Cg_endo) cc_final: 0.7743 (Cg_exo) REVERT: A 1191 TYR cc_start: 0.7804 (t80) cc_final: 0.7594 (t80) REVERT: A 1224 MET cc_start: 0.5357 (mpp) cc_final: 0.5016 (tpp) outliers start: 108 outliers final: 71 residues processed: 1005 average time/residue: 0.2137 time to fit residues: 344.3352 Evaluate side-chains 1026 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 947 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 95 CYS Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 390 CYS Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 585 GLN Chi-restraints excluded: chain B residue 615 THR Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 792 ILE Chi-restraints excluded: chain B residue 802 ASN Chi-restraints excluded: chain B residue 842 ASN Chi-restraints excluded: chain B residue 960 PHE Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1083 ILE Chi-restraints excluded: chain B residue 1124 SER Chi-restraints excluded: chain X residue 7 TRP Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 353 GLU Chi-restraints excluded: chain C residue 455 ARG Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain C residue 665 ILE Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 698 ILE Chi-restraints excluded: chain C residue 725 CYS Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain C residue 792 ILE Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 803 MET Chi-restraints excluded: chain C residue 948 ILE Chi-restraints excluded: chain C residue 960 PHE Chi-restraints excluded: chain C residue 1047 ASN Chi-restraints excluded: chain C residue 1076 GLU Chi-restraints excluded: chain C residue 1082 LEU Chi-restraints excluded: chain C residue 1102 THR Chi-restraints excluded: chain C residue 1120 LYS Chi-restraints excluded: chain C residue 1194 SER Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 390 CYS Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 483 CYS Chi-restraints excluded: chain A residue 484 PHE Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 665 ILE Chi-restraints excluded: chain A residue 698 ILE Chi-restraints excluded: chain A residue 706 ASN Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 805 GLU Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 960 PHE Chi-restraints excluded: chain A residue 999 MET Chi-restraints excluded: chain A residue 1034 ILE Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1112 MET Chi-restraints excluded: chain A residue 1124 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 339 optimal weight: 0.8980 chunk 279 optimal weight: 3.9990 chunk 155 optimal weight: 7.9990 chunk 242 optimal weight: 0.7980 chunk 320 optimal weight: 3.9990 chunk 372 optimal weight: 1.9990 chunk 186 optimal weight: 3.9990 chunk 376 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 315 optimal weight: 4.9990 chunk 321 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 802 ASN ** B1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 573 GLN C 738 GLN C 844 ASN ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1035 GLN ** C1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 GLN A 303 GLN A 731 ASN A 867 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.147021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.119376 restraints weight = 55371.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.123742 restraints weight = 27362.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.126563 restraints weight = 16303.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.128425 restraints weight = 11162.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.129627 restraints weight = 8484.366| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.3903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 33774 Z= 0.214 Angle : 0.681 17.743 46053 Z= 0.356 Chirality : 0.048 0.700 5196 Planarity : 0.004 0.062 5889 Dihedral : 5.137 49.165 4887 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.72 % Allowed : 20.58 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.13), residues: 4170 helix: 0.56 (0.18), residues: 810 sheet: -0.13 (0.16), residues: 1017 loop : -1.06 (0.13), residues: 2343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 328 TYR 0.040 0.002 TYR C 274 PHE 0.030 0.002 PHE C 285 TRP 0.053 0.003 TRP D 94 HIS 0.010 0.001 HIS B 177 Details of bonding type rmsd covalent geometry : bond 0.00456 (33690) covalent geometry : angle 0.65516 (45870) SS BOND : bond 0.00753 ( 69) SS BOND : angle 2.12497 ( 138) hydrogen bonds : bond 0.04170 ( 1128) hydrogen bonds : angle 5.59761 ( 3162) link_NAG-ASN : bond 0.00702 ( 15) link_NAG-ASN : angle 4.88868 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1073 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 974 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 87 TYR cc_start: 0.5171 (m-80) cc_final: 0.4766 (m-80) REVERT: D 89 GLN cc_start: 0.6929 (tm-30) cc_final: 0.6480 (tm-30) REVERT: B 28 ASP cc_start: 0.7555 (t0) cc_final: 0.7178 (t0) REVERT: B 75 TYR cc_start: 0.8235 (m-80) cc_final: 0.7682 (m-80) REVERT: B 100 ILE cc_start: 0.8431 (mp) cc_final: 0.8153 (mm) REVERT: B 108 LYS cc_start: 0.8053 (tttt) cc_final: 0.7641 (tttt) REVERT: B 119 TYR cc_start: 0.6937 (m-80) cc_final: 0.6734 (m-80) REVERT: B 138 VAL cc_start: 0.7896 (t) cc_final: 0.7622 (p) REVERT: B 234 THR cc_start: 0.7376 (p) cc_final: 0.6918 (t) REVERT: B 259 LYS cc_start: 0.8699 (tppt) cc_final: 0.8352 (tppt) REVERT: B 280 GLN cc_start: 0.7393 (mm-40) cc_final: 0.7056 (mm110) REVERT: B 297 GLU cc_start: 0.7608 (tt0) cc_final: 0.7218 (tt0) REVERT: B 299 LYS cc_start: 0.8181 (mttt) cc_final: 0.7575 (ttmm) REVERT: B 301 LYS cc_start: 0.8202 (tptp) cc_final: 0.7945 (tptt) REVERT: B 329 LYS cc_start: 0.8725 (tttt) cc_final: 0.8353 (tttt) REVERT: B 367 LEU cc_start: 0.8574 (mt) cc_final: 0.8352 (mp) REVERT: B 368 MET cc_start: 0.7985 (mtm) cc_final: 0.7701 (mtm) REVERT: B 398 LYS cc_start: 0.8207 (ttpp) cc_final: 0.7999 (ttmt) REVERT: B 403 ASN cc_start: 0.8128 (t0) cc_final: 0.7660 (t0) REVERT: B 405 ARG cc_start: 0.8217 (tpp-160) cc_final: 0.7781 (tpp80) REVERT: B 418 GLN cc_start: 0.7725 (tt0) cc_final: 0.7327 (tt0) REVERT: B 488 LYS cc_start: 0.8106 (ttpt) cc_final: 0.7831 (ttpt) REVERT: B 635 ILE cc_start: 0.8130 (mp) cc_final: 0.7811 (pt) REVERT: B 648 GLN cc_start: 0.8118 (mp10) cc_final: 0.7659 (mp10) REVERT: B 671 MET cc_start: 0.7129 (mmm) cc_final: 0.6828 (mmm) REVERT: B 673 ARG cc_start: 0.7620 (mtp85) cc_final: 0.7007 (ttm110) REVERT: B 680 VAL cc_start: 0.9044 (t) cc_final: 0.8834 (p) REVERT: B 709 LEU cc_start: 0.8329 (mt) cc_final: 0.7753 (tt) REVERT: B 714 GLN cc_start: 0.7944 (tp40) cc_final: 0.7680 (tm-30) REVERT: B 731 ASN cc_start: 0.6116 (t0) cc_final: 0.5761 (t0) REVERT: B 751 ASP cc_start: 0.7629 (t0) cc_final: 0.7319 (t0) REVERT: B 817 ASP cc_start: 0.7711 (t0) cc_final: 0.7346 (t0) REVERT: B 857 THR cc_start: 0.8276 (m) cc_final: 0.8016 (p) REVERT: B 860 GLN cc_start: 0.8047 (mt0) cc_final: 0.7677 (mt0) REVERT: B 918 LEU cc_start: 0.7817 (mt) cc_final: 0.7238 (mm) REVERT: B 957 GLU cc_start: 0.7330 (mm-30) cc_final: 0.7064 (mm-30) REVERT: B 960 PHE cc_start: 0.8125 (OUTLIER) cc_final: 0.7880 (m-80) REVERT: B 999 MET cc_start: 0.7860 (mmm) cc_final: 0.7489 (mmt) REVERT: B 1021 GLN cc_start: 0.7359 (tp40) cc_final: 0.7034 (tp40) REVERT: B 1035 GLN cc_start: 0.7992 (mm-40) cc_final: 0.7095 (tp40) REVERT: B 1039 ASN cc_start: 0.7795 (m-40) cc_final: 0.7549 (m-40) REVERT: B 1049 LEU cc_start: 0.8770 (tp) cc_final: 0.8563 (tt) REVERT: B 1062 SER cc_start: 0.8571 (t) cc_final: 0.7689 (p) REVERT: B 1073 LEU cc_start: 0.8038 (pp) cc_final: 0.7282 (pp) REVERT: B 1076 GLU cc_start: 0.7459 (mt-10) cc_final: 0.6842 (mt-10) REVERT: B 1079 ILE cc_start: 0.9055 (mt) cc_final: 0.8814 (mm) REVERT: B 1083 ILE cc_start: 0.8759 (OUTLIER) cc_final: 0.8461 (mt) REVERT: B 1096 GLN cc_start: 0.7940 (mm-40) cc_final: 0.7688 (mm-40) REVERT: B 1110 GLN cc_start: 0.8312 (tp-100) cc_final: 0.7813 (tp40) REVERT: B 1114 LYS cc_start: 0.8498 (mttm) cc_final: 0.8215 (tttm) REVERT: B 1116 ASN cc_start: 0.7834 (m-40) cc_final: 0.7306 (t0) REVERT: B 1120 LYS cc_start: 0.8332 (mmmm) cc_final: 0.8086 (mmmm) REVERT: B 1144 TYR cc_start: 0.7077 (m-80) cc_final: 0.6755 (m-80) REVERT: B 1147 TYR cc_start: 0.7739 (t80) cc_final: 0.7486 (t80) REVERT: B 1150 HIS cc_start: 0.7785 (m90) cc_final: 0.7506 (m-70) REVERT: B 1157 LYS cc_start: 0.7871 (mmmt) cc_final: 0.7034 (mmmt) REVERT: B 1187 ASN cc_start: 0.8259 (m-40) cc_final: 0.7440 (t0) REVERT: F 89 GLN cc_start: 0.7215 (tm-30) cc_final: 0.7010 (tm-30) REVERT: C 88 ARG cc_start: 0.7643 (mtt90) cc_final: 0.7166 (mtt90) REVERT: C 108 LYS cc_start: 0.8210 (tttt) cc_final: 0.7661 (tttt) REVERT: C 119 TYR cc_start: 0.6803 (m-80) cc_final: 0.6530 (m-80) REVERT: C 200 LYS cc_start: 0.7922 (tptp) cc_final: 0.7535 (mppt) REVERT: C 206 ASP cc_start: 0.7268 (t70) cc_final: 0.6805 (p0) REVERT: C 229 ASP cc_start: 0.6883 (p0) cc_final: 0.6345 (p0) REVERT: C 240 VAL cc_start: 0.8324 (t) cc_final: 0.8087 (p) REVERT: C 248 HIS cc_start: 0.7393 (m170) cc_final: 0.6856 (m170) REVERT: C 250 TYR cc_start: 0.7516 (t80) cc_final: 0.7151 (t80) REVERT: C 299 LYS cc_start: 0.8350 (mttt) cc_final: 0.7955 (mttt) REVERT: C 301 LYS cc_start: 0.8658 (tptp) cc_final: 0.8097 (ttmm) REVERT: C 329 LYS cc_start: 0.8737 (tttt) cc_final: 0.8308 (tttt) REVERT: C 379 ASN cc_start: 0.8348 (t0) cc_final: 0.7836 (t0) REVERT: C 403 ASN cc_start: 0.8023 (t0) cc_final: 0.7689 (t0) REVERT: C 405 ARG cc_start: 0.8195 (tpp-160) cc_final: 0.7499 (tpp80) REVERT: C 408 ASP cc_start: 0.7406 (m-30) cc_final: 0.7148 (m-30) REVERT: C 437 LEU cc_start: 0.8573 (mt) cc_final: 0.8188 (mt) REVERT: C 455 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.7683 (ptm160) REVERT: C 456 PHE cc_start: 0.7336 (m-80) cc_final: 0.7023 (m-10) REVERT: C 476 ASP cc_start: 0.7287 (m-30) cc_final: 0.6842 (m-30) REVERT: C 485 LYS cc_start: 0.7532 (ttmm) cc_final: 0.7328 (ttmm) REVERT: C 488 LYS cc_start: 0.7964 (tppt) cc_final: 0.7757 (tppt) REVERT: C 543 THR cc_start: 0.8079 (m) cc_final: 0.7764 (p) REVERT: C 581 ASP cc_start: 0.6614 (m-30) cc_final: 0.6404 (m-30) REVERT: C 612 LYS cc_start: 0.8096 (ptpp) cc_final: 0.6484 (ttpp) REVERT: C 644 TYR cc_start: 0.7783 (m-80) cc_final: 0.7461 (m-80) REVERT: C 653 ASP cc_start: 0.7963 (t0) cc_final: 0.7394 (p0) REVERT: C 663 ASP cc_start: 0.7494 (t0) cc_final: 0.7152 (t0) REVERT: C 670 PHE cc_start: 0.8237 (m-80) cc_final: 0.7884 (m-10) REVERT: C 671 MET cc_start: 0.6959 (mmm) cc_final: 0.6453 (mmm) REVERT: C 731 ASN cc_start: 0.6286 (t0) cc_final: 0.6021 (t0) REVERT: C 772 GLU cc_start: 0.7711 (tp30) cc_final: 0.6983 (tp30) REVERT: C 803 MET cc_start: 0.6628 (OUTLIER) cc_final: 0.6191 (tmm) REVERT: C 817 ASP cc_start: 0.7665 (t0) cc_final: 0.7462 (t0) REVERT: C 830 LYS cc_start: 0.8440 (mmmm) cc_final: 0.8178 (mmmm) REVERT: C 854 LEU cc_start: 0.8075 (mt) cc_final: 0.7805 (mp) REVERT: C 860 GLN cc_start: 0.8225 (mt0) cc_final: 0.7919 (mt0) REVERT: C 874 LYS cc_start: 0.8321 (mmtt) cc_final: 0.7976 (mmtt) REVERT: C 915 LYS cc_start: 0.8440 (mmmt) cc_final: 0.8062 (mmmt) REVERT: C 948 ILE cc_start: 0.7684 (OUTLIER) cc_final: 0.7364 (mm) REVERT: C 949 LYS cc_start: 0.8032 (tppp) cc_final: 0.7718 (ttmm) REVERT: C 1009 ILE cc_start: 0.8574 (tp) cc_final: 0.7849 (tp) REVERT: C 1013 PHE cc_start: 0.8060 (m-80) cc_final: 0.7257 (m-80) REVERT: C 1039 ASN cc_start: 0.7629 (m-40) cc_final: 0.7334 (m-40) REVERT: C 1049 LEU cc_start: 0.8815 (tp) cc_final: 0.8574 (tt) REVERT: C 1055 ARG cc_start: 0.7683 (ptp-170) cc_final: 0.7248 (mtm110) REVERT: C 1083 ILE cc_start: 0.8543 (mt) cc_final: 0.8132 (mm) REVERT: C 1096 GLN cc_start: 0.7967 (mt0) cc_final: 0.7556 (mm-40) REVERT: C 1116 ASN cc_start: 0.7748 (m-40) cc_final: 0.7316 (t0) REVERT: C 1120 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.7745 (mmtt) REVERT: C 1124 SER cc_start: 0.7832 (p) cc_final: 0.7513 (p) REVERT: C 1157 LYS cc_start: 0.7951 (mmmt) cc_final: 0.7098 (mmmt) REVERT: H 33 TYR cc_start: 0.6530 (m-10) cc_final: 0.6211 (m-10) REVERT: L 35 TRP cc_start: 0.7205 (m100) cc_final: 0.6750 (m100) REVERT: A 24 ASP cc_start: 0.7054 (t0) cc_final: 0.6798 (t0) REVERT: A 28 ASP cc_start: 0.7914 (t0) cc_final: 0.7704 (t0) REVERT: A 108 LYS cc_start: 0.8130 (tttt) cc_final: 0.7711 (tttt) REVERT: A 111 LYS cc_start: 0.8417 (mmmt) cc_final: 0.8152 (mmtt) REVERT: A 138 VAL cc_start: 0.8089 (t) cc_final: 0.7779 (p) REVERT: A 200 LYS cc_start: 0.7822 (tptp) cc_final: 0.7384 (mppt) REVERT: A 259 LYS cc_start: 0.8761 (tppt) cc_final: 0.8373 (tppt) REVERT: A 297 GLU cc_start: 0.7141 (tt0) cc_final: 0.6877 (tt0) REVERT: A 299 LYS cc_start: 0.8460 (mttp) cc_final: 0.8194 (mttp) REVERT: A 313 GLU cc_start: 0.7373 (mm-30) cc_final: 0.7082 (mm-30) REVERT: A 314 LEU cc_start: 0.8281 (mt) cc_final: 0.7673 (mt) REVERT: A 379 ASN cc_start: 0.8017 (t0) cc_final: 0.7696 (t0) REVERT: A 418 GLN cc_start: 0.7556 (tt0) cc_final: 0.7213 (tt0) REVERT: A 448 ASN cc_start: 0.8420 (OUTLIER) cc_final: 0.8005 (m-40) REVERT: A 476 ASP cc_start: 0.7114 (m-30) cc_final: 0.6786 (m-30) REVERT: A 543 THR cc_start: 0.7861 (m) cc_final: 0.7621 (p) REVERT: A 585 GLN cc_start: 0.8031 (pt0) cc_final: 0.7458 (pm20) REVERT: A 644 TYR cc_start: 0.7846 (m-80) cc_final: 0.7144 (m-80) REVERT: A 649 ASN cc_start: 0.7884 (m-40) cc_final: 0.7433 (p0) REVERT: A 652 TYR cc_start: 0.8095 (m-80) cc_final: 0.7874 (m-80) REVERT: A 653 ASP cc_start: 0.7483 (p0) cc_final: 0.7144 (p0) REVERT: A 663 ASP cc_start: 0.7339 (t0) cc_final: 0.6848 (t0) REVERT: A 671 MET cc_start: 0.7031 (mmm) cc_final: 0.6576 (mmm) REVERT: A 702 TYR cc_start: 0.8543 (t80) cc_final: 0.8217 (t80) REVERT: A 707 ASN cc_start: 0.7868 (m110) cc_final: 0.7323 (m110) REVERT: A 772 GLU cc_start: 0.7159 (tp30) cc_final: 0.6621 (tp30) REVERT: A 774 PHE cc_start: 0.8408 (m-80) cc_final: 0.8109 (m-80) REVERT: A 860 GLN cc_start: 0.8028 (mt0) cc_final: 0.7485 (mt0) REVERT: A 866 MET cc_start: 0.7214 (tpp) cc_final: 0.6759 (tpp) REVERT: A 938 ASP cc_start: 0.7589 (t0) cc_final: 0.7253 (t70) REVERT: A 949 LYS cc_start: 0.8253 (tppp) cc_final: 0.8032 (ttmm) REVERT: A 957 GLU cc_start: 0.7457 (mm-30) cc_final: 0.7124 (mm-30) REVERT: A 973 PHE cc_start: 0.7876 (m-80) cc_final: 0.7521 (m-80) REVERT: A 1035 GLN cc_start: 0.8074 (mm-40) cc_final: 0.7676 (tp40) REVERT: A 1055 ARG cc_start: 0.7782 (ptp-170) cc_final: 0.7304 (mtm110) REVERT: A 1084 ASN cc_start: 0.8224 (t0) cc_final: 0.7969 (t0) REVERT: A 1128 PHE cc_start: 0.7692 (t80) cc_final: 0.7393 (t80) REVERT: A 1177 PRO cc_start: 0.8146 (Cg_endo) cc_final: 0.7778 (Cg_exo) REVERT: A 1191 TYR cc_start: 0.7837 (t80) cc_final: 0.7637 (t80) REVERT: A 1224 MET cc_start: 0.5369 (mpp) cc_final: 0.5018 (tpp) outliers start: 99 outliers final: 82 residues processed: 1017 average time/residue: 0.2145 time to fit residues: 346.5796 Evaluate side-chains 1047 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 958 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 95 CYS Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 390 CYS Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 615 THR Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 697 ASN Chi-restraints excluded: chain B residue 792 ILE Chi-restraints excluded: chain B residue 799 THR Chi-restraints excluded: chain B residue 800 ILE Chi-restraints excluded: chain B residue 802 ASN Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 960 PHE Chi-restraints excluded: chain B residue 1032 VAL Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1083 ILE Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain B residue 1124 SER Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 353 GLU Chi-restraints excluded: chain C residue 364 MET Chi-restraints excluded: chain C residue 455 ARG Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain C residue 665 ILE Chi-restraints excluded: chain C residue 694 LEU Chi-restraints excluded: chain C residue 698 ILE Chi-restraints excluded: chain C residue 725 CYS Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain C residue 792 ILE Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 803 MET Chi-restraints excluded: chain C residue 839 PHE Chi-restraints excluded: chain C residue 844 ASN Chi-restraints excluded: chain C residue 948 ILE Chi-restraints excluded: chain C residue 960 PHE Chi-restraints excluded: chain C residue 1047 ASN Chi-restraints excluded: chain C residue 1067 LEU Chi-restraints excluded: chain C residue 1076 GLU Chi-restraints excluded: chain C residue 1082 LEU Chi-restraints excluded: chain C residue 1102 THR Chi-restraints excluded: chain C residue 1118 CYS Chi-restraints excluded: chain C residue 1120 LYS Chi-restraints excluded: chain C residue 1194 SER Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 390 CYS Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 483 CYS Chi-restraints excluded: chain A residue 484 PHE Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 665 ILE Chi-restraints excluded: chain A residue 698 ILE Chi-restraints excluded: chain A residue 706 ASN Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 805 GLU Chi-restraints excluded: chain A residue 849 GLU Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 960 PHE Chi-restraints excluded: chain A residue 999 MET Chi-restraints excluded: chain A residue 1034 ILE Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1112 MET Chi-restraints excluded: chain A residue 1124 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 191 optimal weight: 2.9990 chunk 369 optimal weight: 3.9990 chunk 18 optimal weight: 8.9990 chunk 87 optimal weight: 0.9980 chunk 77 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 190 optimal weight: 1.9990 chunk 21 optimal weight: 0.4980 chunk 256 optimal weight: 4.9990 chunk 240 optimal weight: 0.8980 chunk 172 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 248 HIS B 590 ASN B 802 ASN ** B1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN C 573 GLN C 844 ASN ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 GLN A 303 GLN A 475 HIS A 731 ASN ** A1134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.148864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.121076 restraints weight = 54949.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.125520 restraints weight = 26867.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.128398 restraints weight = 15901.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.130291 restraints weight = 10834.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.131530 restraints weight = 8212.366| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.3968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 33774 Z= 0.144 Angle : 0.655 16.562 46053 Z= 0.340 Chirality : 0.047 0.672 5196 Planarity : 0.004 0.064 5889 Dihedral : 4.884 39.725 4887 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.78 % Allowed : 20.99 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.13), residues: 4170 helix: 0.71 (0.18), residues: 795 sheet: -0.07 (0.16), residues: 1008 loop : -1.05 (0.13), residues: 2367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG Z 66 TYR 0.045 0.002 TYR C 68 PHE 0.033 0.002 PHE B1182 TRP 0.055 0.002 TRP D 94 HIS 0.024 0.002 HIS A1134 Details of bonding type rmsd covalent geometry : bond 0.00317 (33690) covalent geometry : angle 0.62816 (45870) SS BOND : bond 0.00670 ( 69) SS BOND : angle 2.11775 ( 138) hydrogen bonds : bond 0.03873 ( 1128) hydrogen bonds : angle 5.48524 ( 3162) link_NAG-ASN : bond 0.00703 ( 15) link_NAG-ASN : angle 4.74709 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1063 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 962 time to evaluate : 1.159 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: Z 7 TRP cc_start: 0.7943 (p-90) cc_final: 0.7598 (p90) REVERT: D 87 TYR cc_start: 0.5108 (m-80) cc_final: 0.4681 (m-80) REVERT: D 89 GLN cc_start: 0.6913 (tm-30) cc_final: 0.6418 (tm-30) REVERT: B 47 LEU cc_start: 0.8594 (tp) cc_final: 0.7814 (pp) REVERT: B 68 TYR cc_start: 0.7212 (m-80) cc_final: 0.6899 (m-80) REVERT: B 75 TYR cc_start: 0.8222 (m-80) cc_final: 0.7633 (m-80) REVERT: B 100 ILE cc_start: 0.8436 (mp) cc_final: 0.8149 (mm) REVERT: B 108 LYS cc_start: 0.8065 (tttt) cc_final: 0.7635 (tttt) REVERT: B 119 TYR cc_start: 0.6888 (m-80) cc_final: 0.6583 (m-80) REVERT: B 138 VAL cc_start: 0.7881 (t) cc_final: 0.7585 (p) REVERT: B 141 GLN cc_start: 0.6920 (OUTLIER) cc_final: 0.6690 (pm20) REVERT: B 234 THR cc_start: 0.7378 (p) cc_final: 0.6935 (t) REVERT: B 259 LYS cc_start: 0.8687 (tppt) cc_final: 0.8333 (tppt) REVERT: B 280 GLN cc_start: 0.7395 (mm-40) cc_final: 0.7043 (mm110) REVERT: B 297 GLU cc_start: 0.7574 (tt0) cc_final: 0.7135 (tt0) REVERT: B 299 LYS cc_start: 0.8095 (mttt) cc_final: 0.7497 (ttmm) REVERT: B 301 LYS cc_start: 0.8200 (tptp) cc_final: 0.7896 (tptt) REVERT: B 329 LYS cc_start: 0.8722 (tttt) cc_final: 0.8334 (tttt) REVERT: B 368 MET cc_start: 0.7987 (mtm) cc_final: 0.7702 (mtm) REVERT: B 398 LYS cc_start: 0.8226 (ttpp) cc_final: 0.7986 (ttmt) REVERT: B 403 ASN cc_start: 0.8108 (t0) cc_final: 0.7629 (t0) REVERT: B 405 ARG cc_start: 0.8212 (tpp-160) cc_final: 0.7771 (tpp80) REVERT: B 418 GLN cc_start: 0.7711 (tt0) cc_final: 0.7230 (tt0) REVERT: B 488 LYS cc_start: 0.8078 (ttpt) cc_final: 0.7817 (ttpt) REVERT: B 635 ILE cc_start: 0.8079 (mp) cc_final: 0.7745 (pt) REVERT: B 648 GLN cc_start: 0.7983 (mp10) cc_final: 0.7515 (mp10) REVERT: B 673 ARG cc_start: 0.7616 (mtp85) cc_final: 0.7009 (ttm110) REVERT: B 680 VAL cc_start: 0.9030 (t) cc_final: 0.8807 (p) REVERT: B 701 ASN cc_start: 0.7998 (t0) cc_final: 0.7656 (t0) REVERT: B 709 LEU cc_start: 0.8282 (mt) cc_final: 0.7694 (tt) REVERT: B 714 GLN cc_start: 0.7950 (tp40) cc_final: 0.7661 (tm-30) REVERT: B 731 ASN cc_start: 0.5931 (t0) cc_final: 0.5616 (t0) REVERT: B 751 ASP cc_start: 0.7658 (t0) cc_final: 0.7330 (t0) REVERT: B 803 MET cc_start: 0.6256 (tmm) cc_final: 0.5968 (tmm) REVERT: B 817 ASP cc_start: 0.7688 (t0) cc_final: 0.7289 (t0) REVERT: B 857 THR cc_start: 0.8275 (m) cc_final: 0.7996 (p) REVERT: B 860 GLN cc_start: 0.8023 (mt0) cc_final: 0.7640 (mt0) REVERT: B 866 MET cc_start: 0.7136 (tpp) cc_final: 0.6781 (mpp) REVERT: B 918 LEU cc_start: 0.7777 (mt) cc_final: 0.7137 (mm) REVERT: B 954 LEU cc_start: 0.7881 (mt) cc_final: 0.7476 (mp) REVERT: B 957 GLU cc_start: 0.7402 (mm-30) cc_final: 0.7106 (mm-30) REVERT: B 960 PHE cc_start: 0.8120 (OUTLIER) cc_final: 0.7856 (m-80) REVERT: B 1021 GLN cc_start: 0.7262 (tp40) cc_final: 0.6939 (tp40) REVERT: B 1035 GLN cc_start: 0.7986 (mm-40) cc_final: 0.6963 (tp40) REVERT: B 1049 LEU cc_start: 0.8767 (tp) cc_final: 0.8553 (tt) REVERT: B 1062 SER cc_start: 0.8533 (t) cc_final: 0.7624 (p) REVERT: B 1073 LEU cc_start: 0.8093 (pp) cc_final: 0.7412 (pt) REVERT: B 1076 GLU cc_start: 0.7443 (mt-10) cc_final: 0.6805 (mt-10) REVERT: B 1079 ILE cc_start: 0.9010 (mt) cc_final: 0.8790 (mm) REVERT: B 1083 ILE cc_start: 0.8708 (OUTLIER) cc_final: 0.8402 (mt) REVERT: B 1096 GLN cc_start: 0.8027 (mm-40) cc_final: 0.7547 (mm-40) REVERT: B 1110 GLN cc_start: 0.8282 (tp-100) cc_final: 0.7825 (tp40) REVERT: B 1114 LYS cc_start: 0.8455 (mttm) cc_final: 0.8096 (tttm) REVERT: B 1116 ASN cc_start: 0.7788 (m-40) cc_final: 0.7261 (t0) REVERT: B 1120 LYS cc_start: 0.8254 (mmmm) cc_final: 0.8025 (mmmm) REVERT: B 1144 TYR cc_start: 0.6939 (m-80) cc_final: 0.6616 (m-80) REVERT: B 1150 HIS cc_start: 0.7810 (m90) cc_final: 0.7406 (m-70) REVERT: B 1153 TYR cc_start: 0.7350 (t80) cc_final: 0.6837 (t80) REVERT: B 1157 LYS cc_start: 0.7830 (mmmt) cc_final: 0.7003 (mmmt) REVERT: B 1182 PHE cc_start: 0.7311 (m-10) cc_final: 0.7003 (m-10) REVERT: B 1187 ASN cc_start: 0.8234 (m-40) cc_final: 0.7404 (t0) REVERT: X 66 ARG cc_start: 0.6946 (ptm-80) cc_final: 0.6205 (ttp80) REVERT: F 35 TRP cc_start: 0.7046 (m100) cc_final: 0.6819 (m100) REVERT: C 88 ARG cc_start: 0.7633 (mtt90) cc_final: 0.7160 (mtt90) REVERT: C 108 LYS cc_start: 0.8182 (tttt) cc_final: 0.7624 (tttt) REVERT: C 200 LYS cc_start: 0.7880 (tptp) cc_final: 0.7489 (mppt) REVERT: C 206 ASP cc_start: 0.7188 (t70) cc_final: 0.6774 (p0) REVERT: C 229 ASP cc_start: 0.6867 (p0) cc_final: 0.6335 (p0) REVERT: C 248 HIS cc_start: 0.7354 (m170) cc_final: 0.6840 (m170) REVERT: C 250 TYR cc_start: 0.7451 (t80) cc_final: 0.7116 (t80) REVERT: C 295 MET cc_start: 0.6902 (tpt) cc_final: 0.6445 (tpt) REVERT: C 297 GLU cc_start: 0.6874 (OUTLIER) cc_final: 0.6607 (mm-30) REVERT: C 299 LYS cc_start: 0.8289 (mttt) cc_final: 0.7843 (mttt) REVERT: C 301 LYS cc_start: 0.8665 (tptp) cc_final: 0.8227 (ttmt) REVERT: C 329 LYS cc_start: 0.8750 (tttt) cc_final: 0.8279 (tttt) REVERT: C 379 ASN cc_start: 0.8273 (t0) cc_final: 0.7866 (t0) REVERT: C 403 ASN cc_start: 0.8002 (t0) cc_final: 0.7647 (t0) REVERT: C 405 ARG cc_start: 0.8170 (tpp-160) cc_final: 0.7476 (tpp80) REVERT: C 408 ASP cc_start: 0.7419 (m-30) cc_final: 0.7175 (m-30) REVERT: C 437 LEU cc_start: 0.8582 (mt) cc_final: 0.8225 (mt) REVERT: C 455 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.7672 (ptm160) REVERT: C 456 PHE cc_start: 0.7245 (m-80) cc_final: 0.6924 (m-10) REVERT: C 485 LYS cc_start: 0.7493 (ttmm) cc_final: 0.7277 (ttmm) REVERT: C 488 LYS cc_start: 0.8035 (tppt) cc_final: 0.7695 (tppt) REVERT: C 543 THR cc_start: 0.8098 (m) cc_final: 0.7793 (p) REVERT: C 581 ASP cc_start: 0.6609 (m-30) cc_final: 0.6319 (m-30) REVERT: C 612 LYS cc_start: 0.8078 (ptpp) cc_final: 0.5671 (mtmm) REVERT: C 644 TYR cc_start: 0.7698 (m-80) cc_final: 0.7407 (m-80) REVERT: C 653 ASP cc_start: 0.7945 (t0) cc_final: 0.7349 (p0) REVERT: C 670 PHE cc_start: 0.8187 (m-80) cc_final: 0.7863 (m-10) REVERT: C 671 MET cc_start: 0.6902 (mmm) cc_final: 0.6578 (mmm) REVERT: C 723 LEU cc_start: 0.8696 (mm) cc_final: 0.8426 (mt) REVERT: C 731 ASN cc_start: 0.6247 (t0) cc_final: 0.5986 (t0) REVERT: C 738 GLN cc_start: 0.7554 (mm110) cc_final: 0.7069 (mm110) REVERT: C 772 GLU cc_start: 0.7645 (tp30) cc_final: 0.6321 (tp30) REVERT: C 803 MET cc_start: 0.6607 (OUTLIER) cc_final: 0.6157 (tmm) REVERT: C 817 ASP cc_start: 0.7611 (t0) cc_final: 0.7401 (t0) REVERT: C 830 LYS cc_start: 0.8427 (mmmm) cc_final: 0.8164 (mmmm) REVERT: C 860 GLN cc_start: 0.8214 (mt0) cc_final: 0.7921 (mt0) REVERT: C 874 LYS cc_start: 0.8237 (mmtt) cc_final: 0.7897 (mmtt) REVERT: C 915 LYS cc_start: 0.8417 (mmmt) cc_final: 0.8030 (mmmt) REVERT: C 948 ILE cc_start: 0.7621 (OUTLIER) cc_final: 0.7365 (mm) REVERT: C 949 LYS cc_start: 0.7907 (tppp) cc_final: 0.7589 (ttmm) REVERT: C 954 LEU cc_start: 0.7909 (mt) cc_final: 0.7688 (mm) REVERT: C 999 MET cc_start: 0.7808 (mmm) cc_final: 0.7607 (mmt) REVERT: C 1009 ILE cc_start: 0.8557 (tp) cc_final: 0.7820 (tp) REVERT: C 1013 PHE cc_start: 0.8011 (m-80) cc_final: 0.7243 (m-80) REVERT: C 1049 LEU cc_start: 0.8801 (tp) cc_final: 0.8568 (tt) REVERT: C 1083 ILE cc_start: 0.8542 (mt) cc_final: 0.8159 (mm) REVERT: C 1096 GLN cc_start: 0.7894 (mt0) cc_final: 0.7631 (mm-40) REVERT: C 1116 ASN cc_start: 0.7798 (m-40) cc_final: 0.7329 (t0) REVERT: C 1124 SER cc_start: 0.7814 (p) cc_final: 0.7508 (p) REVERT: C 1157 LYS cc_start: 0.7925 (mmmt) cc_final: 0.7086 (mmmt) REVERT: H 33 TYR cc_start: 0.6459 (m-10) cc_final: 0.6117 (m-10) REVERT: L 35 TRP cc_start: 0.7193 (m100) cc_final: 0.6728 (m100) REVERT: A 24 ASP cc_start: 0.7158 (t0) cc_final: 0.6938 (t0) REVERT: A 28 ASP cc_start: 0.7890 (t0) cc_final: 0.7670 (t0) REVERT: A 108 LYS cc_start: 0.8120 (tttt) cc_final: 0.7715 (tttt) REVERT: A 111 LYS cc_start: 0.8479 (mmmt) cc_final: 0.8097 (mmtt) REVERT: A 138 VAL cc_start: 0.8066 (t) cc_final: 0.7724 (p) REVERT: A 184 ARG cc_start: 0.6471 (mtt180) cc_final: 0.6227 (mmt90) REVERT: A 259 LYS cc_start: 0.8734 (tppt) cc_final: 0.8347 (tppt) REVERT: A 297 GLU cc_start: 0.7111 (tt0) cc_final: 0.6873 (tt0) REVERT: A 313 GLU cc_start: 0.7373 (mm-30) cc_final: 0.7099 (mm-30) REVERT: A 314 LEU cc_start: 0.8259 (mt) cc_final: 0.7689 (mt) REVERT: A 368 MET cc_start: 0.7765 (mtm) cc_final: 0.7213 (mtm) REVERT: A 379 ASN cc_start: 0.8024 (t0) cc_final: 0.7709 (t0) REVERT: A 382 ASP cc_start: 0.7586 (p0) cc_final: 0.7270 (m-30) REVERT: A 418 GLN cc_start: 0.7518 (tt0) cc_final: 0.7179 (tt0) REVERT: A 448 ASN cc_start: 0.8449 (OUTLIER) cc_final: 0.7970 (m110) REVERT: A 476 ASP cc_start: 0.7084 (m-30) cc_final: 0.6738 (m-30) REVERT: A 585 GLN cc_start: 0.8090 (pt0) cc_final: 0.7508 (pm20) REVERT: A 587 ASP cc_start: 0.6282 (p0) cc_final: 0.5968 (t0) REVERT: A 644 TYR cc_start: 0.7834 (m-80) cc_final: 0.7139 (m-80) REVERT: A 649 ASN cc_start: 0.7811 (m-40) cc_final: 0.7400 (p0) REVERT: A 652 TYR cc_start: 0.8059 (m-80) cc_final: 0.7808 (m-80) REVERT: A 653 ASP cc_start: 0.7439 (p0) cc_final: 0.7117 (p0) REVERT: A 663 ASP cc_start: 0.7315 (t0) cc_final: 0.6797 (t0) REVERT: A 671 MET cc_start: 0.6998 (mmm) cc_final: 0.6550 (mmm) REVERT: A 707 ASN cc_start: 0.7797 (m110) cc_final: 0.7254 (m110) REVERT: A 723 LEU cc_start: 0.8645 (mm) cc_final: 0.8340 (mm) REVERT: A 725 CYS cc_start: 0.5184 (OUTLIER) cc_final: 0.4730 (t) REVERT: A 772 GLU cc_start: 0.7171 (tp30) cc_final: 0.6639 (tp30) REVERT: A 774 PHE cc_start: 0.8391 (m-80) cc_final: 0.8103 (m-80) REVERT: A 860 GLN cc_start: 0.7982 (mt0) cc_final: 0.7483 (mt0) REVERT: A 866 MET cc_start: 0.7183 (tpp) cc_final: 0.6628 (tpp) REVERT: A 918 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7716 (tp) REVERT: A 938 ASP cc_start: 0.7638 (t0) cc_final: 0.7124 (t70) REVERT: A 957 GLU cc_start: 0.7415 (mm-30) cc_final: 0.7097 (mm-30) REVERT: A 973 PHE cc_start: 0.7834 (m-80) cc_final: 0.7465 (m-80) REVERT: A 1035 GLN cc_start: 0.8059 (mm-40) cc_final: 0.7551 (tp40) REVERT: A 1038 VAL cc_start: 0.8777 (t) cc_final: 0.8525 (p) REVERT: A 1055 ARG cc_start: 0.7678 (ptp-170) cc_final: 0.7214 (mtm110) REVERT: A 1084 ASN cc_start: 0.8223 (t0) cc_final: 0.7956 (t0) REVERT: A 1128 PHE cc_start: 0.7725 (t80) cc_final: 0.7441 (t80) REVERT: A 1177 PRO cc_start: 0.8108 (Cg_endo) cc_final: 0.7733 (Cg_exo) REVERT: A 1224 MET cc_start: 0.5343 (mpp) cc_final: 0.5014 (tpp) outliers start: 101 outliers final: 70 residues processed: 1008 average time/residue: 0.2133 time to fit residues: 344.3415 Evaluate side-chains 1025 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 945 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 95 CYS Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 390 CYS Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 615 THR Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain B residue 792 ILE Chi-restraints excluded: chain B residue 805 GLU Chi-restraints excluded: chain B residue 839 PHE Chi-restraints excluded: chain B residue 960 PHE Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1083 ILE Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain B residue 1124 SER Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 353 GLU Chi-restraints excluded: chain C residue 364 MET Chi-restraints excluded: chain C residue 455 ARG Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain C residue 665 ILE Chi-restraints excluded: chain C residue 680 VAL Chi-restraints excluded: chain C residue 698 ILE Chi-restraints excluded: chain C residue 700 CYS Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain C residue 792 ILE Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 803 MET Chi-restraints excluded: chain C residue 839 PHE Chi-restraints excluded: chain C residue 948 ILE Chi-restraints excluded: chain C residue 960 PHE Chi-restraints excluded: chain C residue 1047 ASN Chi-restraints excluded: chain C residue 1082 LEU Chi-restraints excluded: chain C residue 1102 THR Chi-restraints excluded: chain C residue 1194 SER Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 390 CYS Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 483 CYS Chi-restraints excluded: chain A residue 484 PHE Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 665 ILE Chi-restraints excluded: chain A residue 698 ILE Chi-restraints excluded: chain A residue 706 ASN Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 805 GLU Chi-restraints excluded: chain A residue 849 GLU Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 960 PHE Chi-restraints excluded: chain A residue 999 MET Chi-restraints excluded: chain A residue 1034 ILE Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1112 MET Chi-restraints excluded: chain A residue 1124 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 252 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 338 optimal weight: 0.9980 chunk 119 optimal weight: 7.9990 chunk 174 optimal weight: 9.9990 chunk 104 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 358 optimal weight: 0.0980 chunk 297 optimal weight: 3.9990 chunk 288 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 189 HIS B 802 ASN B1041 ASN B1054 ASN ** B1134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 573 GLN C 844 ASN ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 HIS A 280 GLN A 380 ASN A 403 ASN A 731 ASN ** A1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1046 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.147745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.120054 restraints weight = 56651.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.124487 restraints weight = 27980.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.127415 restraints weight = 16657.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.129306 restraints weight = 11344.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.130237 restraints weight = 8635.925| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 33774 Z= 0.137 Angle : 0.651 16.259 46053 Z= 0.337 Chirality : 0.046 0.648 5196 Planarity : 0.004 0.065 5889 Dihedral : 4.695 35.947 4887 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.25 % Allowed : 21.98 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.13), residues: 4170 helix: 0.75 (0.19), residues: 786 sheet: -0.05 (0.16), residues: 1017 loop : -1.01 (0.13), residues: 2367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Z 66 TYR 0.062 0.001 TYR C 68 PHE 0.029 0.001 PHE B1182 TRP 0.049 0.002 TRP D 94 HIS 0.010 0.001 HIS A 248 Details of bonding type rmsd covalent geometry : bond 0.00305 (33690) covalent geometry : angle 0.62484 (45870) SS BOND : bond 0.00614 ( 69) SS BOND : angle 2.11097 ( 138) hydrogen bonds : bond 0.03754 ( 1128) hydrogen bonds : angle 5.41101 ( 3162) link_NAG-ASN : bond 0.00739 ( 15) link_NAG-ASN : angle 4.72969 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8340 Ramachandran restraints generated. 4170 Oldfield, 0 Emsley, 4170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1045 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 963 time to evaluate : 1.083 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: Z 7 TRP cc_start: 0.7925 (p-90) cc_final: 0.7571 (p90) REVERT: Z 58 ASN cc_start: 0.7000 (t0) cc_final: 0.6532 (m-40) REVERT: D 87 TYR cc_start: 0.5141 (m-80) cc_final: 0.4672 (m-80) REVERT: D 89 GLN cc_start: 0.6879 (tm-30) cc_final: 0.6385 (tm-30) REVERT: B 28 ASP cc_start: 0.7573 (t0) cc_final: 0.7187 (t0) REVERT: B 47 LEU cc_start: 0.8591 (tp) cc_final: 0.7818 (pp) REVERT: B 68 TYR cc_start: 0.7139 (m-80) cc_final: 0.6858 (m-80) REVERT: B 75 TYR cc_start: 0.8216 (m-80) cc_final: 0.7645 (m-80) REVERT: B 100 ILE cc_start: 0.8447 (mp) cc_final: 0.8130 (mm) REVERT: B 108 LYS cc_start: 0.8066 (tttt) cc_final: 0.7626 (tttt) REVERT: B 138 VAL cc_start: 0.7910 (t) cc_final: 0.7626 (p) REVERT: B 141 GLN cc_start: 0.6905 (OUTLIER) cc_final: 0.6658 (pm20) REVERT: B 234 THR cc_start: 0.7352 (p) cc_final: 0.6958 (t) REVERT: B 259 LYS cc_start: 0.8681 (tppt) cc_final: 0.8328 (tppt) REVERT: B 280 GLN cc_start: 0.7372 (mm-40) cc_final: 0.7136 (mm110) REVERT: B 297 GLU cc_start: 0.7561 (tt0) cc_final: 0.7101 (tt0) REVERT: B 299 LYS cc_start: 0.8115 (mttt) cc_final: 0.7530 (ttmm) REVERT: B 301 LYS cc_start: 0.8216 (tptp) cc_final: 0.7915 (tptt) REVERT: B 317 TYR cc_start: 0.5666 (t80) cc_final: 0.5120 (t80) REVERT: B 329 LYS cc_start: 0.8697 (tttt) cc_final: 0.8329 (tttt) REVERT: B 336 ASN cc_start: 0.8611 (m-40) cc_final: 0.8335 (m-40) REVERT: B 364 MET cc_start: 0.6902 (OUTLIER) cc_final: 0.6268 (mmm) REVERT: B 368 MET cc_start: 0.7940 (mtm) cc_final: 0.7673 (mtm) REVERT: B 403 ASN cc_start: 0.8067 (t0) cc_final: 0.7624 (t0) REVERT: B 405 ARG cc_start: 0.8184 (tpp-160) cc_final: 0.7869 (tpp80) REVERT: B 418 GLN cc_start: 0.7582 (tt0) cc_final: 0.7184 (tt0) REVERT: B 435 TYR cc_start: 0.8082 (p90) cc_final: 0.7786 (p90) REVERT: B 488 LYS cc_start: 0.8050 (ttpt) cc_final: 0.7780 (ttpt) REVERT: B 635 ILE cc_start: 0.8092 (mp) cc_final: 0.7717 (pt) REVERT: B 653 ASP cc_start: 0.7797 (t0) cc_final: 0.7371 (p0) REVERT: B 662 ARG cc_start: 0.7631 (ptm160) cc_final: 0.7269 (ttt90) REVERT: B 671 MET cc_start: 0.7094 (mmm) cc_final: 0.6797 (mmm) REVERT: B 673 ARG cc_start: 0.7619 (mtp85) cc_final: 0.6948 (ttm110) REVERT: B 680 VAL cc_start: 0.9072 (t) cc_final: 0.8799 (p) REVERT: B 701 ASN cc_start: 0.7979 (t0) cc_final: 0.7669 (t0) REVERT: B 709 LEU cc_start: 0.8311 (mt) cc_final: 0.7927 (tt) REVERT: B 714 GLN cc_start: 0.7931 (tp40) cc_final: 0.7637 (tm-30) REVERT: B 717 ASN cc_start: 0.7705 (m110) cc_final: 0.7293 (p0) REVERT: B 731 ASN cc_start: 0.6009 (t0) cc_final: 0.5703 (t0) REVERT: B 751 ASP cc_start: 0.7661 (t0) cc_final: 0.7305 (t0) REVERT: B 803 MET cc_start: 0.6366 (tmm) cc_final: 0.5898 (tmm) REVERT: B 805 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7087 (mt-10) REVERT: B 817 ASP cc_start: 0.7673 (t0) cc_final: 0.7301 (t0) REVERT: B 857 THR cc_start: 0.8239 (m) cc_final: 0.7970 (p) REVERT: B 860 GLN cc_start: 0.8016 (mt0) cc_final: 0.7656 (mt0) REVERT: B 866 MET cc_start: 0.7063 (tpp) cc_final: 0.6738 (mpp) REVERT: B 918 LEU cc_start: 0.7741 (mt) cc_final: 0.7171 (mm) REVERT: B 954 LEU cc_start: 0.7825 (mt) cc_final: 0.7417 (mp) REVERT: B 957 GLU cc_start: 0.7378 (mm-30) cc_final: 0.7093 (mm-30) REVERT: B 960 PHE cc_start: 0.8126 (OUTLIER) cc_final: 0.7861 (m-80) REVERT: B 1021 GLN cc_start: 0.7250 (tp40) cc_final: 0.6909 (tp40) REVERT: B 1049 LEU cc_start: 0.8773 (tp) cc_final: 0.8573 (tt) REVERT: B 1062 SER cc_start: 0.8562 (t) cc_final: 0.7639 (p) REVERT: B 1073 LEU cc_start: 0.8160 (pp) cc_final: 0.7593 (pt) REVERT: B 1076 GLU cc_start: 0.7412 (mt-10) cc_final: 0.6791 (mt-10) REVERT: B 1079 ILE cc_start: 0.9006 (mt) cc_final: 0.8778 (mm) REVERT: B 1083 ILE cc_start: 0.8706 (OUTLIER) cc_final: 0.8403 (mt) REVERT: B 1096 GLN cc_start: 0.8015 (mm-40) cc_final: 0.7525 (mm-40) REVERT: B 1110 GLN cc_start: 0.8275 (tp-100) cc_final: 0.7821 (tp40) REVERT: B 1114 LYS cc_start: 0.8445 (mttm) cc_final: 0.8199 (tttm) REVERT: B 1116 ASN cc_start: 0.7734 (m-40) cc_final: 0.7238 (t0) REVERT: B 1120 LYS cc_start: 0.8290 (mmmm) cc_final: 0.8067 (mmmm) REVERT: B 1144 TYR cc_start: 0.6886 (m-80) cc_final: 0.6597 (m-80) REVERT: B 1150 HIS cc_start: 0.7824 (m90) cc_final: 0.7419 (m-70) REVERT: B 1157 LYS cc_start: 0.7801 (mmmt) cc_final: 0.6975 (mmmt) REVERT: B 1182 PHE cc_start: 0.7340 (m-10) cc_final: 0.7008 (m-10) REVERT: B 1187 ASN cc_start: 0.8228 (m-40) cc_final: 0.7409 (t0) REVERT: X 66 ARG cc_start: 0.6957 (ptm-80) cc_final: 0.6242 (ttp80) REVERT: F 49 TYR cc_start: 0.7690 (p90) cc_final: 0.7054 (p90) REVERT: C 24 ASP cc_start: 0.7482 (t0) cc_final: 0.7136 (t70) REVERT: C 88 ARG cc_start: 0.7626 (mtt90) cc_final: 0.7129 (mtt90) REVERT: C 108 LYS cc_start: 0.8191 (tttt) cc_final: 0.7619 (tttt) REVERT: C 156 GLN cc_start: 0.7740 (mm-40) cc_final: 0.7259 (mp10) REVERT: C 200 LYS cc_start: 0.7887 (tptp) cc_final: 0.7507 (mppt) REVERT: C 206 ASP cc_start: 0.7123 (t70) cc_final: 0.6766 (p0) REVERT: C 229 ASP cc_start: 0.6843 (p0) cc_final: 0.6326 (p0) REVERT: C 240 VAL cc_start: 0.8346 (t) cc_final: 0.8115 (p) REVERT: C 248 HIS cc_start: 0.7327 (m170) cc_final: 0.6788 (m170) REVERT: C 250 TYR cc_start: 0.7433 (t80) cc_final: 0.7128 (t80) REVERT: C 259 LYS cc_start: 0.8758 (tppt) cc_final: 0.8375 (tppt) REVERT: C 295 MET cc_start: 0.6921 (tpt) cc_final: 0.6423 (tpt) REVERT: C 297 GLU cc_start: 0.6924 (OUTLIER) cc_final: 0.6650 (mm-30) REVERT: C 299 LYS cc_start: 0.8295 (mttt) cc_final: 0.7842 (mttt) REVERT: C 301 LYS cc_start: 0.8664 (tptp) cc_final: 0.8161 (tppt) REVERT: C 329 LYS cc_start: 0.8736 (tttt) cc_final: 0.8245 (tttt) REVERT: C 379 ASN cc_start: 0.8284 (t0) cc_final: 0.7910 (t0) REVERT: C 403 ASN cc_start: 0.7955 (t0) cc_final: 0.7657 (t0) REVERT: C 405 ARG cc_start: 0.8135 (tpp-160) cc_final: 0.7506 (tpp80) REVERT: C 408 ASP cc_start: 0.7389 (m-30) cc_final: 0.7139 (m-30) REVERT: C 437 LEU cc_start: 0.8555 (mt) cc_final: 0.8233 (mt) REVERT: C 488 LYS cc_start: 0.8107 (tppt) cc_final: 0.7829 (tppt) REVERT: C 543 THR cc_start: 0.7923 (m) cc_final: 0.7701 (p) REVERT: C 581 ASP cc_start: 0.6551 (m-30) cc_final: 0.6282 (m-30) REVERT: C 612 LYS cc_start: 0.8082 (ptpp) cc_final: 0.6259 (ttpp) REVERT: C 644 TYR cc_start: 0.7672 (m-80) cc_final: 0.7361 (m-80) REVERT: C 653 ASP cc_start: 0.7903 (t0) cc_final: 0.7341 (p0) REVERT: C 670 PHE cc_start: 0.8217 (m-80) cc_final: 0.7857 (m-10) REVERT: C 671 MET cc_start: 0.6965 (mmm) cc_final: 0.6592 (mmm) REVERT: C 701 ASN cc_start: 0.8012 (t0) cc_final: 0.7695 (t0) REVERT: C 719 PHE cc_start: 0.8100 (p90) cc_final: 0.7583 (p90) REVERT: C 723 LEU cc_start: 0.8613 (mm) cc_final: 0.8385 (mt) REVERT: C 731 ASN cc_start: 0.6225 (t0) cc_final: 0.5867 (t0) REVERT: C 738 GLN cc_start: 0.7623 (mm110) cc_final: 0.7241 (mm110) REVERT: C 772 GLU cc_start: 0.7692 (tp30) cc_final: 0.6329 (tp30) REVERT: C 803 MET cc_start: 0.6555 (OUTLIER) cc_final: 0.6147 (tmm) REVERT: C 817 ASP cc_start: 0.7544 (t0) cc_final: 0.7268 (t0) REVERT: C 830 LYS cc_start: 0.8439 (mmmm) cc_final: 0.8171 (mmmm) REVERT: C 854 LEU cc_start: 0.8092 (mt) cc_final: 0.7859 (mp) REVERT: C 860 GLN cc_start: 0.8200 (mt0) cc_final: 0.7898 (mt0) REVERT: C 874 LYS cc_start: 0.8212 (mmtt) cc_final: 0.7893 (mmtt) REVERT: C 915 LYS cc_start: 0.8393 (mmmt) cc_final: 0.8016 (mmmt) REVERT: C 927 TYR cc_start: 0.8051 (m-80) cc_final: 0.7759 (m-80) REVERT: C 948 ILE cc_start: 0.7608 (OUTLIER) cc_final: 0.7349 (mm) REVERT: C 954 LEU cc_start: 0.7909 (mt) cc_final: 0.7667 (mm) REVERT: C 964 THR cc_start: 0.8515 (m) cc_final: 0.8264 (p) REVERT: C 969 SER cc_start: 0.8563 (m) cc_final: 0.8168 (p) REVERT: C 1009 ILE cc_start: 0.8547 (tp) cc_final: 0.7820 (tp) REVERT: C 1013 PHE cc_start: 0.8020 (m-80) cc_final: 0.7218 (m-80) REVERT: C 1049 LEU cc_start: 0.8799 (tp) cc_final: 0.8597 (tt) REVERT: C 1083 ILE cc_start: 0.8552 (mt) cc_final: 0.8161 (mm) REVERT: C 1116 ASN cc_start: 0.7744 (m-40) cc_final: 0.7302 (t0) REVERT: C 1124 SER cc_start: 0.7805 (p) cc_final: 0.7502 (p) REVERT: C 1157 LYS cc_start: 0.7901 (mmmt) cc_final: 0.7090 (mmmt) REVERT: H 33 TYR cc_start: 0.6411 (m-10) cc_final: 0.6074 (m-10) REVERT: L 35 TRP cc_start: 0.7185 (m100) cc_final: 0.6747 (m100) REVERT: A 24 ASP cc_start: 0.7114 (t0) cc_final: 0.6800 (t0) REVERT: A 28 ASP cc_start: 0.7904 (t0) cc_final: 0.7668 (t0) REVERT: A 108 LYS cc_start: 0.8120 (tttt) cc_final: 0.7694 (tttt) REVERT: A 111 LYS cc_start: 0.8455 (mmmt) cc_final: 0.8079 (mmtt) REVERT: A 138 VAL cc_start: 0.8039 (t) cc_final: 0.7693 (p) REVERT: A 184 ARG cc_start: 0.6481 (mtt180) cc_final: 0.6167 (mtt90) REVERT: A 200 LYS cc_start: 0.7820 (tptp) cc_final: 0.7367 (mppt) REVERT: A 259 LYS cc_start: 0.8750 (tppt) cc_final: 0.8361 (tppt) REVERT: A 297 GLU cc_start: 0.7116 (tt0) cc_final: 0.6901 (tt0) REVERT: A 313 GLU cc_start: 0.7415 (mm-30) cc_final: 0.7150 (mm-30) REVERT: A 314 LEU cc_start: 0.8313 (mt) cc_final: 0.7694 (mt) REVERT: A 364 MET cc_start: 0.6926 (mmm) cc_final: 0.6385 (tmm) REVERT: A 368 MET cc_start: 0.7739 (mtm) cc_final: 0.6442 (mtm) REVERT: A 382 ASP cc_start: 0.7597 (p0) cc_final: 0.7333 (m-30) REVERT: A 423 ARG cc_start: 0.7935 (tpp-160) cc_final: 0.7668 (tpp-160) REVERT: A 448 ASN cc_start: 0.8421 (OUTLIER) cc_final: 0.8041 (m-40) REVERT: A 585 GLN cc_start: 0.8064 (pt0) cc_final: 0.7497 (pm20) REVERT: A 587 ASP cc_start: 0.6240 (p0) cc_final: 0.6012 (t0) REVERT: A 644 TYR cc_start: 0.7810 (m-80) cc_final: 0.7106 (m-80) REVERT: A 649 ASN cc_start: 0.7827 (m-40) cc_final: 0.7403 (p0) REVERT: A 652 TYR cc_start: 0.8042 (m-80) cc_final: 0.7791 (m-80) REVERT: A 653 ASP cc_start: 0.7456 (p0) cc_final: 0.7130 (p0) REVERT: A 663 ASP cc_start: 0.7323 (t0) cc_final: 0.6787 (t0) REVERT: A 671 MET cc_start: 0.6972 (mmm) cc_final: 0.6539 (mmm) REVERT: A 702 TYR cc_start: 0.8412 (t80) cc_final: 0.8056 (t80) REVERT: A 707 ASN cc_start: 0.7740 (m110) cc_final: 0.7199 (m110) REVERT: A 725 CYS cc_start: 0.5182 (OUTLIER) cc_final: 0.4824 (t) REVERT: A 772 GLU cc_start: 0.7153 (tp30) cc_final: 0.6620 (tp30) REVERT: A 774 PHE cc_start: 0.8355 (m-80) cc_final: 0.8088 (m-80) REVERT: A 860 GLN cc_start: 0.7908 (mt0) cc_final: 0.7457 (mt0) REVERT: A 866 MET cc_start: 0.7169 (tpp) cc_final: 0.6717 (tpp) REVERT: A 938 ASP cc_start: 0.7542 (t0) cc_final: 0.7113 (t70) REVERT: A 951 LEU cc_start: 0.8340 (mt) cc_final: 0.8093 (mm) REVERT: A 957 GLU cc_start: 0.7409 (mm-30) cc_final: 0.7050 (mm-30) REVERT: A 973 PHE cc_start: 0.7865 (m-80) cc_final: 0.7504 (m-80) REVERT: A 1035 GLN cc_start: 0.7992 (mm-40) cc_final: 0.7681 (tp40) REVERT: A 1055 ARG cc_start: 0.7716 (ptp-170) cc_final: 0.7241 (mtm110) REVERT: A 1084 ASN cc_start: 0.8195 (t0) cc_final: 0.7930 (t0) REVERT: A 1128 PHE cc_start: 0.7714 (t80) cc_final: 0.7470 (t80) REVERT: A 1177 PRO cc_start: 0.8079 (Cg_endo) cc_final: 0.7696 (Cg_exo) REVERT: A 1224 MET cc_start: 0.5309 (mpp) cc_final: 0.4989 (tpp) outliers start: 82 outliers final: 61 residues processed: 998 average time/residue: 0.2131 time to fit residues: 339.1491 Evaluate side-chains 1025 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 954 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 95 CYS Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 390 CYS Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 615 THR Chi-restraints excluded: chain B residue 792 ILE Chi-restraints excluded: chain B residue 805 GLU Chi-restraints excluded: chain B residue 839 PHE Chi-restraints excluded: chain B residue 960 PHE Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1083 ILE Chi-restraints excluded: chain B residue 1124 SER Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 353 GLU Chi-restraints excluded: chain C residue 364 MET Chi-restraints excluded: chain C residue 589 CYS Chi-restraints excluded: chain C residue 665 ILE Chi-restraints excluded: chain C residue 680 VAL Chi-restraints excluded: chain C residue 698 ILE Chi-restraints excluded: chain C residue 700 CYS Chi-restraints excluded: chain C residue 750 VAL Chi-restraints excluded: chain C residue 792 ILE Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 803 MET Chi-restraints excluded: chain C residue 948 ILE Chi-restraints excluded: chain C residue 1047 ASN Chi-restraints excluded: chain C residue 1082 LEU Chi-restraints excluded: chain C residue 1194 SER Chi-restraints excluded: chain H residue 60 ASN Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 127 ILE 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 230 THR Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 378 CYS Chi-restraints excluded: chain A residue 390 CYS Chi-restraints excluded: chain A residue 391 PHE Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 483 CYS Chi-restraints excluded: chain A residue 484 PHE Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 589 CYS Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 665 ILE Chi-restraints excluded: chain A residue 698 ILE Chi-restraints excluded: chain A residue 706 ASN Chi-restraints excluded: chain A residue 725 CYS Chi-restraints excluded: chain A residue 805 GLU Chi-restraints excluded: chain A residue 849 GLU Chi-restraints excluded: chain A residue 960 PHE Chi-restraints excluded: chain A residue 999 MET Chi-restraints excluded: chain A residue 1034 ILE Chi-restraints excluded: chain A residue 1046 ASN Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1112 MET Chi-restraints excluded: chain A residue 1124 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 6 optimal weight: 5.9990 chunk 412 optimal weight: 4.9990 chunk 366 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 123 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 242 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 230 optimal weight: 3.9990 chunk 229 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 248 HIS B 802 ASN B1039 ASN ** B1064 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 573 GLN C 844 ASN ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 HIS A 280 GLN ** A 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 ASN ** A1041 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.149207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.121624 restraints weight = 55087.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.125989 restraints weight = 27131.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.128837 restraints weight = 16162.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.130689 restraints weight = 11030.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.131887 restraints weight = 8390.377| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.4089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.161 33774 Z= 0.196 Angle : 0.776 59.192 46053 Z= 0.429 Chirality : 0.046 0.647 5196 Planarity : 0.004 0.065 5889 Dihedral : 4.696 35.939 4887 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.31 % Allowed : 22.18 % Favored : 75.52 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.13), residues: 4170 helix: 0.72 (0.19), residues: 786 sheet: -0.04 (0.16), residues: 1017 loop : -1.01 (0.13), residues: 2367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 143 TYR 0.087 0.002 TYR C 274 PHE 0.026 0.002 PHE C 285 TRP 0.041 0.002 TRP F 94 HIS 0.008 0.001 HIS A 248 Details of bonding type rmsd covalent geometry : bond 0.00398 (33690) covalent geometry : angle 0.74751 (45870) SS BOND : bond 0.00693 ( 69) SS BOND : angle 2.85470 ( 138) hydrogen bonds : bond 0.03801 ( 1128) hydrogen bonds : angle 5.41988 ( 3162) link_NAG-ASN : bond 0.00742 ( 15) link_NAG-ASN : angle 4.72652 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7125.44 seconds wall clock time: 123 minutes 5.43 seconds (7385.43 seconds total)