Starting phenix.real_space_refine on Mon Jul 6 05:29:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7pnq_13550/07_2026/7pnq_13550.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pnq_13550/07_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_13550/07_2026/7pnq_13550.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pnq_13550/07_2026/7pnq_13550.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7pnq_13550/07_2026/7pnq_13550.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7pnq_13550/07_2026/7pnq_13550.cif" model { file = "/net/cci-nas-00/data/ceres_data/7pnq_13550/07_2026/7pnq_13550.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pnq_13550/07_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-6108/lib/python3.11/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 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 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 chiralities: 5 Time building chain proxies: 7.46, per 1000 atoms: 0.23 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: 2.79 Conformation dependent library (CDL) restraints added in 1.5 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: 1.48 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: 10.06 Time building geometry restraints manager: 3.83 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 - 17.02: 17979 17.02 - 34.04: 1554 34.04 - 51.05: 260 51.05 - 68.07: 55 68.07 - 85.09: 18 Dihedral angle restraints: 19866 sinusoidal: 7596 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 19863 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: 0.09 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: 0.010 Normalize map: mean=0, sd=1: 3.470 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: 0.040 Extract box with map and model: 0.610 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 34.620 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5596 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 : 12.816 85.088 11835 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/Z covalent geometry : bond 0.00338 / 0.17 (33678) covalent geometry : angle 0.64391 / 0.35 (45849) SS BOND : bond 0.00241 / 0.14 ( 69) SS BOND : angle 1.19111 / 0.83 ( 138) hydrogen bonds : bond 0.24020 / 15.64 ( 1186) hydrogen bonds : angle 8.41374 / 5.86 ( 3381) link_NAG-ASN : bond 0.01599 / 0.94 ( 15) link_NAG-ASN : angle 7.14542 / 4.67 ( 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 : 1.195 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: 0.2242 time to fit residues: 290.8381 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 : 1.210 ------------------------------------------------------------------------------- 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... 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 B1054 ASN B1096 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4677 r_free = 0.4677 target = 0.216328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.184181 restraints weight = 59815.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.189367 restraints weight = 32120.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.192678 restraints weight = 20073.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.194740 restraints weight = 14121.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.196075 restraints weight = 10973.591| |-----------------------------------------------------------------------------| r_work (final): 0.4396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6015 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 33762 Z= 0.133 Angle : 0.609 14.611 46032 Z= 0.321 Chirality : 0.046 0.483 5196 Planarity : 0.005 0.089 5883 Dihedral : 4.289 21.458 4572 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.33 % Favored : 96.59 % Rotamer: Outliers : 1.15 % Allowed : 9.01 % Favored : 89.83 % 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: -0.13 (0.17), residues: 783 sheet: -0.18 (0.16), residues: 996 loop : -0.88 (0.12), residues: 2391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 467 TYR 0.023 0.001 TYR A 274 PHE 0.021 0.001 PHE B 484 TRP 0.028 0.001 TRP B 452 HIS 0.017 0.001 HIS B 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 (33678) covalent geometry : angle 0.58393 / 0.31 (45849) SS BOND : bond 0.00590 / 0.27 ( 69) SS BOND : angle 1.75950 / 1.34 ( 138) hydrogen bonds : bond 0.04651 / 3.02 ( 1186) hydrogen bonds : angle 6.26552 / 4.38 ( 3381) link_NAG-ASN : bond 0.00928 / 0.55 ( 15) link_NAG-ASN : angle 4.80615 / 3.12 ( 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 700 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 658 time to evaluate : 1.226 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: 0.6919 (mp) cc_final: 0.6662 (mm) REVERT: C 57 TYR cc_start: 0.6528 (m-80) cc_final: 0.6004 (m-80) REVERT: C 106 LYS cc_start: 0.8093 (tttt) cc_final: 0.7201 (tttm) REVERT: C 143 ARG cc_start: 0.4000 (ttt180) cc_final: 0.3476 (ttt180) REVERT: C 213 TYR cc_start: 0.6770 (m-80) cc_final: 0.5762 (m-80) REVERT: C 230 THR cc_start: 0.7543 (m) cc_final: 0.7201 (t) REVERT: C 289 ASP cc_start: 0.6175 (t0) cc_final: 0.5836 (t70) REVERT: C 292 SER cc_start: 0.8289 (t) cc_final: 0.7609 (p) REVERT: C 293 ASP cc_start: 0.7482 (p0) cc_final: 0.6915 (p0) REVERT: C 295 MET cc_start: 0.5729 (ptm) cc_final: 0.5509 (ptm) REVERT: C 355 LYS cc_start: 0.7262 (tttp) cc_final: 0.7036 (tptm) REVERT: C 357 PHE cc_start: 0.7302 (m-10) cc_final: 0.6418 (m-10) REVERT: C 435 TYR cc_start: 0.7391 (p90) cc_final: 0.6812 (p90) REVERT: C 451 THR cc_start: 0.6449 (p) cc_final: 0.5327 (m) REVERT: C 481 GLN cc_start: 0.7497 (tt0) cc_final: 0.7212 (tt0) REVERT: C 611 GLN cc_start: 0.7438 (tm-30) cc_final: 0.7079 (tm-30) REVERT: C 653 ASP cc_start: 0.7601 (t0) cc_final: 0.7396 (t70) REVERT: C 663 ASP cc_start: 0.7519 (t0) cc_final: 0.7217 (t0) REVERT: C 671 MET cc_start: 0.6621 (mmm) cc_final: 0.6037 (mmm) REVERT: C 720 ASP cc_start: 0.6348 (m-30) cc_final: 0.6109 (m-30) REVERT: C 835 GLU cc_start: 0.7006 (mt-10) cc_final: 0.6638 (mm-30) REVERT: C 841 ASP cc_start: 0.7329 (m-30) cc_final: 0.6984 (m-30) REVERT: C 938 ASP cc_start: 0.8277 (t0) cc_final: 0.8048 (t0) REVERT: C 950 VAL cc_start: 0.6671 (t) cc_final: 0.6258 (p) REVERT: C 1043 GLU cc_start: 0.7261 (mt-10) cc_final: 0.6906 (mt-10) REVERT: C 1051 GLN cc_start: 0.7473 (mm-40) cc_final: 0.7121 (tp-100) REVERT: C 1056 PHE cc_start: 0.8083 (m-80) cc_final: 0.7621 (m-80) REVERT: H 94 TYR cc_start: 0.4747 (m-80) cc_final: 0.4476 (m-80) REVERT: L 35 TRP cc_start: 0.4854 (m100) cc_final: 0.4589 (m100) REVERT: A 78 MET cc_start: 0.5635 (mmp) cc_final: 0.5406 (mmt) REVERT: A 106 LYS cc_start: 0.7972 (tttt) cc_final: 0.7401 (tttm) REVERT: A 143 ARG cc_start: 0.3593 (ttp-170) cc_final: 0.3102 (ttp-170) REVERT: A 230 THR cc_start: 0.7636 (m) cc_final: 0.7058 (p) REVERT: A 298 ILE cc_start: 0.7479 (mm) cc_final: 0.7226 (mt) REVERT: A 326 TYR cc_start: 0.7467 (t80) cc_final: 0.7249 (t80) REVERT: A 379 ASN cc_start: 0.7845 (t0) cc_final: 0.7368 (t0) REVERT: A 380 ASN cc_start: 0.7974 (m-40) cc_final: 0.7637 (m110) REVERT: A 409 LEU cc_start: 0.8296 (mt) cc_final: 0.8092 (mp) REVERT: A 435 TYR cc_start: 0.7577 (p90) cc_final: 0.7027 (p90) REVERT: A 624 ASN cc_start: 0.6577 (p0) cc_final: 0.6161 (p0) REVERT: A 631 LEU cc_start: 0.8852 (mt) cc_final: 0.8476 (mp) REVERT: A 642 THR cc_start: 0.8150 (p) cc_final: 0.7785 (t) REVERT: A 663 ASP cc_start: 0.7343 (t0) cc_final: 0.7126 (t0) REVERT: A 671 MET cc_start: 0.6548 (mmm) cc_final: 0.6164 (mmm) REVERT: A 699 LYS cc_start: 0.6511 (mmmt) cc_final: 0.6186 (mmmm) REVERT: A 720 ASP cc_start: 0.6296 (m-30) cc_final: 0.5923 (m-30) REVERT: A 723 LEU cc_start: 0.7231 (mt) cc_final: 0.6994 (mt) REVERT: A 804 VAL cc_start: 0.1158 (m) cc_final: 0.0362 (t) REVERT: A 833 LEU cc_start: 0.7276 (tp) cc_final: 0.6775 (tp) REVERT: A 852 GLU cc_start: 0.7390 (mt-10) cc_final: 0.7046 (mt-10) REVERT: A 1005 ASN cc_start: 0.4555 (p0) cc_final: 0.4126 (p0) REVERT: A 1049 LEU cc_start: 0.8787 (tp) cc_final: 0.8577 (tt) REVERT: A 1050 GLN cc_start: 0.8083 (mm-40) cc_final: 0.7655 (mm-40) REVERT: A 1059 ILE cc_start: 0.8091 (pt) cc_final: 0.7582 (mt) REVERT: A 1080 ASP cc_start: 0.7793 (t0) cc_final: 0.7578 (t70) REVERT: A 1105 LYS cc_start: 0.8543 (ttmt) cc_final: 0.8330 (mtpt) REVERT: F 4 MET cc_start: 0.4306 (tpt) cc_final: 0.4066 (tpt) REVERT: B 203 PHE cc_start: 0.7363 (m-80) cc_final: 0.6944 (m-80) REVERT: B 289 ASP cc_start: 0.6866 (t0) cc_final: 0.6406 (t70) REVERT: B 293 ASP cc_start: 0.7261 (p0) cc_final: 0.6783 (p0) REVERT: B 295 MET cc_start: 0.5936 (ptm) cc_final: 0.5662 (ptm) REVERT: B 340 TRP cc_start: 0.7964 (t-100) cc_final: 0.7343 (t-100) REVERT: B 380 ASN cc_start: 0.7922 (m-40) cc_final: 0.7675 (m-40) REVERT: B 455 ARG cc_start: 0.7271 (mtp-110) cc_final: 0.6995 (ttp80) REVERT: B 475 HIS cc_start: 0.5861 (m90) cc_final: 0.5500 (m90) REVERT: B 591 ILE cc_start: 0.7798 (mt) cc_final: 0.7394 (mm) REVERT: B 596 ILE cc_start: 0.7987 (mp) cc_final: 0.7786 (mt) REVERT: B 642 THR cc_start: 0.8114 (p) cc_final: 0.7786 (t) REVERT: B 663 ASP cc_start: 0.7265 (t0) cc_final: 0.6776 (t0) REVERT: B 666 THR cc_start: 0.7507 (p) cc_final: 0.7125 (p) REVERT: B 671 MET cc_start: 0.6735 (mmm) cc_final: 0.6442 (mmm) REVERT: B 711 ARG cc_start: 0.6892 (mtm180) cc_final: 0.6665 (mtm180) REVERT: B 720 ASP cc_start: 0.6645 (m-30) cc_final: 0.6253 (m-30) REVERT: B 835 GLU cc_start: 0.6894 (mt-10) cc_final: 0.6515 (mt-10) REVERT: B 852 GLU cc_start: 0.6880 (mt-10) cc_final: 0.6478 (mt-10) REVERT: B 910 ASP cc_start: 0.7124 (m-30) cc_final: 0.6922 (m-30) REVERT: B 951 LEU cc_start: 0.7158 (mt) cc_final: 0.6528 (mp) REVERT: B 1064 GLN cc_start: 0.7853 (tt0) cc_final: 0.7571 (tt0) REVERT: B 1105 LYS cc_start: 0.8243 (tttm) cc_final: 0.7949 (mtpp) REVERT: B 1131 ASN cc_start: 0.6863 (m-40) cc_final: 0.6660 (m-40) outliers start: 42 outliers final: 25 residues processed: 674 average time/residue: 0.2178 time to fit residues: 239.7148 Evaluate side-chains 645 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 620 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 369 optimal weight: 5.9990 chunk 371 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 22 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 376 optimal weight: 1.9990 chunk 341 optimal weight: 0.9990 chunk 339 optimal weight: 0.7980 chunk 256 optimal weight: 2.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 380 ASN C 707 ASN C 858 GLN C1064 GLN L 92 ASN A 208 ASN A 273 GLN A 418 GLN A 552 HIS 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** B1050 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.203698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.171589 restraints weight = 58772.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.176707 restraints weight = 31257.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.179941 restraints weight = 19354.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.182069 restraints weight = 13500.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.183407 restraints weight = 10401.196| |-----------------------------------------------------------------------------| r_work (final): 0.4270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6247 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 33762 Z= 0.204 Angle : 0.674 13.777 46032 Z= 0.358 Chirality : 0.048 0.428 5196 Planarity : 0.005 0.043 5883 Dihedral : 4.602 24.860 4572 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.74 % Favored : 96.19 % Rotamer: Outliers : 1.84 % Allowed : 10.80 % Favored : 87.36 % 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: -0.80 (0.12), residues: 4170 helix: -0.12 (0.17), residues: 786 sheet: 0.02 (0.17), residues: 930 loop : -0.87 (0.12), residues: 2454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 201 TYR 0.026 0.002 TYR A 274 PHE 0.032 0.003 PHE C 456 TRP 0.029 0.002 TRP B 452 HIS 0.012 0.002 HIS A 552 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.20 (33678) covalent geometry : angle 0.65771 / 0.35 (45849) SS BOND : bond 0.00874 / 0.53 ( 69) SS BOND : angle 1.45478 / 1.03 ( 138) hydrogen bonds : bond 0.04822 / 3.24 ( 1186) hydrogen bonds : angle 6.08527 / 4.21 ( 3381) link_NAG-ASN : bond 0.00862 / 0.52 ( 15) link_NAG-ASN : angle 4.17279 / 2.67 ( 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 793 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 726 time to evaluate : 1.211 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 64 LEU cc_start: 0.8176 (tp) cc_final: 0.7922 (tp) REVERT: C 78 MET cc_start: 0.6082 (mmp) cc_final: 0.5836 (mmp) REVERT: C 106 LYS cc_start: 0.8228 (tttt) cc_final: 0.7446 (tttm) REVERT: C 143 ARG cc_start: 0.4522 (ttt180) cc_final: 0.3682 (mtp180) REVERT: C 230 THR cc_start: 0.8005 (m) cc_final: 0.7653 (p) REVERT: C 234 THR cc_start: 0.8158 (p) cc_final: 0.7824 (t) REVERT: C 274 TYR cc_start: 0.6739 (m-10) cc_final: 0.6527 (m-80) REVERT: C 289 ASP cc_start: 0.7050 (t0) cc_final: 0.6119 (t70) REVERT: C 311 VAL cc_start: 0.6916 (t) cc_final: 0.6678 (p) REVERT: C 327 ARG cc_start: 0.7050 (mmm160) cc_final: 0.6759 (mmm-85) REVERT: C 377 THR cc_start: 0.7637 (OUTLIER) cc_final: 0.7296 (p) REVERT: C 379 ASN cc_start: 0.8323 (t0) cc_final: 0.8120 (t0) REVERT: C 401 ILE cc_start: 0.7925 (mm) cc_final: 0.7540 (mt) REVERT: C 425 ASP cc_start: 0.7545 (t70) cc_final: 0.7143 (t70) REVERT: C 451 THR cc_start: 0.6426 (p) cc_final: 0.5477 (m) REVERT: C 645 ASN cc_start: 0.8008 (t0) cc_final: 0.7737 (p0) REVERT: C 648 GLN cc_start: 0.7409 (mt0) cc_final: 0.7173 (mt0) REVERT: C 663 ASP cc_start: 0.7549 (t0) cc_final: 0.7342 (t0) REVERT: C 673 ARG cc_start: 0.7255 (mtp85) cc_final: 0.6441 (mtt90) REVERT: C 720 ASP cc_start: 0.6604 (m-30) cc_final: 0.6349 (m-30) REVERT: C 728 ASN cc_start: 0.8505 (m-40) cc_final: 0.8221 (m-40) REVERT: C 799 THR cc_start: 0.3830 (t) cc_final: 0.2762 (m) REVERT: C 807 ILE cc_start: 0.6969 (mt) cc_final: 0.6568 (pt) REVERT: C 816 ILE cc_start: 0.8110 (mm) cc_final: 0.7905 (mt) REVERT: C 833 LEU cc_start: 0.7794 (tp) cc_final: 0.7302 (tt) REVERT: C 835 GLU cc_start: 0.7013 (mt-10) cc_final: 0.6735 (mm-30) REVERT: C 1043 GLU cc_start: 0.7265 (mt-10) cc_final: 0.6846 (mt-10) REVERT: C 1046 ASN cc_start: 0.8341 (t0) cc_final: 0.8112 (t0) REVERT: C 1076 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7586 (mt-10) REVERT: A 78 MET cc_start: 0.5995 (mmp) cc_final: 0.5750 (mmt) REVERT: A 106 LYS cc_start: 0.8197 (tttt) cc_final: 0.7749 (ttpp) REVERT: A 143 ARG cc_start: 0.3974 (ttp-170) cc_final: 0.2710 (mtp180) REVERT: A 230 THR cc_start: 0.7894 (m) cc_final: 0.7472 (p) REVERT: A 235 LYS cc_start: 0.7849 (mtmm) cc_final: 0.7346 (mtmm) REVERT: A 293 ASP cc_start: 0.7840 (p0) cc_final: 0.7418 (p0) REVERT: A 298 ILE cc_start: 0.7802 (mm) cc_final: 0.7577 (mt) REVERT: A 377 THR cc_start: 0.7782 (m) cc_final: 0.7460 (p) REVERT: A 379 ASN cc_start: 0.8152 (t0) cc_final: 0.7653 (t0) REVERT: A 380 ASN cc_start: 0.8125 (m-40) cc_final: 0.7783 (m110) REVERT: A 401 ILE cc_start: 0.8070 (mm) cc_final: 0.7711 (mt) REVERT: A 446 ARG cc_start: 0.6219 (ptp90) cc_final: 0.5715 (ptp-170) REVERT: A 481 GLN cc_start: 0.7745 (tt0) cc_final: 0.7364 (tp40) REVERT: A 601 ASN cc_start: 0.7800 (p0) cc_final: 0.7310 (p0) REVERT: A 602 SER cc_start: 0.8071 (t) cc_final: 0.7559 (m) REVERT: A 631 LEU cc_start: 0.8791 (mt) cc_final: 0.8427 (mp) REVERT: A 633 GLN cc_start: 0.7484 (mm-40) cc_final: 0.7056 (mm-40) REVERT: A 635 ILE cc_start: 0.7995 (pt) cc_final: 0.7721 (pt) REVERT: A 642 THR cc_start: 0.8230 (p) cc_final: 0.7881 (t) REVERT: A 661 PHE cc_start: 0.7703 (p90) cc_final: 0.7390 (p90) REVERT: A 668 ARG cc_start: 0.7243 (mtp85) cc_final: 0.7037 (ttp-110) REVERT: A 671 MET cc_start: 0.6367 (mmm) cc_final: 0.5910 (mmm) REVERT: A 679 ARG cc_start: 0.6571 (mtp85) cc_final: 0.6028 (mtp85) REVERT: A 711 ARG cc_start: 0.7429 (mtm180) cc_final: 0.7168 (mtm180) REVERT: A 728 ASN cc_start: 0.8547 (m-40) cc_final: 0.8281 (m-40) REVERT: A 799 THR cc_start: 0.4343 (t) cc_final: 0.3372 (m) REVERT: A 833 LEU cc_start: 0.7515 (tp) cc_final: 0.7104 (tt) REVERT: A 848 THR cc_start: 0.8232 (p) cc_final: 0.7908 (p) REVERT: A 852 GLU cc_start: 0.7552 (mt-10) cc_final: 0.7095 (mt-10) REVERT: A 863 ASN cc_start: 0.6351 (t0) cc_final: 0.5646 (t0) REVERT: A 910 ASP cc_start: 0.7570 (p0) cc_final: 0.7324 (m-30) REVERT: A 928 ASN cc_start: 0.7847 (t0) cc_final: 0.7534 (m-40) REVERT: A 938 ASP cc_start: 0.8344 (t0) cc_final: 0.8123 (t0) REVERT: A 948 ILE cc_start: 0.8347 (mm) cc_final: 0.8145 (mp) REVERT: A 949 LYS cc_start: 0.8172 (mttt) cc_final: 0.7927 (mttt) REVERT: A 1050 GLN cc_start: 0.8128 (mm-40) cc_final: 0.7679 (mm-40) REVERT: A 1059 ILE cc_start: 0.8358 (pt) cc_final: 0.8060 (mt) REVERT: A 1064 GLN cc_start: 0.8192 (tt0) cc_final: 0.7943 (tt0) REVERT: A 1079 ILE cc_start: 0.8478 (mt) cc_final: 0.8069 (mm) REVERT: A 1080 ASP cc_start: 0.7911 (t0) cc_final: 0.7456 (t0) REVERT: F 65 SER cc_start: 0.7476 (t) cc_final: 0.7224 (p) REVERT: B 57 TYR cc_start: 0.7422 (m-80) cc_final: 0.6513 (m-80) REVERT: B 106 LYS cc_start: 0.8247 (ttmm) cc_final: 0.7875 (ttmm) REVERT: B 230 THR cc_start: 0.7872 (m) cc_final: 0.7581 (t) REVERT: B 235 LYS cc_start: 0.8016 (pttm) cc_final: 0.7716 (pttm) REVERT: B 252 MET cc_start: 0.7184 (ptp) cc_final: 0.6943 (tpt) REVERT: B 293 ASP cc_start: 0.7140 (p0) cc_final: 0.6748 (p0) REVERT: B 295 MET cc_start: 0.6545 (ptm) cc_final: 0.6337 (ptm) REVERT: B 312 TYR cc_start: 0.7144 (m-80) cc_final: 0.6909 (m-10) REVERT: B 340 TRP cc_start: 0.8128 (t-100) cc_final: 0.7837 (t-100) REVERT: B 355 LYS cc_start: 0.7492 (tptt) cc_final: 0.7239 (tptm) REVERT: B 357 PHE cc_start: 0.7358 (m-10) cc_final: 0.7082 (m-10) REVERT: B 379 ASN cc_start: 0.8093 (t0) cc_final: 0.7760 (t0) REVERT: B 382 ASP cc_start: 0.7249 (p0) cc_final: 0.7045 (p0) REVERT: B 425 ASP cc_start: 0.7539 (t70) cc_final: 0.7181 (p0) REVERT: B 591 ILE cc_start: 0.8113 (mt) cc_final: 0.7634 (mm) REVERT: B 596 ILE cc_start: 0.8112 (mp) cc_final: 0.7874 (mt) REVERT: B 645 ASN cc_start: 0.8158 (t0) cc_final: 0.7900 (t0) REVERT: B 654 SER cc_start: 0.8462 (m) cc_final: 0.8114 (p) REVERT: B 663 ASP cc_start: 0.7272 (t0) cc_final: 0.6930 (t0) REVERT: B 671 MET cc_start: 0.6702 (mmm) cc_final: 0.6018 (mmm) REVERT: B 711 ARG cc_start: 0.7400 (mtm180) cc_final: 0.7107 (mtm180) REVERT: B 720 ASP cc_start: 0.6687 (m-30) cc_final: 0.6289 (m-30) REVERT: B 799 THR cc_start: 0.4017 (t) cc_final: 0.3100 (m) REVERT: B 822 VAL cc_start: 0.8674 (t) cc_final: 0.8418 (p) REVERT: B 852 GLU cc_start: 0.7118 (mt-10) cc_final: 0.6718 (mt-10) REVERT: B 910 ASP cc_start: 0.7266 (m-30) cc_final: 0.6974 (m-30) REVERT: B 948 ILE cc_start: 0.8472 (mm) cc_final: 0.8225 (mp) REVERT: B 949 LYS cc_start: 0.8151 (mttt) cc_final: 0.7906 (mttt) REVERT: B 999 MET cc_start: 0.2960 (tmm) cc_final: 0.2756 (tpp) REVERT: B 1043 GLU cc_start: 0.7550 (mt-10) cc_final: 0.7336 (mt-10) REVERT: B 1065 GLU cc_start: 0.7223 (mt-10) cc_final: 0.6617 (mm-30) REVERT: B 1076 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7353 (mt-10) REVERT: B 1083 ILE cc_start: 0.8589 (pt) cc_final: 0.8376 (mt) REVERT: B 1091 ASN cc_start: 0.8455 (m110) cc_final: 0.8184 (m110) REVERT: B 1105 LYS cc_start: 0.8375 (tttm) cc_final: 0.8094 (mtpp) outliers start: 67 outliers final: 40 residues processed: 754 average time/residue: 0.2166 time to fit residues: 266.8359 Evaluate side-chains 706 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 665 time to evaluate : 1.198 ------------------------------------------------------------------------------- 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 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 377 THR 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 L residue 65 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 740 CYS 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 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: 0.0670 chunk 96 optimal weight: 6.9990 chunk 306 optimal weight: 8.9990 chunk 164 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 265 optimal weight: 0.5980 chunk 275 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 351 optimal weight: 0.1980 chunk 140 optimal weight: 30.0000 chunk 237 optimal weight: 0.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C1050 GLN C1096 GLN C1226 ASN A 552 HIS ** A 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 793 GLN A 858 GLN A1054 ASN ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN B 336 ASN B 380 ASN B 802 ASN B 858 GLN ** B 867 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1078 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.201738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.169749 restraints weight = 58555.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.174778 restraints weight = 31319.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.178074 restraints weight = 19460.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.180243 restraints weight = 13578.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.181646 restraints weight = 10407.719| |-----------------------------------------------------------------------------| r_work (final): 0.4294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6206 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 33762 Z= 0.116 Angle : 0.596 12.746 46032 Z= 0.308 Chirality : 0.046 0.433 5196 Planarity : 0.004 0.038 5883 Dihedral : 4.249 23.510 4572 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.31 % Favored : 96.62 % Rotamer: Outliers : 1.79 % Allowed : 13.41 % Favored : 84.80 % 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: -0.51 (0.13), residues: 4170 helix: 0.56 (0.19), residues: 762 sheet: 0.06 (0.17), residues: 966 loop : -0.78 (0.12), residues: 2442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1055 TYR 0.031 0.001 TYR C 963 PHE 0.023 0.002 PHE C 960 TRP 0.032 0.001 TRP B 452 HIS 0.009 0.001 HIS B 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (33678) covalent geometry : angle 0.57766 / 0.30 (45849) SS BOND : bond 0.00288 / 0.17 ( 69) SS BOND : angle 1.59314 / 1.09 ( 138) hydrogen bonds : bond 0.03936 / 2.62 ( 1186) hydrogen bonds : angle 5.76339 / 3.99 ( 3381) link_NAG-ASN : bond 0.00816 / 0.49 ( 15) link_NAG-ASN : angle 3.90600 / 2.50 ( 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 753 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 688 time to evaluate : 1.061 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: C 78 MET cc_start: 0.5915 (mmp) cc_final: 0.5675 (mmt) REVERT: C 106 LYS cc_start: 0.8235 (tttt) cc_final: 0.7406 (tttm) REVERT: C 143 ARG cc_start: 0.4422 (ttt180) cc_final: 0.4165 (ttt180) REVERT: C 230 THR cc_start: 0.7801 (m) cc_final: 0.7460 (p) REVERT: C 234 THR cc_start: 0.8145 (p) cc_final: 0.7863 (t) REVERT: C 289 ASP cc_start: 0.6850 (t0) cc_final: 0.6117 (t70) REVERT: C 311 VAL cc_start: 0.6961 (t) cc_final: 0.6728 (p) REVERT: C 327 ARG cc_start: 0.7157 (mmm160) cc_final: 0.6850 (mmm-85) REVERT: C 344 LYS cc_start: 0.7819 (ptpt) cc_final: 0.7352 (ptpt) REVERT: C 355 LYS cc_start: 0.7498 (tppt) cc_final: 0.7124 (tptm) REVERT: C 357 PHE cc_start: 0.7371 (m-10) cc_final: 0.6552 (m-10) REVERT: C 379 ASN cc_start: 0.8335 (t0) cc_final: 0.7690 (t0) REVERT: C 380 ASN cc_start: 0.8290 (m-40) cc_final: 0.8038 (m-40) REVERT: C 401 ILE cc_start: 0.7946 (mm) cc_final: 0.7540 (mt) REVERT: C 425 ASP cc_start: 0.7591 (t70) cc_final: 0.7187 (t70) REVERT: C 451 THR cc_start: 0.6541 (p) cc_final: 0.5498 (m) REVERT: C 452 TRP cc_start: 0.7317 (p-90) cc_final: 0.6955 (p90) REVERT: C 611 GLN cc_start: 0.7622 (tp-100) cc_final: 0.7335 (tm-30) REVERT: C 633 GLN cc_start: 0.7320 (mm-40) cc_final: 0.6995 (mm-40) REVERT: C 720 ASP cc_start: 0.6638 (m-30) cc_final: 0.6410 (m-30) REVERT: C 728 ASN cc_start: 0.8544 (m-40) cc_final: 0.8071 (m-40) REVERT: C 799 THR cc_start: 0.4080 (t) cc_final: 0.3002 (m) REVERT: C 807 ILE cc_start: 0.6960 (mt) cc_final: 0.6582 (pt) REVERT: C 816 ILE cc_start: 0.8071 (mm) cc_final: 0.7846 (mt) REVERT: C 833 LEU cc_start: 0.7676 (tp) cc_final: 0.7181 (tt) REVERT: C 917 LYS cc_start: 0.6435 (ptmm) cc_final: 0.6161 (ptmm) REVERT: C 1043 GLU cc_start: 0.7322 (mt-10) cc_final: 0.6884 (mt-10) REVERT: C 1046 ASN cc_start: 0.8337 (t0) cc_final: 0.8097 (t0) REVERT: C 1050 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.7514 (mm-40) REVERT: C 1052 LEU cc_start: 0.8731 (tp) cc_final: 0.8464 (tp) REVERT: C 1069 ARG cc_start: 0.8148 (mtp180) cc_final: 0.7884 (ptm160) REVERT: A 78 MET cc_start: 0.5809 (mmp) cc_final: 0.5588 (mmt) REVERT: A 106 LYS cc_start: 0.8214 (tttt) cc_final: 0.7703 (ttpp) REVERT: A 143 ARG cc_start: 0.3945 (ttp-170) cc_final: 0.2721 (mtp180) REVERT: A 200 LYS cc_start: 0.7614 (mptt) cc_final: 0.7407 (mptt) REVERT: A 230 THR cc_start: 0.7818 (m) cc_final: 0.7460 (p) REVERT: A 235 LYS cc_start: 0.7839 (mtmm) cc_final: 0.7299 (mtmm) REVERT: A 291 MET cc_start: 0.6811 (mmp) cc_final: 0.6481 (mmp) REVERT: A 293 ASP cc_start: 0.7801 (p0) cc_final: 0.7425 (p0) REVERT: A 295 MET cc_start: 0.6418 (ptm) cc_final: 0.6207 (ptm) REVERT: A 298 ILE cc_start: 0.7813 (mm) cc_final: 0.7530 (mt) REVERT: A 329 LYS cc_start: 0.7511 (tttp) cc_final: 0.7294 (tptt) REVERT: A 377 THR cc_start: 0.7900 (m) cc_final: 0.7521 (p) REVERT: A 379 ASN cc_start: 0.8157 (t0) cc_final: 0.7663 (t0) REVERT: A 380 ASN cc_start: 0.8117 (m-40) cc_final: 0.7746 (m110) REVERT: A 446 ARG cc_start: 0.6182 (ptp90) cc_final: 0.5508 (ptp-170) REVERT: A 601 ASN cc_start: 0.7559 (p0) cc_final: 0.7336 (p0) REVERT: A 602 SER cc_start: 0.7812 (t) cc_final: 0.7312 (m) REVERT: A 606 CYS cc_start: 0.5185 (m) cc_final: 0.4694 (m) REVERT: A 631 LEU cc_start: 0.8747 (mt) cc_final: 0.8448 (mp) REVERT: A 635 ILE cc_start: 0.8098 (pt) cc_final: 0.7808 (pt) REVERT: A 642 THR cc_start: 0.8228 (p) cc_final: 0.7893 (t) REVERT: A 661 PHE cc_start: 0.7636 (p90) cc_final: 0.7194 (p90) REVERT: A 663 ASP cc_start: 0.7351 (t0) cc_final: 0.7101 (t0) REVERT: A 668 ARG cc_start: 0.7210 (mtp85) cc_final: 0.6970 (ttp-110) REVERT: A 679 ARG cc_start: 0.6476 (mtp85) cc_final: 0.6257 (mtp85) REVERT: A 685 HIS cc_start: 0.7327 (t-90) cc_final: 0.6734 (t-90) REVERT: A 699 LYS cc_start: 0.6776 (mmmm) cc_final: 0.6367 (mmmm) REVERT: A 711 ARG cc_start: 0.7375 (mtm180) cc_final: 0.7104 (mtm180) REVERT: A 714 GLN cc_start: 0.8044 (mm-40) cc_final: 0.7754 (mp-120) REVERT: A 720 ASP cc_start: 0.6608 (m-30) cc_final: 0.6018 (m-30) REVERT: A 728 ASN cc_start: 0.8556 (m-40) cc_final: 0.8292 (m-40) REVERT: A 799 THR cc_start: 0.4405 (t) cc_final: 0.3445 (m) REVERT: A 804 VAL cc_start: 0.4506 (OUTLIER) cc_final: 0.4262 (p) REVERT: A 830 LYS cc_start: 0.8156 (mttt) cc_final: 0.7909 (mmmm) REVERT: A 833 LEU cc_start: 0.7393 (tp) cc_final: 0.7008 (tt) REVERT: A 848 THR cc_start: 0.8204 (p) cc_final: 0.7792 (p) REVERT: A 852 GLU cc_start: 0.7525 (mt-10) cc_final: 0.7029 (mt-10) REVERT: A 863 ASN cc_start: 0.6332 (t0) cc_final: 0.5824 (t0) REVERT: A 866 MET cc_start: 0.5580 (ptp) cc_final: 0.5347 (ptp) REVERT: A 910 ASP cc_start: 0.7602 (p0) cc_final: 0.7331 (m-30) REVERT: A 928 ASN cc_start: 0.7846 (t0) cc_final: 0.7571 (m-40) REVERT: A 938 ASP cc_start: 0.8294 (t0) cc_final: 0.8075 (t0) REVERT: A 1050 GLN cc_start: 0.8137 (mm-40) cc_final: 0.7282 (mm-40) REVERT: A 1059 ILE cc_start: 0.8384 (pt) cc_final: 0.8003 (mt) REVERT: A 1064 GLN cc_start: 0.8054 (tt0) cc_final: 0.7657 (tt0) REVERT: F 65 SER cc_start: 0.7445 (t) cc_final: 0.7183 (p) REVERT: B 230 THR cc_start: 0.7862 (m) cc_final: 0.7610 (t) REVERT: B 235 LYS cc_start: 0.7979 (pttm) cc_final: 0.7659 (pttm) REVERT: B 252 MET cc_start: 0.7208 (ptp) cc_final: 0.6896 (tpt) REVERT: B 293 ASP cc_start: 0.7178 (p0) cc_final: 0.6750 (p0) REVERT: B 295 MET cc_start: 0.6249 (ptm) cc_final: 0.6045 (ptm) REVERT: B 340 TRP cc_start: 0.8060 (t-100) cc_final: 0.7796 (t-100) REVERT: B 379 ASN cc_start: 0.8276 (t0) cc_final: 0.7850 (t0) REVERT: B 380 ASN cc_start: 0.8177 (m-40) cc_final: 0.7975 (m110) REVERT: B 425 ASP cc_start: 0.7551 (t70) cc_final: 0.7229 (t70) REVERT: B 591 ILE cc_start: 0.8110 (mt) cc_final: 0.7608 (mm) REVERT: B 596 ILE cc_start: 0.8147 (mp) cc_final: 0.7861 (mt) REVERT: B 662 ARG cc_start: 0.7883 (ptm160) cc_final: 0.7567 (ptp-170) REVERT: B 663 ASP cc_start: 0.7215 (t0) cc_final: 0.6838 (t0) REVERT: B 671 MET cc_start: 0.6608 (mmm) cc_final: 0.6151 (mmm) REVERT: B 720 ASP cc_start: 0.6817 (m-30) cc_final: 0.6457 (m-30) REVERT: B 799 THR cc_start: 0.4214 (t) cc_final: 0.3269 (m) REVERT: B 802 ASN cc_start: 0.6499 (OUTLIER) cc_final: 0.6231 (p0) REVERT: B 852 GLU cc_start: 0.7102 (mt-10) cc_final: 0.6603 (mt-10) REVERT: B 910 ASP cc_start: 0.7249 (m-30) cc_final: 0.6935 (m-30) REVERT: B 913 PHE cc_start: 0.7884 (m-80) cc_final: 0.7630 (m-80) REVERT: B 949 LYS cc_start: 0.8032 (mttt) cc_final: 0.7796 (mttt) REVERT: B 1043 GLU cc_start: 0.7499 (mt-10) cc_final: 0.7209 (mt-10) REVERT: B 1065 GLU cc_start: 0.7279 (mt-10) cc_final: 0.6857 (mm-30) REVERT: B 1091 ASN cc_start: 0.8475 (m110) cc_final: 0.7967 (m110) REVERT: B 1105 LYS cc_start: 0.8431 (tttm) cc_final: 0.8111 (mtpp) REVERT: B 1210 MET cc_start: 0.3414 (ppp) cc_final: 0.1722 (pmm) outliers start: 65 outliers final: 44 residues processed: 720 average time/residue: 0.1985 time to fit residues: 233.4414 Evaluate side-chains 701 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 654 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 65 SER Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 44 THR 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 1050 GLN Chi-restraints excluded: chain C residue 1062 SER Chi-restraints excluded: chain C residue 1096 GLN Chi-restraints excluded: chain C residue 1099 SER Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain A residue 40 THR 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 284 ILE Chi-restraints excluded: chain A residue 363 ASN Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 740 CYS Chi-restraints excluded: chain A residue 749 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 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 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 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 802 ASN Chi-restraints excluded: chain B residue 866 MET Chi-restraints excluded: chain B residue 940 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 236 optimal weight: 0.9980 chunk 134 optimal weight: 10.0000 chunk 394 optimal weight: 4.9990 chunk 142 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 chunk 119 optimal weight: 0.0270 chunk 215 optimal weight: 2.9990 chunk 209 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 255 optimal weight: 4.9990 chunk 152 optimal weight: 20.0000 overall best weight: 2.2044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 418 GLN C 648 GLN C 793 GLN C 802 ASN L 6 GLN L 90 GLN ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 273 GLN A 280 GLN A 793 GLN A 858 GLN A1091 ASN F 90 GLN ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 336 ASN B 590 ASN ** B 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 858 GLN ** B 867 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1050 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.192287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.160027 restraints weight = 58310.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.164937 restraints weight = 31200.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.168065 restraints weight = 19447.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.170203 restraints weight = 13677.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.171612 restraints weight = 10612.360| |-----------------------------------------------------------------------------| r_work (final): 0.4171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6418 moved from start: 0.4861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.109 33762 Z= 0.286 Angle : 0.753 12.112 46032 Z= 0.406 Chirality : 0.051 0.380 5196 Planarity : 0.005 0.068 5883 Dihedral : 4.982 26.880 4572 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.16 % Favored : 94.80 % Rotamer: Outliers : 2.91 % Allowed : 14.26 % Favored : 82.82 % 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: -0.99 (0.12), residues: 4170 helix: 0.04 (0.18), residues: 738 sheet: -0.23 (0.17), residues: 927 loop : -1.04 (0.12), residues: 2505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 571 TYR 0.034 0.003 TYR C 963 PHE 0.033 0.003 PHE A 104 TRP 0.033 0.003 TRP B 452 HIS 0.008 0.002 HIS C 552 Details of bonding type rmsd/Z covalent geometry : bond 0.00602 / 0.29 (33678) covalent geometry : angle 0.73649 / 0.40 (45849) SS BOND : bond 0.00556 / 0.34 ( 69) SS BOND : angle 1.99030 / 1.32 ( 138) hydrogen bonds : bond 0.04997 / 3.34 ( 1186) hydrogen bonds : angle 6.26609 / 4.33 ( 3381) link_NAG-ASN : bond 0.00578 / 0.33 ( 15) link_NAG-ASN : angle 3.88859 / 2.50 ( 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 843 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 737 time to evaluate : 1.175 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: 0.3420 (OUTLIER) cc_final: 0.3125 (tpt) REVERT: C 57 TYR cc_start: 0.7558 (m-80) cc_final: 0.7005 (m-80) REVERT: C 78 MET cc_start: 0.6180 (mmp) cc_final: 0.5969 (mmp) REVERT: C 143 ARG cc_start: 0.4445 (ttt180) cc_final: 0.3184 (mtp180) REVERT: C 205 TYR cc_start: 0.8069 (p90) cc_final: 0.7780 (p90) REVERT: C 230 THR cc_start: 0.7958 (m) cc_final: 0.7658 (p) REVERT: C 235 LYS cc_start: 0.7594 (mtmm) cc_final: 0.7218 (mtmm) REVERT: C 240 VAL cc_start: 0.8959 (t) cc_final: 0.8742 (p) REVERT: C 252 MET cc_start: 0.7109 (pmm) cc_final: 0.6659 (tpt) REVERT: C 311 VAL cc_start: 0.7117 (t) cc_final: 0.6915 (p) REVERT: C 344 LYS cc_start: 0.8113 (ptpt) cc_final: 0.7761 (ptpt) REVERT: C 367 LEU cc_start: 0.8614 (mt) cc_final: 0.8412 (mt) REVERT: C 377 THR cc_start: 0.7732 (OUTLIER) cc_final: 0.7444 (p) REVERT: C 379 ASN cc_start: 0.8514 (t0) cc_final: 0.7822 (t0) REVERT: C 380 ASN cc_start: 0.8348 (m-40) cc_final: 0.7987 (m-40) REVERT: C 425 ASP cc_start: 0.7516 (t70) cc_final: 0.7124 (t0) REVERT: C 606 CYS cc_start: 0.4916 (m) cc_final: 0.4614 (m) REVERT: C 671 MET cc_start: 0.6093 (mmm) cc_final: 0.5548 (mtp) REVERT: C 673 ARG cc_start: 0.7407 (mtp180) cc_final: 0.7038 (mtt-85) REVERT: C 685 HIS cc_start: 0.7567 (t-90) cc_final: 0.7285 (t-90) REVERT: C 720 ASP cc_start: 0.7012 (m-30) cc_final: 0.6791 (m-30) REVERT: C 728 ASN cc_start: 0.8525 (m-40) cc_final: 0.8035 (m-40) REVERT: C 807 ILE cc_start: 0.7100 (mt) cc_final: 0.6833 (pt) REVERT: C 816 ILE cc_start: 0.8257 (mm) cc_final: 0.8055 (mt) REVERT: C 835 GLU cc_start: 0.6935 (mm-30) cc_final: 0.6708 (mm-30) REVERT: C 849 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.6947 (pt0) REVERT: C 852 GLU cc_start: 0.7309 (mt-10) cc_final: 0.6730 (mt-10) REVERT: C 940 ILE cc_start: 0.8016 (tp) cc_final: 0.7778 (tt) REVERT: C 965 LEU cc_start: 0.8008 (tt) cc_final: 0.7780 (tt) REVERT: C 1043 GLU cc_start: 0.7492 (mt-10) cc_final: 0.7102 (mt-10) REVERT: C 1046 ASN cc_start: 0.8405 (t0) cc_final: 0.8195 (t0) REVERT: C 1052 LEU cc_start: 0.8841 (tp) cc_final: 0.8505 (tp) REVERT: C 1074 GLU cc_start: 0.7773 (tt0) cc_final: 0.7348 (tt0) REVERT: C 1105 LYS cc_start: 0.8382 (ptmt) cc_final: 0.7990 (mtmm) REVERT: C 1224 MET cc_start: 0.4425 (tpp) cc_final: 0.4207 (tpp) REVERT: A 78 MET cc_start: 0.6058 (mmp) cc_final: 0.5853 (mmt) REVERT: A 99 PHE cc_start: 0.7336 (t80) cc_final: 0.6950 (t80) REVERT: A 106 LYS cc_start: 0.8254 (tttt) cc_final: 0.7744 (ttpp) REVERT: A 143 ARG cc_start: 0.4375 (ttp-170) cc_final: 0.3105 (mtp180) REVERT: A 230 THR cc_start: 0.7846 (m) cc_final: 0.7570 (p) REVERT: A 235 LYS cc_start: 0.7906 (mtmm) cc_final: 0.7458 (mtmm) REVERT: A 291 MET cc_start: 0.6985 (mmp) cc_final: 0.6739 (mmt) REVERT: A 293 ASP cc_start: 0.7704 (p0) cc_final: 0.7419 (p0) REVERT: A 298 ILE cc_start: 0.8056 (mm) cc_final: 0.7812 (mt) REVERT: A 315 ASN cc_start: 0.7676 (p0) cc_final: 0.7435 (p0) REVERT: A 344 LYS cc_start: 0.8258 (ptpt) cc_final: 0.7870 (ptpt) REVERT: A 357 PHE cc_start: 0.7392 (m-10) cc_final: 0.7192 (m-80) REVERT: A 368 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.8193 (mtt) REVERT: A 377 THR cc_start: 0.8074 (m) cc_final: 0.7724 (p) REVERT: A 379 ASN cc_start: 0.8408 (t0) cc_final: 0.7904 (t0) REVERT: A 380 ASN cc_start: 0.8165 (m-40) cc_final: 0.7916 (m110) REVERT: A 409 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8393 (mp) REVERT: A 425 ASP cc_start: 0.7364 (t70) cc_final: 0.6978 (p0) REVERT: A 451 THR cc_start: 0.6870 (p) cc_final: 0.5923 (m) REVERT: A 602 SER cc_start: 0.8024 (t) cc_final: 0.7396 (m) REVERT: A 606 CYS cc_start: 0.5105 (m) cc_final: 0.4835 (m) REVERT: A 631 LEU cc_start: 0.8792 (mt) cc_final: 0.8505 (mp) REVERT: A 635 ILE cc_start: 0.8105 (pt) cc_final: 0.7822 (pt) REVERT: A 668 ARG cc_start: 0.7444 (mtp85) cc_final: 0.7233 (ttp-110) REVERT: A 671 MET cc_start: 0.6063 (mmm) cc_final: 0.5825 (mmm) REVERT: A 728 ASN cc_start: 0.8518 (m-40) cc_final: 0.8226 (m-40) REVERT: A 804 VAL cc_start: 0.7064 (OUTLIER) cc_final: 0.6760 (p) REVERT: A 830 LYS cc_start: 0.8221 (mttt) cc_final: 0.7993 (mmmm) REVERT: A 849 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.6935 (pt0) REVERT: A 852 GLU cc_start: 0.7654 (mt-10) cc_final: 0.7107 (mt-10) REVERT: A 863 ASN cc_start: 0.6505 (t0) cc_final: 0.6133 (t0) REVERT: A 910 ASP cc_start: 0.7710 (p0) cc_final: 0.7487 (p0) REVERT: A 928 ASN cc_start: 0.8082 (t0) cc_final: 0.7853 (m-40) REVERT: A 1050 GLN cc_start: 0.8108 (mm-40) cc_final: 0.7347 (mm-40) REVERT: A 1059 ILE cc_start: 0.8477 (pt) cc_final: 0.8217 (mt) REVERT: A 1064 GLN cc_start: 0.8208 (tt0) cc_final: 0.7897 (tt0) REVERT: B 143 ARG cc_start: 0.4841 (ttt180) cc_final: 0.4191 (ttp-170) REVERT: B 205 TYR cc_start: 0.8107 (p90) cc_final: 0.7846 (p90) REVERT: B 230 THR cc_start: 0.8030 (m) cc_final: 0.7731 (p) REVERT: B 235 LYS cc_start: 0.7973 (pttm) cc_final: 0.7624 (pttm) REVERT: B 246 LEU cc_start: 0.6683 (mt) cc_final: 0.6312 (mt) REVERT: B 252 MET cc_start: 0.7285 (ptp) cc_final: 0.7058 (ptp) REVERT: B 322 ILE cc_start: 0.8273 (mm) cc_final: 0.8053 (mm) REVERT: B 329 LYS cc_start: 0.7830 (tptt) cc_final: 0.7416 (tptt) REVERT: B 340 TRP cc_start: 0.8328 (t-100) cc_final: 0.8028 (t-100) REVERT: B 344 LYS cc_start: 0.8039 (ptpt) cc_final: 0.7609 (ptpt) REVERT: B 374 ASP cc_start: 0.7623 (t70) cc_final: 0.7405 (t0) REVERT: B 379 ASN cc_start: 0.8252 (t0) cc_final: 0.7783 (t0) REVERT: B 380 ASN cc_start: 0.8189 (m-40) cc_final: 0.7892 (m110) REVERT: B 547 VAL cc_start: 0.8510 (p) cc_final: 0.8294 (m) REVERT: B 559 LYS cc_start: 0.7628 (pttt) cc_final: 0.7263 (pttt) REVERT: B 591 ILE cc_start: 0.8253 (mt) cc_final: 0.7737 (mm) REVERT: B 596 ILE cc_start: 0.8231 (OUTLIER) cc_final: 0.7959 (mt) REVERT: B 652 TYR cc_start: 0.7731 (m-80) cc_final: 0.7308 (m-80) REVERT: B 654 SER cc_start: 0.8483 (m) cc_final: 0.8167 (p) REVERT: B 663 ASP cc_start: 0.7239 (t0) cc_final: 0.6926 (t0) REVERT: B 671 MET cc_start: 0.6508 (mmm) cc_final: 0.6094 (mmm) REVERT: B 679 ARG cc_start: 0.6900 (mmm-85) cc_final: 0.6644 (mmm-85) REVERT: B 711 ARG cc_start: 0.7682 (mtm180) cc_final: 0.7457 (mtm180) REVERT: B 830 LYS cc_start: 0.8278 (mttp) cc_final: 0.7939 (mmtp) REVERT: B 852 GLU cc_start: 0.7385 (mt-10) cc_final: 0.6958 (mt-10) REVERT: B 927 TYR cc_start: 0.8147 (m-80) cc_final: 0.7870 (m-80) REVERT: B 949 LYS cc_start: 0.8397 (mttt) cc_final: 0.8039 (mttt) REVERT: B 1043 GLU cc_start: 0.7621 (mt-10) cc_final: 0.7342 (mt-10) REVERT: B 1073 LEU cc_start: 0.7743 (tt) cc_final: 0.7517 (tt) REVERT: B 1091 ASN cc_start: 0.8364 (m110) cc_final: 0.7923 (m110) REVERT: B 1105 LYS cc_start: 0.8512 (tttm) cc_final: 0.8166 (mtpp) outliers start: 106 outliers final: 56 residues processed: 787 average time/residue: 0.1976 time to fit residues: 254.4840 Evaluate side-chains 752 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 688 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 32 TYR Chi-restraints excluded: chain Y residue 4 MET Chi-restraints excluded: chain C residue 40 THR 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 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 839 PHE 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 90 GLN Chi-restraints excluded: chain A residue 40 THR 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 368 MET Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 409 LEU Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 740 CYS Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 802 ASN Chi-restraints excluded: chain A residue 803 MET Chi-restraints excluded: chain A residue 804 VAL 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 1060 SER Chi-restraints excluded: chain D residue 32 TYR 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 F residue 90 GLN 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 237 LEU Chi-restraints excluded: chain B residue 292 SER 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 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 769 THR Chi-restraints excluded: chain B residue 836 TYR Chi-restraints excluded: chain B residue 855 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 408 optimal weight: 5.9990 chunk 346 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 50 optimal weight: 0.4980 chunk 306 optimal weight: 9.9990 chunk 213 optimal weight: 3.9990 chunk 19 optimal weight: 20.0000 chunk 196 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 377 optimal weight: 1.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Y 90 GLN ** C 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1096 GLN C1133 ASN ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 273 GLN A 380 ASN A 474 ASN A 552 HIS A 573 GLN A 655 ASN A 714 GLN A1133 ASN ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN B 280 GLN B 714 GLN ** B 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.190222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.157795 restraints weight = 57963.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.162740 restraints weight = 30831.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.165971 restraints weight = 19182.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.167930 restraints weight = 13440.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.169398 restraints weight = 10427.657| |-----------------------------------------------------------------------------| r_work (final): 0.4162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6456 moved from start: 0.5556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 33762 Z= 0.255 Angle : 0.728 14.344 46032 Z= 0.389 Chirality : 0.050 0.388 5196 Planarity : 0.005 0.060 5883 Dihedral : 5.025 27.066 4572 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.72 % Favored : 95.25 % Rotamer: Outliers : 3.13 % Allowed : 16.02 % Favored : 80.85 % 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: -1.14 (0.12), residues: 4170 helix: 0.03 (0.18), residues: 738 sheet: -0.41 (0.16), residues: 981 loop : -1.16 (0.12), residues: 2451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1125 TYR 0.033 0.002 TYR A1147 PHE 0.026 0.003 PHE B1013 TRP 0.035 0.002 TRP B 452 HIS 0.013 0.002 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00531 / 0.25 (33678) covalent geometry : angle 0.71017 / 0.38 (45849) SS BOND : bond 0.00540 / 0.32 ( 69) SS BOND : angle 2.14020 / 1.53 ( 138) hydrogen bonds : bond 0.04737 / 3.19 ( 1186) hydrogen bonds : angle 6.21527 / 4.28 ( 3381) link_NAG-ASN : bond 0.00589 / 0.34 ( 15) link_NAG-ASN : angle 3.80396 / 2.46 ( 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 850 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 736 time to evaluate : 0.996 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: Y 4 MET cc_start: 0.3628 (OUTLIER) cc_final: 0.3400 (tpt) REVERT: C 57 TYR cc_start: 0.7524 (m-80) cc_final: 0.7030 (m-80) REVERT: C 78 MET cc_start: 0.6191 (mmp) cc_final: 0.5975 (mmp) REVERT: C 143 ARG cc_start: 0.4376 (ttt180) cc_final: 0.4129 (ttt180) REVERT: C 200 LYS cc_start: 0.8108 (mptt) cc_final: 0.7896 (mppt) REVERT: C 205 TYR cc_start: 0.8121 (p90) cc_final: 0.7823 (p90) REVERT: C 230 THR cc_start: 0.7876 (m) cc_final: 0.7559 (p) REVERT: C 235 LYS cc_start: 0.7559 (mtmm) cc_final: 0.7347 (mtmm) REVERT: C 240 VAL cc_start: 0.8898 (t) cc_final: 0.8636 (p) REVERT: C 311 VAL cc_start: 0.7211 (t) cc_final: 0.6995 (p) REVERT: C 327 ARG cc_start: 0.7499 (mmm160) cc_final: 0.7280 (mmm-85) REVERT: C 343 ASP cc_start: 0.7459 (t70) cc_final: 0.6840 (p0) REVERT: C 344 LYS cc_start: 0.8383 (ptpt) cc_final: 0.7505 (ptpt) REVERT: C 361 ASN cc_start: 0.7425 (m-40) cc_final: 0.7204 (m-40) REVERT: C 367 LEU cc_start: 0.8657 (mt) cc_final: 0.8454 (mt) REVERT: C 377 THR cc_start: 0.7654 (OUTLIER) cc_final: 0.7390 (p) REVERT: C 379 ASN cc_start: 0.8449 (t0) cc_final: 0.7848 (t0) REVERT: C 380 ASN cc_start: 0.8349 (m-40) cc_final: 0.7987 (m-40) REVERT: C 389 MET cc_start: 0.7267 (tpp) cc_final: 0.7028 (mmm) REVERT: C 398 LYS cc_start: 0.8366 (pttt) cc_final: 0.7609 (pttm) REVERT: C 671 MET cc_start: 0.6070 (mmm) cc_final: 0.5672 (mtp) REVERT: C 673 ARG cc_start: 0.7316 (mtp180) cc_final: 0.6990 (mtt-85) REVERT: C 685 HIS cc_start: 0.7606 (t-90) cc_final: 0.7334 (t-90) REVERT: C 728 ASN cc_start: 0.8485 (m-40) cc_final: 0.7962 (m-40) REVERT: C 807 ILE cc_start: 0.7149 (mt) cc_final: 0.6740 (pt) REVERT: C 835 GLU cc_start: 0.7043 (mm-30) cc_final: 0.6789 (mm-30) REVERT: C 849 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7018 (pt0) REVERT: C 852 GLU cc_start: 0.7309 (mt-10) cc_final: 0.6675 (mt-10) REVERT: C 855 ASP cc_start: 0.7790 (OUTLIER) cc_final: 0.7517 (p0) REVERT: C 858 GLN cc_start: 0.7879 (mt0) cc_final: 0.7647 (mt0) REVERT: C 946 LYS cc_start: 0.8320 (mmtp) cc_final: 0.8061 (mmtm) REVERT: C 965 LEU cc_start: 0.7936 (tt) cc_final: 0.7674 (tt) REVERT: C 1028 ASN cc_start: 0.6339 (p0) cc_final: 0.6038 (p0) REVERT: C 1043 GLU cc_start: 0.7490 (mt-10) cc_final: 0.7209 (mt-10) REVERT: C 1046 ASN cc_start: 0.8292 (t0) cc_final: 0.8039 (t0) REVERT: C 1051 GLN cc_start: 0.7590 (mm-40) cc_final: 0.7213 (mm-40) REVERT: C 1052 LEU cc_start: 0.8947 (tp) cc_final: 0.8607 (tp) REVERT: C 1074 GLU cc_start: 0.7821 (tt0) cc_final: 0.7460 (tt0) REVERT: C 1079 ILE cc_start: 0.8733 (mt) cc_final: 0.8393 (mm) REVERT: C 1147 TYR cc_start: 0.6016 (t80) cc_final: 0.5792 (t80) REVERT: C 1183 VAL cc_start: 0.2963 (m) cc_final: 0.2532 (p) REVERT: C 1224 MET cc_start: 0.4344 (tpp) cc_final: 0.4104 (tpp) REVERT: A 64 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7628 (mp) REVERT: A 78 MET cc_start: 0.5958 (mmp) cc_final: 0.5755 (mmt) REVERT: A 106 LYS cc_start: 0.8184 (tttt) cc_final: 0.7688 (ttpp) REVERT: A 143 ARG cc_start: 0.4283 (ttp-170) cc_final: 0.2984 (mtp180) REVERT: A 200 LYS cc_start: 0.7744 (mptt) cc_final: 0.7352 (mppt) REVERT: A 230 THR cc_start: 0.7833 (m) cc_final: 0.7555 (p) REVERT: A 235 LYS cc_start: 0.7814 (mtmm) cc_final: 0.7408 (mtmm) REVERT: A 293 ASP cc_start: 0.7654 (p0) cc_final: 0.7384 (p0) REVERT: A 298 ILE cc_start: 0.8022 (mm) cc_final: 0.7779 (mt) REVERT: A 313 GLU cc_start: 0.7027 (mm-30) cc_final: 0.6762 (tm-30) REVERT: A 315 ASN cc_start: 0.7736 (p0) cc_final: 0.7361 (p0) REVERT: A 326 TYR cc_start: 0.7614 (t80) cc_final: 0.6859 (t80) REVERT: A 344 LYS cc_start: 0.8253 (ptpt) cc_final: 0.7942 (ptpt) REVERT: A 357 PHE cc_start: 0.7261 (m-10) cc_final: 0.6943 (m-80) REVERT: A 363 ASN cc_start: 0.4538 (OUTLIER) cc_final: 0.4212 (p0) REVERT: A 377 THR cc_start: 0.8078 (m) cc_final: 0.7743 (p) REVERT: A 379 ASN cc_start: 0.8338 (t0) cc_final: 0.7970 (t0) REVERT: A 397 ASP cc_start: 0.7203 (p0) cc_final: 0.6877 (p0) REVERT: A 425 ASP cc_start: 0.7379 (t70) cc_final: 0.7013 (p0) REVERT: A 601 ASN cc_start: 0.7198 (p0) cc_final: 0.6955 (p0) REVERT: A 602 SER cc_start: 0.7841 (t) cc_final: 0.7297 (m) REVERT: A 631 LEU cc_start: 0.8864 (mt) cc_final: 0.8536 (mp) REVERT: A 635 ILE cc_start: 0.8114 (pt) cc_final: 0.7837 (pt) REVERT: A 663 ASP cc_start: 0.7210 (t0) cc_final: 0.6855 (t0) REVERT: A 668 ARG cc_start: 0.7454 (mtp85) cc_final: 0.7246 (ttp-110) REVERT: A 718 TYR cc_start: 0.6184 (p90) cc_final: 0.5892 (p90) REVERT: A 728 ASN cc_start: 0.8442 (m-40) cc_final: 0.8089 (m110) REVERT: A 833 LEU cc_start: 0.7579 (tp) cc_final: 0.7256 (mm) REVERT: A 849 GLU cc_start: 0.7654 (pt0) cc_final: 0.6839 (pt0) REVERT: A 852 GLU cc_start: 0.7629 (mt-10) cc_final: 0.6998 (mt-10) REVERT: A 928 ASN cc_start: 0.7923 (t0) cc_final: 0.7532 (m-40) REVERT: A 1005 ASN cc_start: 0.4583 (p0) cc_final: 0.4259 (p0) REVERT: A 1050 GLN cc_start: 0.8071 (mm-40) cc_final: 0.7354 (mm-40) REVERT: A 1059 ILE cc_start: 0.8486 (pt) cc_final: 0.8161 (mt) REVERT: A 1064 GLN cc_start: 0.8183 (tt0) cc_final: 0.7940 (tt0) REVERT: A 1147 TYR cc_start: 0.6049 (OUTLIER) cc_final: 0.5711 (t80) REVERT: B 64 LEU cc_start: 0.8154 (tp) cc_final: 0.7670 (tt) REVERT: B 106 LYS cc_start: 0.8563 (ttpp) cc_final: 0.8330 (ttmm) REVERT: B 143 ARG cc_start: 0.4791 (ttt180) cc_final: 0.4479 (ttt180) REVERT: B 189 HIS cc_start: 0.8615 (p-80) cc_final: 0.8327 (p-80) REVERT: B 200 LYS cc_start: 0.7699 (mppt) cc_final: 0.7447 (mppt) REVERT: B 230 THR cc_start: 0.8012 (m) cc_final: 0.7712 (p) REVERT: B 235 LYS cc_start: 0.7975 (pttm) cc_final: 0.7591 (pttm) REVERT: B 237 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8438 (mp) REVERT: B 252 MET cc_start: 0.7284 (ptp) cc_final: 0.7074 (ptp) REVERT: B 298 ILE cc_start: 0.7967 (mm) cc_final: 0.7649 (mm) REVERT: B 326 TYR cc_start: 0.7856 (t80) cc_final: 0.7236 (t80) REVERT: B 329 LYS cc_start: 0.7998 (tptt) cc_final: 0.7688 (tptt) REVERT: B 374 ASP cc_start: 0.7698 (t70) cc_final: 0.7436 (t0) REVERT: B 379 ASN cc_start: 0.8211 (t0) cc_final: 0.7742 (t0) REVERT: B 380 ASN cc_start: 0.8180 (m-40) cc_final: 0.7829 (m110) REVERT: B 397 ASP cc_start: 0.7094 (OUTLIER) cc_final: 0.6418 (p0) REVERT: B 446 ARG cc_start: 0.5880 (mpp80) cc_final: 0.5552 (mpp80) REVERT: B 477 VAL cc_start: 0.7803 (OUTLIER) cc_final: 0.6864 (m) REVERT: B 545 SER cc_start: 0.8410 (p) cc_final: 0.8204 (t) REVERT: B 547 VAL cc_start: 0.8508 (p) cc_final: 0.8267 (m) REVERT: B 559 LYS cc_start: 0.7729 (pttt) cc_final: 0.7314 (pttt) REVERT: B 591 ILE cc_start: 0.8307 (mt) cc_final: 0.7889 (mm) REVERT: B 596 ILE cc_start: 0.8260 (OUTLIER) cc_final: 0.7982 (mt) REVERT: B 601 ASN cc_start: 0.7846 (p0) cc_final: 0.7509 (p0) REVERT: B 646 SER cc_start: 0.8765 (m) cc_final: 0.8520 (t) REVERT: B 652 TYR cc_start: 0.7664 (m-80) cc_final: 0.7273 (m-80) REVERT: B 654 SER cc_start: 0.8382 (m) cc_final: 0.8070 (p) REVERT: B 663 ASP cc_start: 0.7340 (t0) cc_final: 0.6963 (t0) REVERT: B 671 MET cc_start: 0.6332 (mmm) cc_final: 0.6043 (mmm) REVERT: B 849 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.6939 (pt0) REVERT: B 852 GLU cc_start: 0.7371 (mt-10) cc_final: 0.6988 (mt-10) REVERT: B 928 ASN cc_start: 0.8094 (t0) cc_final: 0.7722 (m-40) REVERT: B 949 LYS cc_start: 0.8363 (mttt) cc_final: 0.7770 (ttmt) REVERT: B 1043 GLU cc_start: 0.7537 (mt-10) cc_final: 0.7333 (mt-10) REVERT: B 1065 GLU cc_start: 0.7512 (mt-10) cc_final: 0.6991 (mm-30) REVERT: B 1067 LEU cc_start: 0.8680 (tp) cc_final: 0.8207 (tt) REVERT: B 1073 LEU cc_start: 0.7838 (tt) cc_final: 0.7574 (tt) REVERT: B 1074 GLU cc_start: 0.7982 (tt0) cc_final: 0.7684 (tp30) REVERT: B 1105 LYS cc_start: 0.8574 (tttm) cc_final: 0.8164 (mtpp) outliers start: 114 outliers final: 72 residues processed: 795 average time/residue: 0.2010 time to fit residues: 258.8649 Evaluate side-chains 780 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 696 time to evaluate : 1.163 ------------------------------------------------------------------------------- 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 4 MET Chi-restraints excluded: chain Y residue 14 SER Chi-restraints excluded: chain Y residue 90 GLN Chi-restraints excluded: chain C residue 40 THR 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 284 ILE 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 433 LEU Chi-restraints excluded: chain C residue 570 CYS 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 769 THR Chi-restraints excluded: chain C residue 834 VAL 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 1045 LEU 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 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 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 407 VAL Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 623 VAL Chi-restraints excluded: chain A residue 638 GLU Chi-restraints excluded: chain A residue 740 CYS Chi-restraints excluded: chain A residue 749 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 804 VAL 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 1102 THR Chi-restraints excluded: chain A residue 1147 TYR 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 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 237 LEU 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 353 GLU 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 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 623 VAL 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 846 ILE Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 855 ASP Chi-restraints excluded: chain B residue 1068 SER 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: 0.9980 chunk 198 optimal weight: 0.9990 chunk 285 optimal weight: 6.9990 chunk 317 optimal weight: 0.9990 chunk 6 optimal weight: 0.0980 chunk 187 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 220 optimal weight: 1.9990 chunk 185 optimal weight: 0.8980 chunk 141 optimal weight: 20.0000 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 858 GLN L 90 GLN A 280 GLN A 474 ASN A 552 HIS A 573 GLN A1133 ASN ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 858 GLN B1133 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.193059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.161167 restraints weight = 57798.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.166106 restraints weight = 30621.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.169344 restraints weight = 18973.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.171414 restraints weight = 13238.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.172846 restraints weight = 10205.485| |-----------------------------------------------------------------------------| r_work (final): 0.4201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6395 moved from start: 0.5695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 33762 Z= 0.150 Angle : 0.685 21.205 46032 Z= 0.354 Chirality : 0.051 1.412 5196 Planarity : 0.004 0.041 5883 Dihedral : 4.801 37.679 4572 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.39 % Favored : 95.56 % Rotamer: Outliers : 2.58 % Allowed : 17.48 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.95 (0.13), residues: 4170 helix: 0.52 (0.19), residues: 720 sheet: -0.41 (0.17), residues: 963 loop : -1.08 (0.12), residues: 2487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 679 TYR 0.030 0.002 TYR D 94 PHE 0.041 0.002 PHE A 99 TRP 0.033 0.002 TRP B 452 HIS 0.007 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 (33678) covalent geometry : angle 0.65815 / 0.35 (45849) SS BOND : bond 0.00766 / 0.45 ( 69) SS BOND : angle 2.15682 / 1.42 ( 138) hydrogen bonds : bond 0.04119 / 2.75 ( 1186) hydrogen bonds : angle 5.94471 / 4.10 ( 3381) link_NAG-ASN : bond 0.01392 / 0.83 ( 15) link_NAG-ASN : angle 4.98496 / 3.09 ( 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 815 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 721 time to evaluate : 1.024 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: X 45 LEU cc_start: 0.7089 (mt) cc_final: 0.6832 (mt) REVERT: Y 4 MET cc_start: 0.3628 (OUTLIER) cc_final: 0.3390 (tpt) REVERT: C 78 MET cc_start: 0.6095 (mmp) cc_final: 0.5867 (mmp) REVERT: C 111 LYS cc_start: 0.8893 (mtpt) cc_final: 0.8583 (mtpp) REVERT: C 143 ARG cc_start: 0.4305 (ttt180) cc_final: 0.3427 (mtp180) REVERT: C 200 LYS cc_start: 0.8111 (mptt) cc_final: 0.7829 (mppt) REVERT: C 205 TYR cc_start: 0.8016 (p90) cc_final: 0.7725 (p90) REVERT: C 230 THR cc_start: 0.7869 (m) cc_final: 0.7571 (p) REVERT: C 235 LYS cc_start: 0.7589 (mtmm) cc_final: 0.7232 (mtmm) REVERT: C 240 VAL cc_start: 0.8892 (t) cc_final: 0.8607 (p) REVERT: C 301 LYS cc_start: 0.7752 (tptm) cc_final: 0.7105 (ttmt) REVERT: C 355 LYS cc_start: 0.7637 (tppt) cc_final: 0.7238 (tptm) REVERT: C 357 PHE cc_start: 0.7493 (m-10) cc_final: 0.6956 (m-10) REVERT: C 361 ASN cc_start: 0.7418 (m-40) cc_final: 0.7209 (m-40) REVERT: C 363 ASN cc_start: 0.5949 (OUTLIER) cc_final: 0.5460 (p0) REVERT: C 377 THR cc_start: 0.7468 (OUTLIER) cc_final: 0.7174 (p) REVERT: C 379 ASN cc_start: 0.8406 (t0) cc_final: 0.7662 (t0) REVERT: C 380 ASN cc_start: 0.8297 (OUTLIER) cc_final: 0.7882 (m-40) REVERT: C 612 LYS cc_start: 0.7361 (ptmm) cc_final: 0.7020 (ptpp) REVERT: C 671 MET cc_start: 0.6061 (mmm) cc_final: 0.5605 (mtp) REVERT: C 673 ARG cc_start: 0.7296 (mtp180) cc_final: 0.6964 (mtt-85) REVERT: C 685 HIS cc_start: 0.7502 (t-90) cc_final: 0.7278 (t-90) REVERT: C 728 ASN cc_start: 0.8497 (m-40) cc_final: 0.8024 (m-40) REVERT: C 807 ILE cc_start: 0.7046 (mt) cc_final: 0.6646 (pt) REVERT: C 833 LEU cc_start: 0.7834 (tp) cc_final: 0.7605 (mt) REVERT: C 835 GLU cc_start: 0.6976 (mm-30) cc_final: 0.6710 (mm-30) REVERT: C 849 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7003 (pt0) REVERT: C 852 GLU cc_start: 0.7298 (mt-10) cc_final: 0.6654 (mt-10) REVERT: C 858 GLN cc_start: 0.7857 (OUTLIER) cc_final: 0.7632 (mt0) REVERT: C 965 LEU cc_start: 0.7839 (tt) cc_final: 0.7574 (tt) REVERT: C 1028 ASN cc_start: 0.6220 (p0) cc_final: 0.5935 (p0) REVERT: C 1043 GLU cc_start: 0.7338 (mt-10) cc_final: 0.7014 (mt-10) REVERT: C 1046 ASN cc_start: 0.8260 (t0) cc_final: 0.7996 (t0) REVERT: C 1051 GLN cc_start: 0.7438 (mm-40) cc_final: 0.6857 (mm110) REVERT: C 1052 LEU cc_start: 0.8821 (tp) cc_final: 0.8474 (tp) REVERT: C 1059 ILE cc_start: 0.8763 (mt) cc_final: 0.8527 (mm) REVERT: C 1065 GLU cc_start: 0.7398 (mt-10) cc_final: 0.6930 (mm-30) REVERT: C 1069 ARG cc_start: 0.8174 (mtp180) cc_final: 0.7693 (ptm160) REVERT: C 1074 GLU cc_start: 0.7708 (tt0) cc_final: 0.7341 (tt0) REVERT: C 1076 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7499 (mt-10) REVERT: C 1079 ILE cc_start: 0.8700 (mt) cc_final: 0.8372 (mm) REVERT: A 106 LYS cc_start: 0.8207 (tttt) cc_final: 0.7725 (ttpp) REVERT: A 143 ARG cc_start: 0.3938 (ttp-170) cc_final: 0.2661 (mtp180) REVERT: A 187 LEU cc_start: 0.6819 (tp) cc_final: 0.6518 (tp) REVERT: A 200 LYS cc_start: 0.7650 (mptt) cc_final: 0.7298 (mppt) REVERT: A 230 THR cc_start: 0.7759 (OUTLIER) cc_final: 0.7471 (p) REVERT: A 235 LYS cc_start: 0.7764 (mtmm) cc_final: 0.7365 (mtmm) REVERT: A 293 ASP cc_start: 0.7617 (p0) cc_final: 0.7320 (p0) REVERT: A 298 ILE cc_start: 0.8011 (mm) cc_final: 0.7758 (mt) REVERT: A 315 ASN cc_start: 0.7645 (p0) cc_final: 0.7180 (p0) REVERT: A 326 TYR cc_start: 0.7509 (t80) cc_final: 0.6869 (t80) REVERT: A 329 LYS cc_start: 0.8088 (tttp) cc_final: 0.7875 (tttp) REVERT: A 344 LYS cc_start: 0.8209 (ptpt) cc_final: 0.7849 (ptpt) REVERT: A 346 VAL cc_start: 0.8567 (p) cc_final: 0.8341 (m) REVERT: A 377 THR cc_start: 0.8042 (m) cc_final: 0.7640 (p) REVERT: A 379 ASN cc_start: 0.8257 (t0) cc_final: 0.7864 (t0) REVERT: A 382 ASP cc_start: 0.7713 (OUTLIER) cc_final: 0.7379 (p0) REVERT: A 425 ASP cc_start: 0.7309 (t70) cc_final: 0.6937 (p0) REVERT: A 602 SER cc_start: 0.7625 (t) cc_final: 0.7110 (m) REVERT: A 631 LEU cc_start: 0.8896 (mt) cc_final: 0.8568 (mp) REVERT: A 635 ILE cc_start: 0.8048 (pt) cc_final: 0.7789 (pt) REVERT: A 652 TYR cc_start: 0.7465 (m-80) cc_final: 0.7173 (m-80) REVERT: A 663 ASP cc_start: 0.7084 (t0) cc_final: 0.6729 (t0) REVERT: A 668 ARG cc_start: 0.7417 (mtp85) cc_final: 0.7216 (ttp-110) REVERT: A 718 TYR cc_start: 0.6130 (p90) cc_final: 0.5827 (p90) REVERT: A 728 ASN cc_start: 0.8498 (m-40) cc_final: 0.8131 (m110) REVERT: A 849 GLU cc_start: 0.7618 (pt0) cc_final: 0.6770 (pt0) REVERT: A 852 GLU cc_start: 0.7552 (mt-10) cc_final: 0.6912 (mt-10) REVERT: A 863 ASN cc_start: 0.6816 (t0) cc_final: 0.6357 (t0) REVERT: A 928 ASN cc_start: 0.7616 (t0) cc_final: 0.7349 (m-40) REVERT: A 1050 GLN cc_start: 0.7984 (mm-40) cc_final: 0.7198 (mm-40) REVERT: A 1059 ILE cc_start: 0.8457 (pt) cc_final: 0.8121 (mt) REVERT: A 1200 GLU cc_start: 0.5187 (mp0) cc_final: 0.2104 (tm-30) REVERT: D 112 ASP cc_start: 0.7810 (OUTLIER) cc_final: 0.7315 (m-30) REVERT: B 64 LEU cc_start: 0.8017 (tp) cc_final: 0.7608 (tt) REVERT: B 106 LYS cc_start: 0.8492 (ttpp) cc_final: 0.8282 (ttmm) REVERT: B 143 ARG cc_start: 0.4725 (ttt180) cc_final: 0.4257 (ttp-170) REVERT: B 189 HIS cc_start: 0.8540 (p-80) cc_final: 0.8292 (p-80) REVERT: B 230 THR cc_start: 0.7882 (m) cc_final: 0.7603 (p) REVERT: B 235 LYS cc_start: 0.7955 (pttm) cc_final: 0.7574 (pttm) REVERT: B 237 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8334 (mp) REVERT: B 298 ILE cc_start: 0.7974 (mm) cc_final: 0.7478 (mm) REVERT: B 322 ILE cc_start: 0.8209 (mm) cc_final: 0.7965 (mm) REVERT: B 326 TYR cc_start: 0.7688 (t80) cc_final: 0.7072 (t80) REVERT: B 329 LYS cc_start: 0.7909 (tptt) cc_final: 0.7628 (tptt) REVERT: B 379 ASN cc_start: 0.8176 (t0) cc_final: 0.7911 (t0) REVERT: B 397 ASP cc_start: 0.7051 (OUTLIER) cc_final: 0.6437 (p0) REVERT: B 406 LYS cc_start: 0.8503 (tptt) cc_final: 0.8222 (tptt) REVERT: B 446 ARG cc_start: 0.5831 (mpp80) cc_final: 0.5496 (mpp80) REVERT: B 452 TRP cc_start: 0.7900 (p-90) cc_final: 0.7622 (p-90) REVERT: B 545 SER cc_start: 0.8413 (p) cc_final: 0.8173 (t) REVERT: B 547 VAL cc_start: 0.8512 (p) cc_final: 0.8265 (m) REVERT: B 559 LYS cc_start: 0.7695 (pttt) cc_final: 0.7271 (pttt) REVERT: B 591 ILE cc_start: 0.8291 (mt) cc_final: 0.7895 (mm) REVERT: B 596 ILE cc_start: 0.8274 (OUTLIER) cc_final: 0.8018 (mt) REVERT: B 601 ASN cc_start: 0.7907 (p0) cc_final: 0.7247 (p0) REVERT: B 646 SER cc_start: 0.8731 (m) cc_final: 0.8462 (t) REVERT: B 652 TYR cc_start: 0.7634 (m-80) cc_final: 0.7290 (m-80) REVERT: B 654 SER cc_start: 0.8414 (m) cc_final: 0.8151 (p) REVERT: B 663 ASP cc_start: 0.7298 (t0) cc_final: 0.7062 (t0) REVERT: B 671 MET cc_start: 0.6370 (mmm) cc_final: 0.6021 (mmm) REVERT: B 830 LYS cc_start: 0.8270 (mttp) cc_final: 0.7910 (mmtp) REVERT: B 849 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.6875 (pt0) REVERT: B 852 GLU cc_start: 0.7195 (mt-10) cc_final: 0.6698 (mt-10) REVERT: B 914 ASP cc_start: 0.6369 (p0) cc_final: 0.6074 (p0) REVERT: B 949 LYS cc_start: 0.8279 (mttt) cc_final: 0.7702 (ttmt) REVERT: B 1065 GLU cc_start: 0.7483 (mt-10) cc_final: 0.6928 (mm-30) REVERT: B 1067 LEU cc_start: 0.8554 (tp) cc_final: 0.8234 (tt) REVERT: B 1073 LEU cc_start: 0.7789 (tt) cc_final: 0.7583 (tt) REVERT: B 1074 GLU cc_start: 0.7932 (tt0) cc_final: 0.7666 (tp30) REVERT: B 1105 LYS cc_start: 0.8530 (tttm) cc_final: 0.8039 (mtpp) REVERT: B 1112 MET cc_start: 0.7700 (ptp) cc_final: 0.7438 (mtm) REVERT: B 1210 MET cc_start: 0.3547 (ppp) cc_final: 0.1423 (pmm) outliers start: 94 outliers final: 57 residues processed: 768 average time/residue: 0.1997 time to fit residues: 249.3368 Evaluate side-chains 763 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 693 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 32 TYR Chi-restraints excluded: chain Y residue 4 MET 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 313 GLU 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 380 ASN 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 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 834 VAL 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 1062 SER Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain A residue 40 THR 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 382 ASP Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 740 CYS Chi-restraints excluded: chain A residue 749 CYS 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 855 ASP Chi-restraints excluded: chain A residue 964 THR 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 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 237 LEU 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 394 ILE 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 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 615 THR Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 855 ASP Chi-restraints excluded: chain B residue 858 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 133 optimal weight: 3.9990 chunk 335 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 138 optimal weight: 0.4980 chunk 16 optimal weight: 6.9990 chunk 150 optimal weight: 8.9990 chunk 110 optimal weight: 0.9980 chunk 115 optimal weight: 0.6980 chunk 286 optimal weight: 10.0000 chunk 301 optimal weight: 10.0000 chunk 275 optimal weight: 0.0770 overall best weight: 1.2540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 280 GLN ** C 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 273 GLN A1039 ASN ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.191029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.158637 restraints weight = 57705.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.163576 restraints weight = 30687.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.166722 restraints weight = 19091.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.168870 restraints weight = 13382.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.170188 restraints weight = 10350.234| |-----------------------------------------------------------------------------| r_work (final): 0.4171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6439 moved from start: 0.5971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 33762 Z= 0.182 Angle : 0.691 15.392 46032 Z= 0.361 Chirality : 0.048 0.382 5196 Planarity : 0.004 0.043 5883 Dihedral : 4.767 31.312 4572 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.92 % Favored : 95.04 % Rotamer: Outliers : 2.50 % Allowed : 18.19 % Favored : 79.31 % 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: -0.99 (0.13), residues: 4170 helix: 0.38 (0.19), residues: 735 sheet: -0.33 (0.17), residues: 933 loop : -1.11 (0.12), residues: 2502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 679 TYR 0.040 0.002 TYR C1147 PHE 0.024 0.002 PHE C1056 TRP 0.030 0.002 TRP D 114 HIS 0.008 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.18 (33678) covalent geometry : angle 0.67577 / 0.36 (45849) SS BOND : bond 0.00444 / 0.27 ( 69) SS BOND : angle 1.88476 / 1.29 ( 138) hydrogen bonds : bond 0.04236 / 2.84 ( 1186) hydrogen bonds : angle 5.94480 / 4.10 ( 3381) link_NAG-ASN : bond 0.00855 / 0.44 ( 15) link_NAG-ASN : angle 3.52975 / 2.28 ( 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 808 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 717 time to evaluate : 1.437 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: X 45 LEU cc_start: 0.7138 (mt) cc_final: 0.6892 (mt) REVERT: Y 4 MET cc_start: 0.3742 (OUTLIER) cc_final: 0.3515 (tpt) REVERT: C 78 MET cc_start: 0.6165 (mmp) cc_final: 0.5953 (mmp) REVERT: C 103 ILE cc_start: 0.7932 (pt) cc_final: 0.7499 (tt) REVERT: C 143 ARG cc_start: 0.4321 (ttt180) cc_final: 0.3449 (mtp180) REVERT: C 205 TYR cc_start: 0.8077 (p90) cc_final: 0.7768 (p90) REVERT: C 230 THR cc_start: 0.7875 (m) cc_final: 0.7595 (p) REVERT: C 235 LYS cc_start: 0.7666 (mtmm) cc_final: 0.7446 (mtmm) REVERT: C 240 VAL cc_start: 0.8909 (t) cc_final: 0.8639 (p) REVERT: C 315 ASN cc_start: 0.7430 (p0) cc_final: 0.6947 (p0) REVERT: C 327 ARG cc_start: 0.7424 (mmm-85) cc_final: 0.7077 (mmm-85) REVERT: C 355 LYS cc_start: 0.7615 (tppt) cc_final: 0.7192 (tptm) REVERT: C 357 PHE cc_start: 0.7513 (m-10) cc_final: 0.6894 (m-10) REVERT: C 361 ASN cc_start: 0.7488 (m-40) cc_final: 0.7264 (m-40) REVERT: C 379 ASN cc_start: 0.8428 (t0) cc_final: 0.8091 (t0) REVERT: C 479 TYR cc_start: 0.7293 (p90) cc_final: 0.6879 (p90) REVERT: C 671 MET cc_start: 0.6007 (mmm) cc_final: 0.5550 (mtp) REVERT: C 673 ARG cc_start: 0.7187 (mtp180) cc_final: 0.6879 (mtt-85) REVERT: C 728 ASN cc_start: 0.8496 (m-40) cc_final: 0.8038 (m-40) REVERT: C 807 ILE cc_start: 0.7175 (mt) cc_final: 0.6804 (pt) REVERT: C 833 LEU cc_start: 0.7904 (tp) cc_final: 0.7680 (mt) REVERT: C 835 GLU cc_start: 0.7004 (mm-30) cc_final: 0.6717 (mm-30) REVERT: C 849 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7047 (pt0) REVERT: C 852 GLU cc_start: 0.7368 (mt-10) cc_final: 0.6649 (mt-10) REVERT: C 855 ASP cc_start: 0.7823 (OUTLIER) cc_final: 0.7510 (p0) REVERT: C 946 LYS cc_start: 0.8352 (mmtm) cc_final: 0.8069 (mttm) REVERT: C 965 LEU cc_start: 0.7819 (tt) cc_final: 0.7544 (tt) REVERT: C 1028 ASN cc_start: 0.6312 (p0) cc_final: 0.6008 (p0) REVERT: C 1043 GLU cc_start: 0.7387 (mt-10) cc_final: 0.7033 (mt-10) REVERT: C 1046 ASN cc_start: 0.8275 (t0) cc_final: 0.8044 (t0) REVERT: C 1051 GLN cc_start: 0.7464 (mm-40) cc_final: 0.6929 (mm110) REVERT: C 1065 GLU cc_start: 0.7417 (mt-10) cc_final: 0.7053 (mt-10) REVERT: C 1069 ARG cc_start: 0.8213 (mtp180) cc_final: 0.7710 (ptm160) REVERT: C 1074 GLU cc_start: 0.7743 (tt0) cc_final: 0.7406 (tt0) REVERT: C 1076 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7496 (mt-10) REVERT: C 1079 ILE cc_start: 0.8741 (mt) cc_final: 0.8419 (mm) REVERT: C 1080 ASP cc_start: 0.7744 (t0) cc_final: 0.7473 (t0) REVERT: C 1114 LYS cc_start: 0.7425 (ptpt) cc_final: 0.7191 (ptpp) REVERT: C 1183 VAL cc_start: 0.2941 (m) cc_final: 0.2582 (p) REVERT: A 143 ARG cc_start: 0.4068 (ttp-170) cc_final: 0.2789 (mtp180) REVERT: A 187 LEU cc_start: 0.6889 (tp) cc_final: 0.6577 (tp) REVERT: A 200 LYS cc_start: 0.7684 (mptt) cc_final: 0.7338 (mppt) REVERT: A 230 THR cc_start: 0.7767 (OUTLIER) cc_final: 0.7489 (p) REVERT: A 235 LYS cc_start: 0.7781 (mtmm) cc_final: 0.7397 (mtmm) REVERT: A 273 GLN cc_start: 0.7316 (pt0) cc_final: 0.7100 (pt0) REVERT: A 291 MET cc_start: 0.6740 (mmp) cc_final: 0.6376 (mmt) REVERT: A 293 ASP cc_start: 0.7589 (p0) cc_final: 0.7304 (p0) REVERT: A 298 ILE cc_start: 0.8024 (mm) cc_final: 0.7795 (mt) REVERT: A 315 ASN cc_start: 0.7699 (p0) cc_final: 0.7299 (p0) REVERT: A 326 TYR cc_start: 0.7561 (t80) cc_final: 0.6964 (t80) REVERT: A 344 LYS cc_start: 0.8350 (ptpt) cc_final: 0.7995 (ptpt) REVERT: A 379 ASN cc_start: 0.8206 (t0) cc_final: 0.7801 (t0) REVERT: A 425 ASP cc_start: 0.7256 (t70) cc_final: 0.6840 (t0) REVERT: A 435 TYR cc_start: 0.7733 (p90) cc_final: 0.7182 (p90) REVERT: A 481 GLN cc_start: 0.7686 (tt0) cc_final: 0.7317 (tp40) REVERT: A 602 SER cc_start: 0.7737 (t) cc_final: 0.7242 (m) REVERT: A 630 ILE cc_start: 0.7973 (mp) cc_final: 0.7370 (tp) REVERT: A 631 LEU cc_start: 0.8934 (mt) cc_final: 0.8585 (mt) REVERT: A 635 ILE cc_start: 0.8020 (pt) cc_final: 0.7734 (pt) REVERT: A 652 TYR cc_start: 0.7464 (m-80) cc_final: 0.7202 (m-80) REVERT: A 663 ASP cc_start: 0.7120 (t0) cc_final: 0.6768 (t0) REVERT: A 673 ARG cc_start: 0.7007 (mtp85) cc_final: 0.6798 (mtp85) REVERT: A 718 TYR cc_start: 0.6128 (p90) cc_final: 0.5849 (p90) REVERT: A 728 ASN cc_start: 0.8491 (m-40) cc_final: 0.8110 (m110) REVERT: A 849 GLU cc_start: 0.7657 (pt0) cc_final: 0.6780 (pt0) REVERT: A 852 GLU cc_start: 0.7541 (mt-10) cc_final: 0.6909 (mt-10) REVERT: A 863 ASN cc_start: 0.6935 (t0) cc_final: 0.6525 (t0) REVERT: A 928 ASN cc_start: 0.7631 (t0) cc_final: 0.7330 (m-40) REVERT: A 965 LEU cc_start: 0.7628 (tt) cc_final: 0.7424 (tt) REVERT: A 1050 GLN cc_start: 0.7974 (mm-40) cc_final: 0.7183 (mm-40) REVERT: A 1059 ILE cc_start: 0.8428 (pt) cc_final: 0.7988 (mt) REVERT: D 112 ASP cc_start: 0.7840 (OUTLIER) cc_final: 0.7309 (m-30) REVERT: B 64 LEU cc_start: 0.8076 (tp) cc_final: 0.7811 (tt) REVERT: B 106 LYS cc_start: 0.8499 (ttpp) cc_final: 0.8292 (ttmm) REVERT: B 143 ARG cc_start: 0.4767 (ttt180) cc_final: 0.4292 (ttp-170) REVERT: B 189 HIS cc_start: 0.8610 (p-80) cc_final: 0.8335 (p-80) REVERT: B 230 THR cc_start: 0.7894 (m) cc_final: 0.7620 (p) REVERT: B 235 LYS cc_start: 0.7972 (pttm) cc_final: 0.7608 (pttm) REVERT: B 237 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8351 (mp) REVERT: B 322 ILE cc_start: 0.8296 (mm) cc_final: 0.8061 (mm) REVERT: B 326 TYR cc_start: 0.7743 (t80) cc_final: 0.7191 (t80) REVERT: B 329 LYS cc_start: 0.7945 (tptt) cc_final: 0.7640 (tptt) REVERT: B 379 ASN cc_start: 0.8188 (t0) cc_final: 0.7948 (t0) REVERT: B 410 GLN cc_start: 0.7816 (OUTLIER) cc_final: 0.7392 (mp10) REVERT: B 477 VAL cc_start: 0.7884 (OUTLIER) cc_final: 0.6983 (m) REVERT: B 545 SER cc_start: 0.8435 (p) cc_final: 0.8168 (t) REVERT: B 547 VAL cc_start: 0.8555 (p) cc_final: 0.8295 (m) REVERT: B 549 ILE cc_start: 0.8131 (OUTLIER) cc_final: 0.7857 (tt) REVERT: B 559 LYS cc_start: 0.7792 (pttt) cc_final: 0.7464 (pttt) REVERT: B 591 ILE cc_start: 0.8379 (mt) cc_final: 0.8007 (mm) REVERT: B 596 ILE cc_start: 0.8308 (OUTLIER) cc_final: 0.8039 (mt) REVERT: B 599 ASP cc_start: 0.7443 (t0) cc_final: 0.6962 (t70) REVERT: B 646 SER cc_start: 0.8747 (m) cc_final: 0.8450 (t) REVERT: B 652 TYR cc_start: 0.7632 (m-80) cc_final: 0.7278 (m-80) REVERT: B 654 SER cc_start: 0.8396 (m) cc_final: 0.8174 (p) REVERT: B 671 MET cc_start: 0.6372 (mmm) cc_final: 0.6030 (mmm) REVERT: B 830 LYS cc_start: 0.8254 (mttp) cc_final: 0.7896 (mmtp) REVERT: B 833 LEU cc_start: 0.7802 (tp) cc_final: 0.7457 (tt) REVERT: B 849 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.6931 (pt0) REVERT: B 852 GLU cc_start: 0.7293 (mt-10) cc_final: 0.6795 (mt-10) REVERT: B 949 LYS cc_start: 0.8310 (mttt) cc_final: 0.7707 (ttmt) REVERT: B 1051 GLN cc_start: 0.7608 (mm-40) cc_final: 0.7264 (mm-40) REVERT: B 1065 GLU cc_start: 0.7383 (mt-10) cc_final: 0.6899 (mm-30) REVERT: B 1067 LEU cc_start: 0.8532 (tp) cc_final: 0.8178 (tt) REVERT: B 1074 GLU cc_start: 0.7980 (tt0) cc_final: 0.7664 (tp30) REVERT: B 1105 LYS cc_start: 0.8548 (tttm) cc_final: 0.8049 (mtpp) REVERT: B 1210 MET cc_start: 0.3513 (ppp) cc_final: 0.1444 (pmm) outliers start: 91 outliers final: 65 residues processed: 762 average time/residue: 0.2157 time to fit residues: 268.1135 Evaluate side-chains 772 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 696 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 32 TYR Chi-restraints excluded: chain Y residue 4 MET 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 244 MET 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 570 CYS 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 786 VAL Chi-restraints excluded: chain C residue 803 MET Chi-restraints excluded: chain C residue 834 VAL 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 857 THR 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 382 ASP Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 688 SER Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 803 MET 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 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 56 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 237 LEU 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 394 ILE 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 549 ILE Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 855 ASP 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: 1.9990 chunk 90 optimal weight: 1.9990 chunk 209 optimal weight: 0.5980 chunk 94 optimal weight: 1.9990 chunk 22 optimal weight: 8.9990 chunk 397 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 352 optimal weight: 0.4980 chunk 115 optimal weight: 0.8980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 101 ASN C 418 GLN ** C 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 842 ASN ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 101 ASN A 280 GLN A 573 GLN ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.190496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.158503 restraints weight = 57202.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.163445 restraints weight = 30335.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.166543 restraints weight = 18779.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.168713 restraints weight = 13226.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.169911 restraints weight = 10176.457| |-----------------------------------------------------------------------------| r_work (final): 0.4169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6443 moved from start: 0.6206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.119 33762 Z= 0.178 Angle : 0.699 16.599 46032 Z= 0.365 Chirality : 0.048 0.376 5196 Planarity : 0.004 0.041 5883 Dihedral : 4.814 29.851 4572 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.20 % Favored : 94.75 % Rotamer: Outliers : 2.34 % Allowed : 18.85 % Favored : 78.81 % 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: -0.99 (0.13), residues: 4170 helix: 0.32 (0.19), residues: 738 sheet: -0.25 (0.17), residues: 921 loop : -1.14 (0.12), residues: 2511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 679 TYR 0.045 0.002 TYR C1147 PHE 0.025 0.002 PHE A 458 TRP 0.033 0.002 TRP Y 35 HIS 0.008 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.18 (33678) covalent geometry : angle 0.68307 / 0.36 (45849) SS BOND : bond 0.00622 / 0.34 ( 69) SS BOND : angle 1.96028 / 1.32 ( 138) hydrogen bonds : bond 0.04216 / 2.83 ( 1186) hydrogen bonds : angle 5.96993 / 4.11 ( 3381) link_NAG-ASN : bond 0.00661 / 0.39 ( 15) link_NAG-ASN : angle 3.62158 / 2.36 ( 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 820 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 735 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 45 LEU cc_start: 0.7141 (mt) cc_final: 0.6892 (mt) REVERT: C 78 MET cc_start: 0.6171 (mmp) cc_final: 0.5940 (mmp) REVERT: C 143 ARG cc_start: 0.4268 (ttt180) cc_final: 0.3105 (mtp180) REVERT: C 200 LYS cc_start: 0.8133 (mptt) cc_final: 0.7844 (mppt) REVERT: C 205 TYR cc_start: 0.8075 (p90) cc_final: 0.7798 (p90) REVERT: C 230 THR cc_start: 0.7884 (m) cc_final: 0.7609 (p) REVERT: C 235 LYS cc_start: 0.7653 (mtmm) cc_final: 0.7367 (mtmm) REVERT: C 240 VAL cc_start: 0.8903 (t) cc_final: 0.8623 (p) REVERT: C 315 ASN cc_start: 0.7585 (p0) cc_final: 0.7046 (p0) REVERT: C 355 LYS cc_start: 0.7551 (tppt) cc_final: 0.7145 (tptm) REVERT: C 357 PHE cc_start: 0.7522 (m-10) cc_final: 0.6897 (m-10) REVERT: C 361 ASN cc_start: 0.7503 (m-40) cc_final: 0.7294 (m-40) REVERT: C 379 ASN cc_start: 0.8257 (t0) cc_final: 0.7348 (t0) REVERT: C 380 ASN cc_start: 0.8442 (m-40) cc_final: 0.7707 (m-40) REVERT: C 416 TYR cc_start: 0.7869 (m-10) cc_final: 0.7622 (m-80) REVERT: C 479 TYR cc_start: 0.7295 (p90) cc_final: 0.6889 (p90) REVERT: C 671 MET cc_start: 0.5970 (mmm) cc_final: 0.5460 (mtp) REVERT: C 673 ARG cc_start: 0.7078 (mtp180) cc_final: 0.6873 (mtp180) REVERT: C 728 ASN cc_start: 0.8506 (m-40) cc_final: 0.8010 (m-40) REVERT: C 807 ILE cc_start: 0.7208 (mt) cc_final: 0.6807 (pt) REVERT: C 833 LEU cc_start: 0.7877 (tp) cc_final: 0.7633 (mt) REVERT: C 835 GLU cc_start: 0.6993 (mm-30) cc_final: 0.6667 (mm-30) REVERT: C 849 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7044 (pt0) REVERT: C 852 GLU cc_start: 0.7376 (mt-10) cc_final: 0.6672 (mt-10) REVERT: C 855 ASP cc_start: 0.7823 (OUTLIER) cc_final: 0.7489 (p0) REVERT: C 914 ASP cc_start: 0.6698 (p0) cc_final: 0.6377 (p0) REVERT: C 938 ASP cc_start: 0.8294 (t0) cc_final: 0.8027 (t0) REVERT: C 965 LEU cc_start: 0.7806 (tt) cc_final: 0.7528 (tt) REVERT: C 1028 ASN cc_start: 0.6642 (p0) cc_final: 0.6421 (p0) REVERT: C 1043 GLU cc_start: 0.7358 (mt-10) cc_final: 0.6996 (mt-10) REVERT: C 1046 ASN cc_start: 0.8258 (t0) cc_final: 0.8012 (t0) REVERT: C 1051 GLN cc_start: 0.7435 (mm-40) cc_final: 0.7107 (mm-40) REVERT: C 1065 GLU cc_start: 0.7367 (mt-10) cc_final: 0.7017 (mt-10) REVERT: C 1069 ARG cc_start: 0.8225 (mtp180) cc_final: 0.7700 (ptm160) REVERT: C 1074 GLU cc_start: 0.7772 (tt0) cc_final: 0.7441 (tt0) REVERT: C 1076 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7485 (mt-10) REVERT: C 1079 ILE cc_start: 0.8696 (mt) cc_final: 0.8323 (mm) REVERT: C 1080 ASP cc_start: 0.7758 (t0) cc_final: 0.7482 (t0) REVERT: C 1114 LYS cc_start: 0.7346 (ptpt) cc_final: 0.7101 (ptpp) REVERT: A 143 ARG cc_start: 0.4073 (ttp-170) cc_final: 0.2811 (mtp180) REVERT: A 187 LEU cc_start: 0.6916 (tp) cc_final: 0.6599 (tp) REVERT: A 200 LYS cc_start: 0.7740 (mptt) cc_final: 0.7374 (mppt) REVERT: A 230 THR cc_start: 0.7800 (OUTLIER) cc_final: 0.7545 (p) REVERT: A 235 LYS cc_start: 0.7780 (mtmm) cc_final: 0.7415 (mtmm) REVERT: A 291 MET cc_start: 0.6791 (mmp) cc_final: 0.6255 (mmp) REVERT: A 293 ASP cc_start: 0.7577 (p0) cc_final: 0.7313 (p0) REVERT: A 298 ILE cc_start: 0.8014 (mm) cc_final: 0.7773 (mt) REVERT: A 313 GLU cc_start: 0.6584 (tm-30) cc_final: 0.6150 (tm-30) REVERT: A 315 ASN cc_start: 0.7538 (p0) cc_final: 0.7201 (p0) REVERT: A 326 TYR cc_start: 0.7510 (t80) cc_final: 0.7031 (t80) REVERT: A 329 LYS cc_start: 0.8139 (tttp) cc_final: 0.7854 (tptt) REVERT: A 344 LYS cc_start: 0.8399 (ptpt) cc_final: 0.8031 (ptpt) REVERT: A 379 ASN cc_start: 0.8059 (t0) cc_final: 0.7735 (t0) REVERT: A 425 ASP cc_start: 0.7282 (t70) cc_final: 0.6839 (t0) REVERT: A 435 TYR cc_start: 0.7763 (p90) cc_final: 0.7211 (p90) REVERT: A 479 TYR cc_start: 0.7622 (p90) cc_final: 0.7263 (p90) REVERT: A 490 PHE cc_start: 0.7933 (t80) cc_final: 0.7722 (t80) REVERT: A 602 SER cc_start: 0.7650 (t) cc_final: 0.7157 (m) REVERT: A 612 LYS cc_start: 0.7434 (ptpt) cc_final: 0.7171 (ptmm) REVERT: A 630 ILE cc_start: 0.7961 (mp) cc_final: 0.7410 (tp) REVERT: A 631 LEU cc_start: 0.8855 (mt) cc_final: 0.8596 (mt) REVERT: A 635 ILE cc_start: 0.8018 (pt) cc_final: 0.7713 (pt) REVERT: A 652 TYR cc_start: 0.7450 (m-80) cc_final: 0.7203 (m-80) REVERT: A 663 ASP cc_start: 0.7059 (t0) cc_final: 0.6653 (t0) REVERT: A 673 ARG cc_start: 0.6891 (mtp85) cc_final: 0.6675 (mtt90) REVERT: A 718 TYR cc_start: 0.6091 (p90) cc_final: 0.5827 (p90) REVERT: A 768 PHE cc_start: 0.6800 (m-10) cc_final: 0.6288 (m-10) REVERT: A 830 LYS cc_start: 0.8253 (mttt) cc_final: 0.7972 (mmmm) REVERT: A 833 LEU cc_start: 0.7457 (tp) cc_final: 0.7176 (mm) REVERT: A 848 THR cc_start: 0.8083 (p) cc_final: 0.7151 (t) REVERT: A 849 GLU cc_start: 0.7670 (pt0) cc_final: 0.6809 (pt0) REVERT: A 852 GLU cc_start: 0.7513 (mt-10) cc_final: 0.6821 (mt-10) REVERT: A 863 ASN cc_start: 0.6944 (t0) cc_final: 0.6571 (t0) REVERT: A 928 ASN cc_start: 0.7647 (t0) cc_final: 0.7429 (m-40) REVERT: A 1050 GLN cc_start: 0.7960 (mm-40) cc_final: 0.7140 (mm-40) REVERT: A 1059 ILE cc_start: 0.8436 (pt) cc_final: 0.8117 (mm) REVERT: A 1196 TYR cc_start: 0.6808 (t80) cc_final: 0.6570 (t80) REVERT: D 112 ASP cc_start: 0.7806 (OUTLIER) cc_final: 0.7283 (m-30) REVERT: B 64 LEU cc_start: 0.8024 (tp) cc_final: 0.7756 (tt) REVERT: B 143 ARG cc_start: 0.4910 (ttt180) cc_final: 0.4342 (ttp-170) REVERT: B 189 HIS cc_start: 0.8617 (p-80) cc_final: 0.8283 (p-80) REVERT: B 203 PHE cc_start: 0.7404 (m-10) cc_final: 0.7180 (m-10) REVERT: B 205 TYR cc_start: 0.7983 (p90) cc_final: 0.7706 (p90) REVERT: B 230 THR cc_start: 0.7893 (m) cc_final: 0.7620 (p) REVERT: B 235 LYS cc_start: 0.7990 (pttm) cc_final: 0.7639 (pttm) REVERT: B 298 ILE cc_start: 0.7986 (mm) cc_final: 0.7547 (mm) REVERT: B 322 ILE cc_start: 0.8247 (mm) cc_final: 0.8029 (mm) REVERT: B 326 TYR cc_start: 0.7616 (t80) cc_final: 0.7071 (t80) REVERT: B 329 LYS cc_start: 0.7988 (tptt) cc_final: 0.7637 (tttp) REVERT: B 389 MET cc_start: 0.7554 (mmp) cc_final: 0.7339 (mmm) REVERT: B 410 GLN cc_start: 0.7823 (mm-40) cc_final: 0.7387 (mp10) REVERT: B 544 LYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7648 (ptmm) REVERT: B 545 SER cc_start: 0.8395 (p) cc_final: 0.8137 (t) REVERT: B 547 VAL cc_start: 0.8577 (p) cc_final: 0.8298 (m) REVERT: B 559 LYS cc_start: 0.7898 (pttt) cc_final: 0.7482 (pttt) REVERT: B 591 ILE cc_start: 0.8401 (mt) cc_final: 0.7986 (mm) REVERT: B 596 ILE cc_start: 0.8302 (OUTLIER) cc_final: 0.8015 (mt) REVERT: B 599 ASP cc_start: 0.7439 (t0) cc_final: 0.6952 (t70) REVERT: B 601 ASN cc_start: 0.7951 (p0) cc_final: 0.7548 (p0) REVERT: B 646 SER cc_start: 0.8727 (m) cc_final: 0.8443 (t) REVERT: B 652 TYR cc_start: 0.7630 (m-80) cc_final: 0.7262 (m-80) REVERT: B 663 ASP cc_start: 0.7309 (t0) cc_final: 0.7014 (t0) REVERT: B 671 MET cc_start: 0.6369 (mmm) cc_final: 0.6007 (mmm) REVERT: B 833 LEU cc_start: 0.7752 (tp) cc_final: 0.7458 (tt) REVERT: B 849 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.6970 (pt0) REVERT: B 852 GLU cc_start: 0.7280 (mt-10) cc_final: 0.6822 (mt-10) REVERT: B 949 LYS cc_start: 0.8298 (mttt) cc_final: 0.8048 (ttmt) REVERT: B 960 PHE cc_start: 0.7964 (m-10) cc_final: 0.7658 (m-80) REVERT: B 1051 GLN cc_start: 0.7572 (mm-40) cc_final: 0.7211 (mm-40) REVERT: B 1065 GLU cc_start: 0.7319 (mt-10) cc_final: 0.6897 (mm-30) REVERT: B 1067 LEU cc_start: 0.8521 (tp) cc_final: 0.8167 (tt) REVERT: B 1074 GLU cc_start: 0.8011 (tt0) cc_final: 0.7686 (tp30) REVERT: B 1105 LYS cc_start: 0.8583 (tttm) cc_final: 0.8035 (mtpp) REVERT: B 1210 MET cc_start: 0.3475 (ppp) cc_final: 0.1510 (pmm) outliers start: 85 outliers final: 68 residues processed: 778 average time/residue: 0.2077 time to fit residues: 262.4951 Evaluate side-chains 793 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 718 time to evaluate : 1.165 ------------------------------------------------------------------------------- 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 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 418 GLN Chi-restraints excluded: chain C residue 430 SER 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 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 786 VAL Chi-restraints excluded: chain C residue 834 VAL 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 56 VAL 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 246 LEU 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 394 ILE Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 749 CYS 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 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 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 292 SER Chi-restraints excluded: chain B residue 311 VAL Chi-restraints excluded: chain B residue 340 TRP 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 394 ILE Chi-restraints excluded: chain B residue 397 ASP Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 544 LYS Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 615 THR Chi-restraints excluded: chain B residue 846 ILE Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 855 ASP Chi-restraints excluded: chain B residue 858 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 148 optimal weight: 4.9990 chunk 257 optimal weight: 9.9990 chunk 59 optimal weight: 2.9990 chunk 12 optimal weight: 10.0000 chunk 303 optimal weight: 0.7980 chunk 320 optimal weight: 0.8980 chunk 236 optimal weight: 0.0370 chunk 5 optimal weight: 5.9990 chunk 237 optimal weight: 0.3980 chunk 170 optimal weight: 0.8980 chunk 96 optimal weight: 4.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 418 GLN ** C 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 273 GLN A 573 GLN ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1039 ASN ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 858 GLN ** B 867 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1133 ASN B1141 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.192706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.160792 restraints weight = 57704.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.165721 restraints weight = 30459.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.168948 restraints weight = 18825.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.171086 restraints weight = 13103.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.172436 restraints weight = 10080.674| |-----------------------------------------------------------------------------| r_work (final): 0.4191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6400 moved from start: 0.6290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 33762 Z= 0.136 Angle : 0.690 17.448 46032 Z= 0.357 Chirality : 0.047 0.378 5196 Planarity : 0.004 0.040 5883 Dihedral : 4.680 28.722 4572 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.63 % Favored : 95.35 % Rotamer: Outliers : 2.03 % Allowed : 19.48 % Favored : 78.48 % 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: -0.88 (0.13), residues: 4170 helix: 0.53 (0.19), residues: 720 sheet: -0.18 (0.17), residues: 921 loop : -1.09 (0.12), residues: 2529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 679 TYR 0.062 0.002 TYR B 274 PHE 0.031 0.002 PHE A 821 TRP 0.041 0.002 TRP Y 35 HIS 0.005 0.001 HIS B 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (33678) covalent geometry : angle 0.67518 / 0.35 (45849) SS BOND : bond 0.00504 / 0.27 ( 69) SS BOND : angle 1.88716 / 1.28 ( 138) hydrogen bonds : bond 0.03985 / 2.66 ( 1186) hydrogen bonds : angle 5.86236 / 4.05 ( 3381) link_NAG-ASN : bond 0.00726 / 0.41 ( 15) link_NAG-ASN : angle 3.50513 / 2.28 ( 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 787 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 713 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 45 LEU cc_start: 0.7097 (mt) cc_final: 0.6842 (mt) REVERT: C 78 MET cc_start: 0.6104 (mmp) cc_final: 0.5882 (mmp) REVERT: C 111 LYS cc_start: 0.8827 (mtpp) cc_final: 0.8592 (tttm) REVERT: C 143 ARG cc_start: 0.4275 (ttt180) cc_final: 0.4019 (ttp-170) REVERT: C 200 LYS cc_start: 0.8139 (mptt) cc_final: 0.7837 (mppt) REVERT: C 205 TYR cc_start: 0.7973 (p90) cc_final: 0.7650 (p90) REVERT: C 230 THR cc_start: 0.7846 (m) cc_final: 0.7574 (p) REVERT: C 235 LYS cc_start: 0.7612 (mtmm) cc_final: 0.7291 (mtmm) REVERT: C 240 VAL cc_start: 0.8876 (t) cc_final: 0.8576 (p) REVERT: C 355 LYS cc_start: 0.7567 (tppt) cc_final: 0.7280 (tptm) REVERT: C 357 PHE cc_start: 0.7531 (m-10) cc_final: 0.6881 (m-10) REVERT: C 379 ASN cc_start: 0.8134 (t0) cc_final: 0.7754 (t0) REVERT: C 380 ASN cc_start: 0.8397 (OUTLIER) cc_final: 0.7818 (m-40) REVERT: C 479 TYR cc_start: 0.7239 (p90) cc_final: 0.6798 (p90) REVERT: C 481 GLN cc_start: 0.7971 (tp40) cc_final: 0.7711 (tp40) REVERT: C 671 MET cc_start: 0.5972 (mmm) cc_final: 0.5462 (mtp) REVERT: C 673 ARG cc_start: 0.6984 (mtp180) cc_final: 0.6780 (mtp180) REVERT: C 728 ASN cc_start: 0.8512 (m-40) cc_final: 0.8054 (m-40) REVERT: C 807 ILE cc_start: 0.7184 (mt) cc_final: 0.6803 (pt) REVERT: C 833 LEU cc_start: 0.7820 (tp) cc_final: 0.7384 (tt) REVERT: C 835 GLU cc_start: 0.6957 (mm-30) cc_final: 0.6647 (mm-30) REVERT: C 839 PHE cc_start: 0.8737 (OUTLIER) cc_final: 0.8297 (t80) REVERT: C 849 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7080 (pt0) REVERT: C 852 GLU cc_start: 0.7361 (mt-10) cc_final: 0.6646 (mt-10) REVERT: C 855 ASP cc_start: 0.7850 (OUTLIER) cc_final: 0.7526 (p0) REVERT: C 965 LEU cc_start: 0.7785 (tt) cc_final: 0.7502 (tt) REVERT: C 1043 GLU cc_start: 0.7362 (mt-10) cc_final: 0.6985 (mt-10) REVERT: C 1046 ASN cc_start: 0.8212 (t0) cc_final: 0.7989 (t0) REVERT: C 1051 GLN cc_start: 0.7351 (mm-40) cc_final: 0.6969 (mm-40) REVERT: C 1065 GLU cc_start: 0.7363 (mt-10) cc_final: 0.7008 (mt-10) REVERT: C 1069 ARG cc_start: 0.8278 (mtp180) cc_final: 0.7970 (ptm160) REVERT: C 1074 GLU cc_start: 0.7707 (tt0) cc_final: 0.7388 (tt0) REVERT: C 1076 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7441 (mt-10) REVERT: C 1078 GLN cc_start: 0.8528 (mm-40) cc_final: 0.8028 (mm-40) REVERT: C 1080 ASP cc_start: 0.7633 (t0) cc_final: 0.7367 (t0) REVERT: C 1114 LYS cc_start: 0.7261 (ptpt) cc_final: 0.7008 (ptpp) REVERT: A 143 ARG cc_start: 0.4058 (ttp-170) cc_final: 0.2802 (mtp180) REVERT: A 187 LEU cc_start: 0.6708 (tp) cc_final: 0.6396 (tp) REVERT: A 200 LYS cc_start: 0.7771 (mptt) cc_final: 0.7408 (mppt) REVERT: A 230 THR cc_start: 0.7780 (OUTLIER) cc_final: 0.7527 (p) REVERT: A 235 LYS cc_start: 0.7784 (mtmm) cc_final: 0.7402 (mtmm) REVERT: A 273 GLN cc_start: 0.7314 (pt0) cc_final: 0.7091 (pt0) REVERT: A 291 MET cc_start: 0.6750 (mmp) cc_final: 0.6293 (mmt) REVERT: A 293 ASP cc_start: 0.7539 (p0) cc_final: 0.7217 (p0) REVERT: A 298 ILE cc_start: 0.7965 (mm) cc_final: 0.7717 (mt) REVERT: A 313 GLU cc_start: 0.6543 (tm-30) cc_final: 0.6175 (tm-30) REVERT: A 329 LYS cc_start: 0.8085 (tttp) cc_final: 0.7808 (tptt) REVERT: A 344 LYS cc_start: 0.8393 (ptpt) cc_final: 0.8035 (tptp) REVERT: A 379 ASN cc_start: 0.8125 (t0) cc_final: 0.7852 (t0) REVERT: A 382 ASP cc_start: 0.7633 (OUTLIER) cc_final: 0.7340 (p0) REVERT: A 425 ASP cc_start: 0.7275 (t70) cc_final: 0.6832 (t0) REVERT: A 435 TYR cc_start: 0.7724 (p90) cc_final: 0.7194 (p90) REVERT: A 490 PHE cc_start: 0.7854 (t80) cc_final: 0.7641 (t80) REVERT: A 602 SER cc_start: 0.7596 (t) cc_final: 0.7087 (m) REVERT: A 630 ILE cc_start: 0.7844 (mp) cc_final: 0.7281 (tp) REVERT: A 631 LEU cc_start: 0.8797 (mt) cc_final: 0.8507 (mt) REVERT: A 635 ILE cc_start: 0.8013 (pt) cc_final: 0.7720 (pt) REVERT: A 644 TYR cc_start: 0.7538 (m-80) cc_final: 0.7177 (m-80) REVERT: A 663 ASP cc_start: 0.6973 (t0) cc_final: 0.6597 (t0) REVERT: A 718 TYR cc_start: 0.6091 (p90) cc_final: 0.5832 (p90) REVERT: A 768 PHE cc_start: 0.6880 (m-10) cc_final: 0.6320 (m-10) REVERT: A 830 LYS cc_start: 0.8245 (mttt) cc_final: 0.7955 (mmmm) REVERT: A 833 LEU cc_start: 0.7423 (tp) cc_final: 0.7108 (mm) REVERT: A 848 THR cc_start: 0.8034 (p) cc_final: 0.7096 (t) REVERT: A 849 GLU cc_start: 0.7638 (pt0) cc_final: 0.6796 (pt0) REVERT: A 852 GLU cc_start: 0.7537 (mt-10) cc_final: 0.6796 (mt-10) REVERT: A 863 ASN cc_start: 0.6669 (t0) cc_final: 0.6297 (t0) REVERT: A 866 MET cc_start: 0.5623 (ptp) cc_final: 0.4837 (ptp) REVERT: A 928 ASN cc_start: 0.7519 (t0) cc_final: 0.7315 (m-40) REVERT: A 965 LEU cc_start: 0.7575 (tt) cc_final: 0.7351 (tt) REVERT: A 1050 GLN cc_start: 0.7902 (mm-40) cc_final: 0.7078 (mm-40) REVERT: A 1059 ILE cc_start: 0.8382 (pt) cc_final: 0.8107 (mm) REVERT: D 112 ASP cc_start: 0.7755 (OUTLIER) cc_final: 0.7258 (m-30) REVERT: B 64 LEU cc_start: 0.7966 (tp) cc_final: 0.7741 (tt) REVERT: B 143 ARG cc_start: 0.4833 (ttt180) cc_final: 0.4540 (ttt180) REVERT: B 203 PHE cc_start: 0.7424 (m-10) cc_final: 0.7195 (m-10) REVERT: B 230 THR cc_start: 0.7858 (m) cc_final: 0.7569 (p) REVERT: B 235 LYS cc_start: 0.7985 (pttm) cc_final: 0.7636 (pttm) REVERT: B 298 ILE cc_start: 0.7902 (mm) cc_final: 0.7675 (mm) REVERT: B 322 ILE cc_start: 0.8251 (mm) cc_final: 0.8024 (mm) REVERT: B 326 TYR cc_start: 0.7553 (t80) cc_final: 0.7075 (t80) REVERT: B 329 LYS cc_start: 0.7966 (tptt) cc_final: 0.7648 (tptt) REVERT: B 344 LYS cc_start: 0.8389 (ptpp) cc_final: 0.8066 (ptpp) REVERT: B 437 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7317 (mt) REVERT: B 477 VAL cc_start: 0.7902 (OUTLIER) cc_final: 0.7027 (m) REVERT: B 547 VAL cc_start: 0.8556 (p) cc_final: 0.8271 (m) REVERT: B 559 LYS cc_start: 0.7917 (pttt) cc_final: 0.7502 (pttt) REVERT: B 591 ILE cc_start: 0.8322 (mt) cc_final: 0.7973 (mm) REVERT: B 596 ILE cc_start: 0.8383 (OUTLIER) cc_final: 0.8091 (mt) REVERT: B 599 ASP cc_start: 0.7432 (t0) cc_final: 0.6931 (t70) REVERT: B 601 ASN cc_start: 0.7946 (p0) cc_final: 0.7383 (p0) REVERT: B 646 SER cc_start: 0.8711 (m) cc_final: 0.8428 (t) REVERT: B 663 ASP cc_start: 0.7227 (t0) cc_final: 0.6950 (t0) REVERT: B 671 MET cc_start: 0.6342 (mmm) cc_final: 0.5985 (mmm) REVERT: B 830 LYS cc_start: 0.8218 (mttt) cc_final: 0.7977 (mmtp) REVERT: B 833 LEU cc_start: 0.7624 (tp) cc_final: 0.6877 (tt) REVERT: B 849 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.6982 (pt0) REVERT: B 852 GLU cc_start: 0.7229 (mt-10) cc_final: 0.6784 (mt-10) REVERT: B 949 LYS cc_start: 0.8245 (mttt) cc_final: 0.7992 (ttmt) REVERT: B 960 PHE cc_start: 0.7963 (m-10) cc_final: 0.7689 (m-80) REVERT: B 1051 GLN cc_start: 0.7525 (mm-40) cc_final: 0.7077 (mm-40) REVERT: B 1056 PHE cc_start: 0.8202 (m-80) cc_final: 0.7903 (m-80) REVERT: B 1065 GLU cc_start: 0.7336 (mt-10) cc_final: 0.7012 (mm-30) REVERT: B 1067 LEU cc_start: 0.8500 (tp) cc_final: 0.8168 (tt) REVERT: B 1074 GLU cc_start: 0.7885 (tt0) cc_final: 0.7637 (tp30) REVERT: B 1105 LYS cc_start: 0.8578 (tttm) cc_final: 0.8009 (mtpp) REVERT: B 1210 MET cc_start: 0.3383 (ppp) cc_final: 0.1589 (pmm) outliers start: 74 outliers final: 56 residues processed: 751 average time/residue: 0.2116 time to fit residues: 258.0845 Evaluate side-chains 762 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 695 time to evaluate : 1.220 ------------------------------------------------------------------------------- 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 311 VAL Chi-restraints excluded: chain C residue 317 TYR Chi-restraints excluded: chain C residue 380 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 430 SER 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 786 VAL Chi-restraints excluded: chain C residue 834 VAL 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 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 372 GLN Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 394 ILE Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 749 CYS Chi-restraints excluded: chain A residue 834 VAL Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 1060 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 56 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 340 TRP 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 409 LEU Chi-restraints excluded: chain B residue 437 LEU Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 615 THR Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 858 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 417 random chunks: chunk 386 optimal weight: 0.0980 chunk 400 optimal weight: 3.9990 chunk 4 optimal weight: 9.9990 chunk 291 optimal weight: 0.9980 chunk 116 optimal weight: 0.0670 chunk 112 optimal weight: 0.7980 chunk 309 optimal weight: 0.7980 chunk 253 optimal weight: 0.2980 chunk 27 optimal weight: 0.7980 chunk 136 optimal weight: 0.9990 chunk 393 optimal weight: 0.3980 overall best weight: 0.3318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 380 ASN B 633 GLN B 655 ASN B 858 GLN ** B 867 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1039 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.193737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.161937 restraints weight = 57895.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.166860 restraints weight = 30686.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.170045 restraints weight = 19007.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.172149 restraints weight = 13249.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.173480 restraints weight = 10221.128| |-----------------------------------------------------------------------------| r_work (final): 0.4214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6373 moved from start: 0.6348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 33762 Z= 0.123 Angle : 0.685 17.738 46032 Z= 0.352 Chirality : 0.047 0.375 5196 Planarity : 0.004 0.039 5883 Dihedral : 4.561 28.799 4572 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.53 % Favored : 95.42 % Rotamer: Outliers : 2.03 % Allowed : 19.70 % Favored : 78.26 % 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: -0.84 (0.13), residues: 4170 helix: 0.45 (0.19), residues: 738 sheet: -0.28 (0.17), residues: 957 loop : -0.98 (0.12), residues: 2475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 679 TYR 0.048 0.001 TYR B 274 PHE 0.024 0.002 PHE C 490 TRP 0.050 0.002 TRP Y 35 HIS 0.006 0.001 HIS B 177 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (33678) covalent geometry : angle 0.67116 / 0.35 (45849) SS BOND : bond 0.00591 / 0.32 ( 69) SS BOND : angle 1.76677 / 1.18 ( 138) hydrogen bonds : bond 0.03831 / 2.56 ( 1186) hydrogen bonds : angle 5.72300 / 3.95 ( 3381) link_NAG-ASN : bond 0.00729 / 0.42 ( 15) link_NAG-ASN : angle 3.35357 / 2.16 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6743.63 seconds wall clock time: 116 minutes 57.71 seconds (7017.71 seconds total)