Starting phenix.real_space_refine on Fri Mar 6 17:46:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pnq_13550/03_2026/7pnq_13550.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pnq_13550/03_2026/7pnq_13550.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pnq_13550/03_2026/7pnq_13550.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pnq_13550/03_2026/7pnq_13550.map" model { file = "/net/cci-nas-00/data/ceres_data/7pnq_13550/03_2026/7pnq_13550.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pnq_13550/03_2026/7pnq_13550.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.034 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 20931 2.51 5 N 5418 2.21 5 O 6375 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32925 Number of models: 1 Model: "" Number of chains: 12 Chain: "X" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 953 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "Y" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 802 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: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 953 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "L" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 802 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: "D" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 953 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "F" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 802 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: "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 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 Time building chain proxies: 6.69, per 1000 atoms: 0.20 Number of scatterers: 32925 At special positions: 0 Unit cell: (150.165, 152.295, 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 6375 8.00 N 5418 7.00 C 20931 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=69, symmetry=0 Simple disulfide: pdb=" SG CYS X 22 " - pdb=" SG CYS X 95 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 23 " - pdb=" SG CYS Y 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 700 " - pdb=" SG CYS A 725 " distance=2.03 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 818 " - pdb=" SG CYS A 840 " distance=2.03 Simple disulfide: pdb=" SG CYS A 823 " - pdb=" SG CYS A 829 " distance=2.03 Simple disulfide: pdb=" SG CYS A 930 " - pdb=" SG CYS A 941 " distance=2.03 Simple disulfide: pdb=" SG CYS A1118 " - pdb=" SG CYS A1129 " distance=2.04 Simple disulfide: pdb=" SG CYS A1168 " - pdb=" SG CYS A1213 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 95 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 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 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: 2.58 Conformation dependent library (CDL) restraints added in 1.3 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: 93 helices and 75 sheets defined 22.3% alpha, 32.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain 'X' and resid 60 through 64 removed outlier: 3.734A pdb=" N LYS X 64 " --> pdb=" O PRO X 61 " (cutoff:3.500A) Processing helix chain 'X' and resid 86 through 90 removed outlier: 3.711A pdb=" N THR X 90 " --> pdb=" O ALA X 87 " (cutoff:3.500A) Processing helix chain 'Y' and resid 79 through 83 removed outlier: 4.172A pdb=" N PHE Y 83 " --> pdb=" O SER Y 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 92 removed outlier: 3.601A 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 Processing helix chain 'C' and resid 336 through 342 removed outlier: 3.556A pdb=" N ASN C 342 " --> pdb=" O GLU C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 371 removed outlier: 4.016A pdb=" N SER C 369 " --> pdb=" O SER C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 388 removed outlier: 3.845A 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: 3.502A pdb=" N ASP C 408 " --> pdb=" O ARG C 405 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 421 Processing helix chain 'C' and resid 450 through 456 Processing helix chain 'C' and resid 459 through 464 removed outlier: 3.515A pdb=" N PHE C 464 " --> pdb=" O GLU C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 561 No H-bonds generated for 'chain 'C' and resid 559 through 561' 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 Processing helix chain 'C' and resid 826 through 833 Processing helix chain 'C' and resid 836 through 866 removed outlier: 3.595A 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 915 removed outlier: 4.229A pdb=" N LYS C 915 " --> pdb=" O LEU C 911 " (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 Processing helix chain 'C' and resid 983 through 994 Processing helix chain 'C' and resid 999 through 1004 removed outlier: 4.051A 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 1062 through 1070 Processing helix chain 'C' and resid 1071 through 1119 removed outlier: 3.618A pdb=" N ALA C1077 " --> pdb=" O LEU C1073 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 64 removed outlier: 3.723A pdb=" N LYS H 64 " --> pdb=" O PRO H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 90 removed outlier: 3.699A pdb=" N THR H 90 " --> pdb=" O ALA H 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.181A pdb=" N PHE L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 92 removed outlier: 3.599A 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 Processing helix chain 'A' and resid 336 through 342 Processing helix chain 'A' and resid 363 through 371 removed outlier: 3.990A pdb=" N SER A 369 " --> pdb=" O SER A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 388 removed outlier: 3.838A 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: 3.641A pdb=" N GLN A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 421 Processing helix chain 'A' and resid 450 through 456 Processing helix chain 'A' and resid 459 through 464 Processing helix chain 'A' and resid 559 through 561 No H-bonds generated for 'chain 'A' and resid 559 through 561' Processing helix chain 'A' and resid 565 through 568 Processing helix chain 'A' and resid 572 through 575 removed outlier: 3.744A pdb=" N PHE A 575 " --> pdb=" O PRO A 572 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 572 through 575' Processing helix chain 'A' and resid 699 through 708 Processing helix chain 'A' and resid 817 through 823 Processing helix chain 'A' and resid 826 through 833 Processing helix chain 'A' and resid 836 through 866 removed outlier: 3.600A 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: 4.215A pdb=" N LYS A 915 " --> pdb=" O LEU A 911 " (cutoff:3.500A) removed outlier: 4.041A 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 Processing helix chain 'A' and resid 983 through 994 Processing helix chain 'A' and resid 999 through 1004 removed outlier: 4.054A 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: 3.581A pdb=" N ALA A1077 " --> pdb=" O LEU A1073 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 64 removed outlier: 3.727A pdb=" N LYS D 64 " --> pdb=" O PRO D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 90 removed outlier: 3.697A pdb=" N THR D 90 " --> pdb=" O ALA D 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 83 removed outlier: 4.170A pdb=" N PHE F 83 " --> pdb=" O SER F 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 92 removed outlier: 3.608A 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 Processing helix chain 'B' and resid 336 through 342 Processing helix chain 'B' and resid 363 through 371 removed outlier: 4.076A pdb=" N SER B 369 " --> pdb=" O SER B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 388 removed outlier: 3.896A 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: 3.500A pdb=" N ASP B 408 " --> pdb=" O ARG B 405 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 421 Processing helix chain 'B' and resid 450 through 456 Processing helix chain 'B' and resid 459 through 464 removed outlier: 3.506A pdb=" N PHE B 464 " --> pdb=" O GLU B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 561 No H-bonds generated for 'chain 'B' and resid 559 through 561' Processing helix chain 'B' and resid 565 through 568 Processing helix chain 'B' and resid 572 through 575 removed outlier: 3.757A pdb=" N PHE B 575 " --> pdb=" O PRO B 572 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 572 through 575' Processing helix chain 'B' and resid 699 through 708 Processing helix chain 'B' and resid 817 through 823 Processing helix chain 'B' and resid 826 through 833 Processing helix chain 'B' and resid 836 through 866 removed outlier: 3.584A 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 915 removed outlier: 4.207A pdb=" N LYS B 915 " --> pdb=" O LEU B 911 " (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 Processing helix chain 'B' and resid 983 through 994 Processing helix chain 'B' and resid 999 through 1004 removed outlier: 4.034A 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 1062 through 1070 Processing helix chain 'B' and resid 1071 through 1119 removed outlier: 3.626A pdb=" N ALA B1077 " --> pdb=" O LEU B1073 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'X' and resid 4 through 7 removed outlier: 3.712A pdb=" N TRP X 7 " --> pdb=" O THR X 21 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N THR X 21 " --> pdb=" O TRP X 7 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N GLU X 16 " --> pdb=" O SER X 84 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'X' and resid 50 through 51 removed outlier: 4.070A pdb=" N TYR X 33 " --> pdb=" O GLY X 98 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'X' and resid 100 through 101 Processing sheet with id=AA4, first strand: chain 'Y' and resid 4 through 7 removed outlier: 3.640A pdb=" N THR Y 5 " --> pdb=" O ARG Y 24 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N SER Y 7 " --> pdb=" O SER Y 22 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER Y 22 " --> pdb=" O SER Y 7 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA Y 19 " --> pdb=" O ILE Y 75 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N CYS Y 23 " --> pdb=" O PHE Y 71 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE Y 71 " --> pdb=" O CYS Y 23 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU Y 70 " --> pdb=" O SER Y 67 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'Y' and resid 10 through 13 removed outlier: 6.307A pdb=" N LEU Y 11 " --> pdb=" O GLU Y 105 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LEU Y 33 " --> pdb=" O TYR Y 49 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N TYR Y 49 " --> pdb=" O LEU Y 33 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N TRP Y 35 " --> pdb=" O LEU Y 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 26 through 27 Processing sheet with id=AA7, first strand: chain 'C' and resid 36 through 40 removed outlier: 5.101A pdb=" N TYR C 75 " --> pdb=" O SER C 37 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N THR C 74 " --> pdb=" O PRO C 268 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLY C 102 " --> pdb=" O LEU C 269 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR C 213 " --> pdb=" O THR C 228 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR C 222 " --> pdb=" O GLU C 219 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE C 238 " --> pdb=" O ALA C 225 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N PHE C 227 " --> pdb=" O PHE C 236 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N PHE C 236 " --> pdb=" O PHE C 227 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 61 through 69 removed outlier: 3.957A pdb=" N ASN C 286 " --> pdb=" O ALA C 277 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 55 through 56 removed outlier: 6.249A pdb=" N VAL C 56 " --> pdb=" O TYR B 652 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY B 660 " --> pdb=" O LEU B 651 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N TYR B 659 " --> pdb=" O ILE B 672 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY B 632 " --> pdb=" O TYR B 625 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY B 634 " --> pdb=" O VAL B 623 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 97 through 98 removed outlier: 3.581A pdb=" N TYR C 249 " --> pdb=" O SER C 97 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL C 139 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN C 141 " --> pdb=" O GLU C 160 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLY C 157 " --> pdb=" O TYR C 205 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TYR C 205 " --> pdb=" O GLY C 157 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 110 through 114 removed outlier: 3.523A pdb=" N LYS C 114 " --> pdb=" O VAL C 117 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 174 through 175 removed outlier: 7.146A pdb=" N THR C 174 " --> pdb=" O THR C 255 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 310 through 318 removed outlier: 3.636A pdb=" N PHE C 684 " --> pdb=" O GLY C 310 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL C 680 " --> pdb=" O LEU C 314 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLY C 316 " --> pdb=" O GLY C 678 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N GLY C 678 " --> pdb=" O GLY C 316 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N ARG C 679 " --> pdb=" O ARG C 696 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N ARG C 696 " --> pdb=" O ARG C 679 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE C 719 " --> pdb=" O VAL C 726 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 324 through 327 removed outlier: 3.525A pdb=" N GLY C 634 " --> pdb=" O VAL C 623 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY C 632 " --> pdb=" O TYR C 625 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N TYR C 659 " --> pdb=" O ILE C 672 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY C 660 " --> pdb=" O LEU C 651 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 353 through 357 removed outlier: 3.871A pdb=" N GLU C 353 " --> pdb=" O LYS C 398 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS C 398 " --> pdb=" O GLU C 353 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N PHE C 391 " --> pdb=" O VAL C 600 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N VAL C 600 " --> pdb=" O PHE C 391 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER C 393 " --> pdb=" O HIS C 598 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N ASN C 436 " --> pdb=" O ALA C 373 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ALA C 373 " --> pdb=" O ASN C 436 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.567A pdb=" N PHE C 391 " --> pdb=" O VAL C 600 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N VAL C 600 " --> pdb=" O PHE C 391 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER C 393 " --> pdb=" O HIS C 598 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS C 588 " --> pdb=" O GLN C 585 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 476 through 480 Processing sheet with id=AB9, first strand: chain 'C' and resid 484 through 485 Processing sheet with id=AC1, first strand: chain 'C' and resid 563 through 564 Processing sheet with id=AC2, first strand: chain 'C' and resid 730 through 737 removed outlier: 6.857A pdb=" N TYR C 730 " --> pdb=" O PHE C 768 " (cutoff:3.500A) removed outlier: 8.853A pdb=" N ASN C 770 " --> pdb=" O TYR C 730 " (cutoff:3.500A) removed outlier: 9.577A pdb=" N SER C 732 " --> pdb=" O ASN C 770 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N TYR C 748 " --> pdb=" O VAL C 744 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU C 742 " --> pdb=" O VAL C 750 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 777 through 779 Processing sheet with id=AC4, first strand: chain 'C' and resid 790 through 807 removed outlier: 6.493A pdb=" N LYS C1157 " --> pdb=" O SER C 796 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N PHE C 798 " --> pdb=" O PRO C1155 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ILE C 800 " --> pdb=" O TYR C1153 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N TYR C1153 " --> pdb=" O ILE C 800 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ASN C 802 " --> pdb=" O PHE C1151 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N PHE C1151 " --> pdb=" O ASN C 802 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N VAL C 804 " --> pdb=" O ILE C1149 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ILE C1149 " --> pdb=" O VAL C 804 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N PHE C 806 " --> pdb=" O TYR C1147 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N TYR C1147 " --> pdb=" O PHE C 806 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY C1145 " --> pdb=" O ALA C1142 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA C1142 " --> pdb=" O GLY C1145 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE C1136 " --> pdb=" O PHE C1151 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N TYR C1153 " --> pdb=" O HIS C1134 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N HIS C1134 " --> pdb=" O TYR C1153 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 790 through 807 removed outlier: 6.493A pdb=" N LYS C1157 " --> pdb=" O SER C 796 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N PHE C 798 " --> pdb=" O PRO C1155 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N ILE C 800 " --> pdb=" O TYR C1153 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N TYR C1153 " --> pdb=" O ILE C 800 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ASN C 802 " --> pdb=" O PHE C1151 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N PHE C1151 " --> pdb=" O ASN C 802 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N VAL C 804 " --> pdb=" O ILE C1149 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ILE C1149 " --> pdb=" O VAL C 804 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N PHE C 806 " --> pdb=" O TYR C1147 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N TYR C1147 " --> pdb=" O PHE C 806 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ARG C1162 " --> pdb=" O ASN C1184 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ASN C1184 " --> pdb=" O ARG C1162 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR C1192 " --> pdb=" O TYR C1181 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 813 through 816 removed outlier: 4.089A pdb=" N LYS C 813 " --> pdb=" O LEU C 951 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 870 through 872 Processing sheet with id=AC8, first strand: chain 'C' and resid 882 through 883 removed outlier: 3.674A pdb=" N VAL C 883 " --> pdb=" O ILE C 886 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE C 886 " --> pdb=" O VAL C 883 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'C' and resid 1167 through 1168 removed outlier: 3.609A pdb=" N LEU C1167 " --> pdb=" O ILE C1175 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA C1176 " --> pdb=" O VAL C1208 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 4 through 7 removed outlier: 3.712A pdb=" N TRP H 7 " --> pdb=" O THR H 21 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N THR H 21 " --> pdb=" O TRP H 7 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N GLU H 16 " --> pdb=" O SER H 84 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 33 through 39 removed outlier: 4.077A pdb=" N TYR H 33 " --> pdb=" O GLY H 98 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 100 through 101 Processing sheet with id=AD4, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.573A pdb=" N THR L 5 " --> pdb=" O ARG L 24 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER L 7 " --> pdb=" O SER L 22 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER L 22 " --> pdb=" O SER L 7 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N CYS L 23 " --> pdb=" O PHE L 71 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N PHE L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.324A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 26 through 27 Processing sheet with id=AD7, first strand: chain 'A' and resid 36 through 40 removed outlier: 5.098A pdb=" N TYR A 75 " --> pdb=" O SER A 37 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N THR A 74 " --> pdb=" O PRO A 268 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLY A 102 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR A 213 " --> pdb=" O THR A 228 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR A 222 " --> pdb=" O GLU A 219 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE A 238 " --> pdb=" O ALA A 225 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N PHE A 227 " --> pdb=" O PHE A 236 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N PHE A 236 " --> pdb=" O PHE A 227 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 61 through 69 removed outlier: 3.934A pdb=" N ASN A 286 " --> pdb=" O ALA A 277 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 97 through 98 removed outlier: 3.674A pdb=" N TYR A 249 " --> pdb=" O SER A 97 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL A 139 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN A 141 " --> pdb=" O GLU A 160 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLY A 157 " --> pdb=" O TYR A 205 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR A 205 " --> pdb=" O GLY A 157 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG A 201 " --> pdb=" O VAL A 161 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'A' and resid 110 through 114 removed outlier: 3.524A pdb=" N LYS A 114 " --> pdb=" O VAL A 117 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 187 through 189 removed outlier: 7.460A pdb=" N TRP A 188 " --> pdb=" O CYS A 169 " (cutoff:3.500A) removed outlier: 8.990A pdb=" N THR A 255 " --> pdb=" O PRO A 172 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N THR A 174 " --> pdb=" O THR A 255 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 310 through 318 removed outlier: 3.649A pdb=" N PHE A 684 " --> pdb=" O GLY A 310 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL A 680 " --> pdb=" O LEU A 314 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLY A 316 " --> pdb=" O GLY A 678 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N GLY A 678 " --> pdb=" O GLY A 316 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ARG A 679 " --> pdb=" O ARG A 696 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ARG A 696 " --> pdb=" O ARG A 679 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE A 719 " --> pdb=" O VAL A 726 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'A' and resid 324 through 327 removed outlier: 3.532A pdb=" N GLY A 634 " --> pdb=" O VAL A 623 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY A 632 " --> pdb=" O TYR A 625 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N TYR A 659 " --> pdb=" O ILE A 672 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY A 660 " --> pdb=" O LEU A 651 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 355 through 357 removed outlier: 6.567A pdb=" N PHE A 391 " --> pdb=" O VAL A 600 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N VAL A 600 " --> pdb=" O PHE A 391 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER A 393 " --> pdb=" O HIS A 598 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N ASN A 436 " --> pdb=" O ALA A 373 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ALA A 373 " --> pdb=" O ASN A 436 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.567A pdb=" N PHE A 391 " --> pdb=" O VAL A 600 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N VAL A 600 " --> pdb=" O PHE A 391 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER A 393 " --> pdb=" O HIS A 598 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS A 588 " --> pdb=" O GLN A 585 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'A' and resid 476 through 480 Processing sheet with id=AE8, first strand: chain 'A' and resid 484 through 485 Processing sheet with id=AE9, first strand: chain 'A' and resid 563 through 564 Processing sheet with id=AF1, first strand: chain 'A' and resid 730 through 737 removed outlier: 6.838A pdb=" N TYR A 730 " --> pdb=" O PHE A 768 " (cutoff:3.500A) removed outlier: 8.841A pdb=" N ASN A 770 " --> pdb=" O TYR A 730 " (cutoff:3.500A) removed outlier: 9.586A pdb=" N SER A 732 " --> pdb=" O ASN A 770 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TYR A 748 " --> pdb=" O VAL A 744 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LEU A 742 " --> pdb=" O VAL A 750 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'A' and resid 777 through 779 Processing sheet with id=AF3, first strand: chain 'A' and resid 790 through 807 removed outlier: 6.510A pdb=" N LYS A1157 " --> pdb=" O SER A 796 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N PHE A 798 " --> pdb=" O PRO A1155 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ILE A 800 " --> pdb=" O TYR A1153 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N TYR A1153 " --> pdb=" O ILE A 800 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ASN A 802 " --> pdb=" O PHE A1151 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N PHE A1151 " --> pdb=" O ASN A 802 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N VAL A 804 " --> pdb=" O ILE A1149 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ILE A1149 " --> pdb=" O VAL A 804 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N PHE A 806 " --> pdb=" O TYR A1147 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N TYR A1147 " --> pdb=" O PHE A 806 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE A1136 " --> pdb=" O PHE A1151 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N TYR A1153 " --> pdb=" O HIS A1134 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N HIS A1134 " --> pdb=" O TYR A1153 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'A' and resid 790 through 807 removed outlier: 6.510A pdb=" N LYS A1157 " --> pdb=" O SER A 796 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N PHE A 798 " --> pdb=" O PRO A1155 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ILE A 800 " --> pdb=" O TYR A1153 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N TYR A1153 " --> pdb=" O ILE A 800 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ASN A 802 " --> pdb=" O PHE A1151 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N PHE A1151 " --> pdb=" O ASN A 802 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N VAL A 804 " --> pdb=" O ILE A1149 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ILE A1149 " --> pdb=" O VAL A 804 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N PHE A 806 " --> pdb=" O TYR A1147 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N TYR A1147 " --> pdb=" O PHE A 806 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ARG A1162 " --> pdb=" O ASN A1184 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ASN A1184 " --> pdb=" O ARG A1162 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR A1192 " --> pdb=" O TYR A1181 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'A' and resid 813 through 816 removed outlier: 4.082A pdb=" N LYS A 813 " --> pdb=" O LEU A 951 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'A' and resid 882 through 883 removed outlier: 3.716A pdb=" N VAL A 883 " --> pdb=" O ILE A 886 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE A 886 " --> pdb=" O VAL A 883 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'A' and resid 1167 through 1168 removed outlier: 3.609A pdb=" N LEU A1167 " --> pdb=" O ILE A1175 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA A1176 " --> pdb=" O VAL A1208 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.715A pdb=" N TRP D 7 " --> pdb=" O THR D 21 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N THR D 21 " --> pdb=" O TRP D 7 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N GLU D 16 " --> pdb=" O SER D 84 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 33 through 39 removed outlier: 4.068A pdb=" N TYR D 33 " --> pdb=" O GLY D 98 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 100 through 101 Processing sheet with id=AG2, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.538A pdb=" N THR F 5 " --> pdb=" O ARG F 24 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER F 7 " --> pdb=" O SER F 22 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER F 22 " --> pdb=" O SER F 7 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA F 19 " --> pdb=" O ILE F 75 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N CYS F 23 " --> pdb=" O PHE F 71 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N PHE F 71 " --> pdb=" O CYS F 23 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU F 70 " --> pdb=" O SER F 67 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.329A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'B' and resid 26 through 27 Processing sheet with id=AG5, first strand: chain 'B' and resid 36 through 40 removed outlier: 5.104A pdb=" N TYR B 75 " --> pdb=" O SER B 37 " (cutoff:3.500A) removed outlier: 8.355A pdb=" N THR B 74 " --> pdb=" O PRO B 268 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLY B 102 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR B 213 " --> pdb=" O THR B 228 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR B 222 " --> pdb=" O GLU B 219 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE B 238 " --> pdb=" O ALA B 225 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N PHE B 227 " --> pdb=" O PHE B 236 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N PHE B 236 " --> pdb=" O PHE B 227 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'B' and resid 61 through 69 removed outlier: 3.510A pdb=" N GLY B 66 " --> pdb=" O ARG B 272 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASN B 286 " --> pdb=" O ALA B 277 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'B' and resid 97 through 98 removed outlier: 3.588A pdb=" N TYR B 249 " --> pdb=" O SER B 97 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL B 139 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN B 141 " --> pdb=" O GLU B 160 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLY B 157 " --> pdb=" O TYR B 205 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR B 205 " --> pdb=" O GLY B 157 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG B 201 " --> pdb=" O VAL B 161 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'B' and resid 110 through 114 removed outlier: 3.531A pdb=" N LYS B 114 " --> pdb=" O VAL B 117 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'B' and resid 187 through 189 removed outlier: 7.440A pdb=" N TRP B 188 " --> pdb=" O CYS B 169 " (cutoff:3.500A) removed outlier: 8.888A pdb=" N THR B 255 " --> pdb=" O PRO B 172 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N THR B 174 " --> pdb=" O THR B 255 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'B' and resid 310 through 318 removed outlier: 3.670A pdb=" N PHE B 684 " --> pdb=" O GLY B 310 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL B 680 " --> pdb=" O LEU B 314 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLY B 316 " --> pdb=" O GLY B 678 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N GLY B 678 " --> pdb=" O GLY B 316 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N ARG B 679 " --> pdb=" O ARG B 696 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N ARG B 696 " --> pdb=" O ARG B 679 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE B 719 " --> pdb=" O VAL B 726 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'B' and resid 353 through 357 removed outlier: 3.922A pdb=" N GLU B 353 " --> pdb=" O LYS B 398 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS B 398 " --> pdb=" O GLU B 353 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N PHE B 391 " --> pdb=" O VAL B 600 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N VAL B 600 " --> pdb=" O PHE B 391 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER B 393 " --> pdb=" O HIS B 598 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU B 437 " --> pdb=" O CYS B 589 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ASN B 436 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ALA B 373 " --> pdb=" O ASN B 436 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.582A pdb=" N PHE B 391 " --> pdb=" O VAL B 600 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N VAL B 600 " --> pdb=" O PHE B 391 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER B 393 " --> pdb=" O HIS B 598 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS B 588 " --> pdb=" O GLN B 585 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'B' and resid 476 through 480 Processing sheet with id=AH5, first strand: chain 'B' and resid 484 through 485 Processing sheet with id=AH6, first strand: chain 'B' and resid 563 through 564 Processing sheet with id=AH7, first strand: chain 'B' and resid 730 through 737 removed outlier: 6.864A pdb=" N TYR B 730 " --> pdb=" O PHE B 768 " (cutoff:3.500A) removed outlier: 8.849A pdb=" N ASN B 770 " --> pdb=" O TYR B 730 " (cutoff:3.500A) removed outlier: 9.592A pdb=" N SER B 732 " --> pdb=" O ASN B 770 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N TYR B 748 " --> pdb=" O VAL B 744 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LEU B 742 " --> pdb=" O VAL B 750 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'B' and resid 790 through 807 removed outlier: 6.530A pdb=" N LYS B1157 " --> pdb=" O SER B 796 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N PHE B 798 " --> pdb=" O PRO B1155 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ILE B 800 " --> pdb=" O TYR B1153 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N TYR B1153 " --> pdb=" O ILE B 800 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ASN B 802 " --> pdb=" O PHE B1151 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N PHE B1151 " --> pdb=" O ASN B 802 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL B 804 " --> pdb=" O ILE B1149 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N ILE B1149 " --> pdb=" O VAL B 804 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N PHE B 806 " --> pdb=" O TYR B1147 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N TYR B1147 " --> pdb=" O PHE B 806 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY B1145 " --> pdb=" O ALA B1142 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA B1142 " --> pdb=" O GLY B1145 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE B1136 " --> pdb=" O PHE B1151 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N TYR B1153 " --> pdb=" O HIS B1134 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N HIS B1134 " --> pdb=" O TYR B1153 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'B' and resid 790 through 807 removed outlier: 6.530A pdb=" N LYS B1157 " --> pdb=" O SER B 796 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N PHE B 798 " --> pdb=" O PRO B1155 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ILE B 800 " --> pdb=" O TYR B1153 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N TYR B1153 " --> pdb=" O ILE B 800 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ASN B 802 " --> pdb=" O PHE B1151 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N PHE B1151 " --> pdb=" O ASN B 802 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL B 804 " --> pdb=" O ILE B1149 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N ILE B1149 " --> pdb=" O VAL B 804 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N PHE B 806 " --> pdb=" O TYR B1147 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N TYR B1147 " --> pdb=" O PHE B 806 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ARG B1162 " --> pdb=" O ASN B1184 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ASN B1184 " --> pdb=" O ARG B1162 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR B1192 " --> pdb=" O TYR B1181 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'B' and resid 813 through 816 removed outlier: 4.110A pdb=" N LYS B 813 " --> pdb=" O LEU B 951 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'B' and resid 882 through 883 removed outlier: 3.666A pdb=" N VAL B 883 " --> pdb=" O ILE B 886 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE B 886 " --> pdb=" O VAL B 883 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI2 Processing sheet with id=AI3, first strand: chain 'B' and resid 1167 through 1168 removed outlier: 3.625A pdb=" N LEU B1167 " --> pdb=" O ILE B1175 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA B1176 " --> pdb=" O VAL B1208 " (cutoff:3.500A) 1228 hydrogen bonds defined for protein. 3381 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: 8.33 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: 10511 1.34 - 1.47: 8533 1.47 - 1.59: 14373 1.59 - 1.71: 0 1.71 - 1.83: 261 Bond restraints: 33678 Sorted by residual: bond pdb=" C1 NAG A1405 " pdb=" O5 NAG A1405 " ideal model delta sigma weight residual 1.406 1.508 -0.102 2.00e-02 2.50e+03 2.58e+01 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 2.55e+01 bond pdb=" C1 NAG C1405 " pdb=" O5 NAG C1405 " ideal model delta sigma weight residual 1.406 1.506 -0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" C1 NAG C1401 " pdb=" O5 NAG C1401 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 7.03e+00 bond pdb=" C1 NAG A1401 " pdb=" O5 NAG A1401 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.86e+00 ... (remaining 33673 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 44812 1.92 - 3.84: 920 3.84 - 5.76: 85 5.76 - 7.68: 26 7.68 - 9.60: 6 Bond angle restraints: 45849 Sorted by residual: angle pdb=" C GLY C1130 " pdb=" N ASN C1131 " pdb=" CA ASN C1131 " ideal model delta sigma weight residual 121.54 131.14 -9.60 1.91e+00 2.74e-01 2.53e+01 angle pdb=" C GLY A1130 " pdb=" N ASN A1131 " pdb=" CA ASN A1131 " ideal model delta sigma weight residual 121.54 131.11 -9.57 1.91e+00 2.74e-01 2.51e+01 angle pdb=" C GLY B1130 " pdb=" N ASN B1131 " pdb=" CA ASN B1131 " ideal model delta sigma weight residual 121.54 131.10 -9.56 1.91e+00 2.74e-01 2.50e+01 angle pdb=" C ASN B 379 " pdb=" N ASN B 380 " pdb=" CA ASN B 380 " ideal model delta sigma weight residual 121.54 128.09 -6.55 1.91e+00 2.74e-01 1.17e+01 angle pdb=" C ASN A 379 " pdb=" N ASN A 380 " pdb=" CA ASN A 380 " ideal model delta sigma weight residual 121.54 127.99 -6.45 1.91e+00 2.74e-01 1.14e+01 ... (remaining 45844 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.68: 18890 21.68 - 43.37: 1141 43.37 - 65.05: 120 65.05 - 86.73: 21 86.73 - 108.42: 9 Dihedral angle restraints: 20181 sinusoidal: 7911 harmonic: 12270 Sorted by residual: 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 93.00 147.35 -54.35 1 1.00e+01 1.00e-02 4.00e+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 93.00 146.89 -53.89 1 1.00e+01 1.00e-02 3.94e+01 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 93.00 146.68 -53.68 1 1.00e+01 1.00e-02 3.91e+01 ... (remaining 20178 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.125: 5085 0.125 - 0.250: 105 0.250 - 0.374: 3 0.374 - 0.499: 0 0.499 - 0.624: 3 Chirality restraints: 5196 Sorted by residual: 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 -1.78 -0.62 2.00e-01 2.50e+01 9.73e+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 -1.78 -0.62 2.00e-01 2.50e+01 9.66e+00 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 -1.83 -0.57 2.00e-01 2.50e+01 8.07e+00 ... (remaining 5193 not shown) Planarity restraints: 5898 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 889 " -0.047 5.00e-02 4.00e+02 7.10e-02 8.07e+00 pdb=" N PRO A 890 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO A 890 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 890 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 889 " 0.047 5.00e-02 4.00e+02 7.06e-02 7.98e+00 pdb=" N PRO C 890 " -0.122 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 6.96e-02 7.76e+00 pdb=" N PRO B 890 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO B 890 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 890 " -0.039 5.00e-02 4.00e+02 ... (remaining 5895 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 10146 2.83 - 3.34: 26483 3.34 - 3.86: 54527 3.86 - 4.38: 60124 4.38 - 4.90: 107610 Nonbonded interactions: 258890 Sorted by model distance: nonbonded pdb=" OH TYR A 836 " pdb=" OD1 ASP A1080 " model vdw 2.308 3.040 nonbonded pdb=" OG SER A 348 " pdb=" OD1 ASN A 351 " model vdw 2.322 3.040 nonbonded pdb=" OH TYR C 836 " pdb=" OD1 ASP C1080 " model vdw 2.323 3.040 nonbonded pdb=" OG SER B 348 " pdb=" OD1 ASN B 351 " model vdw 2.324 3.040 nonbonded pdb=" O CYS C 930 " pdb=" OH TYR C 945 " model vdw 2.326 3.040 ... (remaining 258885 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: 0.04 Found NCS groups: ncs_group { reference = chain 'X' selection = chain 'H' selection = chain 'D' } ncs_group { reference = chain 'Y' selection = chain 'L' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'A' selection = chain 'B' } 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: 2.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 30.630 Find NCS groups from input model: 0.200 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5577 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 0.102 33762 Z= 0.170 Angle : 0.683 21.052 46032 Z= 0.359 Chirality : 0.050 0.624 5196 Planarity : 0.006 0.071 5883 Dihedral : 13.235 108.416 12150 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.00 % Favored : 96.93 % Rotamer: Outliers : 0.03 % Allowed : 0.27 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.17 % 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: -1.49 (0.12), residues: 4170 helix: -1.30 (0.16), residues: 798 sheet: -0.28 (0.17), residues: 924 loop : -1.16 (0.11), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1125 TYR 0.014 0.001 TYR A 625 PHE 0.017 0.001 PHE B 122 TRP 0.015 0.001 TRP D 114 HIS 0.005 0.001 HIS B 215 Details of bonding type rmsd covalent geometry : bond 0.00338 (33678) covalent geometry : angle 0.64391 (45849) SS BOND : bond 0.00241 ( 69) SS BOND : angle 1.19111 ( 138) hydrogen bonds : bond 0.24020 ( 1186) hydrogen bonds : angle 8.41374 ( 3381) link_NAG-ASN : bond 0.01599 ( 15) link_NAG-ASN : angle 7.14542 ( 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 805 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 804 time to evaluate : 1.059 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: X 33 TYR cc_start: 0.5912 (m-10) cc_final: 0.5550 (m-10) REVERT: C 57 TYR cc_start: 0.6261 (m-80) cc_final: 0.5556 (m-80) REVERT: C 61 THR cc_start: 0.6315 (p) cc_final: 0.5958 (p) REVERT: C 199 TYR cc_start: 0.6412 (t80) cc_final: 0.5184 (t80) REVERT: C 233 VAL cc_start: 0.5972 (m) cc_final: 0.5682 (m) REVERT: C 289 ASP cc_start: 0.5961 (t0) cc_final: 0.5291 (t0) REVERT: C 292 SER cc_start: 0.8653 (t) cc_final: 0.7998 (p) REVERT: C 293 ASP cc_start: 0.7146 (p0) cc_final: 0.6554 (p0) REVERT: C 301 LYS cc_start: 0.7295 (tptp) cc_final: 0.7035 (ttpt) REVERT: C 326 TYR cc_start: 0.7282 (t80) cc_final: 0.7028 (t80) REVERT: C 380 ASN cc_start: 0.7691 (m-40) cc_final: 0.7275 (m110) REVERT: C 382 ASP cc_start: 0.7137 (p0) cc_final: 0.6890 (p0) REVERT: C 411 LEU cc_start: 0.8709 (tp) cc_final: 0.8470 (tt) REVERT: C 848 THR cc_start: 0.6150 (t) cc_final: 0.5883 (p) REVERT: C 946 LYS cc_start: 0.7318 (mmtp) cc_final: 0.6955 (mtpp) REVERT: C 950 VAL cc_start: 0.6539 (t) cc_final: 0.6324 (m) REVERT: C 1051 GLN cc_start: 0.5902 (mm-40) cc_final: 0.5327 (mm-40) REVERT: C 1056 PHE cc_start: 0.7955 (m-80) cc_final: 0.7743 (m-80) REVERT: C 1059 ILE cc_start: 0.8444 (pt) cc_final: 0.8243 (mt) REVERT: H 94 TYR cc_start: 0.4982 (m-80) cc_final: 0.4754 (m-80) REVERT: A 230 THR cc_start: 0.7323 (m) cc_final: 0.6720 (p) REVERT: A 298 ILE cc_start: 0.7236 (mm) cc_final: 0.7032 (mt) REVERT: A 301 LYS cc_start: 0.7035 (tptp) cc_final: 0.6627 (ttmt) REVERT: A 326 TYR cc_start: 0.7556 (t80) cc_final: 0.7318 (t80) REVERT: A 340 TRP cc_start: 0.7380 (t-100) cc_final: 0.7178 (t-100) REVERT: A 379 ASN cc_start: 0.7518 (t0) cc_final: 0.7289 (t0) REVERT: A 380 ASN cc_start: 0.7616 (m-40) cc_final: 0.7395 (m110) REVERT: A 409 LEU cc_start: 0.8033 (mt) cc_final: 0.7779 (mp) REVERT: A 411 LEU cc_start: 0.8645 (tp) cc_final: 0.8316 (tt) REVERT: A 631 LEU cc_start: 0.8651 (mt) cc_final: 0.8438 (mt) REVERT: A 642 THR cc_start: 0.7811 (p) cc_final: 0.7513 (t) REVERT: A 720 ASP cc_start: 0.4861 (m-30) cc_final: 0.4549 (m-30) REVERT: A 723 LEU cc_start: 0.6758 (mt) cc_final: 0.6501 (mt) REVERT: A 835 GLU cc_start: 0.6069 (mt-10) cc_final: 0.5772 (mt-10) REVERT: A 838 SER cc_start: 0.6185 (t) cc_final: 0.4985 (t) REVERT: A 848 THR cc_start: 0.5880 (t) cc_final: 0.5437 (p) REVERT: A 950 VAL cc_start: 0.6374 (t) cc_final: 0.5967 (t) REVERT: A 951 LEU cc_start: 0.6116 (mt) cc_final: 0.5624 (mp) REVERT: A 1059 ILE cc_start: 0.8048 (pt) cc_final: 0.7633 (mt) REVERT: B 289 ASP cc_start: 0.6859 (t0) cc_final: 0.6428 (t70) REVERT: B 293 ASP cc_start: 0.7268 (p0) cc_final: 0.6525 (p0) REVERT: B 301 LYS cc_start: 0.7086 (tptp) cc_final: 0.6723 (ttpt) REVERT: B 591 ILE cc_start: 0.7981 (mt) cc_final: 0.7679 (mm) REVERT: B 596 ILE cc_start: 0.7973 (mp) cc_final: 0.7742 (mt) REVERT: B 642 THR cc_start: 0.7769 (p) cc_final: 0.7504 (t) REVERT: B 666 THR cc_start: 0.7337 (p) cc_final: 0.6949 (p) REVERT: B 720 ASP cc_start: 0.5299 (m-30) cc_final: 0.4853 (m-30) REVERT: B 951 LEU cc_start: 0.6412 (mt) cc_final: 0.6027 (mp) REVERT: B 1067 LEU cc_start: 0.7483 (mt) cc_final: 0.7264 (mp) outliers start: 1 outliers final: 0 residues processed: 805 average time/residue: 0.2100 time to fit residues: 270.9475 Evaluate side-chains 643 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 643 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 3.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 0.0470 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.0030 chunk 207 optimal weight: 0.6980 chunk 401 optimal weight: 0.8980 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 0.6980 overall best weight: 0.4688 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 303 GLN ** C 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 552 HIS C 655 ASN C 851 ASN C1050 GLN ** C1064 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1096 GLN L 92 ASN A 208 ASN A 303 GLN A 475 HIS ** A 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 ASN ** A 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 844 ASN A1054 ASN F 92 ASN B 167 ASN ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 HIS B 303 GLN B 363 ASN B 552 HIS ** B 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 728 ASN B 802 ASN B 851 ASN B 858 GLN B1054 ASN B1096 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.216067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.183228 restraints weight = 59199.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.188436 restraints weight = 31888.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.191654 restraints weight = 19968.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.193695 restraints weight = 14170.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.194994 restraints weight = 11113.906| |-----------------------------------------------------------------------------| r_work (final): 0.4398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5970 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 33762 Z= 0.129 Angle : 0.612 14.831 46032 Z= 0.320 Chirality : 0.046 0.503 5196 Planarity : 0.005 0.102 5883 Dihedral : 6.751 99.829 4887 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.31 % Favored : 96.62 % Rotamer: Outliers : 1.24 % Allowed : 8.79 % Favored : 89.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.17 % 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: -0.87 (0.12), residues: 4170 helix: -0.12 (0.17), residues: 786 sheet: -0.17 (0.16), residues: 996 loop : -0.88 (0.12), residues: 2388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 76 TYR 0.024 0.001 TYR A 274 PHE 0.020 0.001 PHE B 484 TRP 0.029 0.001 TRP B 452 HIS 0.017 0.001 HIS B 177 Details of bonding type rmsd covalent geometry : bond 0.00276 (33678) covalent geometry : angle 0.58519 (45849) SS BOND : bond 0.00486 ( 69) SS BOND : angle 1.84594 ( 138) hydrogen bonds : bond 0.04792 ( 1186) hydrogen bonds : angle 6.26788 ( 3381) link_NAG-ASN : bond 0.01133 ( 15) link_NAG-ASN : angle 4.88249 ( 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 702 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 657 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: X 69 ILE cc_start: 0.6904 (mp) cc_final: 0.6654 (mm) REVERT: C 57 TYR cc_start: 0.6536 (m-80) cc_final: 0.6007 (m-80) REVERT: C 106 LYS cc_start: 0.8105 (tttt) cc_final: 0.7242 (tttm) REVERT: C 143 ARG cc_start: 0.4044 (ttt180) cc_final: 0.3514 (ttt180) REVERT: C 213 TYR cc_start: 0.6761 (m-80) cc_final: 0.5840 (m-80) REVERT: C 230 THR cc_start: 0.7523 (m) cc_final: 0.7174 (t) REVERT: C 289 ASP cc_start: 0.6172 (t0) cc_final: 0.5849 (t70) REVERT: C 292 SER cc_start: 0.8224 (t) cc_final: 0.7548 (p) REVERT: C 293 ASP cc_start: 0.7457 (p0) cc_final: 0.6907 (p0) REVERT: C 295 MET cc_start: 0.5802 (ptm) cc_final: 0.5569 (ptm) REVERT: C 355 LYS cc_start: 0.7310 (tttp) cc_final: 0.7066 (tptm) REVERT: C 357 PHE cc_start: 0.7301 (m-10) cc_final: 0.6411 (m-10) REVERT: C 435 TYR cc_start: 0.7391 (p90) cc_final: 0.6814 (p90) REVERT: C 451 THR cc_start: 0.6430 (p) cc_final: 0.5292 (m) REVERT: C 481 GLN cc_start: 0.7477 (tt0) cc_final: 0.7199 (tt0) REVERT: C 611 GLN cc_start: 0.7444 (tm-30) cc_final: 0.7087 (tm-30) REVERT: C 653 ASP cc_start: 0.7622 (t0) cc_final: 0.7412 (t70) REVERT: C 663 ASP cc_start: 0.7513 (t0) cc_final: 0.7230 (t0) REVERT: C 671 MET cc_start: 0.6626 (mmm) cc_final: 0.6055 (mmm) REVERT: C 720 ASP cc_start: 0.6296 (m-30) cc_final: 0.6054 (m-30) REVERT: C 835 GLU cc_start: 0.6994 (mt-10) cc_final: 0.6637 (mm-30) REVERT: C 841 ASP cc_start: 0.7300 (m-30) cc_final: 0.6957 (m-30) REVERT: C 938 ASP cc_start: 0.8277 (t0) cc_final: 0.8060 (t0) REVERT: C 950 VAL cc_start: 0.6678 (t) cc_final: 0.6138 (p) REVERT: C 1043 GLU cc_start: 0.7180 (mt-10) cc_final: 0.6832 (mt-10) REVERT: C 1051 GLN cc_start: 0.7393 (mm-40) cc_final: 0.7085 (tp-100) REVERT: C 1056 PHE cc_start: 0.8086 (m-80) cc_final: 0.7631 (m-80) REVERT: C 1059 ILE cc_start: 0.8591 (pt) cc_final: 0.8388 (mt) REVERT: L 35 TRP cc_start: 0.4963 (m100) cc_final: 0.4683 (m100) REVERT: A 78 MET cc_start: 0.5533 (mmp) cc_final: 0.5312 (mmt) REVERT: A 106 LYS cc_start: 0.8008 (tttt) cc_final: 0.7444 (tttm) REVERT: A 143 ARG cc_start: 0.3700 (ttp-170) cc_final: 0.3195 (ttp-170) REVERT: A 230 THR cc_start: 0.7635 (m) cc_final: 0.7060 (p) REVERT: A 298 ILE cc_start: 0.7499 (mm) cc_final: 0.7225 (mt) REVERT: A 326 TYR cc_start: 0.7404 (t80) cc_final: 0.7182 (t80) REVERT: A 379 ASN cc_start: 0.7838 (t0) cc_final: 0.7410 (t0) REVERT: A 380 ASN cc_start: 0.7977 (m-40) cc_final: 0.7704 (m-40) REVERT: A 409 LEU cc_start: 0.8288 (mt) cc_final: 0.8081 (mp) REVERT: A 435 TYR cc_start: 0.7569 (p90) cc_final: 0.7021 (p90) REVERT: A 624 ASN cc_start: 0.6615 (p0) cc_final: 0.6195 (p0) REVERT: A 631 LEU cc_start: 0.8784 (mt) cc_final: 0.8429 (mp) REVERT: A 642 THR cc_start: 0.8151 (p) cc_final: 0.7792 (t) REVERT: A 663 ASP cc_start: 0.7359 (t0) cc_final: 0.7121 (t0) REVERT: A 671 MET cc_start: 0.6584 (mmm) cc_final: 0.6235 (mmm) REVERT: A 699 LYS cc_start: 0.6459 (mmmt) cc_final: 0.6140 (mmmm) REVERT: A 720 ASP cc_start: 0.6147 (m-30) cc_final: 0.5794 (m-30) REVERT: A 723 LEU cc_start: 0.7204 (mt) cc_final: 0.6977 (mt) REVERT: A 804 VAL cc_start: 0.1180 (m) cc_final: 0.0383 (t) REVERT: A 833 LEU cc_start: 0.7302 (tp) cc_final: 0.6806 (tp) REVERT: A 852 GLU cc_start: 0.7358 (mt-10) cc_final: 0.6988 (mt-10) REVERT: A 1005 ASN cc_start: 0.4554 (p0) cc_final: 0.4077 (p0) REVERT: A 1049 LEU cc_start: 0.8786 (tp) cc_final: 0.8572 (tt) REVERT: A 1050 GLN cc_start: 0.8074 (mm-40) cc_final: 0.7650 (mm-40) REVERT: A 1059 ILE cc_start: 0.8092 (pt) cc_final: 0.7575 (mt) REVERT: A 1080 ASP cc_start: 0.7766 (t0) cc_final: 0.7546 (t70) REVERT: A 1105 LYS cc_start: 0.8548 (ttmt) cc_final: 0.8333 (mtpt) REVERT: F 4 MET cc_start: 0.4251 (tpt) cc_final: 0.3993 (tpt) REVERT: B 203 PHE cc_start: 0.7329 (m-80) cc_final: 0.6894 (m-80) REVERT: B 289 ASP cc_start: 0.6878 (t0) cc_final: 0.6420 (t70) REVERT: B 293 ASP cc_start: 0.7270 (p0) cc_final: 0.6781 (p0) REVERT: B 295 MET cc_start: 0.5904 (ptm) cc_final: 0.5627 (ptm) REVERT: B 340 TRP cc_start: 0.7953 (t-100) cc_final: 0.7353 (t-100) REVERT: B 380 ASN cc_start: 0.7927 (m-40) cc_final: 0.7676 (m-40) REVERT: B 455 ARG cc_start: 0.7261 (mtp-110) cc_final: 0.7007 (ttp80) REVERT: B 591 ILE cc_start: 0.7817 (mt) cc_final: 0.7419 (mm) REVERT: B 596 ILE cc_start: 0.8000 (mp) cc_final: 0.7782 (mt) REVERT: B 642 THR cc_start: 0.8117 (p) cc_final: 0.7788 (t) REVERT: B 663 ASP cc_start: 0.7269 (t0) cc_final: 0.6747 (t0) REVERT: B 666 THR cc_start: 0.7511 (p) cc_final: 0.7150 (p) REVERT: B 671 MET cc_start: 0.6743 (mmm) cc_final: 0.6440 (mmm) REVERT: B 673 ARG cc_start: 0.7174 (mtp85) cc_final: 0.6971 (mtp85) REVERT: B 711 ARG cc_start: 0.6873 (mtm180) cc_final: 0.6636 (mtm180) REVERT: B 720 ASP cc_start: 0.6545 (m-30) cc_final: 0.6149 (m-30) REVERT: B 835 GLU cc_start: 0.6904 (mt-10) cc_final: 0.6549 (mt-10) REVERT: B 852 GLU cc_start: 0.6889 (mt-10) cc_final: 0.6488 (mt-10) REVERT: B 951 LEU cc_start: 0.7151 (mt) cc_final: 0.6524 (mp) REVERT: B 1050 GLN cc_start: 0.8049 (mm-40) cc_final: 0.7848 (mm-40) REVERT: B 1064 GLN cc_start: 0.7863 (tt0) cc_final: 0.7581 (tt0) REVERT: B 1105 LYS cc_start: 0.8268 (tttm) cc_final: 0.7960 (mtpp) outliers start: 45 outliers final: 26 residues processed: 674 average time/residue: 0.2003 time to fit residues: 219.8950 Evaluate side-chains 647 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 621 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 83 SER Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain C residue 317 TYR Chi-restraints excluded: chain C residue 397 ASP Chi-restraints excluded: chain C residue 615 THR Chi-restraints excluded: chain C residue 741 ASP Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 1045 LEU Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 615 THR Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 701 ASN Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 948 ILE Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 397 ASP Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 600 VAL Chi-restraints excluded: chain B residue 615 THR Chi-restraints excluded: chain B residue 769 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 133 optimal weight: 7.9990 chunk 369 optimal weight: 2.9990 chunk 371 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 22 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 376 optimal weight: 1.9990 chunk 341 optimal weight: 0.6980 chunk 339 optimal weight: 0.9980 chunk 256 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 380 ASN C 418 GLN C 707 ASN ** C1064 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 92 ASN A 208 ASN A 418 GLN A 655 ASN A 714 GLN ** A 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 793 GLN A 858 GLN A1064 GLN A1226 ASN F 92 ASN B 167 ASN ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 HIS B 215 HIS B 714 GLN B 728 ASN B 858 GLN ** B 867 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.205915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.173862 restraints weight = 58726.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.178901 restraints weight = 31265.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.182057 restraints weight = 19479.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.184059 restraints weight = 13753.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.185364 restraints weight = 10749.091| |-----------------------------------------------------------------------------| r_work (final): 0.4266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6220 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 33762 Z= 0.219 Angle : 0.680 14.130 46032 Z= 0.362 Chirality : 0.048 0.455 5196 Planarity : 0.005 0.044 5883 Dihedral : 6.442 95.579 4887 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.86 % Favored : 96.07 % Rotamer: Outliers : 1.81 % Allowed : 10.80 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.17 % 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: -0.85 (0.12), residues: 4170 helix: -0.14 (0.17), residues: 786 sheet: -0.04 (0.17), residues: 897 loop : -0.90 (0.12), residues: 2487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C1069 TYR 0.026 0.002 TYR A 274 PHE 0.025 0.003 PHE C 456 TRP 0.029 0.002 TRP B 452 HIS 0.009 0.002 HIS B 552 Details of bonding type rmsd covalent geometry : bond 0.00455 (33678) covalent geometry : angle 0.66240 (45849) SS BOND : bond 0.00831 ( 69) SS BOND : angle 1.49447 ( 138) hydrogen bonds : bond 0.04856 ( 1186) hydrogen bonds : angle 6.13818 ( 3381) link_NAG-ASN : bond 0.00852 ( 15) link_NAG-ASN : angle 4.38447 ( 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 791 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 725 time to evaluate : 0.956 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: C 78 MET cc_start: 0.6116 (mmp) cc_final: 0.5868 (mmp) REVERT: C 106 LYS cc_start: 0.8275 (tttt) cc_final: 0.7484 (tttm) REVERT: C 143 ARG cc_start: 0.4522 (ttt180) cc_final: 0.3603 (mtp180) REVERT: C 205 TYR cc_start: 0.7828 (p90) cc_final: 0.7466 (p90) REVERT: C 230 THR cc_start: 0.7985 (m) cc_final: 0.7626 (p) REVERT: C 289 ASP cc_start: 0.7092 (t0) cc_final: 0.6019 (t70) REVERT: C 292 SER cc_start: 0.8145 (t) cc_final: 0.7676 (p) REVERT: C 311 VAL cc_start: 0.6963 (t) cc_final: 0.6722 (p) REVERT: C 327 ARG cc_start: 0.7044 (mmm160) cc_final: 0.6690 (mmm-85) REVERT: C 401 ILE cc_start: 0.7937 (mm) cc_final: 0.7543 (mt) REVERT: C 425 ASP cc_start: 0.7542 (t70) cc_final: 0.7131 (t0) REVERT: C 451 THR cc_start: 0.6425 (p) cc_final: 0.5413 (m) REVERT: C 556 LEU cc_start: 0.7432 (mt) cc_final: 0.7073 (mm) REVERT: C 645 ASN cc_start: 0.8055 (t0) cc_final: 0.7712 (p0) REVERT: C 648 GLN cc_start: 0.7410 (mt0) cc_final: 0.7115 (mt0) REVERT: C 663 ASP cc_start: 0.7582 (t0) cc_final: 0.7377 (t0) REVERT: C 671 MET cc_start: 0.6432 (mmm) cc_final: 0.6224 (mmm) REVERT: C 673 ARG cc_start: 0.7235 (mtp85) cc_final: 0.6424 (mtt90) REVERT: C 720 ASP cc_start: 0.6613 (m-30) cc_final: 0.6356 (m-30) REVERT: C 728 ASN cc_start: 0.8494 (m-40) cc_final: 0.8215 (m-40) REVERT: C 799 THR cc_start: 0.3857 (t) cc_final: 0.2784 (m) REVERT: C 807 ILE cc_start: 0.6974 (mt) cc_final: 0.6571 (pt) REVERT: C 816 ILE cc_start: 0.8106 (mm) cc_final: 0.7887 (mt) REVERT: C 833 LEU cc_start: 0.7818 (tp) cc_final: 0.7334 (tt) REVERT: C 835 GLU cc_start: 0.7002 (mt-10) cc_final: 0.6715 (mm-30) REVERT: C 917 LYS cc_start: 0.6462 (ptmm) cc_final: 0.6169 (ptmm) REVERT: C 1043 GLU cc_start: 0.7262 (mt-10) cc_final: 0.6852 (mt-10) REVERT: C 1046 ASN cc_start: 0.8340 (t0) cc_final: 0.8104 (t0) REVERT: C 1051 GLN cc_start: 0.7575 (mm-40) cc_final: 0.7002 (mm-40) REVERT: C 1079 ILE cc_start: 0.8659 (mt) cc_final: 0.8371 (mm) REVERT: A 78 MET cc_start: 0.6028 (mmp) cc_final: 0.5796 (mmt) REVERT: A 106 LYS cc_start: 0.8175 (tttt) cc_final: 0.7710 (ttpp) REVERT: A 143 ARG cc_start: 0.3972 (ttp-170) cc_final: 0.2732 (mtp180) REVERT: A 230 THR cc_start: 0.7884 (m) cc_final: 0.7471 (p) REVERT: A 235 LYS cc_start: 0.7854 (mtmm) cc_final: 0.7360 (mtmm) REVERT: A 329 LYS cc_start: 0.7547 (tttp) cc_final: 0.7304 (tttp) REVERT: A 377 THR cc_start: 0.7792 (m) cc_final: 0.7448 (p) REVERT: A 379 ASN cc_start: 0.8131 (t0) cc_final: 0.7695 (t0) REVERT: A 380 ASN cc_start: 0.8128 (m-40) cc_final: 0.7801 (m-40) REVERT: A 401 ILE cc_start: 0.8085 (mm) cc_final: 0.7742 (mt) REVERT: A 446 ARG cc_start: 0.6223 (ptp90) cc_final: 0.5702 (ptp-170) REVERT: A 481 GLN cc_start: 0.7719 (tt0) cc_final: 0.7369 (tp40) REVERT: A 601 ASN cc_start: 0.7796 (p0) cc_final: 0.7376 (p0) REVERT: A 602 SER cc_start: 0.8090 (t) cc_final: 0.7585 (m) REVERT: A 631 LEU cc_start: 0.8858 (mt) cc_final: 0.8463 (mp) REVERT: A 635 ILE cc_start: 0.8004 (pt) cc_final: 0.7739 (pt) REVERT: A 642 THR cc_start: 0.8230 (p) cc_final: 0.7884 (t) REVERT: A 661 PHE cc_start: 0.7735 (p90) cc_final: 0.7437 (p90) REVERT: A 668 ARG cc_start: 0.7229 (mtp85) cc_final: 0.7020 (ttp-110) REVERT: A 671 MET cc_start: 0.6430 (mmm) cc_final: 0.5967 (mmm) REVERT: A 711 ARG cc_start: 0.7411 (mtm180) cc_final: 0.7142 (mtm180) REVERT: A 723 LEU cc_start: 0.7565 (mt) cc_final: 0.7359 (mt) REVERT: A 728 ASN cc_start: 0.8526 (m-40) cc_final: 0.8263 (m-40) REVERT: A 799 THR cc_start: 0.4307 (t) cc_final: 0.3335 (m) REVERT: A 830 LYS cc_start: 0.8263 (mttt) cc_final: 0.8020 (mmmm) REVERT: A 852 GLU cc_start: 0.7549 (mt-10) cc_final: 0.6993 (mt-10) REVERT: A 863 ASN cc_start: 0.6372 (t0) cc_final: 0.5957 (t0) REVERT: A 910 ASP cc_start: 0.7602 (p0) cc_final: 0.7321 (m-30) REVERT: A 928 ASN cc_start: 0.7828 (t0) cc_final: 0.7537 (m-40) REVERT: A 938 ASP cc_start: 0.8368 (t0) cc_final: 0.8136 (t0) REVERT: A 948 ILE cc_start: 0.8422 (mm) cc_final: 0.8146 (mp) REVERT: A 949 LYS cc_start: 0.8165 (mttt) cc_final: 0.7918 (mttt) REVERT: A 1050 GLN cc_start: 0.8136 (mm-40) cc_final: 0.7691 (mm-40) REVERT: A 1059 ILE cc_start: 0.8354 (pt) cc_final: 0.8072 (mt) REVERT: A 1065 GLU cc_start: 0.7169 (mt-10) cc_final: 0.6951 (mt-10) REVERT: A 1079 ILE cc_start: 0.8466 (mt) cc_final: 0.8086 (mm) REVERT: A 1080 ASP cc_start: 0.7889 (t0) cc_final: 0.7442 (t0) REVERT: A 1097 GLN cc_start: 0.8354 (tp40) cc_final: 0.7996 (tp40) REVERT: B 57 TYR cc_start: 0.7437 (m-80) cc_final: 0.6551 (m-80) REVERT: B 106 LYS cc_start: 0.8264 (ttmm) cc_final: 0.7905 (ttmm) REVERT: B 230 THR cc_start: 0.7882 (m) cc_final: 0.7623 (t) REVERT: B 235 LYS cc_start: 0.8041 (pttm) cc_final: 0.7739 (pttm) REVERT: B 252 MET cc_start: 0.7251 (ptp) cc_final: 0.6915 (tpt) REVERT: B 293 ASP cc_start: 0.7166 (p0) cc_final: 0.6786 (p0) REVERT: B 295 MET cc_start: 0.6596 (ptm) cc_final: 0.6383 (ptm) REVERT: B 312 TYR cc_start: 0.7141 (m-80) cc_final: 0.6807 (m-10) REVERT: B 340 TRP cc_start: 0.8132 (t-100) cc_final: 0.7841 (t-100) REVERT: B 379 ASN cc_start: 0.8302 (t0) cc_final: 0.7693 (t0) REVERT: B 380 ASN cc_start: 0.8312 (m-40) cc_final: 0.7991 (m-40) REVERT: B 425 ASP cc_start: 0.7532 (t70) cc_final: 0.7167 (p0) REVERT: B 559 LYS cc_start: 0.7266 (pttt) cc_final: 0.6952 (pttt) REVERT: B 591 ILE cc_start: 0.8117 (mt) cc_final: 0.7657 (mm) REVERT: B 596 ILE cc_start: 0.8104 (mp) cc_final: 0.7887 (mt) REVERT: B 645 ASN cc_start: 0.8210 (t0) cc_final: 0.7956 (t0) REVERT: B 654 SER cc_start: 0.8484 (m) cc_final: 0.8124 (p) REVERT: B 663 ASP cc_start: 0.7279 (t0) cc_final: 0.6946 (t0) REVERT: B 671 MET cc_start: 0.6714 (mmm) cc_final: 0.6021 (mmm) REVERT: B 679 ARG cc_start: 0.6358 (mmm-85) cc_final: 0.6149 (mmm-85) REVERT: B 711 ARG cc_start: 0.7413 (mtm180) cc_final: 0.7186 (mtm180) REVERT: B 720 ASP cc_start: 0.6701 (m-30) cc_final: 0.6299 (m-30) REVERT: B 799 THR cc_start: 0.4063 (t) cc_final: 0.3159 (m) REVERT: B 822 VAL cc_start: 0.8712 (t) cc_final: 0.8439 (p) REVERT: B 852 GLU cc_start: 0.7117 (mt-10) cc_final: 0.6726 (mt-10) REVERT: B 948 ILE cc_start: 0.8501 (mm) cc_final: 0.8247 (mp) REVERT: B 1065 GLU cc_start: 0.7168 (mt-10) cc_final: 0.6590 (mm-30) REVERT: B 1069 ARG cc_start: 0.7865 (mtp180) cc_final: 0.7630 (ptm160) REVERT: B 1076 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7405 (mt-10) REVERT: B 1083 ILE cc_start: 0.8598 (pt) cc_final: 0.8354 (mt) REVERT: B 1091 ASN cc_start: 0.8453 (m110) cc_final: 0.8203 (m110) REVERT: B 1105 LYS cc_start: 0.8317 (tttm) cc_final: 0.8043 (mtpp) outliers start: 66 outliers final: 40 residues processed: 752 average time/residue: 0.1994 time to fit residues: 244.3087 Evaluate side-chains 710 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 670 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 83 SER Chi-restraints excluded: chain X residue 103 SER Chi-restraints excluded: chain Y residue 14 SER Chi-restraints excluded: chain Y residue 65 SER Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 199 TYR Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 317 TYR Chi-restraints excluded: chain C residue 397 ASP Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 615 THR Chi-restraints excluded: chain C residue 741 ASP Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 803 MET Chi-restraints excluded: chain C residue 1045 LEU Chi-restraints excluded: chain C residue 1062 SER Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 701 ASN Chi-restraints excluded: chain A residue 802 ASN Chi-restraints excluded: chain A residue 834 VAL Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 1060 SER Chi-restraints excluded: chain A residue 1062 SER Chi-restraints excluded: chain A residue 1141 ASN Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain B residue 37 SER Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain B residue 397 ASP Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 549 ILE Chi-restraints excluded: chain B residue 590 ASN Chi-restraints excluded: chain B residue 615 THR Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 866 MET Chi-restraints excluded: chain B residue 940 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 221 optimal weight: 2.9990 chunk 96 optimal weight: 7.9990 chunk 306 optimal weight: 8.9990 chunk 164 optimal weight: 0.8980 chunk 87 optimal weight: 0.5980 chunk 265 optimal weight: 0.7980 chunk 275 optimal weight: 8.9990 chunk 56 optimal weight: 0.7980 chunk 351 optimal weight: 5.9990 chunk 140 optimal weight: 30.0000 chunk 237 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 802 ASN C1050 GLN C1226 ASN A 552 HIS ** A 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 858 GLN A1054 ASN ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN B 336 ASN B 802 ASN B 858 GLN ** B 867 ASN ** 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 = 0.4581 r_free = 0.4581 target = 0.206102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.173836 restraints weight = 58219.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.178935 restraints weight = 31187.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.182153 restraints weight = 19468.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.184189 restraints weight = 13732.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.185503 restraints weight = 10664.098| |-----------------------------------------------------------------------------| r_work (final): 0.4281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6204 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 33762 Z= 0.132 Angle : 0.614 12.825 46032 Z= 0.315 Chirality : 0.046 0.453 5196 Planarity : 0.004 0.044 5883 Dihedral : 5.887 88.616 4887 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.36 % Favored : 96.59 % Rotamer: Outliers : 2.06 % Allowed : 13.22 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.17 % 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: -0.56 (0.13), residues: 4170 helix: 0.48 (0.18), residues: 762 sheet: 0.07 (0.17), residues: 936 loop : -0.80 (0.12), residues: 2472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 55 TYR 0.028 0.001 TYR B 718 PHE 0.018 0.002 PHE C 376 TRP 0.032 0.002 TRP B 452 HIS 0.007 0.001 HIS B 177 Details of bonding type rmsd covalent geometry : bond 0.00280 (33678) covalent geometry : angle 0.59483 (45849) SS BOND : bond 0.00292 ( 69) SS BOND : angle 1.63332 ( 138) hydrogen bonds : bond 0.04002 ( 1186) hydrogen bonds : angle 5.81562 ( 3381) link_NAG-ASN : bond 0.00807 ( 15) link_NAG-ASN : angle 4.15644 ( 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 758 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 683 time to evaluate : 1.123 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: C 78 MET cc_start: 0.5955 (mmp) cc_final: 0.5744 (mmp) REVERT: C 106 LYS cc_start: 0.8282 (tttt) cc_final: 0.7450 (tttm) REVERT: C 143 ARG cc_start: 0.4440 (ttt180) cc_final: 0.3600 (ttp-170) REVERT: C 200 LYS cc_start: 0.7829 (mptt) cc_final: 0.7608 (mppt) REVERT: C 205 TYR cc_start: 0.7857 (p90) cc_final: 0.7559 (p90) REVERT: C 230 THR cc_start: 0.7801 (m) cc_final: 0.7446 (p) REVERT: C 234 THR cc_start: 0.8149 (p) cc_final: 0.7880 (t) REVERT: C 293 ASP cc_start: 0.7551 (p0) cc_final: 0.7282 (p0) REVERT: C 295 MET cc_start: 0.6497 (ptm) cc_final: 0.6173 (ptm) REVERT: C 311 VAL cc_start: 0.7015 (t) cc_final: 0.6778 (p) REVERT: C 327 ARG cc_start: 0.7121 (mmm160) cc_final: 0.6907 (mmm-85) REVERT: C 344 LYS cc_start: 0.7857 (ptpt) cc_final: 0.7388 (ptpt) REVERT: C 355 LYS cc_start: 0.7545 (tppt) cc_final: 0.7161 (tptm) REVERT: C 357 PHE cc_start: 0.7389 (m-10) cc_final: 0.6500 (m-10) REVERT: C 379 ASN cc_start: 0.8327 (t0) cc_final: 0.7661 (t0) REVERT: C 380 ASN cc_start: 0.8321 (m-40) cc_final: 0.8012 (m110) REVERT: C 401 ILE cc_start: 0.7956 (mm) cc_final: 0.7563 (mt) REVERT: C 425 ASP cc_start: 0.7602 (t70) cc_final: 0.7205 (t70) REVERT: C 451 THR cc_start: 0.6464 (p) cc_final: 0.5570 (m) REVERT: C 452 TRP cc_start: 0.7413 (p-90) cc_final: 0.7202 (p-90) REVERT: C 633 GLN cc_start: 0.7350 (mm-40) cc_final: 0.7067 (mm-40) REVERT: C 663 ASP cc_start: 0.7220 (t0) cc_final: 0.6812 (t0) REVERT: C 671 MET cc_start: 0.6457 (mmm) cc_final: 0.6155 (mmm) REVERT: C 711 ARG cc_start: 0.7502 (mtm180) cc_final: 0.7287 (mtm180) REVERT: C 720 ASP cc_start: 0.6654 (m-30) cc_final: 0.6437 (m-30) REVERT: C 728 ASN cc_start: 0.8540 (m-40) cc_final: 0.8092 (m-40) REVERT: C 799 THR cc_start: 0.4252 (t) cc_final: 0.3204 (m) REVERT: C 807 ILE cc_start: 0.6979 (mt) cc_final: 0.6613 (pt) REVERT: C 816 ILE cc_start: 0.8072 (mm) cc_final: 0.7831 (mt) REVERT: C 833 LEU cc_start: 0.7748 (tp) cc_final: 0.7263 (tt) REVERT: C 917 LYS cc_start: 0.6390 (ptmm) cc_final: 0.6117 (ptmm) REVERT: C 1043 GLU cc_start: 0.7199 (mt-10) cc_final: 0.6790 (mt-10) REVERT: C 1046 ASN cc_start: 0.8268 (t0) cc_final: 0.8009 (t0) REVERT: C 1051 GLN cc_start: 0.7413 (mm-40) cc_final: 0.7060 (mm-40) REVERT: C 1052 LEU cc_start: 0.8727 (tp) cc_final: 0.8326 (tp) REVERT: C 1069 ARG cc_start: 0.8162 (mtp180) cc_final: 0.7899 (ptm160) REVERT: C 1076 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7465 (mt-10) REVERT: C 1079 ILE cc_start: 0.8651 (mt) cc_final: 0.8366 (mm) REVERT: A 78 MET cc_start: 0.5885 (mmp) cc_final: 0.5659 (mmt) REVERT: A 106 LYS cc_start: 0.8206 (tttt) cc_final: 0.7782 (ttpp) REVERT: A 143 ARG cc_start: 0.3962 (ttp-170) cc_final: 0.2744 (mtp180) REVERT: A 230 THR cc_start: 0.7816 (m) cc_final: 0.7462 (p) REVERT: A 235 LYS cc_start: 0.7827 (mtmm) cc_final: 0.7323 (mtmm) REVERT: A 252 MET cc_start: 0.7075 (ptp) cc_final: 0.6861 (pmm) REVERT: A 377 THR cc_start: 0.7914 (m) cc_final: 0.7543 (p) REVERT: A 379 ASN cc_start: 0.8197 (t0) cc_final: 0.7704 (t0) REVERT: A 380 ASN cc_start: 0.8114 (m-40) cc_final: 0.7814 (m110) REVERT: A 446 ARG cc_start: 0.6154 (ptp90) cc_final: 0.5416 (ptp-170) REVERT: A 601 ASN cc_start: 0.7492 (p0) cc_final: 0.7138 (p0) REVERT: A 602 SER cc_start: 0.7909 (t) cc_final: 0.7356 (m) REVERT: A 606 CYS cc_start: 0.5069 (m) cc_final: 0.4662 (m) REVERT: A 631 LEU cc_start: 0.8798 (mt) cc_final: 0.8412 (mp) REVERT: A 633 GLN cc_start: 0.7276 (mm-40) cc_final: 0.6946 (mm-40) REVERT: A 635 ILE cc_start: 0.8122 (pt) cc_final: 0.7866 (pt) REVERT: A 642 THR cc_start: 0.8235 (p) cc_final: 0.7913 (t) REVERT: A 661 PHE cc_start: 0.7694 (p90) cc_final: 0.7243 (p90) REVERT: A 668 ARG cc_start: 0.7247 (mtp85) cc_final: 0.7019 (ttp-110) REVERT: A 679 ARG cc_start: 0.6533 (mtp85) cc_final: 0.6301 (mtp85) REVERT: A 699 LYS cc_start: 0.6766 (mmmm) cc_final: 0.6356 (mmmm) REVERT: A 711 ARG cc_start: 0.7409 (mtm180) cc_final: 0.7125 (mtm180) REVERT: A 720 ASP cc_start: 0.6634 (m-30) cc_final: 0.6075 (m-30) REVERT: A 723 LEU cc_start: 0.7551 (mt) cc_final: 0.7344 (mt) REVERT: A 728 ASN cc_start: 0.8547 (m-40) cc_final: 0.8269 (m-40) REVERT: A 799 THR cc_start: 0.4586 (t) cc_final: 0.3638 (m) REVERT: A 804 VAL cc_start: 0.4864 (OUTLIER) cc_final: 0.4631 (p) REVERT: A 830 LYS cc_start: 0.8226 (mttt) cc_final: 0.7969 (mmmm) REVERT: A 848 THR cc_start: 0.8197 (p) cc_final: 0.7782 (p) REVERT: A 852 GLU cc_start: 0.7504 (mt-10) cc_final: 0.6897 (mt-10) REVERT: A 863 ASN cc_start: 0.6364 (t0) cc_final: 0.5897 (t0) REVERT: A 910 ASP cc_start: 0.7637 (p0) cc_final: 0.7366 (m-30) REVERT: A 928 ASN cc_start: 0.7803 (t0) cc_final: 0.7550 (m-40) REVERT: A 1050 GLN cc_start: 0.8113 (mm-40) cc_final: 0.7271 (mm-40) REVERT: A 1059 ILE cc_start: 0.8391 (pt) cc_final: 0.8024 (mt) REVERT: A 1064 GLN cc_start: 0.8055 (tt0) cc_final: 0.7678 (tt0) REVERT: A 1065 GLU cc_start: 0.7202 (mt-10) cc_final: 0.6763 (mt-10) REVERT: A 1079 ILE cc_start: 0.8430 (mt) cc_final: 0.8070 (mm) REVERT: F 65 SER cc_start: 0.7530 (t) cc_final: 0.7236 (p) REVERT: B 143 ARG cc_start: 0.4546 (ttt180) cc_final: 0.4077 (ttp-170) REVERT: B 230 THR cc_start: 0.7932 (m) cc_final: 0.7673 (t) REVERT: B 235 LYS cc_start: 0.8008 (pttm) cc_final: 0.7679 (pttm) REVERT: B 239 ASN cc_start: 0.8284 (OUTLIER) cc_final: 0.7890 (m-40) REVERT: B 293 ASP cc_start: 0.7179 (p0) cc_final: 0.6779 (p0) REVERT: B 295 MET cc_start: 0.6374 (ptm) cc_final: 0.6158 (ptm) REVERT: B 340 TRP cc_start: 0.8102 (t-100) cc_final: 0.7813 (t-100) REVERT: B 379 ASN cc_start: 0.8174 (t0) cc_final: 0.7627 (t0) REVERT: B 425 ASP cc_start: 0.7529 (t70) cc_final: 0.7221 (t70) REVERT: B 591 ILE cc_start: 0.8175 (mt) cc_final: 0.7679 (mm) REVERT: B 596 ILE cc_start: 0.8157 (mp) cc_final: 0.7850 (mt) REVERT: B 662 ARG cc_start: 0.7909 (ptm160) cc_final: 0.7590 (ptp-170) REVERT: B 663 ASP cc_start: 0.7269 (t0) cc_final: 0.6869 (t0) REVERT: B 671 MET cc_start: 0.6614 (mmm) cc_final: 0.6184 (mmm) REVERT: B 720 ASP cc_start: 0.6788 (m-30) cc_final: 0.6444 (m-30) REVERT: B 799 THR cc_start: 0.4408 (t) cc_final: 0.3481 (m) REVERT: B 852 GLU cc_start: 0.7083 (mt-10) cc_final: 0.6620 (mt-10) REVERT: B 913 PHE cc_start: 0.7888 (m-80) cc_final: 0.7630 (m-80) REVERT: B 1050 GLN cc_start: 0.8038 (mm-40) cc_final: 0.7346 (mm-40) REVERT: B 1064 GLN cc_start: 0.7905 (tt0) cc_final: 0.7697 (tt0) REVERT: B 1065 GLU cc_start: 0.7107 (mt-10) cc_final: 0.6506 (mm-30) REVERT: B 1069 ARG cc_start: 0.7761 (mtp180) cc_final: 0.7530 (ptm160) REVERT: B 1091 ASN cc_start: 0.8444 (m110) cc_final: 0.8083 (m110) REVERT: B 1105 LYS cc_start: 0.8422 (tttm) cc_final: 0.8109 (mtpp) REVERT: B 1112 MET cc_start: 0.7038 (mtm) cc_final: 0.6783 (mtp) REVERT: B 1210 MET cc_start: 0.3335 (ppp) cc_final: 0.1651 (pmm) outliers start: 75 outliers final: 47 residues processed: 713 average time/residue: 0.2071 time to fit residues: 239.8834 Evaluate side-chains 709 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 660 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 32 TYR Chi-restraints excluded: chain X residue 94 TYR Chi-restraints excluded: chain Y residue 65 SER Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 199 TYR Chi-restraints excluded: chain C residue 317 TYR Chi-restraints excluded: chain C residue 363 ASN Chi-restraints excluded: chain C residue 397 ASP Chi-restraints excluded: chain C residue 615 THR Chi-restraints excluded: chain C residue 741 ASP Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 1045 LEU Chi-restraints excluded: chain C residue 1062 SER Chi-restraints excluded: chain C residue 1112 MET Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 363 ASN Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 740 CYS Chi-restraints excluded: chain A residue 802 ASN Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 834 VAL Chi-restraints excluded: chain A residue 855 ASP Chi-restraints excluded: chain A residue 1060 SER Chi-restraints excluded: chain A residue 1062 SER Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 363 ASN Chi-restraints excluded: chain B residue 397 ASP Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 549 ILE Chi-restraints excluded: chain B residue 590 ASN Chi-restraints excluded: chain B residue 615 THR Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 866 MET Chi-restraints excluded: chain B residue 1099 SER Chi-restraints excluded: chain B residue 1103 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 236 optimal weight: 1.9990 chunk 134 optimal weight: 9.9990 chunk 394 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 17 optimal weight: 8.9990 chunk 119 optimal weight: 0.8980 chunk 215 optimal weight: 1.9990 chunk 209 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 255 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 90 GLN C 418 GLN ** C 633 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 648 GLN C 793 GLN C 858 GLN L 6 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 GLN A 552 HIS A 573 GLN A 649 ASN A 714 GLN A 858 GLN A1091 ASN ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 GLN B 336 ASN B 380 ASN B 590 ASN B 858 GLN B1041 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.190468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.157086 restraints weight = 58158.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.162271 restraints weight = 30430.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.165618 restraints weight = 18710.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.167848 restraints weight = 12948.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.169103 restraints weight = 9947.795| |-----------------------------------------------------------------------------| r_work (final): 0.4145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6427 moved from start: 0.5227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 33762 Z= 0.308 Angle : 0.807 12.704 46032 Z= 0.431 Chirality : 0.052 0.394 5196 Planarity : 0.006 0.084 5883 Dihedral : 6.067 73.997 4887 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.64 % Favored : 94.34 % Rotamer: Outliers : 3.19 % Allowed : 14.29 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.17 % 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: -1.17 (0.12), residues: 4170 helix: -0.20 (0.18), residues: 741 sheet: -0.47 (0.17), residues: 969 loop : -1.08 (0.12), residues: 2460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1125 TYR 0.037 0.003 TYR B 963 PHE 0.037 0.003 PHE A 104 TRP 0.033 0.003 TRP B 452 HIS 0.010 0.002 HIS C1150 Details of bonding type rmsd covalent geometry : bond 0.00645 (33678) covalent geometry : angle 0.79004 (45849) SS BOND : bond 0.00516 ( 69) SS BOND : angle 1.84009 ( 138) hydrogen bonds : bond 0.05362 ( 1186) hydrogen bonds : angle 6.47726 ( 3381) link_NAG-ASN : bond 0.00561 ( 15) link_NAG-ASN : angle 4.43954 ( 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 869 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 753 time to evaluate : 1.206 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: C 57 TYR cc_start: 0.7632 (m-80) cc_final: 0.7051 (m-80) REVERT: C 78 MET cc_start: 0.6296 (mmp) cc_final: 0.6065 (mmp) REVERT: C 106 LYS cc_start: 0.8275 (tttt) cc_final: 0.7666 (tttm) REVERT: C 143 ARG cc_start: 0.4351 (ttt180) cc_final: 0.3779 (ttt180) REVERT: C 230 THR cc_start: 0.7969 (m) cc_final: 0.7668 (p) REVERT: C 235 LYS cc_start: 0.7673 (OUTLIER) cc_final: 0.7296 (mtmm) REVERT: C 240 VAL cc_start: 0.8958 (t) cc_final: 0.8743 (p) REVERT: C 311 VAL cc_start: 0.7236 (t) cc_final: 0.7032 (p) REVERT: C 344 LYS cc_start: 0.8220 (ptpt) cc_final: 0.7751 (ptpt) REVERT: C 345 SER cc_start: 0.7906 (t) cc_final: 0.7681 (p) REVERT: C 363 ASN cc_start: 0.5678 (OUTLIER) cc_final: 0.5385 (p0) REVERT: C 377 THR cc_start: 0.7715 (OUTLIER) cc_final: 0.7422 (p) REVERT: C 379 ASN cc_start: 0.8503 (t0) cc_final: 0.8009 (t0) REVERT: C 380 ASN cc_start: 0.8401 (m-40) cc_final: 0.7969 (m-40) REVERT: C 425 ASP cc_start: 0.7493 (t70) cc_final: 0.7056 (t0) REVERT: C 437 LEU cc_start: 0.7744 (mm) cc_final: 0.7511 (mm) REVERT: C 605 THR cc_start: 0.8230 (m) cc_final: 0.7698 (t) REVERT: C 663 ASP cc_start: 0.7378 (t0) cc_final: 0.6927 (t0) REVERT: C 685 HIS cc_start: 0.7592 (t-90) cc_final: 0.7189 (t-90) REVERT: C 711 ARG cc_start: 0.7710 (mtm180) cc_final: 0.7447 (mtm180) REVERT: C 714 GLN cc_start: 0.8092 (mm110) cc_final: 0.7866 (mp-120) REVERT: C 720 ASP cc_start: 0.7116 (m-30) cc_final: 0.6866 (m-30) REVERT: C 728 ASN cc_start: 0.8468 (m-40) cc_final: 0.7975 (m-40) REVERT: C 807 ILE cc_start: 0.7043 (mt) cc_final: 0.6719 (pt) REVERT: C 838 SER cc_start: 0.8020 (OUTLIER) cc_final: 0.7775 (p) REVERT: C 848 THR cc_start: 0.8240 (p) cc_final: 0.7112 (t) REVERT: C 849 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7009 (pt0) REVERT: C 852 GLU cc_start: 0.7350 (mt-10) cc_final: 0.6770 (mt-10) REVERT: C 858 GLN cc_start: 0.7880 (OUTLIER) cc_final: 0.7668 (mt0) REVERT: C 917 LYS cc_start: 0.6675 (ptmm) cc_final: 0.6440 (ptmm) REVERT: C 938 ASP cc_start: 0.8314 (t0) cc_final: 0.8094 (t0) REVERT: C 965 LEU cc_start: 0.8045 (tt) cc_final: 0.7764 (tt) REVERT: C 1043 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7182 (mp0) REVERT: C 1051 GLN cc_start: 0.7547 (mm-40) cc_final: 0.7182 (mm-40) REVERT: C 1052 LEU cc_start: 0.8985 (tp) cc_final: 0.8677 (tp) REVERT: C 1064 GLN cc_start: 0.8194 (tt0) cc_final: 0.7962 (tt0) REVERT: C 1074 GLU cc_start: 0.7808 (tt0) cc_final: 0.7395 (tt0) REVERT: C 1076 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7617 (mt-10) REVERT: C 1078 GLN cc_start: 0.8507 (mm-40) cc_final: 0.8001 (mm-40) REVERT: C 1079 ILE cc_start: 0.8726 (mt) cc_final: 0.8473 (mm) REVERT: C 1224 MET cc_start: 0.4481 (tpp) cc_final: 0.4241 (tpp) REVERT: A 78 MET cc_start: 0.6148 (mmp) cc_final: 0.5941 (mmt) REVERT: A 99 PHE cc_start: 0.7407 (t80) cc_final: 0.6957 (t80) REVERT: A 106 LYS cc_start: 0.8221 (tttt) cc_final: 0.7719 (ttpp) REVERT: A 143 ARG cc_start: 0.4270 (ttp-170) cc_final: 0.2790 (mtp180) REVERT: A 230 THR cc_start: 0.7928 (m) cc_final: 0.7669 (p) REVERT: A 291 MET cc_start: 0.7040 (mmt) cc_final: 0.6808 (mmt) REVERT: A 293 ASP cc_start: 0.7737 (p0) cc_final: 0.7481 (p0) REVERT: A 315 ASN cc_start: 0.7847 (p0) cc_final: 0.7577 (p0) REVERT: A 319 VAL cc_start: 0.8277 (t) cc_final: 0.7996 (p) REVERT: A 344 LYS cc_start: 0.8278 (ptpt) cc_final: 0.7874 (ptpt) REVERT: A 355 LYS cc_start: 0.7563 (tptm) cc_final: 0.7307 (tptm) REVERT: A 363 ASN cc_start: 0.4436 (OUTLIER) cc_final: 0.4007 (p0) REVERT: A 368 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.8169 (mtp) REVERT: A 379 ASN cc_start: 0.8404 (t0) cc_final: 0.8074 (t0) REVERT: A 409 LEU cc_start: 0.8703 (mp) cc_final: 0.8446 (mp) REVERT: A 410 GLN cc_start: 0.8046 (mm-40) cc_final: 0.7789 (mm-40) REVERT: A 417 LEU cc_start: 0.8008 (mt) cc_final: 0.7789 (mp) REVERT: A 425 ASP cc_start: 0.7380 (t70) cc_final: 0.7012 (p0) REVERT: A 451 THR cc_start: 0.6894 (p) cc_final: 0.6008 (m) REVERT: A 601 ASN cc_start: 0.7438 (p0) cc_final: 0.6658 (p0) REVERT: A 602 SER cc_start: 0.8062 (t) cc_final: 0.7505 (m) REVERT: A 605 THR cc_start: 0.8444 (m) cc_final: 0.8168 (t) REVERT: A 631 LEU cc_start: 0.8788 (mt) cc_final: 0.8453 (mp) REVERT: A 635 ILE cc_start: 0.8101 (pt) cc_final: 0.7842 (pt) REVERT: A 668 ARG cc_start: 0.7506 (mtp85) cc_final: 0.7285 (ttp-110) REVERT: A 711 ARG cc_start: 0.7729 (mtm180) cc_final: 0.7455 (mtm180) REVERT: A 714 GLN cc_start: 0.8411 (mm-40) cc_final: 0.8076 (mp-120) REVERT: A 728 ASN cc_start: 0.8430 (m-40) cc_final: 0.8160 (m-40) REVERT: A 830 LYS cc_start: 0.8252 (mttt) cc_final: 0.7988 (mmmm) REVERT: A 848 THR cc_start: 0.8288 (p) cc_final: 0.7640 (t) REVERT: A 849 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.6971 (pt0) REVERT: A 852 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7119 (mt-10) REVERT: A 910 ASP cc_start: 0.7761 (p0) cc_final: 0.7526 (p0) REVERT: A 928 ASN cc_start: 0.8211 (t0) cc_final: 0.8010 (m-40) REVERT: A 949 LYS cc_start: 0.8535 (mttt) cc_final: 0.8327 (mttt) REVERT: A 1050 GLN cc_start: 0.8106 (mm-40) cc_final: 0.7322 (mm-40) REVERT: A 1059 ILE cc_start: 0.8509 (pt) cc_final: 0.8266 (mt) REVERT: A 1065 GLU cc_start: 0.7493 (mt-10) cc_final: 0.6893 (mt-10) REVERT: A 1153 TYR cc_start: 0.6448 (t80) cc_final: 0.6241 (t80) REVERT: B 143 ARG cc_start: 0.4882 (ttt180) cc_final: 0.4222 (ttp-170) REVERT: B 201 ARG cc_start: 0.6821 (ptm160) cc_final: 0.6506 (ptm-80) REVERT: B 205 TYR cc_start: 0.8179 (p90) cc_final: 0.7856 (p90) REVERT: B 230 THR cc_start: 0.8069 (m) cc_final: 0.7864 (p) REVERT: B 235 LYS cc_start: 0.7913 (pttm) cc_final: 0.7551 (pttm) REVERT: B 246 LEU cc_start: 0.6968 (mt) cc_final: 0.6662 (mt) REVERT: B 322 ILE cc_start: 0.8359 (OUTLIER) cc_final: 0.8108 (mm) REVERT: B 329 LYS cc_start: 0.8119 (tttp) cc_final: 0.7836 (tttp) REVERT: B 379 ASN cc_start: 0.8202 (t0) cc_final: 0.7781 (t0) REVERT: B 544 LYS cc_start: 0.7918 (OUTLIER) cc_final: 0.7702 (ptmm) REVERT: B 547 VAL cc_start: 0.8509 (p) cc_final: 0.8265 (m) REVERT: B 559 LYS cc_start: 0.7429 (pttt) cc_final: 0.7030 (pttt) REVERT: B 591 ILE cc_start: 0.8336 (mt) cc_final: 0.7833 (mm) REVERT: B 596 ILE cc_start: 0.8240 (OUTLIER) cc_final: 0.8006 (mt) REVERT: B 610 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8679 (tt) REVERT: B 652 TYR cc_start: 0.7710 (m-80) cc_final: 0.7256 (m-80) REVERT: B 653 ASP cc_start: 0.7700 (t0) cc_final: 0.7488 (t0) REVERT: B 654 SER cc_start: 0.8412 (m) cc_final: 0.8079 (p) REVERT: B 663 ASP cc_start: 0.7263 (t0) cc_final: 0.6962 (t0) REVERT: B 670 PHE cc_start: 0.6965 (m-80) cc_final: 0.6479 (m-80) REVERT: B 671 MET cc_start: 0.6452 (mmm) cc_final: 0.6108 (mmm) REVERT: B 679 ARG cc_start: 0.7062 (mmm-85) cc_final: 0.6827 (mtp85) REVERT: B 685 HIS cc_start: 0.7719 (t-90) cc_final: 0.7456 (t-90) REVERT: B 714 GLN cc_start: 0.8131 (mm-40) cc_final: 0.7881 (mp-120) REVERT: B 803 MET cc_start: 0.4776 (mmm) cc_final: 0.4392 (mmm) REVERT: B 804 VAL cc_start: 0.6750 (OUTLIER) cc_final: 0.6351 (p) REVERT: B 830 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.7978 (mmtp) REVERT: B 835 GLU cc_start: 0.6772 (mm-30) cc_final: 0.6483 (mm-30) REVERT: B 849 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7382 (pt0) REVERT: B 852 GLU cc_start: 0.7411 (mt-10) cc_final: 0.6989 (mt-10) REVERT: B 1050 GLN cc_start: 0.8239 (mm-40) cc_final: 0.7231 (mm-40) REVERT: B 1065 GLU cc_start: 0.7479 (mt-10) cc_final: 0.6841 (mm-30) REVERT: B 1069 ARG cc_start: 0.8089 (mtp180) cc_final: 0.7684 (ptm160) REVERT: B 1074 GLU cc_start: 0.7978 (tt0) cc_final: 0.7745 (tt0) REVERT: B 1091 ASN cc_start: 0.8439 (m110) cc_final: 0.7973 (m110) REVERT: B 1105 LYS cc_start: 0.8536 (tttm) cc_final: 0.8147 (mtpp) outliers start: 116 outliers final: 61 residues processed: 801 average time/residue: 0.1932 time to fit residues: 253.9952 Evaluate side-chains 793 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 716 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 32 TYR Chi-restraints excluded: chain Y residue 14 SER Chi-restraints excluded: chain Y residue 90 GLN Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 199 TYR Chi-restraints excluded: chain C residue 204 THR Chi-restraints excluded: chain C residue 235 LYS Chi-restraints excluded: chain C residue 363 ASN Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 397 ASP Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 615 THR Chi-restraints excluded: chain C residue 741 ASP Chi-restraints excluded: chain C residue 744 VAL Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 829 CYS Chi-restraints excluded: chain C residue 838 SER Chi-restraints excluded: chain C residue 839 PHE Chi-restraints excluded: chain C residue 849 GLU Chi-restraints excluded: chain C residue 858 GLN Chi-restraints excluded: chain C residue 1032 VAL Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 281 ASP Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 363 ASN Chi-restraints excluded: chain A residue 368 MET Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 638 GLU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 802 ASN Chi-restraints excluded: chain A residue 803 MET Chi-restraints excluded: chain A residue 834 VAL Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 849 GLU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 855 ASP Chi-restraints excluded: chain A residue 1060 SER Chi-restraints excluded: chain A residue 1062 SER Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 397 ASP Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 544 LYS Chi-restraints excluded: chain B residue 549 ILE Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 802 ASN Chi-restraints excluded: chain B residue 804 VAL Chi-restraints excluded: chain B residue 830 LYS Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 940 ILE Chi-restraints excluded: chain B residue 1103 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 408 optimal weight: 4.9990 chunk 346 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 50 optimal weight: 0.0870 chunk 306 optimal weight: 10.0000 chunk 213 optimal weight: 7.9990 chunk 19 optimal weight: 20.0000 chunk 196 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 377 optimal weight: 2.9990 overall best weight: 1.1160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1050 GLN C1131 ASN C1133 ASN L 90 GLN A 573 GLN A 858 GLN F 90 GLN ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 GLN ** B1064 GLN ** 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 = 0.4467 r_free = 0.4467 target = 0.192299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.160249 restraints weight = 57986.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.165143 restraints weight = 30979.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.168226 restraints weight = 19268.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.170356 restraints weight = 13547.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.171564 restraints weight = 10487.282| |-----------------------------------------------------------------------------| r_work (final): 0.4187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6361 moved from start: 0.5374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 33762 Z= 0.168 Angle : 0.693 13.676 46032 Z= 0.360 Chirality : 0.048 0.425 5196 Planarity : 0.004 0.045 5883 Dihedral : 5.703 80.127 4887 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.08 % Favored : 95.88 % Rotamer: Outliers : 2.56 % Allowed : 17.07 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.17 % 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: -0.97 (0.13), residues: 4170 helix: 0.34 (0.19), residues: 723 sheet: -0.48 (0.16), residues: 987 loop : -1.01 (0.12), residues: 2460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 679 TYR 0.056 0.002 TYR C 963 PHE 0.024 0.002 PHE C 490 TRP 0.035 0.002 TRP B 452 HIS 0.009 0.002 HIS B 177 Details of bonding type rmsd covalent geometry : bond 0.00360 (33678) covalent geometry : angle 0.66772 (45849) SS BOND : bond 0.00399 ( 69) SS BOND : angle 2.06861 ( 138) hydrogen bonds : bond 0.04230 ( 1186) hydrogen bonds : angle 6.04249 ( 3381) link_NAG-ASN : bond 0.00685 ( 15) link_NAG-ASN : angle 4.81390 ( 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 818 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 725 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 4 MET cc_start: 0.3606 (tpt) cc_final: 0.3405 (tpt) REVERT: C 78 MET cc_start: 0.6086 (mmp) cc_final: 0.5881 (mmp) REVERT: C 143 ARG cc_start: 0.4327 (ttt180) cc_final: 0.3653 (ttp-170) REVERT: C 205 TYR cc_start: 0.8092 (p90) cc_final: 0.7775 (p90) REVERT: C 230 THR cc_start: 0.7810 (m) cc_final: 0.7493 (p) REVERT: C 233 VAL cc_start: 0.6731 (OUTLIER) cc_final: 0.6490 (t) REVERT: C 235 LYS cc_start: 0.7544 (mtmm) cc_final: 0.7186 (mtmm) REVERT: C 240 VAL cc_start: 0.8892 (t) cc_final: 0.8657 (p) REVERT: C 311 VAL cc_start: 0.7169 (t) cc_final: 0.6969 (p) REVERT: C 344 LYS cc_start: 0.8245 (ptpt) cc_final: 0.7886 (ptpt) REVERT: C 361 ASN cc_start: 0.7387 (m-40) cc_final: 0.7175 (m-40) REVERT: C 377 THR cc_start: 0.7555 (OUTLIER) cc_final: 0.7254 (p) REVERT: C 379 ASN cc_start: 0.8360 (t0) cc_final: 0.7957 (t0) REVERT: C 380 ASN cc_start: 0.8334 (m-40) cc_final: 0.7987 (m-40) REVERT: C 671 MET cc_start: 0.6139 (mmm) cc_final: 0.5278 (mtp) REVERT: C 728 ASN cc_start: 0.8467 (m-40) cc_final: 0.7970 (m-40) REVERT: C 807 ILE cc_start: 0.7080 (mt) cc_final: 0.6684 (pt) REVERT: C 833 LEU cc_start: 0.7781 (tp) cc_final: 0.7261 (tt) REVERT: C 848 THR cc_start: 0.8059 (p) cc_final: 0.7084 (t) REVERT: C 849 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.6924 (pt0) REVERT: C 852 GLU cc_start: 0.7311 (mt-10) cc_final: 0.6723 (mt-10) REVERT: C 858 GLN cc_start: 0.7592 (mt0) cc_final: 0.7387 (mt0) REVERT: C 928 ASN cc_start: 0.7986 (t0) cc_final: 0.7728 (m-40) REVERT: C 965 LEU cc_start: 0.7877 (tt) cc_final: 0.7607 (tt) REVERT: C 1043 GLU cc_start: 0.7313 (mt-10) cc_final: 0.7019 (mt-10) REVERT: C 1051 GLN cc_start: 0.7485 (mm-40) cc_final: 0.7265 (tp-100) REVERT: C 1052 LEU cc_start: 0.8844 (tp) cc_final: 0.8518 (tp) REVERT: C 1064 GLN cc_start: 0.8062 (tt0) cc_final: 0.7854 (tt0) REVERT: C 1069 ARG cc_start: 0.8148 (mtp180) cc_final: 0.7905 (ptm160) REVERT: C 1074 GLU cc_start: 0.7612 (tt0) cc_final: 0.7232 (tt0) REVERT: C 1076 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7532 (mt-10) REVERT: C 1078 GLN cc_start: 0.8435 (mm-40) cc_final: 0.8057 (mm-40) REVERT: C 1079 ILE cc_start: 0.8647 (mt) cc_final: 0.8328 (mm) REVERT: A 64 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7510 (mp) REVERT: A 78 MET cc_start: 0.5849 (mmp) cc_final: 0.5616 (mmt) REVERT: A 99 PHE cc_start: 0.7102 (t80) cc_final: 0.6886 (t80) REVERT: A 106 LYS cc_start: 0.8225 (tttt) cc_final: 0.7815 (ttpp) REVERT: A 143 ARG cc_start: 0.4103 (ttp-170) cc_final: 0.2644 (mtp180) REVERT: A 200 LYS cc_start: 0.7584 (mppt) cc_final: 0.7303 (mppt) REVERT: A 230 THR cc_start: 0.7796 (m) cc_final: 0.7523 (p) REVERT: A 291 MET cc_start: 0.6912 (mmt) cc_final: 0.6615 (mmt) REVERT: A 293 ASP cc_start: 0.7702 (p0) cc_final: 0.7435 (p0) REVERT: A 315 ASN cc_start: 0.7726 (p0) cc_final: 0.7339 (p0) REVERT: A 326 TYR cc_start: 0.7558 (t80) cc_final: 0.6958 (t80) REVERT: A 344 LYS cc_start: 0.8172 (ptpt) cc_final: 0.7787 (ptpt) REVERT: A 372 GLN cc_start: 0.7720 (OUTLIER) cc_final: 0.7145 (tm-30) REVERT: A 377 THR cc_start: 0.8015 (m) cc_final: 0.7691 (p) REVERT: A 379 ASN cc_start: 0.8348 (t0) cc_final: 0.8015 (t0) REVERT: A 409 LEU cc_start: 0.8658 (mp) cc_final: 0.8342 (mp) REVERT: A 410 GLN cc_start: 0.7927 (mm-40) cc_final: 0.7605 (mp10) REVERT: A 425 ASP cc_start: 0.7309 (t70) cc_final: 0.6932 (p0) REVERT: A 451 THR cc_start: 0.6821 (p) cc_final: 0.5922 (m) REVERT: A 601 ASN cc_start: 0.7277 (p0) cc_final: 0.6714 (p0) REVERT: A 602 SER cc_start: 0.7951 (t) cc_final: 0.7376 (m) REVERT: A 612 LYS cc_start: 0.7515 (ptpt) cc_final: 0.7310 (ptpt) REVERT: A 631 LEU cc_start: 0.8899 (mt) cc_final: 0.8592 (mp) REVERT: A 635 ILE cc_start: 0.8100 (pt) cc_final: 0.7734 (pt) REVERT: A 699 LYS cc_start: 0.6961 (mmmm) cc_final: 0.6692 (mmmm) REVERT: A 711 ARG cc_start: 0.7622 (mtm180) cc_final: 0.7402 (mtm180) REVERT: A 718 TYR cc_start: 0.6215 (p90) cc_final: 0.5890 (p90) REVERT: A 728 ASN cc_start: 0.8528 (m-40) cc_final: 0.8255 (m-40) REVERT: A 835 GLU cc_start: 0.6884 (OUTLIER) cc_final: 0.6674 (mm-30) REVERT: A 849 GLU cc_start: 0.7559 (pt0) cc_final: 0.6704 (pt0) REVERT: A 852 GLU cc_start: 0.7539 (mt-10) cc_final: 0.6888 (mt-10) REVERT: A 863 ASN cc_start: 0.6744 (t0) cc_final: 0.6281 (t0) REVERT: A 928 ASN cc_start: 0.7918 (t0) cc_final: 0.7709 (m-40) REVERT: A 949 LYS cc_start: 0.8370 (mttt) cc_final: 0.8157 (mttt) REVERT: A 1005 ASN cc_start: 0.4694 (p0) cc_final: 0.4374 (p0) REVERT: A 1050 GLN cc_start: 0.7952 (mm-40) cc_final: 0.7236 (mm-40) REVERT: A 1059 ILE cc_start: 0.8520 (pt) cc_final: 0.8207 (mt) REVERT: A 1064 GLN cc_start: 0.8086 (tt0) cc_final: 0.7800 (tt0) REVERT: A 1065 GLU cc_start: 0.7247 (mt-10) cc_final: 0.6638 (mt-10) REVERT: A 1114 LYS cc_start: 0.7083 (ptpt) cc_final: 0.6846 (pttt) REVERT: D 111 MET cc_start: 0.4426 (tpt) cc_final: 0.4154 (tpt) REVERT: D 112 ASP cc_start: 0.7748 (OUTLIER) cc_final: 0.7437 (m-30) REVERT: B 64 LEU cc_start: 0.8144 (tp) cc_final: 0.7675 (tt) REVERT: B 106 LYS cc_start: 0.8525 (ttpp) cc_final: 0.8275 (ttmm) REVERT: B 143 ARG cc_start: 0.4870 (ttt180) cc_final: 0.4411 (ttp-170) REVERT: B 189 HIS cc_start: 0.8578 (p-80) cc_final: 0.8307 (p-80) REVERT: B 200 LYS cc_start: 0.7771 (mppt) cc_final: 0.7516 (mppt) REVERT: B 230 THR cc_start: 0.7982 (m) cc_final: 0.7686 (p) REVERT: B 235 LYS cc_start: 0.7989 (pttm) cc_final: 0.7648 (pttm) REVERT: B 322 ILE cc_start: 0.8264 (mm) cc_final: 0.8024 (mm) REVERT: B 326 TYR cc_start: 0.7780 (t80) cc_final: 0.7167 (t80) REVERT: B 329 LYS cc_start: 0.8017 (tttp) cc_final: 0.7660 (tttp) REVERT: B 379 ASN cc_start: 0.8190 (t0) cc_final: 0.7785 (t0) REVERT: B 397 ASP cc_start: 0.7088 (OUTLIER) cc_final: 0.6482 (p0) REVERT: B 446 ARG cc_start: 0.5852 (mpp80) cc_final: 0.5555 (mpp80) REVERT: B 477 VAL cc_start: 0.7788 (OUTLIER) cc_final: 0.6811 (m) REVERT: B 547 VAL cc_start: 0.8493 (p) cc_final: 0.8269 (m) REVERT: B 591 ILE cc_start: 0.8383 (mt) cc_final: 0.7887 (mm) REVERT: B 596 ILE cc_start: 0.8272 (OUTLIER) cc_final: 0.8004 (mt) REVERT: B 599 ASP cc_start: 0.7541 (t0) cc_final: 0.7092 (t70) REVERT: B 646 SER cc_start: 0.8751 (m) cc_final: 0.8466 (t) REVERT: B 652 TYR cc_start: 0.7618 (m-80) cc_final: 0.7270 (m-80) REVERT: B 654 SER cc_start: 0.8463 (m) cc_final: 0.8081 (p) REVERT: B 663 ASP cc_start: 0.7184 (t0) cc_final: 0.6910 (t0) REVERT: B 670 PHE cc_start: 0.6746 (m-80) cc_final: 0.6476 (m-80) REVERT: B 671 MET cc_start: 0.6401 (mmm) cc_final: 0.6043 (mmm) REVERT: B 699 LYS cc_start: 0.6867 (mmmm) cc_final: 0.6421 (mmmm) REVERT: B 720 ASP cc_start: 0.7086 (m-30) cc_final: 0.6252 (m-30) REVERT: B 830 LYS cc_start: 0.8275 (OUTLIER) cc_final: 0.7999 (mmtp) REVERT: B 833 LEU cc_start: 0.7750 (tp) cc_final: 0.7180 (tt) REVERT: B 852 GLU cc_start: 0.7239 (mt-10) cc_final: 0.6820 (mt-10) REVERT: B 1050 GLN cc_start: 0.8023 (mm-40) cc_final: 0.7039 (mm-40) REVERT: B 1065 GLU cc_start: 0.7153 (mt-10) cc_final: 0.6569 (mm-30) REVERT: B 1067 LEU cc_start: 0.8584 (tp) cc_final: 0.8244 (tt) REVERT: B 1069 ARG cc_start: 0.7998 (mtp180) cc_final: 0.7621 (ptm160) REVERT: B 1091 ASN cc_start: 0.8373 (m110) cc_final: 0.7925 (m110) REVERT: B 1105 LYS cc_start: 0.8560 (tttm) cc_final: 0.8180 (mtpp) outliers start: 93 outliers final: 55 residues processed: 773 average time/residue: 0.1978 time to fit residues: 249.0751 Evaluate side-chains 768 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 702 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 32 TYR Chi-restraints excluded: chain X residue 103 SER Chi-restraints excluded: chain Y residue 14 SER Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 199 TYR Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 317 TYR Chi-restraints excluded: chain C residue 363 ASN Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 397 ASP Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 570 CYS Chi-restraints excluded: chain C residue 615 THR Chi-restraints excluded: chain C residue 741 ASP Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 849 GLU Chi-restraints excluded: chain C residue 1062 SER Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 363 ASN Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 802 ASN Chi-restraints excluded: chain A residue 803 MET Chi-restraints excluded: chain A residue 834 VAL Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain A residue 855 ASP Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 1060 SER Chi-restraints excluded: chain A residue 1062 SER Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 90 GLN Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 353 GLU Chi-restraints excluded: chain B residue 363 ASN Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 397 ASP Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 544 LYS Chi-restraints excluded: chain B residue 549 ILE Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 830 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 180 optimal weight: 3.9990 chunk 221 optimal weight: 2.9990 chunk 198 optimal weight: 2.9990 chunk 285 optimal weight: 7.9990 chunk 317 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 187 optimal weight: 4.9990 chunk 30 optimal weight: 0.5980 chunk 220 optimal weight: 3.9990 chunk 185 optimal weight: 2.9990 chunk 141 optimal weight: 20.0000 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 90 GLN ** C 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 418 GLN C 573 GLN C 633 GLN ** C 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 714 GLN ** C 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 GLN A 633 GLN A1039 ASN A1133 ASN ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 649 ASN B 655 ASN B 858 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.187315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.154470 restraints weight = 57793.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.159619 restraints weight = 29951.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.162870 restraints weight = 18291.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.165092 restraints weight = 12673.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.166560 restraints weight = 9694.548| |-----------------------------------------------------------------------------| r_work (final): 0.4120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6472 moved from start: 0.6230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 33762 Z= 0.323 Angle : 0.818 16.357 46032 Z= 0.438 Chirality : 0.053 1.003 5196 Planarity : 0.005 0.053 5883 Dihedral : 6.156 73.545 4887 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.40 % Favored : 93.57 % Rotamer: Outliers : 3.05 % Allowed : 17.45 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.43 (0.12), residues: 4170 helix: -0.14 (0.18), residues: 738 sheet: -0.75 (0.16), residues: 969 loop : -1.29 (0.12), residues: 2463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B1125 TYR 0.046 0.003 TYR C 963 PHE 0.037 0.003 PHE A 458 TRP 0.035 0.003 TRP B 452 HIS 0.011 0.002 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00667 (33678) covalent geometry : angle 0.79113 (45849) SS BOND : bond 0.01065 ( 69) SS BOND : angle 2.47726 ( 138) hydrogen bonds : bond 0.05171 ( 1186) hydrogen bonds : angle 6.45514 ( 3381) link_NAG-ASN : bond 0.01013 ( 15) link_NAG-ASN : angle 5.30467 ( 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 853 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 742 time to evaluate : 1.169 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: C 57 TYR cc_start: 0.7611 (m-80) cc_final: 0.7054 (m-80) REVERT: C 78 MET cc_start: 0.6307 (mmp) cc_final: 0.6065 (mmp) REVERT: C 143 ARG cc_start: 0.4257 (ttt180) cc_final: 0.3696 (ttt180) REVERT: C 230 THR cc_start: 0.7962 (m) cc_final: 0.7672 (p) REVERT: C 235 LYS cc_start: 0.7688 (mtmm) cc_final: 0.7319 (mtmm) REVERT: C 240 VAL cc_start: 0.8903 (t) cc_final: 0.8662 (p) REVERT: C 315 ASN cc_start: 0.7497 (p0) cc_final: 0.7291 (p0) REVERT: C 327 ARG cc_start: 0.7380 (mmm-85) cc_final: 0.7144 (mmm-85) REVERT: C 343 ASP cc_start: 0.7623 (t70) cc_final: 0.7155 (p0) REVERT: C 355 LYS cc_start: 0.7700 (tppt) cc_final: 0.7180 (tptm) REVERT: C 357 PHE cc_start: 0.7629 (m-10) cc_final: 0.6948 (m-10) REVERT: C 377 THR cc_start: 0.7622 (OUTLIER) cc_final: 0.7386 (p) REVERT: C 398 LYS cc_start: 0.8527 (pttt) cc_final: 0.7573 (pttm) REVERT: C 465 LYS cc_start: 0.8326 (pttm) cc_final: 0.8020 (pttm) REVERT: C 479 TYR cc_start: 0.7435 (p90) cc_final: 0.7014 (p90) REVERT: C 591 ILE cc_start: 0.8338 (mt) cc_final: 0.8036 (mp) REVERT: C 605 THR cc_start: 0.8329 (OUTLIER) cc_final: 0.7897 (t) REVERT: C 671 MET cc_start: 0.6211 (mmm) cc_final: 0.5747 (mtp) REVERT: C 728 ASN cc_start: 0.8433 (m-40) cc_final: 0.7889 (m-40) REVERT: C 807 ILE cc_start: 0.7212 (mt) cc_final: 0.6802 (pt) REVERT: C 848 THR cc_start: 0.8151 (p) cc_final: 0.7310 (t) REVERT: C 849 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7118 (pt0) REVERT: C 852 GLU cc_start: 0.7385 (mt-10) cc_final: 0.6818 (mt-10) REVERT: C 946 LYS cc_start: 0.8386 (mmtp) cc_final: 0.8130 (mmtm) REVERT: C 965 LEU cc_start: 0.7964 (tt) cc_final: 0.7702 (tt) REVERT: C 1005 ASN cc_start: 0.4710 (p0) cc_final: 0.4388 (t0) REVERT: C 1028 ASN cc_start: 0.6497 (p0) cc_final: 0.6253 (p0) REVERT: C 1043 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7316 (mt-10) REVERT: C 1051 GLN cc_start: 0.7645 (mm-40) cc_final: 0.7248 (mm-40) REVERT: C 1052 LEU cc_start: 0.8945 (tp) cc_final: 0.8654 (tp) REVERT: C 1074 GLU cc_start: 0.7847 (tt0) cc_final: 0.7422 (tt0) REVERT: C 1076 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7588 (mt-10) REVERT: C 1078 GLN cc_start: 0.8492 (mm-40) cc_final: 0.8073 (mm-40) REVERT: C 1114 LYS cc_start: 0.7652 (ptpt) cc_final: 0.7310 (pttm) REVERT: A 78 MET cc_start: 0.6095 (mmp) cc_final: 0.5895 (mmt) REVERT: A 106 LYS cc_start: 0.8242 (tttt) cc_final: 0.7705 (ttpp) REVERT: A 143 ARG cc_start: 0.4327 (ttp-170) cc_final: 0.3081 (mtp180) REVERT: A 230 THR cc_start: 0.7842 (OUTLIER) cc_final: 0.7622 (p) REVERT: A 235 LYS cc_start: 0.7844 (mtmm) cc_final: 0.7429 (mtmm) REVERT: A 293 ASP cc_start: 0.7616 (p0) cc_final: 0.7341 (p0) REVERT: A 315 ASN cc_start: 0.7824 (p0) cc_final: 0.7510 (p0) REVERT: A 344 LYS cc_start: 0.8441 (ptpt) cc_final: 0.8143 (ptpt) REVERT: A 363 ASN cc_start: 0.5075 (OUTLIER) cc_final: 0.4770 (p0) REVERT: A 372 GLN cc_start: 0.7884 (OUTLIER) cc_final: 0.7273 (tm-30) REVERT: A 379 ASN cc_start: 0.8319 (t0) cc_final: 0.7981 (t0) REVERT: A 397 ASP cc_start: 0.7205 (p0) cc_final: 0.6766 (p0) REVERT: A 410 GLN cc_start: 0.7984 (mm-40) cc_final: 0.7649 (mm-40) REVERT: A 424 ILE cc_start: 0.8667 (OUTLIER) cc_final: 0.8171 (pt) REVERT: A 425 ASP cc_start: 0.7289 (t70) cc_final: 0.6804 (t0) REVERT: A 601 ASN cc_start: 0.7350 (p0) cc_final: 0.6652 (p0) REVERT: A 602 SER cc_start: 0.8084 (t) cc_final: 0.7345 (m) REVERT: A 631 LEU cc_start: 0.8926 (mt) cc_final: 0.8522 (mp) REVERT: A 644 TYR cc_start: 0.7664 (m-80) cc_final: 0.6928 (m-80) REVERT: A 652 TYR cc_start: 0.7541 (m-80) cc_final: 0.7197 (m-80) REVERT: A 673 ARG cc_start: 0.7045 (mtp85) cc_final: 0.6807 (mtt90) REVERT: A 718 TYR cc_start: 0.6253 (p90) cc_final: 0.5933 (p90) REVERT: A 728 ASN cc_start: 0.8457 (m-40) cc_final: 0.8164 (m-40) REVERT: A 768 PHE cc_start: 0.6952 (OUTLIER) cc_final: 0.6728 (m-80) REVERT: A 833 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7336 (mt) REVERT: A 835 GLU cc_start: 0.7009 (OUTLIER) cc_final: 0.6783 (mm-30) REVERT: A 849 GLU cc_start: 0.7799 (pt0) cc_final: 0.6990 (pt0) REVERT: A 852 GLU cc_start: 0.7583 (mt-10) cc_final: 0.6890 (mt-10) REVERT: A 863 ASN cc_start: 0.7137 (t0) cc_final: 0.6681 (t0) REVERT: A 928 ASN cc_start: 0.7831 (t0) cc_final: 0.7473 (m-40) REVERT: A 1005 ASN cc_start: 0.4684 (p0) cc_final: 0.4380 (p0) REVERT: A 1050 GLN cc_start: 0.8106 (mm-40) cc_final: 0.7381 (mm-40) REVERT: A 1059 ILE cc_start: 0.8497 (pt) cc_final: 0.8096 (mt) REVERT: A 1065 GLU cc_start: 0.7376 (mt-10) cc_final: 0.6554 (mt-10) REVERT: A 1114 LYS cc_start: 0.7321 (ptpt) cc_final: 0.7082 (pttt) REVERT: A 1196 TYR cc_start: 0.7106 (t80) cc_final: 0.6832 (t80) REVERT: D 33 TYR cc_start: 0.7042 (m-10) cc_final: 0.6692 (m-10) REVERT: D 112 ASP cc_start: 0.7877 (OUTLIER) cc_final: 0.7471 (m-30) REVERT: B 64 LEU cc_start: 0.8033 (tp) cc_final: 0.7631 (tt) REVERT: B 132 VAL cc_start: 0.8035 (t) cc_final: 0.7798 (p) REVERT: B 143 ARG cc_start: 0.4876 (ttt180) cc_final: 0.4271 (ttp-170) REVERT: B 189 HIS cc_start: 0.8663 (p-80) cc_final: 0.8341 (p-80) REVERT: B 230 THR cc_start: 0.8033 (m) cc_final: 0.7790 (p) REVERT: B 235 LYS cc_start: 0.8075 (pttm) cc_final: 0.7700 (pttm) REVERT: B 298 ILE cc_start: 0.7969 (mm) cc_final: 0.7738 (mm) REVERT: B 322 ILE cc_start: 0.8360 (mm) cc_final: 0.8108 (mm) REVERT: B 326 TYR cc_start: 0.7945 (t80) cc_final: 0.7480 (t80) REVERT: B 329 LYS cc_start: 0.8267 (tttp) cc_final: 0.7779 (tttp) REVERT: B 344 LYS cc_start: 0.8472 (ptpt) cc_final: 0.8201 (tptp) REVERT: B 357 PHE cc_start: 0.7333 (m-10) cc_final: 0.7012 (m-10) REVERT: B 379 ASN cc_start: 0.8210 (t0) cc_final: 0.7924 (m110) REVERT: B 397 ASP cc_start: 0.6912 (OUTLIER) cc_final: 0.6181 (p0) REVERT: B 442 VAL cc_start: 0.7808 (p) cc_final: 0.7472 (p) REVERT: B 461 ASP cc_start: 0.7353 (m-30) cc_final: 0.7036 (t70) REVERT: B 477 VAL cc_start: 0.7968 (OUTLIER) cc_final: 0.7118 (m) REVERT: B 478 VAL cc_start: 0.8390 (p) cc_final: 0.8018 (m) REVERT: B 547 VAL cc_start: 0.8501 (p) cc_final: 0.8202 (m) REVERT: B 591 ILE cc_start: 0.8487 (mt) cc_final: 0.8020 (mm) REVERT: B 596 ILE cc_start: 0.8307 (OUTLIER) cc_final: 0.8071 (mt) REVERT: B 599 ASP cc_start: 0.7479 (t0) cc_final: 0.7004 (t70) REVERT: B 646 SER cc_start: 0.8779 (m) cc_final: 0.8501 (t) REVERT: B 652 TYR cc_start: 0.7631 (m-80) cc_final: 0.7217 (m-80) REVERT: B 663 ASP cc_start: 0.7438 (t0) cc_final: 0.7125 (t0) REVERT: B 671 MET cc_start: 0.6410 (mmm) cc_final: 0.6198 (mtt) REVERT: B 805 GLU cc_start: 0.5862 (pm20) cc_final: 0.5639 (pm20) REVERT: B 849 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7111 (pt0) REVERT: B 852 GLU cc_start: 0.7396 (mt-10) cc_final: 0.7016 (mt-10) REVERT: B 861 VAL cc_start: 0.7578 (OUTLIER) cc_final: 0.7330 (t) REVERT: B 928 ASN cc_start: 0.7953 (t0) cc_final: 0.7554 (m-40) REVERT: B 1050 GLN cc_start: 0.8146 (mm-40) cc_final: 0.7197 (mm-40) REVERT: B 1065 GLU cc_start: 0.7502 (mt-10) cc_final: 0.6835 (mm-30) REVERT: B 1067 LEU cc_start: 0.8675 (tp) cc_final: 0.8347 (tt) REVERT: B 1069 ARG cc_start: 0.8143 (mtp180) cc_final: 0.7911 (ptm160) REVERT: B 1074 GLU cc_start: 0.8133 (tt0) cc_final: 0.7829 (tp30) REVERT: B 1105 LYS cc_start: 0.8625 (tttm) cc_final: 0.8041 (mtpp) REVERT: B 1210 MET cc_start: 0.3355 (ppp) cc_final: 0.1258 (pmm) outliers start: 111 outliers final: 68 residues processed: 795 average time/residue: 0.1978 time to fit residues: 256.5937 Evaluate side-chains 800 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 716 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 32 TYR Chi-restraints excluded: chain Y residue 14 SER Chi-restraints excluded: chain Y residue 90 GLN Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 199 TYR Chi-restraints excluded: chain C residue 340 TRP Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 397 ASP Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 570 CYS Chi-restraints excluded: chain C residue 600 VAL Chi-restraints excluded: chain C residue 605 THR Chi-restraints excluded: chain C residue 615 THR Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 741 ASP Chi-restraints excluded: chain C residue 744 VAL Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 803 MET Chi-restraints excluded: chain C residue 839 PHE Chi-restraints excluded: chain C residue 849 GLU Chi-restraints excluded: chain C residue 968 THR Chi-restraints excluded: chain C residue 1045 LEU Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 363 ASN Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 606 CYS Chi-restraints excluded: chain A residue 768 PHE Chi-restraints excluded: chain A residue 802 ASN Chi-restraints excluded: chain A residue 803 MET Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 834 VAL Chi-restraints excluded: chain A residue 835 GLU Chi-restraints excluded: chain A residue 855 ASP Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 1032 VAL Chi-restraints excluded: chain A residue 1060 SER Chi-restraints excluded: chain A residue 1062 SER Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 353 GLU Chi-restraints excluded: chain B residue 363 ASN Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 397 ASP Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 544 LYS Chi-restraints excluded: chain B residue 549 ILE Chi-restraints excluded: chain B residue 570 CYS Chi-restraints excluded: chain B residue 581 ASP Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 846 ILE Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 861 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 133 optimal weight: 4.9990 chunk 335 optimal weight: 0.2980 chunk 114 optimal weight: 3.9990 chunk 138 optimal weight: 20.0000 chunk 16 optimal weight: 0.9980 chunk 150 optimal weight: 7.9990 chunk 110 optimal weight: 0.8980 chunk 115 optimal weight: 0.5980 chunk 286 optimal weight: 6.9990 chunk 301 optimal weight: 10.0000 chunk 275 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 90 GLN C 101 ASN C 280 GLN C 802 ASN ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1050 GLN A 573 GLN A 714 GLN A1039 ASN A1133 ASN ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 336 ASN ** B 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 ASN B 858 GLN B1133 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.191612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.158728 restraints weight = 57721.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.163955 restraints weight = 29901.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.167294 restraints weight = 18262.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.169532 restraints weight = 12649.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.170937 restraints weight = 9684.677| |-----------------------------------------------------------------------------| r_work (final): 0.4174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6384 moved from start: 0.6242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 33762 Z= 0.146 Angle : 0.709 16.031 46032 Z= 0.368 Chirality : 0.047 0.422 5196 Planarity : 0.004 0.045 5883 Dihedral : 5.503 64.919 4887 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.27 % Favored : 95.66 % Rotamer: Outliers : 2.28 % Allowed : 18.77 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.17 % 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: -1.10 (0.12), residues: 4170 helix: 0.28 (0.19), residues: 735 sheet: -0.38 (0.17), residues: 939 loop : -1.20 (0.12), residues: 2496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 679 TYR 0.044 0.002 TYR C 963 PHE 0.038 0.002 PHE A 99 TRP 0.037 0.002 TRP B 452 HIS 0.007 0.001 HIS B 177 Details of bonding type rmsd covalent geometry : bond 0.00318 (33678) covalent geometry : angle 0.68704 (45849) SS BOND : bond 0.00370 ( 69) SS BOND : angle 2.05258 ( 138) hydrogen bonds : bond 0.04093 ( 1186) hydrogen bonds : angle 6.00710 ( 3381) link_NAG-ASN : bond 0.00736 ( 15) link_NAG-ASN : angle 4.54146 ( 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 801 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 718 time to evaluate : 1.110 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: C 78 MET cc_start: 0.6155 (mmp) cc_final: 0.5920 (mmp) REVERT: C 143 ARG cc_start: 0.4428 (ttt180) cc_final: 0.3740 (ttp-170) REVERT: C 205 TYR cc_start: 0.7951 (p90) cc_final: 0.7657 (p90) REVERT: C 230 THR cc_start: 0.7823 (m) cc_final: 0.7550 (p) REVERT: C 235 LYS cc_start: 0.7588 (mtmm) cc_final: 0.7182 (mtmm) REVERT: C 240 VAL cc_start: 0.8852 (t) cc_final: 0.8584 (p) REVERT: C 315 ASN cc_start: 0.7318 (p0) cc_final: 0.7061 (p0) REVERT: C 327 ARG cc_start: 0.7333 (mmm-85) cc_final: 0.7065 (mmm-85) REVERT: C 355 LYS cc_start: 0.7525 (tppt) cc_final: 0.7130 (tptm) REVERT: C 357 PHE cc_start: 0.7530 (m-10) cc_final: 0.6893 (m-10) REVERT: C 364 MET cc_start: 0.7622 (mtp) cc_final: 0.7413 (mtm) REVERT: C 380 ASN cc_start: 0.8420 (m-40) cc_final: 0.7973 (m-40) REVERT: C 406 LYS cc_start: 0.8611 (tptt) cc_final: 0.8298 (tptm) REVERT: C 455 ARG cc_start: 0.7426 (ttm-80) cc_final: 0.7065 (ttm-80) REVERT: C 479 TYR cc_start: 0.7352 (p90) cc_final: 0.6946 (p90) REVERT: C 644 TYR cc_start: 0.7665 (m-80) cc_final: 0.7343 (m-80) REVERT: C 671 MET cc_start: 0.6180 (mmm) cc_final: 0.5540 (mtp) REVERT: C 728 ASN cc_start: 0.8483 (m-40) cc_final: 0.7990 (m-40) REVERT: C 802 ASN cc_start: 0.7269 (OUTLIER) cc_final: 0.6760 (t0) REVERT: C 803 MET cc_start: 0.5897 (OUTLIER) cc_final: 0.5407 (mmm) REVERT: C 807 ILE cc_start: 0.7231 (mt) cc_final: 0.6864 (pt) REVERT: C 833 LEU cc_start: 0.7621 (tp) cc_final: 0.7175 (tt) REVERT: C 848 THR cc_start: 0.8015 (p) cc_final: 0.7082 (t) REVERT: C 849 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7009 (pt0) REVERT: C 852 GLU cc_start: 0.7358 (mt-10) cc_final: 0.6739 (mt-10) REVERT: C 928 ASN cc_start: 0.8048 (t0) cc_final: 0.7719 (m-40) REVERT: C 936 ILE cc_start: 0.6828 (tp) cc_final: 0.6582 (tp) REVERT: C 965 LEU cc_start: 0.7843 (tt) cc_final: 0.7553 (tt) REVERT: C 1005 ASN cc_start: 0.4736 (p0) cc_final: 0.4257 (t0) REVERT: C 1043 GLU cc_start: 0.7378 (mt-10) cc_final: 0.7059 (mt-10) REVERT: C 1050 GLN cc_start: 0.8036 (OUTLIER) cc_final: 0.7438 (mm-40) REVERT: C 1051 GLN cc_start: 0.7560 (mm-40) cc_final: 0.7208 (mm-40) REVERT: C 1052 LEU cc_start: 0.8821 (tp) cc_final: 0.8546 (tp) REVERT: C 1069 ARG cc_start: 0.8233 (mtp180) cc_final: 0.7844 (ptm160) REVERT: C 1074 GLU cc_start: 0.7734 (tt0) cc_final: 0.7352 (tt0) REVERT: C 1076 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7617 (mt-10) REVERT: C 1078 GLN cc_start: 0.8456 (mm-40) cc_final: 0.7985 (mm-40) REVERT: C 1079 ILE cc_start: 0.8558 (mt) cc_final: 0.8161 (mm) REVERT: C 1081 ARG cc_start: 0.8472 (mtt-85) cc_final: 0.8232 (mtt-85) REVERT: C 1105 LYS cc_start: 0.8203 (mtmm) cc_final: 0.7920 (mtpp) REVERT: A 64 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7428 (mp) REVERT: A 143 ARG cc_start: 0.3971 (ttp-170) cc_final: 0.2708 (mtp180) REVERT: A 187 LEU cc_start: 0.7026 (tp) cc_final: 0.6707 (tp) REVERT: A 200 LYS cc_start: 0.7564 (mppt) cc_final: 0.7301 (mppt) REVERT: A 235 LYS cc_start: 0.7771 (mtmm) cc_final: 0.7366 (mtmm) REVERT: A 293 ASP cc_start: 0.7611 (p0) cc_final: 0.7350 (p0) REVERT: A 312 TYR cc_start: 0.7294 (m-10) cc_final: 0.6891 (m-80) REVERT: A 315 ASN cc_start: 0.7679 (p0) cc_final: 0.7335 (p0) REVERT: A 326 TYR cc_start: 0.7527 (t80) cc_final: 0.6909 (t80) REVERT: A 344 LYS cc_start: 0.8391 (ptpt) cc_final: 0.7998 (ptpt) REVERT: A 382 ASP cc_start: 0.7652 (OUTLIER) cc_final: 0.7337 (p0) REVERT: A 397 ASP cc_start: 0.7088 (p0) cc_final: 0.6888 (p0) REVERT: A 424 ILE cc_start: 0.8633 (OUTLIER) cc_final: 0.8103 (pt) REVERT: A 425 ASP cc_start: 0.7279 (t70) cc_final: 0.6762 (t0) REVERT: A 435 TYR cc_start: 0.7791 (p90) cc_final: 0.7148 (p90) REVERT: A 479 TYR cc_start: 0.7641 (p90) cc_final: 0.7353 (p90) REVERT: A 601 ASN cc_start: 0.7303 (p0) cc_final: 0.6728 (p0) REVERT: A 602 SER cc_start: 0.7702 (t) cc_final: 0.7153 (m) REVERT: A 631 LEU cc_start: 0.8865 (mt) cc_final: 0.8507 (mt) REVERT: A 635 ILE cc_start: 0.7945 (pt) cc_final: 0.7632 (pt) REVERT: A 673 ARG cc_start: 0.6947 (mtp85) cc_final: 0.6653 (mtt90) REVERT: A 718 TYR cc_start: 0.6164 (p90) cc_final: 0.5876 (p90) REVERT: A 728 ASN cc_start: 0.8485 (m-40) cc_final: 0.8187 (m-40) REVERT: A 849 GLU cc_start: 0.7688 (pt0) cc_final: 0.6811 (pt0) REVERT: A 852 GLU cc_start: 0.7530 (mt-10) cc_final: 0.6808 (mt-10) REVERT: A 855 ASP cc_start: 0.7683 (OUTLIER) cc_final: 0.7321 (p0) REVERT: A 863 ASN cc_start: 0.7050 (t0) cc_final: 0.6666 (t0) REVERT: A 928 ASN cc_start: 0.7790 (t0) cc_final: 0.7434 (m-40) REVERT: A 1050 GLN cc_start: 0.7984 (mm-40) cc_final: 0.7202 (mm-40) REVERT: A 1059 ILE cc_start: 0.8527 (pt) cc_final: 0.8274 (mt) REVERT: A 1065 GLU cc_start: 0.7273 (mt-10) cc_final: 0.6403 (mt-10) REVERT: A 1114 LYS cc_start: 0.7233 (ptpt) cc_final: 0.6937 (pttt) REVERT: D 112 ASP cc_start: 0.7823 (OUTLIER) cc_final: 0.7269 (m-30) REVERT: B 143 ARG cc_start: 0.4760 (ttt180) cc_final: 0.4193 (ttp-170) REVERT: B 189 HIS cc_start: 0.8613 (p-80) cc_final: 0.8239 (p-80) REVERT: B 230 THR cc_start: 0.7865 (m) cc_final: 0.7602 (p) REVERT: B 235 LYS cc_start: 0.8006 (pttm) cc_final: 0.7631 (pttm) REVERT: B 322 ILE cc_start: 0.8329 (mm) cc_final: 0.8072 (mm) REVERT: B 326 TYR cc_start: 0.7769 (t80) cc_final: 0.7211 (t80) REVERT: B 329 LYS cc_start: 0.8111 (tttp) cc_final: 0.7648 (tttp) REVERT: B 357 PHE cc_start: 0.7157 (m-10) cc_final: 0.6928 (m-10) REVERT: B 397 ASP cc_start: 0.6904 (OUTLIER) cc_final: 0.6214 (p0) REVERT: B 461 ASP cc_start: 0.7222 (m-30) cc_final: 0.6901 (t70) REVERT: B 477 VAL cc_start: 0.7927 (OUTLIER) cc_final: 0.7022 (m) REVERT: B 478 VAL cc_start: 0.8270 (p) cc_final: 0.7820 (m) REVERT: B 544 LYS cc_start: 0.7966 (OUTLIER) cc_final: 0.7672 (ptmm) REVERT: B 545 SER cc_start: 0.8386 (p) cc_final: 0.8164 (t) REVERT: B 549 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7899 (tt) REVERT: B 591 ILE cc_start: 0.8470 (mt) cc_final: 0.8034 (mm) REVERT: B 596 ILE cc_start: 0.8341 (OUTLIER) cc_final: 0.8118 (mt) REVERT: B 599 ASP cc_start: 0.7496 (t0) cc_final: 0.6979 (t70) REVERT: B 646 SER cc_start: 0.8736 (m) cc_final: 0.8441 (t) REVERT: B 652 TYR cc_start: 0.7636 (m-80) cc_final: 0.7244 (m-80) REVERT: B 654 SER cc_start: 0.8352 (m) cc_final: 0.8129 (p) REVERT: B 663 ASP cc_start: 0.7172 (t0) cc_final: 0.6850 (t0) REVERT: B 671 MET cc_start: 0.6407 (mmm) cc_final: 0.6185 (mmm) REVERT: B 699 LYS cc_start: 0.7248 (mmmm) cc_final: 0.7007 (mmmm) REVERT: B 833 LEU cc_start: 0.7622 (tp) cc_final: 0.7125 (tt) REVERT: B 849 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7007 (pt0) REVERT: B 852 GLU cc_start: 0.7236 (mt-10) cc_final: 0.6820 (mt-10) REVERT: B 928 ASN cc_start: 0.7939 (t0) cc_final: 0.7564 (m-40) REVERT: B 960 PHE cc_start: 0.8167 (m-10) cc_final: 0.7721 (m-80) REVERT: B 1050 GLN cc_start: 0.8005 (mm-40) cc_final: 0.6975 (mm-40) REVERT: B 1051 GLN cc_start: 0.7710 (mm-40) cc_final: 0.7300 (mm-40) REVERT: B 1065 GLU cc_start: 0.7278 (mt-10) cc_final: 0.6598 (mm-30) REVERT: B 1067 LEU cc_start: 0.8560 (tp) cc_final: 0.8202 (tt) REVERT: B 1069 ARG cc_start: 0.8085 (mtp180) cc_final: 0.7731 (ptm160) REVERT: B 1074 GLU cc_start: 0.8054 (tt0) cc_final: 0.7803 (tp30) REVERT: B 1105 LYS cc_start: 0.8589 (tttm) cc_final: 0.8029 (mtpp) REVERT: B 1210 MET cc_start: 0.3367 (ppp) cc_final: 0.1502 (pmm) outliers start: 83 outliers final: 52 residues processed: 765 average time/residue: 0.1989 time to fit residues: 248.7479 Evaluate side-chains 763 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 696 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 32 TYR Chi-restraints excluded: chain X residue 103 SER Chi-restraints excluded: chain Y residue 90 GLN Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 199 TYR Chi-restraints excluded: chain C residue 317 TYR Chi-restraints excluded: chain C residue 340 TRP Chi-restraints excluded: chain C residue 397 ASP Chi-restraints excluded: chain C residue 570 CYS Chi-restraints excluded: chain C residue 615 THR Chi-restraints excluded: chain C residue 622 CYS Chi-restraints excluded: chain C residue 741 ASP Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 802 ASN Chi-restraints excluded: chain C residue 803 MET Chi-restraints excluded: chain C residue 839 PHE Chi-restraints excluded: chain C residue 849 GLU Chi-restraints excluded: chain C residue 855 ASP Chi-restraints excluded: chain C residue 1050 GLN Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 363 ASN Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 606 CYS Chi-restraints excluded: chain A residue 802 ASN Chi-restraints excluded: chain A residue 834 VAL Chi-restraints excluded: chain A residue 855 ASP Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 1060 SER Chi-restraints excluded: chain A residue 1062 SER Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain B residue 200 LYS Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 345 SER Chi-restraints excluded: chain B residue 363 ASN Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 397 ASP Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 544 LYS Chi-restraints excluded: chain B residue 549 ILE Chi-restraints excluded: chain B residue 570 CYS Chi-restraints excluded: chain B residue 581 ASP Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 615 THR Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 858 GLN Chi-restraints excluded: chain B residue 964 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 380 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 209 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 22 optimal weight: 9.9990 chunk 397 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 352 optimal weight: 6.9990 chunk 115 optimal weight: 0.6980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 208 ASN C 573 GLN ** C 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 802 ASN ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1050 GLN ** C1131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 GLN ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 633 GLN ** B 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 858 GLN B1039 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.190015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.157900 restraints weight = 57468.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.162889 restraints weight = 30247.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.166161 restraints weight = 18681.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.168322 restraints weight = 12996.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.169507 restraints weight = 9993.062| |-----------------------------------------------------------------------------| r_work (final): 0.4157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6420 moved from start: 0.6456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 33762 Z= 0.188 Angle : 0.720 15.674 46032 Z= 0.375 Chirality : 0.048 0.411 5196 Planarity : 0.004 0.045 5883 Dihedral : 5.248 53.658 4887 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.88 % Favored : 94.08 % Rotamer: Outliers : 2.34 % Allowed : 19.32 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.12), residues: 4170 helix: 0.23 (0.18), residues: 753 sheet: -0.40 (0.17), residues: 888 loop : -1.21 (0.12), residues: 2529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 679 TYR 0.042 0.002 TYR C 963 PHE 0.033 0.002 PHE A 458 TRP 0.032 0.002 TRP Y 35 HIS 0.008 0.001 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00405 (33678) covalent geometry : angle 0.70111 (45849) SS BOND : bond 0.00430 ( 69) SS BOND : angle 1.80135 ( 138) hydrogen bonds : bond 0.04258 ( 1186) hydrogen bonds : angle 6.02364 ( 3381) link_NAG-ASN : bond 0.00674 ( 15) link_NAG-ASN : angle 4.47148 ( 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 795 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 710 time to evaluate : 1.101 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: C 78 MET cc_start: 0.6197 (mmp) cc_final: 0.5956 (mmp) REVERT: C 143 ARG cc_start: 0.4469 (ttt180) cc_final: 0.3623 (ttp-170) REVERT: C 205 TYR cc_start: 0.7908 (p90) cc_final: 0.7566 (p90) REVERT: C 230 THR cc_start: 0.7870 (m) cc_final: 0.7608 (p) REVERT: C 235 LYS cc_start: 0.7645 (mtmm) cc_final: 0.7377 (mtmm) REVERT: C 240 VAL cc_start: 0.8875 (t) cc_final: 0.8639 (p) REVERT: C 315 ASN cc_start: 0.7370 (p0) cc_final: 0.7115 (p0) REVERT: C 380 ASN cc_start: 0.8500 (m-40) cc_final: 0.7769 (m-40) REVERT: C 418 GLN cc_start: 0.7645 (tt0) cc_final: 0.7411 (tt0) REVERT: C 455 ARG cc_start: 0.7492 (ttm-80) cc_final: 0.7128 (ttm-80) REVERT: C 479 TYR cc_start: 0.7344 (p90) cc_final: 0.7009 (p90) REVERT: C 591 ILE cc_start: 0.8452 (mt) cc_final: 0.8194 (mp) REVERT: C 671 MET cc_start: 0.6112 (mmm) cc_final: 0.5442 (mtp) REVERT: C 728 ASN cc_start: 0.8487 (m-40) cc_final: 0.8008 (m-40) REVERT: C 807 ILE cc_start: 0.7279 (mt) cc_final: 0.6965 (pt) REVERT: C 833 LEU cc_start: 0.7746 (tp) cc_final: 0.7321 (tt) REVERT: C 848 THR cc_start: 0.8026 (p) cc_final: 0.7131 (t) REVERT: C 849 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7105 (pt0) REVERT: C 852 GLU cc_start: 0.7366 (mt-10) cc_final: 0.6778 (mt-10) REVERT: C 914 ASP cc_start: 0.6539 (p0) cc_final: 0.6220 (p0) REVERT: C 928 ASN cc_start: 0.8076 (t0) cc_final: 0.7809 (m-40) REVERT: C 965 LEU cc_start: 0.7765 (tt) cc_final: 0.7481 (tt) REVERT: C 1043 GLU cc_start: 0.7386 (mt-10) cc_final: 0.7031 (mt-10) REVERT: C 1051 GLN cc_start: 0.7527 (mm-40) cc_final: 0.7128 (mm-40) REVERT: C 1052 LEU cc_start: 0.8794 (tp) cc_final: 0.8569 (tp) REVERT: C 1064 GLN cc_start: 0.8103 (tt0) cc_final: 0.7700 (tt0) REVERT: C 1069 ARG cc_start: 0.8214 (mtp180) cc_final: 0.7829 (ptm160) REVERT: C 1074 GLU cc_start: 0.7772 (tt0) cc_final: 0.7339 (tt0) REVERT: C 1076 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7598 (mt-10) REVERT: C 1078 GLN cc_start: 0.8485 (mm-40) cc_final: 0.8085 (mm-40) REVERT: C 1081 ARG cc_start: 0.8436 (mtt-85) cc_final: 0.8223 (mtt-85) REVERT: C 1105 LYS cc_start: 0.8185 (mtmm) cc_final: 0.7903 (mtpp) REVERT: C 1210 MET cc_start: 0.2975 (ppp) cc_final: 0.1281 (pmm) REVERT: A 64 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7543 (mp) REVERT: A 99 PHE cc_start: 0.7222 (t80) cc_final: 0.6900 (t80) REVERT: A 143 ARG cc_start: 0.4043 (ttp-170) cc_final: 0.2789 (mtp180) REVERT: A 187 LEU cc_start: 0.7048 (tp) cc_final: 0.6727 (tp) REVERT: A 230 THR cc_start: 0.7781 (OUTLIER) cc_final: 0.7524 (p) REVERT: A 235 LYS cc_start: 0.7780 (mtmm) cc_final: 0.7394 (mtmm) REVERT: A 293 ASP cc_start: 0.7563 (p0) cc_final: 0.7262 (p0) REVERT: A 313 GLU cc_start: 0.6817 (tm-30) cc_final: 0.6102 (tm-30) REVERT: A 315 ASN cc_start: 0.7773 (p0) cc_final: 0.7182 (p0) REVERT: A 326 TYR cc_start: 0.7559 (t80) cc_final: 0.6928 (t80) REVERT: A 344 LYS cc_start: 0.8415 (ptpt) cc_final: 0.8067 (ptpt) REVERT: A 363 ASN cc_start: 0.5026 (OUTLIER) cc_final: 0.4528 (p0) REVERT: A 385 LYS cc_start: 0.8415 (mmmm) cc_final: 0.8194 (mmmm) REVERT: A 397 ASP cc_start: 0.7050 (p0) cc_final: 0.6826 (p0) REVERT: A 425 ASP cc_start: 0.7252 (t70) cc_final: 0.6824 (t0) REVERT: A 435 TYR cc_start: 0.7816 (p90) cc_final: 0.7221 (p90) REVERT: A 479 TYR cc_start: 0.7679 (p90) cc_final: 0.7364 (p90) REVERT: A 601 ASN cc_start: 0.7193 (p0) cc_final: 0.6516 (p0) REVERT: A 602 SER cc_start: 0.7796 (t) cc_final: 0.7221 (m) REVERT: A 631 LEU cc_start: 0.8887 (mt) cc_final: 0.8532 (mt) REVERT: A 633 GLN cc_start: 0.7240 (pp30) cc_final: 0.6975 (pp30) REVERT: A 635 ILE cc_start: 0.7940 (OUTLIER) cc_final: 0.7658 (pt) REVERT: A 652 TYR cc_start: 0.7444 (m-80) cc_final: 0.7235 (m-80) REVERT: A 679 ARG cc_start: 0.6295 (mtp85) cc_final: 0.5670 (mtp85) REVERT: A 718 TYR cc_start: 0.6122 (p90) cc_final: 0.5839 (p90) REVERT: A 728 ASN cc_start: 0.8410 (m-40) cc_final: 0.8059 (m-40) REVERT: A 849 GLU cc_start: 0.7709 (pt0) cc_final: 0.6935 (pt0) REVERT: A 852 GLU cc_start: 0.7518 (mt-10) cc_final: 0.6803 (mt-10) REVERT: A 855 ASP cc_start: 0.7680 (OUTLIER) cc_final: 0.7313 (p0) REVERT: A 863 ASN cc_start: 0.7050 (t0) cc_final: 0.6671 (t0) REVERT: A 866 MET cc_start: 0.5634 (ptp) cc_final: 0.5004 (ptp) REVERT: A 928 ASN cc_start: 0.7668 (t0) cc_final: 0.7349 (m-40) REVERT: A 1050 GLN cc_start: 0.7986 (mm-40) cc_final: 0.7224 (mm-40) REVERT: A 1059 ILE cc_start: 0.8500 (pt) cc_final: 0.8253 (mm) REVERT: A 1065 GLU cc_start: 0.7252 (mt-10) cc_final: 0.6410 (mt-10) REVERT: A 1114 LYS cc_start: 0.7185 (ptpt) cc_final: 0.6917 (pttt) REVERT: A 1196 TYR cc_start: 0.6893 (t80) cc_final: 0.6658 (t80) REVERT: D 112 ASP cc_start: 0.7875 (OUTLIER) cc_final: 0.7347 (m-30) REVERT: B 143 ARG cc_start: 0.4814 (ttt180) cc_final: 0.4458 (ttt180) REVERT: B 230 THR cc_start: 0.7874 (m) cc_final: 0.7616 (p) REVERT: B 235 LYS cc_start: 0.8000 (pttm) cc_final: 0.7631 (pttm) REVERT: B 319 VAL cc_start: 0.8077 (t) cc_final: 0.7763 (m) REVERT: B 322 ILE cc_start: 0.8346 (mm) cc_final: 0.8090 (mm) REVERT: B 326 TYR cc_start: 0.7873 (t80) cc_final: 0.7390 (t80) REVERT: B 329 LYS cc_start: 0.8111 (tttp) cc_final: 0.7678 (tttp) REVERT: B 357 PHE cc_start: 0.7238 (m-10) cc_final: 0.7025 (m-10) REVERT: B 461 ASP cc_start: 0.7197 (m-30) cc_final: 0.6927 (t70) REVERT: B 477 VAL cc_start: 0.7973 (OUTLIER) cc_final: 0.7232 (m) REVERT: B 544 LYS cc_start: 0.7976 (OUTLIER) cc_final: 0.7673 (ptmm) REVERT: B 545 SER cc_start: 0.8420 (p) cc_final: 0.8169 (t) REVERT: B 559 LYS cc_start: 0.7592 (pttt) cc_final: 0.7255 (ptmt) REVERT: B 591 ILE cc_start: 0.8494 (mt) cc_final: 0.8079 (mm) REVERT: B 596 ILE cc_start: 0.8337 (OUTLIER) cc_final: 0.8079 (mt) REVERT: B 599 ASP cc_start: 0.7497 (t0) cc_final: 0.6985 (t70) REVERT: B 646 SER cc_start: 0.8719 (m) cc_final: 0.8428 (t) REVERT: B 652 TYR cc_start: 0.7657 (m-80) cc_final: 0.7300 (m-80) REVERT: B 663 ASP cc_start: 0.7206 (t0) cc_final: 0.6898 (t0) REVERT: B 671 MET cc_start: 0.6461 (mmm) cc_final: 0.6126 (mtt) REVERT: B 699 LYS cc_start: 0.7287 (mmmm) cc_final: 0.7051 (mmmm) REVERT: B 833 LEU cc_start: 0.7688 (tp) cc_final: 0.7429 (tt) REVERT: B 849 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7067 (pt0) REVERT: B 852 GLU cc_start: 0.7257 (mt-10) cc_final: 0.6909 (mt-10) REVERT: B 928 ASN cc_start: 0.7764 (t0) cc_final: 0.7405 (m-40) REVERT: B 949 LYS cc_start: 0.8290 (mttt) cc_final: 0.7947 (ttmt) REVERT: B 1051 GLN cc_start: 0.7796 (mm-40) cc_final: 0.7306 (mm-40) REVERT: B 1065 GLU cc_start: 0.7242 (mt-10) cc_final: 0.6723 (mm-30) REVERT: B 1067 LEU cc_start: 0.8573 (tp) cc_final: 0.8132 (tt) REVERT: B 1069 ARG cc_start: 0.8017 (mtp180) cc_final: 0.7688 (ptm160) REVERT: B 1074 GLU cc_start: 0.8057 (tt0) cc_final: 0.7793 (tp30) REVERT: B 1105 LYS cc_start: 0.8589 (tttm) cc_final: 0.8039 (mtpp) REVERT: B 1112 MET cc_start: 0.7414 (mtm) cc_final: 0.7178 (ptm) REVERT: B 1210 MET cc_start: 0.3589 (ppp) cc_final: 0.1880 (pmm) outliers start: 85 outliers final: 62 residues processed: 754 average time/residue: 0.1897 time to fit residues: 234.7393 Evaluate side-chains 787 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 714 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 32 TYR Chi-restraints excluded: chain X residue 103 SER Chi-restraints excluded: chain Y residue 14 SER Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 199 TYR Chi-restraints excluded: chain C residue 317 TYR Chi-restraints excluded: chain C residue 363 ASN Chi-restraints excluded: chain C residue 391 PHE Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 397 ASP Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain C residue 570 CYS Chi-restraints excluded: chain C residue 615 THR Chi-restraints excluded: chain C residue 622 CYS Chi-restraints excluded: chain C residue 741 ASP Chi-restraints excluded: chain C residue 744 VAL Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 786 VAL Chi-restraints excluded: chain C residue 802 ASN Chi-restraints excluded: chain C residue 803 MET Chi-restraints excluded: chain C residue 839 PHE Chi-restraints excluded: chain C residue 849 GLU Chi-restraints excluded: chain C residue 855 ASP Chi-restraints excluded: chain C residue 1062 SER Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 363 ASN Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 606 CYS Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 802 ASN Chi-restraints excluded: chain A residue 834 VAL Chi-restraints excluded: chain A residue 855 ASP Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 1032 VAL Chi-restraints excluded: chain A residue 1060 SER Chi-restraints excluded: chain A residue 1062 SER Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 363 ASN Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 397 ASP Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 544 LYS Chi-restraints excluded: chain B residue 549 ILE Chi-restraints excluded: chain B residue 570 CYS Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 633 GLN Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 834 VAL Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 964 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 148 optimal weight: 10.0000 chunk 257 optimal weight: 5.9990 chunk 59 optimal weight: 0.7980 chunk 12 optimal weight: 8.9990 chunk 303 optimal weight: 3.9990 chunk 320 optimal weight: 0.9980 chunk 236 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 237 optimal weight: 0.8980 chunk 170 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 90 GLN C 573 GLN C 802 ASN C 842 ASN ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1050 GLN ** C1131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 552 HIS A 573 GLN A1039 ASN ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 453 ASN B 633 GLN ** B 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 858 GLN ** B1141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.189488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.156313 restraints weight = 56975.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.161410 restraints weight = 30047.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.164499 restraints weight = 18577.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.166589 restraints weight = 13153.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.167941 restraints weight = 10229.192| |-----------------------------------------------------------------------------| r_work (final): 0.4138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6450 moved from start: 0.6658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 33762 Z= 0.208 Angle : 0.731 15.761 46032 Z= 0.382 Chirality : 0.048 0.407 5196 Planarity : 0.005 0.045 5883 Dihedral : 5.158 42.990 4887 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.49 % Favored : 94.46 % Rotamer: Outliers : 2.42 % Allowed : 19.46 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.17 % 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: -1.23 (0.13), residues: 4170 helix: 0.11 (0.18), residues: 753 sheet: -0.46 (0.16), residues: 987 loop : -1.28 (0.12), residues: 2430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 571 TYR 0.043 0.002 TYR C 963 PHE 0.040 0.002 PHE A 458 TRP 0.039 0.002 TRP Y 35 HIS 0.011 0.002 HIS A 482 Details of bonding type rmsd covalent geometry : bond 0.00445 (33678) covalent geometry : angle 0.71108 (45849) SS BOND : bond 0.00478 ( 69) SS BOND : angle 1.86393 ( 138) hydrogen bonds : bond 0.04385 ( 1186) hydrogen bonds : angle 6.10086 ( 3381) link_NAG-ASN : bond 0.00659 ( 15) link_NAG-ASN : angle 4.50570 ( 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 804 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 716 time to evaluate : 1.123 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: C 78 MET cc_start: 0.6266 (mmp) cc_final: 0.6021 (mmp) REVERT: C 143 ARG cc_start: 0.4517 (ttt180) cc_final: 0.3794 (ttp-170) REVERT: C 187 LEU cc_start: 0.7027 (tp) cc_final: 0.6660 (tp) REVERT: C 205 TYR cc_start: 0.7907 (p90) cc_final: 0.7576 (p90) REVERT: C 230 THR cc_start: 0.7849 (m) cc_final: 0.7576 (p) REVERT: C 235 LYS cc_start: 0.7662 (mtmm) cc_final: 0.7307 (mtmm) REVERT: C 240 VAL cc_start: 0.8891 (t) cc_final: 0.8663 (p) REVERT: C 279 ASN cc_start: 0.6852 (p0) cc_final: 0.6568 (p0) REVERT: C 315 ASN cc_start: 0.7412 (p0) cc_final: 0.7208 (p0) REVERT: C 355 LYS cc_start: 0.7583 (tppt) cc_final: 0.7317 (tptm) REVERT: C 380 ASN cc_start: 0.8470 (m-40) cc_final: 0.7782 (m-40) REVERT: C 418 GLN cc_start: 0.7679 (tt0) cc_final: 0.7431 (tt0) REVERT: C 455 ARG cc_start: 0.7592 (ttm-80) cc_final: 0.7205 (ttm-80) REVERT: C 479 TYR cc_start: 0.7396 (p90) cc_final: 0.7065 (p90) REVERT: C 591 ILE cc_start: 0.8423 (mt) cc_final: 0.8177 (mp) REVERT: C 671 MET cc_start: 0.6090 (mmm) cc_final: 0.5411 (mtp) REVERT: C 728 ASN cc_start: 0.8481 (m-40) cc_final: 0.7985 (m-40) REVERT: C 807 ILE cc_start: 0.7303 (mt) cc_final: 0.6924 (pt) REVERT: C 833 LEU cc_start: 0.7867 (tp) cc_final: 0.7418 (tt) REVERT: C 839 PHE cc_start: 0.8826 (OUTLIER) cc_final: 0.8335 (t80) REVERT: C 848 THR cc_start: 0.8046 (p) cc_final: 0.7177 (t) REVERT: C 849 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7143 (pt0) REVERT: C 852 GLU cc_start: 0.7445 (mt-10) cc_final: 0.6878 (mt-10) REVERT: C 928 ASN cc_start: 0.8073 (t0) cc_final: 0.7852 (m-40) REVERT: C 965 LEU cc_start: 0.7800 (tt) cc_final: 0.7527 (tt) REVERT: C 1043 GLU cc_start: 0.7332 (mt-10) cc_final: 0.6947 (mt-10) REVERT: C 1050 GLN cc_start: 0.8161 (tp-100) cc_final: 0.7937 (tp40) REVERT: C 1051 GLN cc_start: 0.7564 (mm-40) cc_final: 0.7171 (mm-40) REVERT: C 1064 GLN cc_start: 0.8099 (tt0) cc_final: 0.7697 (tt0) REVERT: C 1069 ARG cc_start: 0.8255 (mtp180) cc_final: 0.7870 (ptm160) REVERT: C 1074 GLU cc_start: 0.7785 (tt0) cc_final: 0.7406 (tt0) REVERT: C 1076 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7651 (mt-10) REVERT: C 1078 GLN cc_start: 0.8477 (mm-40) cc_final: 0.8085 (mm-40) REVERT: C 1081 ARG cc_start: 0.8400 (mtt-85) cc_final: 0.8165 (mtt-85) REVERT: C 1105 LYS cc_start: 0.8167 (mtmm) cc_final: 0.7914 (mtpp) REVERT: C 1114 LYS cc_start: 0.7556 (ptpt) cc_final: 0.7236 (ptpp) REVERT: C 1210 MET cc_start: 0.3288 (ppp) cc_final: 0.1536 (pmm) REVERT: A 64 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7587 (mp) REVERT: A 143 ARG cc_start: 0.4100 (ttp-170) cc_final: 0.2800 (mtp180) REVERT: A 187 LEU cc_start: 0.6859 (tp) cc_final: 0.6552 (tp) REVERT: A 230 THR cc_start: 0.7798 (OUTLIER) cc_final: 0.7533 (p) REVERT: A 235 LYS cc_start: 0.7797 (mtmm) cc_final: 0.7426 (mtmm) REVERT: A 293 ASP cc_start: 0.7522 (p0) cc_final: 0.7242 (p0) REVERT: A 313 GLU cc_start: 0.7043 (OUTLIER) cc_final: 0.6388 (tm-30) REVERT: A 315 ASN cc_start: 0.7748 (p0) cc_final: 0.7182 (p0) REVERT: A 326 TYR cc_start: 0.7516 (t80) cc_final: 0.6852 (t80) REVERT: A 344 LYS cc_start: 0.8504 (ptpt) cc_final: 0.8136 (ptpt) REVERT: A 363 ASN cc_start: 0.4934 (OUTLIER) cc_final: 0.4526 (p0) REVERT: A 372 GLN cc_start: 0.7859 (OUTLIER) cc_final: 0.7239 (tm-30) REVERT: A 397 ASP cc_start: 0.7059 (p0) cc_final: 0.6618 (p0) REVERT: A 424 ILE cc_start: 0.8615 (OUTLIER) cc_final: 0.8130 (pt) REVERT: A 425 ASP cc_start: 0.7249 (t70) cc_final: 0.6741 (t0) REVERT: A 435 TYR cc_start: 0.7850 (p90) cc_final: 0.7253 (p90) REVERT: A 479 TYR cc_start: 0.7682 (p90) cc_final: 0.7414 (p90) REVERT: A 601 ASN cc_start: 0.7171 (p0) cc_final: 0.6516 (p0) REVERT: A 602 SER cc_start: 0.7808 (t) cc_final: 0.7217 (m) REVERT: A 631 LEU cc_start: 0.8795 (mt) cc_final: 0.8499 (mt) REVERT: A 635 ILE cc_start: 0.7910 (OUTLIER) cc_final: 0.7570 (pt) REVERT: A 652 TYR cc_start: 0.7466 (m-80) cc_final: 0.7244 (m-80) REVERT: A 673 ARG cc_start: 0.6999 (mtp85) cc_final: 0.6735 (mtt90) REVERT: A 679 ARG cc_start: 0.6371 (mtp85) cc_final: 0.5706 (mtp85) REVERT: A 728 ASN cc_start: 0.8423 (m-40) cc_final: 0.8072 (m110) REVERT: A 849 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.6950 (pt0) REVERT: A 852 GLU cc_start: 0.7517 (mt-10) cc_final: 0.6793 (mt-10) REVERT: A 855 ASP cc_start: 0.7709 (OUTLIER) cc_final: 0.7360 (p0) REVERT: A 863 ASN cc_start: 0.7057 (t0) cc_final: 0.6681 (t0) REVERT: A 928 ASN cc_start: 0.7658 (t0) cc_final: 0.7394 (m-40) REVERT: A 1050 GLN cc_start: 0.7972 (mm-40) cc_final: 0.7230 (mm-40) REVERT: A 1059 ILE cc_start: 0.8513 (pt) cc_final: 0.8249 (mm) REVERT: A 1065 GLU cc_start: 0.7267 (mt-10) cc_final: 0.6433 (mt-10) REVERT: A 1114 LYS cc_start: 0.7353 (ptpt) cc_final: 0.7091 (pttt) REVERT: A 1196 TYR cc_start: 0.7011 (t80) cc_final: 0.6754 (t80) REVERT: D 78 PHE cc_start: 0.6794 (m-80) cc_final: 0.6494 (m-10) REVERT: D 111 MET cc_start: 0.6138 (OUTLIER) cc_final: 0.5097 (tpt) REVERT: D 112 ASP cc_start: 0.7836 (OUTLIER) cc_final: 0.7272 (m-30) REVERT: B 143 ARG cc_start: 0.4823 (ttt180) cc_final: 0.4285 (ttp-170) REVERT: B 230 THR cc_start: 0.7876 (m) cc_final: 0.7630 (p) REVERT: B 235 LYS cc_start: 0.7990 (pttm) cc_final: 0.7636 (pttm) REVERT: B 319 VAL cc_start: 0.8061 (t) cc_final: 0.7767 (m) REVERT: B 322 ILE cc_start: 0.8282 (mm) cc_final: 0.8021 (mm) REVERT: B 326 TYR cc_start: 0.7874 (t80) cc_final: 0.7378 (t80) REVERT: B 329 LYS cc_start: 0.8168 (tttp) cc_final: 0.7734 (tttp) REVERT: B 357 PHE cc_start: 0.7262 (m-10) cc_final: 0.6904 (m-10) REVERT: B 477 VAL cc_start: 0.8066 (OUTLIER) cc_final: 0.7340 (m) REVERT: B 544 LYS cc_start: 0.7973 (OUTLIER) cc_final: 0.7698 (ptmm) REVERT: B 545 SER cc_start: 0.8420 (p) cc_final: 0.8155 (t) REVERT: B 559 LYS cc_start: 0.7658 (pttt) cc_final: 0.7334 (ptmt) REVERT: B 591 ILE cc_start: 0.8538 (mt) cc_final: 0.8104 (mm) REVERT: B 596 ILE cc_start: 0.8335 (OUTLIER) cc_final: 0.8094 (mt) REVERT: B 599 ASP cc_start: 0.7474 (t0) cc_final: 0.6962 (t70) REVERT: B 646 SER cc_start: 0.8732 (m) cc_final: 0.8458 (t) REVERT: B 652 TYR cc_start: 0.7667 (m-80) cc_final: 0.7352 (m-80) REVERT: B 663 ASP cc_start: 0.7244 (t0) cc_final: 0.6893 (t0) REVERT: B 671 MET cc_start: 0.6506 (mmm) cc_final: 0.6130 (mtt) REVERT: B 699 LYS cc_start: 0.7324 (mmmm) cc_final: 0.7023 (mmmm) REVERT: B 833 LEU cc_start: 0.7751 (tp) cc_final: 0.7230 (tt) REVERT: B 849 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7081 (pt0) REVERT: B 852 GLU cc_start: 0.7262 (mt-10) cc_final: 0.6936 (mt-10) REVERT: B 928 ASN cc_start: 0.7993 (t0) cc_final: 0.7651 (m-40) REVERT: B 949 LYS cc_start: 0.8342 (mttt) cc_final: 0.8013 (ttmt) REVERT: B 1024 PHE cc_start: 0.5993 (m-80) cc_final: 0.5774 (m-80) REVERT: B 1051 GLN cc_start: 0.7720 (mm-40) cc_final: 0.7280 (mm-40) REVERT: B 1056 PHE cc_start: 0.8216 (m-80) cc_final: 0.8008 (m-80) REVERT: B 1065 GLU cc_start: 0.7390 (mt-10) cc_final: 0.6745 (mm-30) REVERT: B 1067 LEU cc_start: 0.8583 (tp) cc_final: 0.8317 (tt) REVERT: B 1074 GLU cc_start: 0.8048 (tt0) cc_final: 0.7838 (tp30) REVERT: B 1105 LYS cc_start: 0.8589 (tttm) cc_final: 0.8041 (mtpp) REVERT: B 1112 MET cc_start: 0.7362 (mtm) cc_final: 0.7154 (ptm) REVERT: B 1210 MET cc_start: 0.3621 (ppp) cc_final: 0.2112 (pmm) outliers start: 88 outliers final: 64 residues processed: 761 average time/residue: 0.1926 time to fit residues: 240.5416 Evaluate side-chains 785 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 704 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 32 TYR Chi-restraints excluded: chain X residue 103 SER Chi-restraints excluded: chain Y residue 14 SER Chi-restraints excluded: chain Y residue 90 GLN Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 199 TYR Chi-restraints excluded: chain C residue 311 VAL Chi-restraints excluded: chain C residue 317 TYR Chi-restraints excluded: chain C residue 363 ASN Chi-restraints excluded: chain C residue 391 PHE Chi-restraints excluded: chain C residue 394 ILE Chi-restraints excluded: chain C residue 397 ASP Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain C residue 570 CYS Chi-restraints excluded: chain C residue 615 THR Chi-restraints excluded: chain C residue 622 CYS Chi-restraints excluded: chain C residue 741 ASP Chi-restraints excluded: chain C residue 744 VAL Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 786 VAL Chi-restraints excluded: chain C residue 803 MET Chi-restraints excluded: chain C residue 839 PHE Chi-restraints excluded: chain C residue 849 GLU Chi-restraints excluded: chain C residue 855 ASP Chi-restraints excluded: chain C residue 1062 SER Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 64 LEU Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 363 ASN Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 606 CYS Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 802 ASN Chi-restraints excluded: chain A residue 834 VAL Chi-restraints excluded: chain A residue 849 GLU Chi-restraints excluded: chain A residue 855 ASP Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 1032 VAL Chi-restraints excluded: chain A residue 1060 SER Chi-restraints excluded: chain A residue 1062 SER Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain D residue 32 TYR Chi-restraints excluded: chain D residue 111 MET Chi-restraints excluded: chain D residue 112 ASP Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 199 TYR Chi-restraints excluded: chain B residue 200 LYS Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 363 ASN Chi-restraints excluded: chain B residue 377 THR Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 397 ASP Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 544 LYS Chi-restraints excluded: chain B residue 549 ILE Chi-restraints excluded: chain B residue 570 CYS Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 633 GLN Chi-restraints excluded: chain B residue 723 LEU Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 834 VAL Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 858 GLN Chi-restraints excluded: chain B residue 964 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 386 optimal weight: 0.9990 chunk 400 optimal weight: 2.9990 chunk 4 optimal weight: 9.9990 chunk 291 optimal weight: 7.9990 chunk 116 optimal weight: 1.9990 chunk 112 optimal weight: 0.0020 chunk 309 optimal weight: 2.9990 chunk 253 optimal weight: 7.9990 chunk 27 optimal weight: 0.9990 chunk 136 optimal weight: 6.9990 chunk 393 optimal weight: 0.9990 overall best weight: 0.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 208 ASN C 280 GLN C 802 ASN ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 GLN ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 858 GLN B1039 ASN ** B1141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.188157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.156285 restraints weight = 57736.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.161194 restraints weight = 30494.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.164428 restraints weight = 18864.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.166564 restraints weight = 13124.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.167940 restraints weight = 10082.497| |-----------------------------------------------------------------------------| r_work (final): 0.4145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6426 moved from start: 0.6676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.352 33762 Z= 0.286 Angle : 0.914 59.196 46032 Z= 0.502 Chirality : 0.049 0.624 5196 Planarity : 0.005 0.163 5883 Dihedral : 5.172 42.920 4887 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.56 % Favored : 94.39 % Rotamer: Outliers : 2.39 % Allowed : 19.95 % Favored : 77.66 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 10.17 % 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: -1.23 (0.13), residues: 4170 helix: 0.10 (0.18), residues: 753 sheet: -0.47 (0.16), residues: 987 loop : -1.28 (0.12), residues: 2430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 571 TYR 0.047 0.002 TYR B 274 PHE 0.035 0.002 PHE A 458 TRP 0.033 0.002 TRP Y 35 HIS 0.008 0.002 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00631 (33678) covalent geometry : angle 0.88332 (45849) SS BOND : bond 0.01274 ( 69) SS BOND : angle 3.62016 ( 138) hydrogen bonds : bond 0.04368 ( 1186) hydrogen bonds : angle 6.10114 ( 3381) link_NAG-ASN : bond 0.00646 ( 15) link_NAG-ASN : angle 4.50699 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6328.02 seconds wall clock time: 109 minutes 44.92 seconds (6584.92 seconds total)