Starting phenix.real_space_refine on Sat Mar 7 09:19:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6scj_10141/03_2026/6scj_10141.cif Found real_map, /net/cci-nas-00/data/ceres_data/6scj_10141/03_2026/6scj_10141.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6scj_10141/03_2026/6scj_10141.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6scj_10141/03_2026/6scj_10141.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6scj_10141/03_2026/6scj_10141.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6scj_10141/03_2026/6scj_10141.map" } resolution = 3.6 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= 0.000 sd= 0.003 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 312 5.16 5 C 24984 2.51 5 N 6890 2.21 5 O 7698 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 162 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39884 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 19693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2551, 19693 Classifications: {'peptide': 2551} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 1, 'PTRANS': 160, 'TRANS': 2389} Chain breaks: 10 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Restraints were copied for chains: B, D Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" N TYR A 24 " occ=0.00 ... (10 atoms not shown) pdb=" OH TYR A 24 " occ=0.00 residue: pdb=" N GLN A 25 " occ=0.00 ... (3 atoms not shown) pdb=" CB GLN A 25 " occ=0.00 residue: pdb=" N VAL A 26 " occ=0.00 ... (3 atoms not shown) pdb=" CB VAL A 26 " occ=0.00 residue: pdb=" N ASP A 27 " occ=0.00 ... (3 atoms not shown) pdb=" CB ASP A 27 " occ=0.00 residue: pdb=" N ALA A 28 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA A 28 " occ=0.00 residue: pdb=" N GLN A 29 " occ=0.00 ... (3 atoms not shown) pdb=" CB GLN A 29 " occ=0.00 residue: pdb=" N TYR B 24 " occ=0.00 ... (10 atoms not shown) pdb=" OH TYR B 24 " occ=0.00 residue: pdb=" N GLN B 25 " occ=0.00 ... (3 atoms not shown) pdb=" CB GLN B 25 " occ=0.00 residue: pdb=" N VAL B 26 " occ=0.00 ... (3 atoms not shown) pdb=" CB VAL B 26 " occ=0.00 residue: pdb=" N ASP B 27 " occ=0.00 ... (3 atoms not shown) pdb=" CB ASP B 27 " occ=0.00 residue: pdb=" N ALA B 28 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA B 28 " occ=0.00 residue: pdb=" N GLN B 29 " occ=0.00 ... (3 atoms not shown) pdb=" CB GLN B 29 " occ=0.00 Time building chain proxies: 37.94, per 1000 atoms: 0.95 Number of scatterers: 39884 At special positions: 0 Unit cell: (268.051, 172.095, 133.504, 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 312 16.00 O 7698 8.00 N 6890 7.00 C 24984 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=120, symmetry=0 Simple disulfide: pdb=" SG CYS A 34 " - pdb=" SG CYS A 52 " distance=2.03 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 70 " distance=2.03 Simple disulfide: pdb=" SG CYS A 72 " - pdb=" SG CYS A 92 " distance=2.03 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS A 120 " distance=2.02 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 138 " distance=2.04 Simple disulfide: pdb=" SG CYS A 140 " - pdb=" SG CYS A 160 " distance=2.03 Simple disulfide: pdb=" SG CYS A 164 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 194 " - pdb=" SG CYS A 235 " distance=2.03 Simple disulfide: pdb=" SG CYS A 237 " - pdb=" SG CYS A 297 " distance=2.03 Simple disulfide: pdb=" SG CYS A 301 " - pdb=" SG CYS A 319 " distance=2.03 Simple disulfide: pdb=" SG CYS A 330 " - pdb=" SG CYS A 336 " distance=2.03 Simple disulfide: pdb=" SG CYS A 338 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 364 " - pdb=" SG CYS A 620 " distance=2.03 Simple disulfide: pdb=" SG CYS A 408 " - pdb=" SG CYS A 608 " distance=2.03 Simple disulfide: pdb=" SG CYS A 631 " - pdb=" SG CYS A 636 " distance=2.03 Simple disulfide: pdb=" SG CYS A 638 " - pdb=" SG CYS A 658 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 687 " distance=2.02 Simple disulfide: pdb=" SG CYS A 698 " - pdb=" SG CYS A 703 " distance=2.03 Simple disulfide: pdb=" SG CYS A 705 " - pdb=" SG CYS A 726 " distance=2.04 Simple disulfide: pdb=" SG CYS A 730 " - pdb=" SG CYS A 763 " distance=2.02 Simple disulfide: pdb=" SG CYS A 774 " - pdb=" SG CYS A 898 " distance=2.03 Simple disulfide: pdb=" SG CYS A 900 " - pdb=" SG CYS A 921 " distance=2.03 Simple disulfide: pdb=" SG CYS A 925 " - pdb=" SG CYS A1031 " distance=2.04 Simple disulfide: pdb=" SG CYS A1042 " - pdb=" SG CYS A1049 " distance=2.03 Simple disulfide: pdb=" SG CYS A1051 " - pdb=" SG CYS A1073 " distance=2.03 Simple disulfide: pdb=" SG CYS A1077 " - pdb=" SG CYS A1108 " distance=2.02 Simple disulfide: pdb=" SG CYS A1126 " - pdb=" SG CYS A1145 " distance=2.04 Simple disulfide: pdb=" SG CYS A1149 " - pdb=" SG CYS A1169 " distance=2.03 Simple disulfide: pdb=" SG CYS A1181 " - pdb=" SG CYS A1188 " distance=2.04 Simple disulfide: pdb=" SG CYS A1190 " - pdb=" SG CYS A1210 " distance=2.02 Simple disulfide: pdb=" SG CYS A1215 " - pdb=" SG CYS A1264 " distance=2.03 Simple disulfide: pdb=" SG CYS A1231 " - pdb=" SG CYS A1245 " distance=2.03 Simple disulfide: pdb=" SG CYS A1306 " - pdb=" SG CYS A1356 " distance=2.04 Simple disulfide: pdb=" SG CYS A1331 " - pdb=" SG CYS A1347 " distance=2.03 Simple disulfide: pdb=" SG CYS A1440 " - pdb=" SG CYS A1459 " distance=2.04 Simple disulfide: pdb=" SG CYS A1462 " - pdb=" SG CYS A1473 " distance=2.03 Simple disulfide: pdb=" SG CYS A1476 " - pdb=" SG CYS A1490 " distance=2.03 Simple disulfide: pdb=" SG CYS A1493 " - pdb=" SG CYS A1510 " distance=2.03 Simple disulfide: pdb=" SG CYS A1514 " - pdb=" SG CYS A1523 " distance=2.03 Simple disulfide: pdb=" SG CYS A1543 " - pdb=" SG CYS A1565 " distance=2.02 Simple disulfide: pdb=" SG CYS A1603 " - pdb=" SG CYS A1627 " distance=2.03 Simple disulfide: pdb=" SG CYS A1607 " - pdb=" SG CYS A1613 " distance=2.03 Simple disulfide: pdb=" SG CYS A1639 " - pdb=" SG CYS A1662 " distance=2.03 Simple disulfide: pdb=" SG CYS A1724 " - pdb=" SG CYS A1749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1728 " - pdb=" SG CYS A1734 " distance=2.03 Simple disulfide: pdb=" SG CYS A1733 " - pdb=" SG CYS A1835 " distance=2.03 Simple disulfide: pdb=" SG CYS A1760 " - pdb=" SG CYS A1777 " distance=2.03 Simple disulfide: pdb=" SG CYS A1893 " - pdb=" SG CYS A1919 " distance=2.03 Simple disulfide: pdb=" SG CYS A1897 " - pdb=" SG CYS A1904 " distance=2.03 Simple disulfide: pdb=" SG CYS A1928 " - pdb=" SG CYS A1939 " distance=2.04 Simple disulfide: pdb=" SG CYS A1996 " - pdb=" SG CYS A2024 " distance=2.03 Simple disulfide: pdb=" SG CYS A2000 " - pdb=" SG CYS A2006 " distance=2.04 Simple disulfide: pdb=" SG CYS A2005 " - pdb=" SG CYS A2076 " distance=2.03 Simple disulfide: pdb=" SG CYS A2035 " - pdb=" SG CYS A2048 " distance=2.03 Simple disulfide: pdb=" SG CYS A2130 " - pdb=" SG CYS A2154 " distance=2.03 Simple disulfide: pdb=" SG CYS A2134 " - pdb=" SG CYS A2140 " distance=2.03 Simple disulfide: pdb=" SG CYS A2163 " - pdb=" SG CYS A2172 " distance=2.03 Simple disulfide: pdb=" SG CYS A2264 " - pdb=" SG CYS A2281 " distance=2.03 Simple disulfide: pdb=" SG CYS A2442 " - pdb=" SG CYS A2453 " distance=2.03 Simple disulfide: pdb=" SG CYS A2591 " - pdb=" SG CYS A2715 " distance=2.04 Simple disulfide: pdb=" SG CYS B 34 " - pdb=" SG CYS B 52 " distance=2.03 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 70 " distance=2.03 Simple disulfide: pdb=" SG CYS B 72 " - pdb=" SG CYS B 92 " distance=2.03 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 120 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 138 " distance=2.04 Simple disulfide: pdb=" SG CYS B 140 " - pdb=" SG CYS B 160 " distance=2.03 Simple disulfide: pdb=" SG CYS B 164 " - pdb=" SG CYS B 183 " distance=2.03 Simple disulfide: pdb=" SG CYS B 194 " - pdb=" SG CYS B 235 " distance=2.03 Simple disulfide: pdb=" SG CYS B 237 " - pdb=" SG CYS B 297 " distance=2.03 Simple disulfide: pdb=" SG CYS B 301 " - pdb=" SG CYS B 319 " distance=2.03 Simple disulfide: pdb=" SG CYS B 330 " - pdb=" SG CYS B 336 " distance=2.03 Simple disulfide: pdb=" SG CYS B 338 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 364 " - pdb=" SG CYS B 620 " distance=2.03 Simple disulfide: pdb=" SG CYS B 408 " - pdb=" SG CYS B 608 " distance=2.03 Simple disulfide: pdb=" SG CYS B 631 " - pdb=" SG CYS B 636 " distance=2.03 Simple disulfide: pdb=" SG CYS B 638 " - pdb=" SG CYS B 658 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 687 " distance=2.02 Simple disulfide: pdb=" SG CYS B 698 " - pdb=" SG CYS B 703 " distance=2.03 Simple disulfide: pdb=" SG CYS B 705 " - pdb=" SG CYS B 726 " distance=2.04 Simple disulfide: pdb=" SG CYS B 730 " - pdb=" SG CYS B 763 " distance=2.02 Simple disulfide: pdb=" SG CYS B 774 " - pdb=" SG CYS B 898 " distance=2.03 Simple disulfide: pdb=" SG CYS B 900 " - pdb=" SG CYS B 921 " distance=2.03 Simple disulfide: pdb=" SG CYS B 925 " - pdb=" SG CYS B1031 " distance=2.04 Simple disulfide: pdb=" SG CYS B1042 " - pdb=" SG CYS B1049 " distance=2.03 Simple disulfide: pdb=" SG CYS B1051 " - pdb=" SG CYS B1073 " distance=2.03 Simple disulfide: pdb=" SG CYS B1077 " - pdb=" SG CYS B1108 " distance=2.02 Simple disulfide: pdb=" SG CYS B1126 " - pdb=" SG CYS B1145 " distance=2.04 Simple disulfide: pdb=" SG CYS B1149 " - pdb=" SG CYS B1169 " distance=2.03 Simple disulfide: pdb=" SG CYS B1181 " - pdb=" SG CYS B1188 " distance=2.04 Simple disulfide: pdb=" SG CYS B1190 " - pdb=" SG CYS B1210 " distance=2.03 Simple disulfide: pdb=" SG CYS B1215 " - pdb=" SG CYS B1264 " distance=2.03 Simple disulfide: pdb=" SG CYS B1231 " - pdb=" SG CYS B1245 " distance=2.03 Simple disulfide: pdb=" SG CYS B1306 " - pdb=" SG CYS B1356 " distance=2.04 Simple disulfide: pdb=" SG CYS B1331 " - pdb=" SG CYS B1347 " distance=2.03 Simple disulfide: pdb=" SG CYS B1440 " - pdb=" SG CYS B1459 " distance=2.04 Simple disulfide: pdb=" SG CYS B1462 " - pdb=" SG CYS B1473 " distance=2.03 Simple disulfide: pdb=" SG CYS B1476 " - pdb=" SG CYS B1490 " distance=2.03 Simple disulfide: pdb=" SG CYS B1493 " - pdb=" SG CYS B1510 " distance=2.03 Simple disulfide: pdb=" SG CYS B1514 " - pdb=" SG CYS B1523 " distance=2.03 Simple disulfide: pdb=" SG CYS B1543 " - pdb=" SG CYS B1565 " distance=2.02 Simple disulfide: pdb=" SG CYS B1603 " - pdb=" SG CYS B1627 " distance=2.03 Simple disulfide: pdb=" SG CYS B1607 " - pdb=" SG CYS B1613 " distance=2.03 Simple disulfide: pdb=" SG CYS B1639 " - pdb=" SG CYS B1662 " distance=2.03 Simple disulfide: pdb=" SG CYS B1724 " - pdb=" SG CYS B1749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1728 " - pdb=" SG CYS B1734 " distance=2.03 Simple disulfide: pdb=" SG CYS B1733 " - pdb=" SG CYS B1835 " distance=2.03 Simple disulfide: pdb=" SG CYS B1760 " - pdb=" SG CYS B1777 " distance=2.03 Simple disulfide: pdb=" SG CYS B1893 " - pdb=" SG CYS B1919 " distance=2.03 Simple disulfide: pdb=" SG CYS B1897 " - pdb=" SG CYS B1904 " distance=2.03 Simple disulfide: pdb=" SG CYS B1928 " - pdb=" SG CYS B1939 " distance=2.04 Simple disulfide: pdb=" SG CYS B1996 " - pdb=" SG CYS B2024 " distance=2.03 Simple disulfide: pdb=" SG CYS B2000 " - pdb=" SG CYS B2006 " distance=2.03 Simple disulfide: pdb=" SG CYS B2005 " - pdb=" SG CYS B2076 " distance=2.03 Simple disulfide: pdb=" SG CYS B2035 " - pdb=" SG CYS B2048 " distance=2.03 Simple disulfide: pdb=" SG CYS B2130 " - pdb=" SG CYS B2154 " distance=2.03 Simple disulfide: pdb=" SG CYS B2134 " - pdb=" SG CYS B2140 " distance=2.03 Simple disulfide: pdb=" SG CYS B2163 " - pdb=" SG CYS B2172 " distance=2.03 Simple disulfide: pdb=" SG CYS B2264 " - pdb=" SG CYS B2281 " distance=2.03 Simple disulfide: pdb=" SG CYS B2442 " - pdb=" SG CYS B2453 " distance=2.03 Simple disulfide: pdb=" SG CYS B2591 " - pdb=" SG CYS B2715 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " NAG-ASN " NAG A2801 " - " ASN A 947 " " NAG A2802 " - " ASN A1220 " " NAG A2803 " - " ASN A1349 " " NAG A2804 " - " ASN A1365 " " NAG A2805 " - " ASN A1716 " " NAG A2809 " - " ASN A2250 " " NAG A2810 " - " ASN A2295 " " NAG A2811 " - " ASN A2582 " " NAG A2812 " - " ASN A2122 " " NAG A2813 " - " ASN A1869 " " NAG A2814 " - " ASN A1774 " " NAG A2815 " - " ASN A 198 " " NAG A2816 " - " ASN A 76 " " NAG A2817 " - " ASN A 484 " " NAG A2818 " - " ASN A 110 " " NAG B2801 " - " ASN B 947 " " NAG B2802 " - " ASN B1220 " " NAG B2803 " - " ASN B1349 " " NAG B2804 " - " ASN B1365 " " NAG B2805 " - " ASN B1716 " " NAG B2809 " - " ASN B2250 " " NAG B2810 " - " ASN B2295 " " NAG B2811 " - " ASN B2582 " " NAG B2812 " - " ASN B2122 " " NAG B2813 " - " ASN B1869 " " NAG B2814 " - " ASN B1774 " " NAG B2815 " - " ASN B 198 " " NAG B2816 " - " ASN B 76 " " NAG B2817 " - " ASN B 484 " " NAG B2818 " - " ASN B 110 " " NAG C 1 " - " ASN A2013 " " NAG D 1 " - " ASN B2013 " Time building additional restraints: 3.72 Conformation dependent library (CDL) restraints added in 1.9 seconds 10116 Ramachandran restraints generated. 5058 Oldfield, 0 Emsley, 5058 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9444 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 68 sheets defined 26.9% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.42 Creating SS restraints... Processing helix chain 'A' and resid 34 through 43 removed outlier: 3.597A pdb=" N GLU A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA A 41 " --> pdb=" O GLN A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 110 removed outlier: 3.571A pdb=" N LEU A 104 " --> pdb=" O LYS A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 174 removed outlier: 3.593A pdb=" N LEU A 172 " --> pdb=" O ASN A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 214 Processing helix chain 'A' and resid 215 through 219 removed outlier: 3.925A pdb=" N VAL A 219 " --> pdb=" O ASP A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 226 removed outlier: 3.687A pdb=" N ARG A 226 " --> pdb=" O SER A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 293 removed outlier: 3.506A pdb=" N ARG A 278 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU A 280 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL A 287 " --> pdb=" O ARG A 283 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 312 removed outlier: 3.704A pdb=" N PHE A 311 " --> pdb=" O THR A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 376 removed outlier: 3.518A pdb=" N GLN A 369 " --> pdb=" O ALA A 365 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 448 removed outlier: 3.716A pdb=" N ARG A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 460 removed outlier: 3.724A pdb=" N ALA A 454 " --> pdb=" O SER A 450 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU A 456 " --> pdb=" O GLY A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 467 Processing helix chain 'A' and resid 468 through 473 Processing helix chain 'A' and resid 475 through 482 Processing helix chain 'A' and resid 497 through 502 removed outlier: 3.721A pdb=" N GLN A 502 " --> pdb=" O SER A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 573 Processing helix chain 'A' and resid 574 through 586 removed outlier: 3.916A pdb=" N LEU A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A 579 " --> pdb=" O PRO A 575 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N HIS A 583 " --> pdb=" O LEU A 579 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER A 586 " --> pdb=" O GLN A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 606 Processing helix chain 'A' and resid 662 through 672 removed outlier: 4.215A pdb=" N ARG A 668 " --> pdb=" O LYS A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 676 Processing helix chain 'A' and resid 730 through 743 removed outlier: 3.776A pdb=" N GLN A 736 " --> pdb=" O LEU A 732 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG A 740 " --> pdb=" O GLN A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 746 No H-bonds generated for 'chain 'A' and resid 744 through 746' Processing helix chain 'A' and resid 780 through 788 removed outlier: 3.758A pdb=" N TRP A 788 " --> pdb=" O LEU A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 806 Processing helix chain 'A' and resid 807 through 815 removed outlier: 4.051A pdb=" N GLU A 811 " --> pdb=" O MET A 807 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALA A 813 " --> pdb=" O TYR A 809 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER A 814 " --> pdb=" O ARG A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 867 Processing helix chain 'A' and resid 872 through 877 removed outlier: 3.799A pdb=" N LEU A 876 " --> pdb=" O LEU A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 949 removed outlier: 4.148A pdb=" N VAL A 932 " --> pdb=" O ALA A 928 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER A 944 " --> pdb=" O GLU A 940 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER A 946 " --> pdb=" O ILE A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 961 Processing helix chain 'A' and resid 979 through 986 removed outlier: 4.264A pdb=" N ALA A 983 " --> pdb=" O ARG A 979 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU A 984 " --> pdb=" O GLU A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1009 removed outlier: 3.584A pdb=" N ALA A 993 " --> pdb=" O GLY A 989 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG A 995 " --> pdb=" O ASP A 991 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA A 998 " --> pdb=" O ILE A 994 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A1002 " --> pdb=" O ALA A 998 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR A1005 " --> pdb=" O THR A1001 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG A1007 " --> pdb=" O SER A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1087 removed outlier: 3.532A pdb=" N SER A1087 " --> pdb=" O SER A1083 " (cutoff:3.500A) Processing helix chain 'A' and resid 1099 through 1101 No H-bonds generated for 'chain 'A' and resid 1099 through 1101' Processing helix chain 'A' and resid 1147 through 1157 Processing helix chain 'A' and resid 1319 through 1328 removed outlier: 3.568A pdb=" N LEU A1325 " --> pdb=" O ILE A1321 " (cutoff:3.500A) Processing helix chain 'A' and resid 1348 through 1352 removed outlier: 3.634A pdb=" N SER A1351 " --> pdb=" O ASN A1348 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N VAL A1352 " --> pdb=" O ASN A1349 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1348 through 1352' Processing helix chain 'A' and resid 1373 through 1375 No H-bonds generated for 'chain 'A' and resid 1373 through 1375' Processing helix chain 'A' and resid 1382 through 1392 removed outlier: 3.560A pdb=" N LEU A1390 " --> pdb=" O ILE A1386 " (cutoff:3.500A) Processing helix chain 'A' and resid 1395 through 1405 Processing helix chain 'A' and resid 1506 through 1510 removed outlier: 3.595A pdb=" N HIS A1509 " --> pdb=" O SER A1506 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N CYS A1510 " --> pdb=" O GLN A1507 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1506 through 1510' Processing helix chain 'A' and resid 1561 through 1567 removed outlier: 3.610A pdb=" N MET A1567 " --> pdb=" O SER A1563 " (cutoff:3.500A) Processing helix chain 'A' and resid 1601 through 1609 removed outlier: 4.000A pdb=" N THR A1605 " --> pdb=" O MET A1601 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASP A1606 " --> pdb=" O GLN A1602 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N CYS A1607 " --> pdb=" O CYS A1603 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR A1608 " --> pdb=" O LEU A1604 " (cutoff:3.500A) Processing helix chain 'A' and resid 1716 through 1726 removed outlier: 3.758A pdb=" N ALA A1720 " --> pdb=" O ASN A1716 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU A1726 " --> pdb=" O LEU A1722 " (cutoff:3.500A) Processing helix chain 'A' and resid 1727 through 1729 No H-bonds generated for 'chain 'A' and resid 1727 through 1729' Processing helix chain 'A' and resid 1848 through 1853 removed outlier: 4.001A pdb=" N THR A1853 " --> pdb=" O ALA A1849 " (cutoff:3.500A) Processing helix chain 'A' and resid 1885 through 1900 removed outlier: 3.873A pdb=" N ASN A1890 " --> pdb=" O ALA A1886 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS A1893 " --> pdb=" O ALA A1889 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN A1899 " --> pdb=" O SER A1895 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU A1900 " --> pdb=" O ARG A1896 " (cutoff:3.500A) Processing helix chain 'A' and resid 1935 through 1939 removed outlier: 4.281A pdb=" N GLY A1938 " --> pdb=" O ASN A1935 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N CYS A1939 " --> pdb=" O ALA A1936 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1935 through 1939' Processing helix chain 'A' and resid 1988 through 2002 removed outlier: 3.696A pdb=" N ARG A1998 " --> pdb=" O PHE A1994 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N CYS A2000 " --> pdb=" O CYS A1996 " (cutoff:3.500A) Processing helix chain 'A' and resid 2015 through 2019 Processing helix chain 'A' and resid 2089 through 2093 Processing helix chain 'A' and resid 2097 through 2099 No H-bonds generated for 'chain 'A' and resid 2097 through 2099' Processing helix chain 'A' and resid 2122 through 2135 removed outlier: 3.575A pdb=" N GLU A2133 " --> pdb=" O LEU A2129 " (cutoff:3.500A) Processing helix chain 'A' and resid 2319 through 2327 Processing helix chain 'A' and resid 2357 through 2374 removed outlier: 3.589A pdb=" N TRP A2365 " --> pdb=" O ALA A2361 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ARG A2371 " --> pdb=" O GLN A2367 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N GLY A2372 " --> pdb=" O THR A2368 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N PHE A2373 " --> pdb=" O HIS A2369 " (cutoff:3.500A) Processing helix chain 'A' and resid 2387 through 2392 removed outlier: 3.681A pdb=" N VAL A2391 " --> pdb=" O GLY A2387 " (cutoff:3.500A) Processing helix chain 'A' and resid 2393 through 2397 Processing helix chain 'A' and resid 2401 through 2405 removed outlier: 3.801A pdb=" N GLN A2405 " --> pdb=" O THR A2402 " (cutoff:3.500A) Processing helix chain 'A' and resid 2425 through 2438 removed outlier: 3.967A pdb=" N GLN A2431 " --> pdb=" O GLU A2427 " (cutoff:3.500A) Processing helix chain 'A' and resid 2453 through 2457 removed outlier: 3.701A pdb=" N LYS A2457 " --> pdb=" O LEU A2454 " (cutoff:3.500A) Processing helix chain 'A' and resid 2460 through 2471 removed outlier: 3.778A pdb=" N THR A2467 " --> pdb=" O ASN A2463 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU A2469 " --> pdb=" O ALA A2465 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA A2471 " --> pdb=" O THR A2467 " (cutoff:3.500A) Processing helix chain 'A' and resid 2491 through 2496 Processing helix chain 'A' and resid 2517 through 2519 No H-bonds generated for 'chain 'A' and resid 2517 through 2519' Processing helix chain 'A' and resid 2520 through 2531 removed outlier: 3.695A pdb=" N GLN A2525 " --> pdb=" O LYS A2521 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N PHE A2526 " --> pdb=" O ALA A2522 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU A2527 " --> pdb=" O VAL A2523 " (cutoff:3.500A) Processing helix chain 'A' and resid 2533 through 2546 removed outlier: 4.231A pdb=" N THR A2537 " --> pdb=" O THR A2533 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N PHE A2539 " --> pdb=" O SER A2535 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN A2541 " --> pdb=" O THR A2537 " (cutoff:3.500A) Processing helix chain 'A' and resid 2553 through 2564 removed outlier: 3.861A pdb=" N ALA A2559 " --> pdb=" O ARG A2555 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TRP A2562 " --> pdb=" O ALA A2558 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR A2563 " --> pdb=" O ALA A2559 " (cutoff:3.500A) Processing helix chain 'A' and resid 2574 through 2589 removed outlier: 3.638A pdb=" N GLU A2581 " --> pdb=" O SER A2577 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR A2587 " --> pdb=" O ALA A2583 " (cutoff:3.500A) Processing helix chain 'A' and resid 2589 through 2602 removed outlier: 3.816A pdb=" N ASP A2595 " --> pdb=" O CYS A2591 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TRP A2600 " --> pdb=" O MET A2596 " (cutoff:3.500A) Processing helix chain 'A' and resid 2633 through 2637 Processing helix chain 'A' and resid 2647 through 2655 removed outlier: 3.875A pdb=" N LYS A2654 " --> pdb=" O SER A2650 " (cutoff:3.500A) Processing helix chain 'A' and resid 2655 through 2666 Processing helix chain 'A' and resid 2713 through 2721 removed outlier: 4.159A pdb=" N SER A2719 " --> pdb=" O CYS A2715 " (cutoff:3.500A) Processing helix chain 'A' and resid 2721 through 2726 Processing helix chain 'B' and resid 34 through 43 removed outlier: 3.596A pdb=" N GLU B 39 " --> pdb=" O GLU B 35 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA B 41 " --> pdb=" O GLN B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 110 removed outlier: 3.572A pdb=" N LEU B 104 " --> pdb=" O LYS B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 174 removed outlier: 3.593A pdb=" N LEU B 172 " --> pdb=" O ASN B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 214 Processing helix chain 'B' and resid 215 through 219 removed outlier: 3.925A pdb=" N VAL B 219 " --> pdb=" O ASP B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 226 removed outlier: 3.687A pdb=" N ARG B 226 " --> pdb=" O SER B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 293 removed outlier: 3.505A pdb=" N ARG B 278 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU B 280 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL B 287 " --> pdb=" O ARG B 283 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL B 290 " --> pdb=" O ALA B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 312 removed outlier: 3.705A pdb=" N PHE B 311 " --> pdb=" O THR B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 376 removed outlier: 3.518A pdb=" N GLN B 369 " --> pdb=" O ALA B 365 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 448 removed outlier: 3.717A pdb=" N ARG B 445 " --> pdb=" O LYS B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 460 removed outlier: 3.725A pdb=" N ALA B 454 " --> pdb=" O SER B 450 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU B 456 " --> pdb=" O GLY B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 467 Processing helix chain 'B' and resid 468 through 473 Processing helix chain 'B' and resid 475 through 482 Processing helix chain 'B' and resid 497 through 502 removed outlier: 3.722A pdb=" N GLN B 502 " --> pdb=" O SER B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 573 Processing helix chain 'B' and resid 574 through 586 removed outlier: 3.915A pdb=" N LEU B 578 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU B 579 " --> pdb=" O PRO B 575 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N HIS B 583 " --> pdb=" O LEU B 579 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER B 586 " --> pdb=" O GLN B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 606 Processing helix chain 'B' and resid 662 through 672 removed outlier: 4.215A pdb=" N ARG B 668 " --> pdb=" O LYS B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 676 Processing helix chain 'B' and resid 730 through 743 removed outlier: 3.776A pdb=" N GLN B 736 " --> pdb=" O LEU B 732 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG B 740 " --> pdb=" O GLN B 736 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 746 No H-bonds generated for 'chain 'B' and resid 744 through 746' Processing helix chain 'B' and resid 780 through 788 removed outlier: 3.759A pdb=" N TRP B 788 " --> pdb=" O LEU B 784 " (cutoff:3.500A) Processing helix chain 'B' and resid 800 through 806 Processing helix chain 'B' and resid 807 through 815 removed outlier: 4.051A pdb=" N GLU B 811 " --> pdb=" O MET B 807 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALA B 813 " --> pdb=" O TYR B 809 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N SER B 814 " --> pdb=" O ARG B 810 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 867 Processing helix chain 'B' and resid 872 through 877 removed outlier: 3.799A pdb=" N LEU B 876 " --> pdb=" O LEU B 872 " (cutoff:3.500A) Processing helix chain 'B' and resid 926 through 949 removed outlier: 4.147A pdb=" N VAL B 932 " --> pdb=" O ALA B 928 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER B 944 " --> pdb=" O GLU B 940 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER B 946 " --> pdb=" O ILE B 942 " (cutoff:3.500A) Processing helix chain 'B' and resid 954 through 961 Processing helix chain 'B' and resid 979 through 986 removed outlier: 4.264A pdb=" N ALA B 983 " --> pdb=" O ARG B 979 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU B 984 " --> pdb=" O GLU B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 989 through 1009 removed outlier: 3.585A pdb=" N ALA B 993 " --> pdb=" O GLY B 989 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG B 995 " --> pdb=" O ASP B 991 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA B 998 " --> pdb=" O ILE B 994 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU B1002 " --> pdb=" O ALA B 998 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N TYR B1005 " --> pdb=" O THR B1001 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG B1007 " --> pdb=" O SER B1003 " (cutoff:3.500A) Processing helix chain 'B' and resid 1077 through 1087 removed outlier: 3.532A pdb=" N SER B1087 " --> pdb=" O SER B1083 " (cutoff:3.500A) Processing helix chain 'B' and resid 1099 through 1101 No H-bonds generated for 'chain 'B' and resid 1099 through 1101' Processing helix chain 'B' and resid 1147 through 1157 Processing helix chain 'B' and resid 1319 through 1328 removed outlier: 3.568A pdb=" N LEU B1325 " --> pdb=" O ILE B1321 " (cutoff:3.500A) Processing helix chain 'B' and resid 1348 through 1352 removed outlier: 3.634A pdb=" N SER B1351 " --> pdb=" O ASN B1348 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N VAL B1352 " --> pdb=" O ASN B1349 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1348 through 1352' Processing helix chain 'B' and resid 1373 through 1375 No H-bonds generated for 'chain 'B' and resid 1373 through 1375' Processing helix chain 'B' and resid 1382 through 1392 removed outlier: 3.561A pdb=" N LEU B1390 " --> pdb=" O ILE B1386 " (cutoff:3.500A) Processing helix chain 'B' and resid 1395 through 1405 Processing helix chain 'B' and resid 1506 through 1510 removed outlier: 3.595A pdb=" N HIS B1509 " --> pdb=" O SER B1506 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N CYS B1510 " --> pdb=" O GLN B1507 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1506 through 1510' Processing helix chain 'B' and resid 1561 through 1567 removed outlier: 3.609A pdb=" N MET B1567 " --> pdb=" O SER B1563 " (cutoff:3.500A) Processing helix chain 'B' and resid 1601 through 1609 removed outlier: 4.000A pdb=" N THR B1605 " --> pdb=" O MET B1601 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASP B1606 " --> pdb=" O GLN B1602 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N CYS B1607 " --> pdb=" O CYS B1603 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR B1608 " --> pdb=" O LEU B1604 " (cutoff:3.500A) Processing helix chain 'B' and resid 1716 through 1726 removed outlier: 3.758A pdb=" N ALA B1720 " --> pdb=" O ASN B1716 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU B1726 " --> pdb=" O LEU B1722 " (cutoff:3.500A) Processing helix chain 'B' and resid 1727 through 1729 No H-bonds generated for 'chain 'B' and resid 1727 through 1729' Processing helix chain 'B' and resid 1848 through 1853 removed outlier: 4.001A pdb=" N THR B1853 " --> pdb=" O ALA B1849 " (cutoff:3.500A) Processing helix chain 'B' and resid 1885 through 1900 removed outlier: 3.873A pdb=" N ASN B1890 " --> pdb=" O ALA B1886 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N CYS B1893 " --> pdb=" O ALA B1889 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN B1899 " --> pdb=" O SER B1895 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU B1900 " --> pdb=" O ARG B1896 " (cutoff:3.500A) Processing helix chain 'B' and resid 1935 through 1939 removed outlier: 4.281A pdb=" N GLY B1938 " --> pdb=" O ASN B1935 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N CYS B1939 " --> pdb=" O ALA B1936 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1935 through 1939' Processing helix chain 'B' and resid 1988 through 2002 removed outlier: 3.695A pdb=" N ARG B1998 " --> pdb=" O PHE B1994 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N CYS B2000 " --> pdb=" O CYS B1996 " (cutoff:3.500A) Processing helix chain 'B' and resid 2015 through 2019 Processing helix chain 'B' and resid 2089 through 2093 Processing helix chain 'B' and resid 2097 through 2099 No H-bonds generated for 'chain 'B' and resid 2097 through 2099' Processing helix chain 'B' and resid 2122 through 2135 removed outlier: 3.574A pdb=" N GLU B2133 " --> pdb=" O LEU B2129 " (cutoff:3.500A) Processing helix chain 'B' and resid 2319 through 2327 Processing helix chain 'B' and resid 2357 through 2374 removed outlier: 3.589A pdb=" N TRP B2365 " --> pdb=" O ALA B2361 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ARG B2371 " --> pdb=" O GLN B2367 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N GLY B2372 " --> pdb=" O THR B2368 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N PHE B2373 " --> pdb=" O HIS B2369 " (cutoff:3.500A) Processing helix chain 'B' and resid 2387 through 2392 removed outlier: 3.682A pdb=" N VAL B2391 " --> pdb=" O GLY B2387 " (cutoff:3.500A) Processing helix chain 'B' and resid 2393 through 2397 Processing helix chain 'B' and resid 2401 through 2405 removed outlier: 3.801A pdb=" N GLN B2405 " --> pdb=" O THR B2402 " (cutoff:3.500A) Processing helix chain 'B' and resid 2425 through 2438 removed outlier: 3.967A pdb=" N GLN B2431 " --> pdb=" O GLU B2427 " (cutoff:3.500A) Processing helix chain 'B' and resid 2453 through 2457 removed outlier: 3.702A pdb=" N LYS B2457 " --> pdb=" O LEU B2454 " (cutoff:3.500A) Processing helix chain 'B' and resid 2460 through 2471 removed outlier: 3.778A pdb=" N THR B2467 " --> pdb=" O ASN B2463 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU B2469 " --> pdb=" O ALA B2465 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA B2471 " --> pdb=" O THR B2467 " (cutoff:3.500A) Processing helix chain 'B' and resid 2491 through 2496 Processing helix chain 'B' and resid 2517 through 2519 No H-bonds generated for 'chain 'B' and resid 2517 through 2519' Processing helix chain 'B' and resid 2520 through 2531 removed outlier: 3.695A pdb=" N GLN B2525 " --> pdb=" O LYS B2521 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N PHE B2526 " --> pdb=" O ALA B2522 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU B2527 " --> pdb=" O VAL B2523 " (cutoff:3.500A) Processing helix chain 'B' and resid 2533 through 2546 removed outlier: 4.231A pdb=" N THR B2537 " --> pdb=" O THR B2533 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N PHE B2539 " --> pdb=" O SER B2535 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN B2541 " --> pdb=" O THR B2537 " (cutoff:3.500A) Processing helix chain 'B' and resid 2553 through 2564 removed outlier: 3.862A pdb=" N ALA B2559 " --> pdb=" O ARG B2555 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TRP B2562 " --> pdb=" O ALA B2558 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR B2563 " --> pdb=" O ALA B2559 " (cutoff:3.500A) Processing helix chain 'B' and resid 2574 through 2589 removed outlier: 3.637A pdb=" N GLU B2581 " --> pdb=" O SER B2577 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR B2587 " --> pdb=" O ALA B2583 " (cutoff:3.500A) Processing helix chain 'B' and resid 2589 through 2602 removed outlier: 3.817A pdb=" N ASP B2595 " --> pdb=" O CYS B2591 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TRP B2600 " --> pdb=" O MET B2596 " (cutoff:3.500A) Processing helix chain 'B' and resid 2633 through 2637 Processing helix chain 'B' and resid 2647 through 2655 removed outlier: 3.876A pdb=" N LYS B2654 " --> pdb=" O SER B2650 " (cutoff:3.500A) Processing helix chain 'B' and resid 2655 through 2666 Processing helix chain 'B' and resid 2713 through 2721 removed outlier: 4.158A pdb=" N SER B2719 " --> pdb=" O CYS B2715 " (cutoff:3.500A) Processing helix chain 'B' and resid 2721 through 2726 Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 63 Processing sheet with id=AA2, first strand: chain 'A' and resid 129 through 130 removed outlier: 5.805A pdb=" N CYS A 140 " --> pdb=" O VAL A 148 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL A 148 " --> pdb=" O CYS A 140 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 192 through 198 Processing sheet with id=AA4, first strand: chain 'A' and resid 328 through 330 Processing sheet with id=AA5, first strand: chain 'A' and resid 629 through 631 removed outlier: 3.566A pdb=" N CYS A 636 " --> pdb=" O VAL A 651 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 696 through 699 removed outlier: 3.645A pdb=" N CYS A 705 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N THR A 716 " --> pdb=" O CYS A 705 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1040 through 1042 Processing sheet with id=AA8, first strand: chain 'A' and resid 1091 through 1092 Processing sheet with id=AA9, first strand: chain 'A' and resid 1118 through 1120 removed outlier: 3.517A pdb=" N GLN A1118 " --> pdb=" O TRP A1125 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TRP A1125 " --> pdb=" O GLN A1118 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER A1120 " --> pdb=" O GLY A1123 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLY A1123 " --> pdb=" O SER A1120 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 1189 through 1191 removed outlier: 8.760A pdb=" N CYS A1190 " --> pdb=" O VAL A1198 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL A1198 " --> pdb=" O CYS A1190 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 1227 through 1231 removed outlier: 3.634A pdb=" N THR A1228 " --> pdb=" O LEU A1248 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU A1230 " --> pdb=" O GLN A1246 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1254 through 1255 removed outlier: 3.644A pdb=" N GLN A1282 " --> pdb=" O TRP A1254 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1369 through 1371 removed outlier: 3.561A pdb=" N GLN A1291 " --> pdb=" O TRP A1437 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1296 through 1297 removed outlier: 3.577A pdb=" N PHE A1296 " --> pdb=" O VAL A1364 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY A1355 " --> pdb=" O GLY A1363 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1333 through 1337 removed outlier: 3.775A pdb=" N THR A1340 " --> pdb=" O THR A1337 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1409 through 1412 removed outlier: 3.501A pdb=" N PHE A1417 " --> pdb=" O LEU A1410 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A1412 " --> pdb=" O LYS A1415 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1466 through 1468 Processing sheet with id=AB9, first strand: chain 'A' and resid 1480 through 1481 Processing sheet with id=AC1, first strand: chain 'A' and resid 1533 through 1535 Processing sheet with id=AC2, first strand: chain 'A' and resid 1626 through 1630 removed outlier: 3.661A pdb=" N SER A1626 " --> pdb=" O SER A1619 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR A1617 " --> pdb=" O ASP A1628 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1705 through 1710 removed outlier: 6.141A pdb=" N CYS A1749 " --> pdb=" O PRO A1707 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N VAL A1709 " --> pdb=" O ILE A1747 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ILE A1747 " --> pdb=" O VAL A1709 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY A1750 " --> pdb=" O VAL A1738 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 1757 through 1759 Processing sheet with id=AC5, first strand: chain 'A' and resid 1856 through 1858 Processing sheet with id=AC6, first strand: chain 'A' and resid 1864 through 1866 removed outlier: 6.259A pdb=" N ILE A1865 " --> pdb=" O LEU A1943 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ARG A1940 " --> pdb=" O VAL A1927 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL A1927 " --> pdb=" O ARG A1940 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'A' and resid 1966 through 1967 Processing sheet with id=AC8, first strand: chain 'A' and resid 1972 through 1974 removed outlier: 3.723A pdb=" N LYS A1972 " --> pdb=" O MET A2034 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE A2142 " --> pdb=" O TYR A2157 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ILE A2183 " --> pdb=" O LEU A2096 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 1977 through 1980 removed outlier: 6.626A pdb=" N SER A1977 " --> pdb=" O ASN A2028 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N THR A2026 " --> pdb=" O ARG A1979 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLY A2008 " --> pdb=" O LEU A2027 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 2012 through 2013 Processing sheet with id=AD2, first strand: chain 'A' and resid 2101 through 2103 removed outlier: 5.819A pdb=" N VAL A2102 " --> pdb=" O LEU A2176 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'A' and resid 2164 through 2165 removed outlier: 3.724A pdb=" N ASN A2171 " --> pdb=" O THR A2164 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 2193 through 2195 removed outlier: 3.568A pdb=" N GLU A2195 " --> pdb=" O VAL A2198 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 2207 through 2210 Processing sheet with id=AD6, first strand: chain 'A' and resid 2214 through 2218 removed outlier: 3.695A pdb=" N SER A2221 " --> pdb=" O VAL A2218 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N GLN A2227 " --> pdb=" O ILE A2288 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ILE A2288 " --> pdb=" O GLN A2227 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N LEU A2229 " --> pdb=" O VAL A2286 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL A2286 " --> pdb=" O LEU A2229 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LEU A2299 " --> pdb=" O VAL A2331 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ALA A2333 " --> pdb=" O LEU A2299 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N PHE A2301 " --> pdb=" O ALA A2333 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL A2298 " --> pdb=" O SER A2381 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N ALA A2383 " --> pdb=" O VAL A2298 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N VAL A2300 " --> pdb=" O ALA A2383 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU A2382 " --> pdb=" O VAL A2411 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N MET A2413 " --> pdb=" O LEU A2382 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ALA A2384 " --> pdb=" O MET A2413 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ALA A2410 " --> pdb=" O LEU A2507 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N GLY A2509 " --> pdb=" O ALA A2410 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LEU A2412 " --> pdb=" O GLY A2509 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N LEU A2506 " --> pdb=" O PHE A2609 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N TYR A2611 " --> pdb=" O LEU A2506 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE A2508 " --> pdb=" O TYR A2611 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N ASN A2696 " --> pdb=" O VAL A2608 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N MET A2610 " --> pdb=" O ASN A2696 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR A2697 " --> pdb=" O ARG A2707 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 2263 through 2264 removed outlier: 5.451A pdb=" N SER A2263 " --> pdb=" O SER A2278 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'B' and resid 61 through 63 Processing sheet with id=AD9, first strand: chain 'B' and resid 129 through 130 removed outlier: 5.805A pdb=" N CYS B 140 " --> pdb=" O VAL B 148 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL B 148 " --> pdb=" O CYS B 140 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 192 through 198 Processing sheet with id=AE2, first strand: chain 'B' and resid 328 through 330 Processing sheet with id=AE3, first strand: chain 'B' and resid 629 through 631 removed outlier: 3.566A pdb=" N CYS B 636 " --> pdb=" O VAL B 651 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 696 through 699 removed outlier: 3.647A pdb=" N CYS B 705 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N THR B 716 " --> pdb=" O CYS B 705 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 1040 through 1042 Processing sheet with id=AE6, first strand: chain 'B' and resid 1091 through 1092 Processing sheet with id=AE7, first strand: chain 'B' and resid 1118 through 1120 removed outlier: 3.517A pdb=" N GLN B1118 " --> pdb=" O TRP B1125 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TRP B1125 " --> pdb=" O GLN B1118 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER B1120 " --> pdb=" O GLY B1123 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLY B1123 " --> pdb=" O SER B1120 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'B' and resid 1189 through 1191 removed outlier: 8.761A pdb=" N CYS B1190 " --> pdb=" O VAL B1198 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL B1198 " --> pdb=" O CYS B1190 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'B' and resid 1227 through 1231 removed outlier: 3.634A pdb=" N THR B1228 " --> pdb=" O LEU B1248 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU B1230 " --> pdb=" O GLN B1246 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 1254 through 1255 removed outlier: 3.643A pdb=" N GLN B1282 " --> pdb=" O TRP B1254 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 1369 through 1371 removed outlier: 3.561A pdb=" N GLN B1291 " --> pdb=" O TRP B1437 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 1296 through 1297 removed outlier: 3.577A pdb=" N PHE B1296 " --> pdb=" O VAL B1364 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY B1355 " --> pdb=" O GLY B1363 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 1333 through 1337 removed outlier: 3.776A pdb=" N THR B1340 " --> pdb=" O THR B1337 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'B' and resid 1409 through 1412 removed outlier: 3.500A pdb=" N PHE B1417 " --> pdb=" O LEU B1410 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU B1412 " --> pdb=" O LYS B1415 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'B' and resid 1466 through 1468 Processing sheet with id=AF7, first strand: chain 'B' and resid 1480 through 1481 Processing sheet with id=AF8, first strand: chain 'B' and resid 1533 through 1535 Processing sheet with id=AF9, first strand: chain 'B' and resid 1626 through 1630 removed outlier: 3.661A pdb=" N SER B1626 " --> pdb=" O SER B1619 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR B1617 " --> pdb=" O ASP B1628 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'B' and resid 1705 through 1710 removed outlier: 6.141A pdb=" N CYS B1749 " --> pdb=" O PRO B1707 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N VAL B1709 " --> pdb=" O ILE B1747 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ILE B1747 " --> pdb=" O VAL B1709 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY B1750 " --> pdb=" O VAL B1738 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'B' and resid 1757 through 1759 Processing sheet with id=AG3, first strand: chain 'B' and resid 1856 through 1858 Processing sheet with id=AG4, first strand: chain 'B' and resid 1864 through 1866 removed outlier: 6.260A pdb=" N ILE B1865 " --> pdb=" O LEU B1943 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG B1940 " --> pdb=" O VAL B1927 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL B1927 " --> pdb=" O ARG B1940 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 'B' and resid 1966 through 1967 Processing sheet with id=AG6, first strand: chain 'B' and resid 1972 through 1974 removed outlier: 3.722A pdb=" N LYS B1972 " --> pdb=" O MET B2034 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE B2142 " --> pdb=" O TYR B2157 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ILE B2183 " --> pdb=" O LEU B2096 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'B' and resid 1977 through 1980 removed outlier: 6.626A pdb=" N SER B1977 " --> pdb=" O ASN B2028 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N THR B2026 " --> pdb=" O ARG B1979 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLY B2008 " --> pdb=" O LEU B2027 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'B' and resid 2012 through 2013 Processing sheet with id=AG9, first strand: chain 'B' and resid 2101 through 2103 removed outlier: 5.820A pdb=" N VAL B2102 " --> pdb=" O LEU B2176 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG9 Processing sheet with id=AH1, first strand: chain 'B' and resid 2164 through 2165 removed outlier: 3.724A pdb=" N ASN B2171 " --> pdb=" O THR B2164 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'B' and resid 2193 through 2195 removed outlier: 3.569A pdb=" N GLU B2195 " --> pdb=" O VAL B2198 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'B' and resid 2207 through 2210 Processing sheet with id=AH4, first strand: chain 'B' and resid 2214 through 2218 removed outlier: 3.695A pdb=" N SER B2221 " --> pdb=" O VAL B2218 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N GLN B2227 " --> pdb=" O ILE B2288 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ILE B2288 " --> pdb=" O GLN B2227 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N LEU B2229 " --> pdb=" O VAL B2286 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL B2286 " --> pdb=" O LEU B2229 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU B2299 " --> pdb=" O VAL B2331 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ALA B2333 " --> pdb=" O LEU B2299 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N PHE B2301 " --> pdb=" O ALA B2333 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL B2298 " --> pdb=" O SER B2381 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N ALA B2383 " --> pdb=" O VAL B2298 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N VAL B2300 " --> pdb=" O ALA B2383 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU B2382 " --> pdb=" O VAL B2411 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N MET B2413 " --> pdb=" O LEU B2382 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ALA B2384 " --> pdb=" O MET B2413 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ALA B2410 " --> pdb=" O LEU B2507 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N GLY B2509 " --> pdb=" O ALA B2410 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU B2412 " --> pdb=" O GLY B2509 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N LEU B2506 " --> pdb=" O PHE B2609 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N TYR B2611 " --> pdb=" O LEU B2506 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE B2508 " --> pdb=" O TYR B2611 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N ASN B2696 " --> pdb=" O VAL B2608 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N MET B2610 " --> pdb=" O ASN B2696 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR B2697 " --> pdb=" O ARG B2707 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'B' and resid 2263 through 2264 removed outlier: 5.452A pdb=" N SER B2263 " --> pdb=" O SER B2278 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH5 916 hydrogen bonds defined for protein. 2472 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.13 Time building geometry restraints manager: 5.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 13184 1.34 - 1.47: 9713 1.47 - 1.60: 17529 1.60 - 1.72: 0 1.72 - 1.85: 380 Bond restraints: 40806 Sorted by residual: bond pdb=" C CYS B1777 " pdb=" N PRO B1778 " ideal model delta sigma weight residual 1.336 1.383 -0.047 1.23e-02 6.61e+03 1.47e+01 bond pdb=" C CYS A1777 " pdb=" N PRO A1778 " ideal model delta sigma weight residual 1.336 1.382 -0.047 1.23e-02 6.61e+03 1.44e+01 bond pdb=" C PRO A1301 " pdb=" N PRO A1302 " ideal model delta sigma weight residual 1.334 1.406 -0.072 2.34e-02 1.83e+03 9.46e+00 bond pdb=" C PRO B1301 " pdb=" N PRO B1302 " ideal model delta sigma weight residual 1.334 1.406 -0.072 2.34e-02 1.83e+03 9.41e+00 bond pdb=" CA PRO A2491 " pdb=" C PRO A2491 " ideal model delta sigma weight residual 1.514 1.502 0.013 5.50e-03 3.31e+04 5.17e+00 ... (remaining 40801 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 53860 2.61 - 5.22: 1251 5.22 - 7.83: 224 7.83 - 10.43: 31 10.43 - 13.04: 10 Bond angle restraints: 55376 Sorted by residual: angle pdb=" N PRO A 864 " pdb=" CA PRO A 864 " pdb=" CB PRO A 864 " ideal model delta sigma weight residual 103.51 110.35 -6.84 9.60e-01 1.09e+00 5.07e+01 angle pdb=" N PRO B 864 " pdb=" CA PRO B 864 " pdb=" CB PRO B 864 " ideal model delta sigma weight residual 103.51 110.31 -6.80 9.60e-01 1.09e+00 5.02e+01 angle pdb=" N PRO B 862 " pdb=" CA PRO B 862 " pdb=" CB PRO B 862 " ideal model delta sigma weight residual 103.25 110.12 -6.87 1.05e+00 9.07e-01 4.28e+01 angle pdb=" N PRO A 862 " pdb=" CA PRO A 862 " pdb=" CB PRO A 862 " ideal model delta sigma weight residual 103.25 110.12 -6.87 1.05e+00 9.07e-01 4.28e+01 angle pdb=" C VAL B1198 " pdb=" N PRO B1199 " pdb=" CA PRO B1199 " ideal model delta sigma weight residual 127.00 140.04 -13.04 2.40e+00 1.74e-01 2.95e+01 ... (remaining 55371 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.10: 24215 21.10 - 42.20: 983 42.20 - 63.30: 86 63.30 - 84.40: 54 84.40 - 105.50: 8 Dihedral angle restraints: 25346 sinusoidal: 10696 harmonic: 14650 Sorted by residual: dihedral pdb=" CB CYS B1728 " pdb=" SG CYS B1728 " pdb=" SG CYS B1734 " pdb=" CB CYS B1734 " ideal model delta sinusoidal sigma weight residual -86.00 -161.81 75.81 1 1.00e+01 1.00e-02 7.25e+01 dihedral pdb=" CB CYS A1728 " pdb=" SG CYS A1728 " pdb=" SG CYS A1734 " pdb=" CB CYS A1734 " ideal model delta sinusoidal sigma weight residual -86.00 -161.78 75.78 1 1.00e+01 1.00e-02 7.24e+01 dihedral pdb=" CB CYS A 364 " pdb=" SG CYS A 364 " pdb=" SG CYS A 620 " pdb=" CB CYS A 620 " ideal model delta sinusoidal sigma weight residual 93.00 158.99 -65.99 1 1.00e+01 1.00e-02 5.69e+01 ... (remaining 25343 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 5127 0.073 - 0.146: 856 0.146 - 0.219: 99 0.219 - 0.292: 16 0.292 - 0.364: 6 Chirality restraints: 6104 Sorted by residual: chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-02 2.50e+03 1.09e+02 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-02 2.50e+03 1.08e+02 chirality pdb=" C1 BMA D 3 " pdb=" O4 NAG D 2 " pdb=" C2 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.31e+01 ... (remaining 6101 not shown) Planarity restraints: 7322 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B2815 " 0.074 2.00e-02 2.50e+03 6.14e-02 4.71e+01 pdb=" C7 NAG B2815 " -0.024 2.00e-02 2.50e+03 pdb=" C8 NAG B2815 " 0.057 2.00e-02 2.50e+03 pdb=" N2 NAG B2815 " -0.096 2.00e-02 2.50e+03 pdb=" O7 NAG B2815 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A2815 " 0.074 2.00e-02 2.50e+03 6.14e-02 4.70e+01 pdb=" C7 NAG A2815 " -0.023 2.00e-02 2.50e+03 pdb=" C8 NAG A2815 " 0.057 2.00e-02 2.50e+03 pdb=" N2 NAG A2815 " -0.097 2.00e-02 2.50e+03 pdb=" O7 NAG A2815 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A2810 " -0.046 2.00e-02 2.50e+03 3.85e-02 1.85e+01 pdb=" C7 NAG A2810 " 0.019 2.00e-02 2.50e+03 pdb=" C8 NAG A2810 " -0.037 2.00e-02 2.50e+03 pdb=" N2 NAG A2810 " 0.059 2.00e-02 2.50e+03 pdb=" O7 NAG A2810 " 0.006 2.00e-02 2.50e+03 ... (remaining 7319 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 7092 2.77 - 3.30: 36616 3.30 - 3.83: 63339 3.83 - 4.37: 73407 4.37 - 4.90: 122833 Nonbonded interactions: 303287 Sorted by model distance: nonbonded pdb=" OH TYR A2721 " pdb=" OH TYR B2721 " model vdw 2.235 3.040 nonbonded pdb=" OG SER A 436 " pdb=" OD1 ASN A 438 " model vdw 2.244 3.040 nonbonded pdb=" OG SER B 436 " pdb=" OD1 ASN B 438 " model vdw 2.244 3.040 nonbonded pdb=" OE1 GLN A 99 " pdb=" OH TYR A 126 " model vdw 2.248 3.040 nonbonded pdb=" OE1 GLN B 99 " pdb=" OH TYR B 126 " model vdw 2.249 3.040 ... (remaining 303282 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 72.520 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 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 : 0.005 0.072 40962 Z= 0.225 Angle : 1.006 13.043 55724 Z= 0.527 Chirality : 0.057 0.364 6104 Planarity : 0.009 0.065 7290 Dihedral : 11.343 105.503 15542 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 13.35 % Favored : 86.58 % Rotamer: Outliers : 0.14 % Allowed : 3.72 % Favored : 96.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.13 % 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: -4.97 (0.09), residues: 5058 helix: -4.37 (0.07), residues: 1168 sheet: -3.03 (0.19), residues: 538 loop : -3.13 (0.09), residues: 3352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 657 TYR 0.034 0.003 TYR A1819 PHE 0.032 0.003 PHE B2659 TRP 0.055 0.003 TRP B2685 HIS 0.008 0.001 HIS A2303 Details of bonding type rmsd covalent geometry : bond 0.00456 (40806) covalent geometry : angle 0.98885 (55376) SS BOND : bond 0.00467 ( 120) SS BOND : angle 1.80210 ( 240) hydrogen bonds : bond 0.30858 ( 916) hydrogen bonds : angle 11.27894 ( 2472) link_BETA1-4 : bond 0.05728 ( 4) link_BETA1-4 : angle 2.57921 ( 12) link_NAG-ASN : bond 0.00270 ( 32) link_NAG-ASN : angle 3.80122 ( 96) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10116 Ramachandran restraints generated. 5058 Oldfield, 0 Emsley, 5058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10116 Ramachandran restraints generated. 5058 Oldfield, 0 Emsley, 5058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 749 residues out of total 4364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 743 time to evaluate : 1.537 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: A 165 GLU cc_start: 0.8791 (mt-10) cc_final: 0.8534 (mt-10) REVERT: A 203 MET cc_start: 0.7676 (mmm) cc_final: 0.7448 (mmt) REVERT: A 291 ILE cc_start: 0.9562 (mm) cc_final: 0.9329 (mt) REVERT: A 460 PHE cc_start: 0.8979 (m-10) cc_final: 0.8754 (m-80) REVERT: A 582 GLN cc_start: 0.8833 (tt0) cc_final: 0.8581 (tt0) REVERT: A 673 MET cc_start: 0.9169 (tpp) cc_final: 0.8731 (tpt) REVERT: A 779 GLU cc_start: 0.6593 (mt-10) cc_final: 0.5494 (tm-30) REVERT: A 803 LEU cc_start: 0.8436 (tp) cc_final: 0.8215 (mm) REVERT: A 1254 TRP cc_start: 0.8039 (m100) cc_final: 0.7715 (m100) REVERT: A 1282 GLN cc_start: 0.8726 (mm-40) cc_final: 0.8121 (mm110) REVERT: A 1283 ARG cc_start: 0.8355 (mtm180) cc_final: 0.8086 (mmm160) REVERT: A 1369 LYS cc_start: 0.8859 (ptmt) cc_final: 0.8572 (tttp) REVERT: A 1528 GLN cc_start: 0.8905 (tm-30) cc_final: 0.8692 (tm-30) REVERT: A 1606 ASP cc_start: 0.7744 (t70) cc_final: 0.7149 (t0) REVERT: A 1609 GLU cc_start: 0.8902 (tt0) cc_final: 0.8236 (pp20) REVERT: A 1705 TYR cc_start: 0.6532 (m-10) cc_final: 0.6278 (m-10) REVERT: A 1753 SER cc_start: 0.5292 (m) cc_final: 0.5009 (t) REVERT: A 1876 LYS cc_start: 0.8565 (mttt) cc_final: 0.8283 (mtpp) REVERT: A 1887 GLN cc_start: 0.8103 (mm-40) cc_final: 0.7811 (tp40) REVERT: A 1930 ASP cc_start: 0.8164 (m-30) cc_final: 0.7572 (t0) REVERT: A 1937 GLN cc_start: 0.8517 (mm-40) cc_final: 0.8091 (mm-40) REVERT: A 1997 GLU cc_start: 0.8853 (mt-10) cc_final: 0.8469 (mt-10) REVERT: A 2286 VAL cc_start: 0.8568 (OUTLIER) cc_final: 0.8330 (t) REVERT: A 2290 GLN cc_start: 0.8734 (tt0) cc_final: 0.8363 (tt0) REVERT: A 2605 ARG cc_start: 0.8079 (mmm160) cc_final: 0.7614 (mmt-90) REVERT: A 2630 PHE cc_start: 0.8378 (m-10) cc_final: 0.8113 (m-10) REVERT: A 2646 LEU cc_start: 0.9280 (mt) cc_final: 0.9023 (mm) REVERT: B 101 GLN cc_start: 0.8060 (pp30) cc_final: 0.7806 (pp30) REVERT: B 165 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8412 (mt-10) REVERT: B 203 MET cc_start: 0.7693 (mmm) cc_final: 0.7341 (mmm) REVERT: B 460 PHE cc_start: 0.8869 (m-10) cc_final: 0.8385 (m-10) REVERT: B 469 GLN cc_start: 0.8448 (mt0) cc_final: 0.8226 (mp10) REVERT: B 582 GLN cc_start: 0.8783 (tt0) cc_final: 0.8581 (tt0) REVERT: B 739 LEU cc_start: 0.9010 (mt) cc_final: 0.8752 (mt) REVERT: B 787 ARG cc_start: 0.7464 (mmp-170) cc_final: 0.7237 (tpm170) REVERT: B 886 PHE cc_start: 0.6515 (m-80) cc_final: 0.6214 (m-80) REVERT: B 1219 PHE cc_start: 0.8565 (m-80) cc_final: 0.8318 (m-80) REVERT: B 1282 GLN cc_start: 0.8883 (mm-40) cc_final: 0.8419 (mm110) REVERT: B 1320 PHE cc_start: 0.8642 (m-10) cc_final: 0.8138 (m-10) REVERT: B 1323 ASP cc_start: 0.8331 (m-30) cc_final: 0.8037 (m-30) REVERT: B 1567 MET cc_start: 0.7761 (ttm) cc_final: 0.7502 (ttm) REVERT: B 1606 ASP cc_start: 0.8028 (t70) cc_final: 0.7480 (t0) REVERT: B 1609 GLU cc_start: 0.8920 (tt0) cc_final: 0.8457 (pp20) REVERT: B 1700 MET cc_start: 0.7566 (pmm) cc_final: 0.7349 (pmm) REVERT: B 1752 LEU cc_start: 0.8763 (mt) cc_final: 0.8561 (mt) REVERT: B 1887 GLN cc_start: 0.8340 (mm-40) cc_final: 0.8045 (tp40) REVERT: B 1908 GLU cc_start: 0.8634 (pt0) cc_final: 0.8393 (pt0) REVERT: B 1930 ASP cc_start: 0.8304 (m-30) cc_final: 0.7666 (t0) REVERT: B 1937 GLN cc_start: 0.8661 (mm-40) cc_final: 0.8429 (mm-40) REVERT: B 2286 VAL cc_start: 0.8660 (OUTLIER) cc_final: 0.8453 (t) REVERT: B 2290 GLN cc_start: 0.8758 (tt0) cc_final: 0.8165 (tt0) REVERT: B 2595 ASP cc_start: 0.8366 (t0) cc_final: 0.8109 (t0) REVERT: B 2605 ARG cc_start: 0.8062 (mmm160) cc_final: 0.7703 (tpp-160) REVERT: B 2629 GLN cc_start: 0.8545 (pt0) cc_final: 0.8320 (mt0) REVERT: B 2646 LEU cc_start: 0.9337 (mt) cc_final: 0.8935 (mm) outliers start: 6 outliers final: 0 residues processed: 747 average time/residue: 0.2837 time to fit residues: 331.9162 Evaluate side-chains 378 residues out of total 4364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 376 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2286 VAL Chi-restraints excluded: chain B residue 2286 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 432 optimal weight: 5.9990 chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 8.9990 chunk 455 optimal weight: 0.0980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 494 optimal weight: 0.8980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.5980 chunk 207 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 GLN A 370 GLN A 468 GLN A 892 HIS A 967 ASN A1207 GLN A1244 GLN A1288 GLN A1332 GLN A1348 ASN ** A1509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1526 ASN A1721 HIS A1741 GLN ** A1787 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1971 GLN A2016 GLN A2266 GLN A2456 GLN A2657 GLN A2669 ASN B 331 GLN B 347 HIS B 468 GLN B 892 HIS B1244 GLN B1288 GLN B1295 HIS B1332 GLN ** B1509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1526 ASN B1528 GLN B1721 HIS B1741 GLN ** B1787 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1971 GLN B2016 GLN B2266 GLN ** B2629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2657 GLN B2669 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.140967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.110729 restraints weight = 96908.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.113872 restraints weight = 49062.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.115885 restraints weight = 27872.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.116022 restraints weight = 25783.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.115950 restraints weight = 20914.194| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 40962 Z= 0.146 Angle : 0.766 14.265 55724 Z= 0.392 Chirality : 0.045 0.361 6104 Planarity : 0.007 0.055 7290 Dihedral : 7.960 70.489 6244 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.05 % Favored : 88.91 % Rotamer: Outliers : 1.96 % Allowed : 8.60 % Favored : 89.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.11 % 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: -3.99 (0.10), residues: 5058 helix: -2.78 (0.11), residues: 1190 sheet: -2.52 (0.19), residues: 600 loop : -2.76 (0.10), residues: 3268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 492 TYR 0.042 0.002 TYR B1819 PHE 0.021 0.001 PHE B1723 TRP 0.028 0.002 TRP A2501 HIS 0.006 0.001 HIS B1721 Details of bonding type rmsd covalent geometry : bond 0.00325 (40806) covalent geometry : angle 0.75174 (55376) SS BOND : bond 0.00419 ( 120) SS BOND : angle 1.63488 ( 240) hydrogen bonds : bond 0.05227 ( 916) hydrogen bonds : angle 6.61775 ( 2472) link_BETA1-4 : bond 0.00570 ( 4) link_BETA1-4 : angle 2.59496 ( 12) link_NAG-ASN : bond 0.00341 ( 32) link_NAG-ASN : angle 2.67943 ( 96) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10116 Ramachandran restraints generated. 5058 Oldfield, 0 Emsley, 5058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10116 Ramachandran restraints generated. 5058 Oldfield, 0 Emsley, 5058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 4364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 443 time to evaluate : 1.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ILE cc_start: 0.9115 (mm) cc_final: 0.8843 (mm) REVERT: A 226 ARG cc_start: 0.8453 (ptm-80) cc_final: 0.7978 (ptp90) REVERT: A 367 GLU cc_start: 0.8341 (tm-30) cc_final: 0.8137 (tm-30) REVERT: A 582 GLN cc_start: 0.8827 (tt0) cc_final: 0.8612 (tt0) REVERT: A 673 MET cc_start: 0.9125 (tpp) cc_final: 0.8801 (tpt) REVERT: A 779 GLU cc_start: 0.7392 (mt-10) cc_final: 0.5713 (tm-30) REVERT: A 1254 TRP cc_start: 0.8028 (m100) cc_final: 0.7706 (m100) REVERT: A 1369 LYS cc_start: 0.9060 (ptmt) cc_final: 0.8800 (tttp) REVERT: A 1528 GLN cc_start: 0.9017 (tm-30) cc_final: 0.8775 (tm-30) REVERT: A 1570 LYS cc_start: 0.9300 (ttpt) cc_final: 0.8987 (ptpp) REVERT: A 1606 ASP cc_start: 0.7706 (t70) cc_final: 0.7279 (t0) REVERT: A 1609 GLU cc_start: 0.8988 (tt0) cc_final: 0.8315 (pp20) REVERT: A 1752 LEU cc_start: 0.8530 (mt) cc_final: 0.7742 (mt) REVERT: A 1876 LYS cc_start: 0.8777 (mttt) cc_final: 0.8486 (mtpp) REVERT: A 1887 GLN cc_start: 0.7950 (mm-40) cc_final: 0.7578 (tp40) REVERT: A 1930 ASP cc_start: 0.8093 (m-30) cc_final: 0.7623 (t0) REVERT: A 1932 MET cc_start: 0.8663 (mtm) cc_final: 0.8439 (mtm) REVERT: A 1937 GLN cc_start: 0.8369 (mm-40) cc_final: 0.8104 (mm-40) REVERT: A 1960 LYS cc_start: 0.8148 (tmtt) cc_final: 0.7842 (tptt) REVERT: A 2540 TYR cc_start: 0.7211 (m-10) cc_final: 0.6574 (m-10) REVERT: A 2605 ARG cc_start: 0.7968 (mmm160) cc_final: 0.7588 (mmt-90) REVERT: A 2630 PHE cc_start: 0.8395 (m-10) cc_final: 0.8126 (m-10) REVERT: A 2647 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7418 (mm-30) REVERT: A 2702 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7412 (mp0) REVERT: B 203 MET cc_start: 0.7799 (mmm) cc_final: 0.7434 (mmm) REVERT: B 460 PHE cc_start: 0.8750 (m-10) cc_final: 0.8469 (m-80) REVERT: B 582 GLN cc_start: 0.8728 (tt0) cc_final: 0.8528 (tt0) REVERT: B 886 PHE cc_start: 0.6590 (m-80) cc_final: 0.6263 (m-80) REVERT: B 985 GLN cc_start: 0.8482 (pp30) cc_final: 0.7695 (pp30) REVERT: B 1513 ASP cc_start: 0.8288 (p0) cc_final: 0.7829 (t0) REVERT: B 1606 ASP cc_start: 0.7941 (t70) cc_final: 0.7539 (t0) REVERT: B 1609 GLU cc_start: 0.8985 (tt0) cc_final: 0.8564 (pp20) REVERT: B 1752 LEU cc_start: 0.8734 (mt) cc_final: 0.7949 (mt) REVERT: B 1797 GLU cc_start: 0.8904 (mm-30) cc_final: 0.8685 (mm-30) REVERT: B 1887 GLN cc_start: 0.8128 (mm-40) cc_final: 0.7752 (tp40) REVERT: B 1930 ASP cc_start: 0.8147 (m-30) cc_final: 0.7605 (t0) REVERT: B 1960 LYS cc_start: 0.8193 (tmtt) cc_final: 0.7876 (tptt) REVERT: B 1965 TYR cc_start: 0.8728 (m-80) cc_final: 0.8271 (m-80) REVERT: B 2028 ASN cc_start: 0.8707 (t0) cc_final: 0.8485 (t0) REVERT: B 2241 ARG cc_start: 0.8084 (mtm-85) cc_final: 0.7664 (ttm110) REVERT: B 2290 GLN cc_start: 0.8771 (tt0) cc_final: 0.8457 (tt0) REVERT: B 2605 ARG cc_start: 0.7921 (mmm160) cc_final: 0.7644 (tpp-160) REVERT: B 2629 GLN cc_start: 0.8665 (pt0) cc_final: 0.8414 (mt0) outliers start: 85 outliers final: 32 residues processed: 506 average time/residue: 0.2443 time to fit residues: 204.3569 Evaluate side-chains 362 residues out of total 4364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 329 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 703 CYS Chi-restraints excluded: chain A residue 741 THR Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 1059 ILE Chi-restraints excluded: chain A residue 1181 CYS Chi-restraints excluded: chain A residue 1348 ASN Chi-restraints excluded: chain A residue 2286 VAL Chi-restraints excluded: chain A residue 2367 GLN Chi-restraints excluded: chain A residue 2423 VAL Chi-restraints excluded: chain A residue 2702 GLU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 703 CYS Chi-restraints excluded: chain B residue 741 THR Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1181 CYS Chi-restraints excluded: chain B residue 1687 THR Chi-restraints excluded: chain B residue 1876 LYS Chi-restraints excluded: chain B residue 2056 HIS Chi-restraints excluded: chain B residue 2144 THR Chi-restraints excluded: chain B residue 2286 VAL Chi-restraints excluded: chain B residue 2367 GLN Chi-restraints excluded: chain B residue 2423 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 292 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 431 optimal weight: 0.8980 chunk 92 optimal weight: 0.8980 chunk 183 optimal weight: 0.6980 chunk 360 optimal weight: 0.6980 chunk 259 optimal weight: 2.9990 chunk 263 optimal weight: 7.9990 chunk 184 optimal weight: 4.9990 chunk 444 optimal weight: 5.9990 chunk 3 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 GLN A 347 HIS A 985 GLN A1207 GLN A1295 HIS ** A1509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1721 HIS A1963 ASN A2426 HIS ** A2463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 469 GLN B 967 ASN B1207 GLN B1295 HIS ** B1509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1706 ASN ** B2466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.140657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.109850 restraints weight = 96693.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.114082 restraints weight = 48685.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.114442 restraints weight = 27125.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.114947 restraints weight = 22942.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.115341 restraints weight = 21843.468| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 40962 Z= 0.140 Angle : 0.725 13.519 55724 Z= 0.369 Chirality : 0.044 0.323 6104 Planarity : 0.006 0.052 7290 Dihedral : 7.084 57.914 6244 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.99 % Favored : 88.97 % Rotamer: Outliers : 2.26 % Allowed : 10.17 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.04 % 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: -3.42 (0.11), residues: 5058 helix: -1.90 (0.13), residues: 1194 sheet: -2.26 (0.19), residues: 606 loop : -2.55 (0.10), residues: 3258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A1202 TYR 0.034 0.002 TYR B1819 PHE 0.022 0.001 PHE A 976 TRP 0.037 0.002 TRP B1254 HIS 0.005 0.001 HIS A1721 Details of bonding type rmsd covalent geometry : bond 0.00313 (40806) covalent geometry : angle 0.70784 (55376) SS BOND : bond 0.00367 ( 120) SS BOND : angle 2.03358 ( 240) hydrogen bonds : bond 0.03735 ( 916) hydrogen bonds : angle 5.88781 ( 2472) link_BETA1-4 : bond 0.00877 ( 4) link_BETA1-4 : angle 2.44485 ( 12) link_NAG-ASN : bond 0.00252 ( 32) link_NAG-ASN : angle 2.28830 ( 96) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10116 Ramachandran restraints generated. 5058 Oldfield, 0 Emsley, 5058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10116 Ramachandran restraints generated. 5058 Oldfield, 0 Emsley, 5058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 4364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 397 time to evaluate : 1.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ILE cc_start: 0.9089 (mm) cc_final: 0.8847 (mm) REVERT: A 226 ARG cc_start: 0.8424 (ptm-80) cc_final: 0.7981 (ptp90) REVERT: A 367 GLU cc_start: 0.8302 (tm-30) cc_final: 0.8062 (tm-30) REVERT: A 582 GLN cc_start: 0.8728 (tt0) cc_final: 0.8514 (tt0) REVERT: A 589 GLU cc_start: 0.8276 (tp30) cc_final: 0.7997 (tp30) REVERT: A 1202 ARG cc_start: 0.8572 (mpp-170) cc_final: 0.7750 (mpp-170) REVERT: A 1320 PHE cc_start: 0.8592 (m-80) cc_final: 0.7465 (m-80) REVERT: A 1323 ASP cc_start: 0.8494 (m-30) cc_final: 0.8249 (m-30) REVERT: A 1369 LYS cc_start: 0.9114 (ptmt) cc_final: 0.8808 (tttp) REVERT: A 1513 ASP cc_start: 0.7856 (p0) cc_final: 0.7369 (t0) REVERT: A 1528 GLN cc_start: 0.8989 (tm-30) cc_final: 0.8771 (tm-30) REVERT: A 1570 LYS cc_start: 0.9246 (ttpt) cc_final: 0.8918 (mttm) REVERT: A 1606 ASP cc_start: 0.7635 (t70) cc_final: 0.7151 (t0) REVERT: A 1609 GLU cc_start: 0.9021 (tt0) cc_final: 0.8347 (pp20) REVERT: A 1752 LEU cc_start: 0.8501 (mt) cc_final: 0.7624 (mt) REVERT: A 1822 LYS cc_start: 0.7327 (tmtt) cc_final: 0.7118 (tmmt) REVERT: A 1887 GLN cc_start: 0.7963 (mm-40) cc_final: 0.7599 (tp40) REVERT: A 1930 ASP cc_start: 0.7995 (m-30) cc_final: 0.7692 (t0) REVERT: A 1960 LYS cc_start: 0.8217 (tmtt) cc_final: 0.7875 (tptt) REVERT: A 2423 VAL cc_start: 0.8334 (OUTLIER) cc_final: 0.8081 (m) REVERT: A 2540 TYR cc_start: 0.7198 (m-10) cc_final: 0.6726 (m-10) REVERT: A 2605 ARG cc_start: 0.7931 (mmm160) cc_final: 0.7526 (mmt-90) REVERT: A 2630 PHE cc_start: 0.8334 (m-10) cc_final: 0.8025 (m-10) REVERT: A 2647 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7466 (mm-30) REVERT: A 2702 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7380 (mp0) REVERT: B 81 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.8017 (mm) REVERT: B 101 GLN cc_start: 0.8451 (mt0) cc_final: 0.8139 (mm-40) REVERT: B 188 GLU cc_start: 0.8282 (pm20) cc_final: 0.7778 (pm20) REVERT: B 203 MET cc_start: 0.7811 (mmm) cc_final: 0.7439 (mmm) REVERT: B 226 ARG cc_start: 0.8294 (ptm-80) cc_final: 0.7869 (ptp90) REVERT: B 460 PHE cc_start: 0.8770 (m-10) cc_final: 0.8521 (m-80) REVERT: B 469 GLN cc_start: 0.8540 (mt0) cc_final: 0.8059 (pm20) REVERT: B 582 GLN cc_start: 0.8711 (tt0) cc_final: 0.8449 (tt0) REVERT: B 886 PHE cc_start: 0.6584 (m-80) cc_final: 0.6241 (m-80) REVERT: B 985 GLN cc_start: 0.8412 (pp30) cc_final: 0.7635 (pp30) REVERT: B 1305 MET cc_start: 0.3246 (ttp) cc_final: 0.2906 (ttp) REVERT: B 1323 ASP cc_start: 0.8728 (m-30) cc_final: 0.8400 (m-30) REVERT: B 1606 ASP cc_start: 0.7868 (t70) cc_final: 0.7263 (t0) REVERT: B 1609 GLU cc_start: 0.9049 (tt0) cc_final: 0.8580 (pp20) REVERT: B 1610 ASP cc_start: 0.7745 (t0) cc_final: 0.7452 (t70) REVERT: B 1752 LEU cc_start: 0.8659 (mt) cc_final: 0.7732 (mt) REVERT: B 1797 GLU cc_start: 0.8993 (mm-30) cc_final: 0.8750 (mm-30) REVERT: B 1960 LYS cc_start: 0.8245 (tmtt) cc_final: 0.7927 (tptt) REVERT: B 1965 TYR cc_start: 0.8637 (m-80) cc_final: 0.8190 (m-80) REVERT: B 2104 ASP cc_start: 0.8588 (t0) cc_final: 0.8293 (t0) REVERT: B 2290 GLN cc_start: 0.8730 (tt0) cc_final: 0.8293 (tt0) REVERT: B 2354 TRP cc_start: 0.7697 (m100) cc_final: 0.7261 (m100) REVERT: B 2423 VAL cc_start: 0.8270 (OUTLIER) cc_final: 0.8008 (m) REVERT: B 2540 TYR cc_start: 0.7142 (m-10) cc_final: 0.6533 (m-10) REVERT: B 2605 ARG cc_start: 0.7897 (mmm160) cc_final: 0.7626 (tpp-160) REVERT: B 2629 GLN cc_start: 0.8715 (pt0) cc_final: 0.8385 (mt0) REVERT: B 2646 LEU cc_start: 0.9310 (mm) cc_final: 0.8971 (tp) outliers start: 98 outliers final: 41 residues processed: 474 average time/residue: 0.2225 time to fit residues: 177.7156 Evaluate side-chains 375 residues out of total 4364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 330 time to evaluate : 1.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 703 CYS Chi-restraints excluded: chain A residue 726 CYS Chi-restraints excluded: chain A residue 741 THR Chi-restraints excluded: chain A residue 985 GLN Chi-restraints excluded: chain A residue 1059 ILE Chi-restraints excluded: chain A residue 1068 LEU Chi-restraints excluded: chain A residue 1181 CYS Chi-restraints excluded: chain A residue 1440 CYS Chi-restraints excluded: chain A residue 1567 MET Chi-restraints excluded: chain A residue 1664 VAL Chi-restraints excluded: chain A residue 1898 VAL Chi-restraints excluded: chain A residue 2034 MET Chi-restraints excluded: chain A residue 2201 VAL Chi-restraints excluded: chain A residue 2286 VAL Chi-restraints excluded: chain A residue 2423 VAL Chi-restraints excluded: chain A residue 2426 HIS Chi-restraints excluded: chain A residue 2702 GLU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 703 CYS Chi-restraints excluded: chain B residue 726 CYS Chi-restraints excluded: chain B residue 741 THR Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1181 CYS Chi-restraints excluded: chain B residue 1346 VAL Chi-restraints excluded: chain B residue 1664 VAL Chi-restraints excluded: chain B residue 1687 THR Chi-restraints excluded: chain B residue 2056 HIS Chi-restraints excluded: chain B residue 2201 VAL Chi-restraints excluded: chain B residue 2286 VAL Chi-restraints excluded: chain B residue 2304 ASN Chi-restraints excluded: chain B residue 2423 VAL Chi-restraints excluded: chain B residue 2625 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 305 optimal weight: 4.9990 chunk 277 optimal weight: 0.0980 chunk 21 optimal weight: 5.9990 chunk 447 optimal weight: 6.9990 chunk 111 optimal weight: 4.9990 chunk 53 optimal weight: 0.0370 chunk 475 optimal weight: 4.9990 chunk 340 optimal weight: 1.9990 chunk 361 optimal weight: 3.9990 chunk 30 optimal weight: 8.9990 chunk 393 optimal weight: 9.9990 overall best weight: 2.2264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 630 GLN A 878 GLN A 985 GLN A1207 GLN ** A1295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1569 GLN ** A2466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 GLN B 630 GLN B 878 GLN B1207 GLN B1295 HIS ** B1509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2426 HIS ** B2466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.135386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.104107 restraints weight = 96487.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.106811 restraints weight = 47513.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.108518 restraints weight = 30845.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.109512 restraints weight = 23656.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.110189 restraints weight = 20278.532| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.102 40962 Z= 0.244 Angle : 0.766 15.137 55724 Z= 0.388 Chirality : 0.046 0.325 6104 Planarity : 0.006 0.157 7290 Dihedral : 6.853 56.715 6244 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.29 % Favored : 88.67 % Rotamer: Outliers : 2.84 % Allowed : 11.11 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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: -3.12 (0.11), residues: 5058 helix: -1.38 (0.14), residues: 1214 sheet: -2.25 (0.19), residues: 610 loop : -2.44 (0.10), residues: 3234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 492 TYR 0.029 0.002 TYR B1819 PHE 0.025 0.002 PHE B 738 TRP 0.030 0.002 TRP B1254 HIS 0.021 0.001 HIS A2426 Details of bonding type rmsd covalent geometry : bond 0.00557 (40806) covalent geometry : angle 0.74999 (55376) SS BOND : bond 0.00462 ( 120) SS BOND : angle 1.99925 ( 240) hydrogen bonds : bond 0.03756 ( 916) hydrogen bonds : angle 5.81257 ( 2472) link_BETA1-4 : bond 0.00231 ( 4) link_BETA1-4 : angle 2.68624 ( 12) link_NAG-ASN : bond 0.00193 ( 32) link_NAG-ASN : angle 2.33543 ( 96) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10116 Ramachandran restraints generated. 5058 Oldfield, 0 Emsley, 5058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10116 Ramachandran restraints generated. 5058 Oldfield, 0 Emsley, 5058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 4364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 351 time to evaluate : 1.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ILE cc_start: 0.9170 (mm) cc_final: 0.8907 (mm) REVERT: A 226 ARG cc_start: 0.8566 (ptm-80) cc_final: 0.8142 (ptp90) REVERT: A 367 GLU cc_start: 0.8333 (tm-30) cc_final: 0.8050 (tm-30) REVERT: A 469 GLN cc_start: 0.8574 (mt0) cc_final: 0.8080 (pm20) REVERT: A 582 GLN cc_start: 0.8786 (tt0) cc_final: 0.8566 (tt0) REVERT: A 589 GLU cc_start: 0.8288 (tp30) cc_final: 0.8034 (tp30) REVERT: A 731 GLN cc_start: 0.8775 (mt0) cc_final: 0.8448 (mt0) REVERT: A 1202 ARG cc_start: 0.8607 (mpp-170) cc_final: 0.7873 (mpp-170) REVERT: A 1320 PHE cc_start: 0.8863 (m-80) cc_final: 0.7884 (m-80) REVERT: A 1369 LYS cc_start: 0.9119 (ptmt) cc_final: 0.8773 (tttp) REVERT: A 1533 GLN cc_start: 0.6783 (OUTLIER) cc_final: 0.5716 (tm-30) REVERT: A 1570 LYS cc_start: 0.9223 (ttpt) cc_final: 0.8934 (mttm) REVERT: A 1606 ASP cc_start: 0.7736 (t70) cc_final: 0.7276 (t0) REVERT: A 1609 GLU cc_start: 0.9066 (tt0) cc_final: 0.8373 (pp20) REVERT: A 1610 ASP cc_start: 0.7951 (t0) cc_final: 0.7630 (t0) REVERT: A 1752 LEU cc_start: 0.8534 (mt) cc_final: 0.8156 (mt) REVERT: A 1797 GLU cc_start: 0.8934 (mm-30) cc_final: 0.8720 (tp30) REVERT: A 1822 LYS cc_start: 0.7504 (tmtt) cc_final: 0.7195 (tmmt) REVERT: A 1887 GLN cc_start: 0.7988 (mm-40) cc_final: 0.7594 (tp40) REVERT: A 1930 ASP cc_start: 0.8172 (m-30) cc_final: 0.7818 (t0) REVERT: A 1960 LYS cc_start: 0.8346 (tmtt) cc_final: 0.8005 (tptt) REVERT: A 2354 TRP cc_start: 0.7949 (m100) cc_final: 0.7714 (m100) REVERT: A 2423 VAL cc_start: 0.8458 (OUTLIER) cc_final: 0.8209 (m) REVERT: A 2466 GLN cc_start: 0.6590 (mt0) cc_final: 0.6267 (mt0) REVERT: A 2540 TYR cc_start: 0.7452 (m-10) cc_final: 0.6962 (m-10) REVERT: A 2605 ARG cc_start: 0.7941 (mmm160) cc_final: 0.7596 (mmt-90) REVERT: A 2630 PHE cc_start: 0.8509 (m-10) cc_final: 0.8136 (m-10) REVERT: A 2647 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7578 (mm-30) REVERT: A 2702 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7489 (mp0) REVERT: B 81 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7999 (mm) REVERT: B 101 GLN cc_start: 0.8522 (mt0) cc_final: 0.8217 (mm-40) REVERT: B 226 ARG cc_start: 0.8341 (ptm-80) cc_final: 0.7963 (ptp90) REVERT: B 460 PHE cc_start: 0.8860 (m-10) cc_final: 0.8603 (m-80) REVERT: B 469 GLN cc_start: 0.8307 (mt0) cc_final: 0.7704 (mp10) REVERT: B 582 GLN cc_start: 0.8745 (tt0) cc_final: 0.8481 (tt0) REVERT: B 731 GLN cc_start: 0.8852 (mt0) cc_final: 0.8348 (mt0) REVERT: B 886 PHE cc_start: 0.6698 (m-80) cc_final: 0.6313 (m-80) REVERT: B 1305 MET cc_start: 0.3650 (OUTLIER) cc_final: 0.3297 (ttp) REVERT: B 1319 VAL cc_start: 0.7900 (OUTLIER) cc_final: 0.7570 (p) REVERT: B 1323 ASP cc_start: 0.8839 (m-30) cc_final: 0.8460 (m-30) REVERT: B 1568 MET cc_start: 0.7779 (tpt) cc_final: 0.7563 (tpt) REVERT: B 1606 ASP cc_start: 0.7914 (t70) cc_final: 0.7322 (t0) REVERT: B 1609 GLU cc_start: 0.9042 (tt0) cc_final: 0.8563 (pp20) REVERT: B 1610 ASP cc_start: 0.7947 (t0) cc_final: 0.7611 (t70) REVERT: B 1752 LEU cc_start: 0.8647 (mt) cc_final: 0.7954 (mt) REVERT: B 1797 GLU cc_start: 0.8976 (mm-30) cc_final: 0.8752 (mm-30) REVERT: B 1887 GLN cc_start: 0.8170 (mm-40) cc_final: 0.7902 (tp40) REVERT: B 1908 GLU cc_start: 0.8387 (pt0) cc_final: 0.8173 (pt0) REVERT: B 1960 LYS cc_start: 0.8373 (tmtt) cc_final: 0.8061 (tptt) REVERT: B 1965 TYR cc_start: 0.8760 (m-80) cc_final: 0.8427 (m-80) REVERT: B 2354 TRP cc_start: 0.7943 (m100) cc_final: 0.7616 (m100) REVERT: B 2423 VAL cc_start: 0.8449 (OUTLIER) cc_final: 0.8202 (m) REVERT: B 2540 TYR cc_start: 0.7440 (m-10) cc_final: 0.6922 (m-10) REVERT: B 2605 ARG cc_start: 0.7993 (mmm160) cc_final: 0.7575 (mmt-90) REVERT: B 2646 LEU cc_start: 0.9429 (mm) cc_final: 0.9115 (tp) outliers start: 123 outliers final: 74 residues processed: 443 average time/residue: 0.2329 time to fit residues: 172.9005 Evaluate side-chains 399 residues out of total 4364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 318 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 703 CYS Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 726 CYS Chi-restraints excluded: chain A residue 741 THR Chi-restraints excluded: chain A residue 985 GLN Chi-restraints excluded: chain A residue 1059 ILE Chi-restraints excluded: chain A residue 1068 LEU Chi-restraints excluded: chain A residue 1111 THR Chi-restraints excluded: chain A residue 1148 LEU Chi-restraints excluded: chain A residue 1152 LEU Chi-restraints excluded: chain A residue 1181 CYS Chi-restraints excluded: chain A residue 1319 VAL Chi-restraints excluded: chain A residue 1440 CYS Chi-restraints excluded: chain A residue 1533 GLN Chi-restraints excluded: chain A residue 1567 MET Chi-restraints excluded: chain A residue 1664 VAL Chi-restraints excluded: chain A residue 1687 THR Chi-restraints excluded: chain A residue 1724 CYS Chi-restraints excluded: chain A residue 1894 LEU Chi-restraints excluded: chain A residue 1898 VAL Chi-restraints excluded: chain A residue 1966 THR Chi-restraints excluded: chain A residue 1982 VAL Chi-restraints excluded: chain A residue 2023 THR Chi-restraints excluded: chain A residue 2034 MET Chi-restraints excluded: chain A residue 2201 VAL Chi-restraints excluded: chain A residue 2238 LEU Chi-restraints excluded: chain A residue 2286 VAL Chi-restraints excluded: chain A residue 2380 VAL Chi-restraints excluded: chain A residue 2391 VAL Chi-restraints excluded: chain A residue 2423 VAL Chi-restraints excluded: chain A residue 2426 HIS Chi-restraints excluded: chain A residue 2482 VAL Chi-restraints excluded: chain A residue 2702 GLU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 622 THR Chi-restraints excluded: chain B residue 703 CYS Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 726 CYS Chi-restraints excluded: chain B residue 741 THR Chi-restraints excluded: chain B residue 1157 LEU Chi-restraints excluded: chain B residue 1181 CYS Chi-restraints excluded: chain B residue 1305 MET Chi-restraints excluded: chain B residue 1319 VAL Chi-restraints excluded: chain B residue 1346 VAL Chi-restraints excluded: chain B residue 1440 CYS Chi-restraints excluded: chain B residue 1664 VAL Chi-restraints excluded: chain B residue 1687 THR Chi-restraints excluded: chain B residue 1876 LYS Chi-restraints excluded: chain B residue 1898 VAL Chi-restraints excluded: chain B residue 1957 LEU Chi-restraints excluded: chain B residue 1966 THR Chi-restraints excluded: chain B residue 1982 VAL Chi-restraints excluded: chain B residue 2201 VAL Chi-restraints excluded: chain B residue 2286 VAL Chi-restraints excluded: chain B residue 2304 ASN Chi-restraints excluded: chain B residue 2357 LEU Chi-restraints excluded: chain B residue 2380 VAL Chi-restraints excluded: chain B residue 2391 VAL Chi-restraints excluded: chain B residue 2423 VAL Chi-restraints excluded: chain B residue 2426 HIS Chi-restraints excluded: chain B residue 2507 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 219 optimal weight: 0.9980 chunk 131 optimal weight: 3.9990 chunk 288 optimal weight: 4.9990 chunk 300 optimal weight: 6.9990 chunk 420 optimal weight: 5.9990 chunk 88 optimal weight: 0.6980 chunk 211 optimal weight: 0.4980 chunk 405 optimal weight: 0.0470 chunk 41 optimal weight: 1.9990 chunk 385 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN A 469 GLN A 985 GLN A1348 ASN ** A1509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2426 HIS ** A2466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2629 GLN B 583 HIS B 985 GLN B1288 GLN ** B1509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1963 ASN ** B2466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2619 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.138099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.107119 restraints weight = 96099.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.109890 restraints weight = 46563.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.111657 restraints weight = 30056.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.112754 restraints weight = 22880.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.113413 restraints weight = 19407.537| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.108 40962 Z= 0.125 Angle : 0.696 15.885 55724 Z= 0.350 Chirality : 0.044 0.313 6104 Planarity : 0.005 0.065 7290 Dihedral : 6.427 57.407 6244 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.22 % Favored : 89.74 % Rotamer: Outliers : 2.45 % Allowed : 12.18 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.86 (0.11), residues: 5058 helix: -0.95 (0.14), residues: 1214 sheet: -2.00 (0.20), residues: 596 loop : -2.38 (0.10), residues: 3248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A1170 TYR 0.025 0.001 TYR A1445 PHE 0.027 0.001 PHE B 738 TRP 0.023 0.001 TRP B2501 HIS 0.021 0.001 HIS B2426 Details of bonding type rmsd covalent geometry : bond 0.00284 (40806) covalent geometry : angle 0.68044 (55376) SS BOND : bond 0.00367 ( 120) SS BOND : angle 1.88172 ( 240) hydrogen bonds : bond 0.03121 ( 916) hydrogen bonds : angle 5.54077 ( 2472) link_BETA1-4 : bond 0.00260 ( 4) link_BETA1-4 : angle 2.34096 ( 12) link_NAG-ASN : bond 0.00268 ( 32) link_NAG-ASN : angle 2.17252 ( 96) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10116 Ramachandran restraints generated. 5058 Oldfield, 0 Emsley, 5058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10116 Ramachandran restraints generated. 5058 Oldfield, 0 Emsley, 5058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 4364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 366 time to evaluate : 1.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8063 (mm) REVERT: A 204 ILE cc_start: 0.9078 (mm) cc_final: 0.8787 (mm) REVERT: A 226 ARG cc_start: 0.8524 (ptm-80) cc_final: 0.8156 (ptp90) REVERT: A 469 GLN cc_start: 0.8593 (mt0) cc_final: 0.8054 (mp10) REVERT: A 582 GLN cc_start: 0.8724 (tt0) cc_final: 0.8509 (tt0) REVERT: A 1152 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8662 (tp) REVERT: A 1202 ARG cc_start: 0.8640 (mpp-170) cc_final: 0.7990 (mpp-170) REVERT: A 1320 PHE cc_start: 0.8860 (m-80) cc_final: 0.7863 (m-80) REVERT: A 1323 ASP cc_start: 0.8758 (m-30) cc_final: 0.8267 (m-30) REVERT: A 1369 LYS cc_start: 0.9112 (ptmt) cc_final: 0.8760 (tttp) REVERT: A 1533 GLN cc_start: 0.6374 (OUTLIER) cc_final: 0.5923 (tm-30) REVERT: A 1570 LYS cc_start: 0.9298 (ttpt) cc_final: 0.9011 (mttt) REVERT: A 1610 ASP cc_start: 0.8060 (t0) cc_final: 0.7761 (t0) REVERT: A 1887 GLN cc_start: 0.7951 (mm-40) cc_final: 0.7567 (tp40) REVERT: A 1930 ASP cc_start: 0.8066 (m-30) cc_final: 0.7849 (t0) REVERT: A 1960 LYS cc_start: 0.8313 (tmtt) cc_final: 0.7972 (tptt) REVERT: A 2423 VAL cc_start: 0.8384 (OUTLIER) cc_final: 0.8153 (m) REVERT: A 2540 TYR cc_start: 0.7201 (m-10) cc_final: 0.6840 (m-10) REVERT: A 2605 ARG cc_start: 0.7831 (mmm160) cc_final: 0.7488 (mmt-90) REVERT: A 2630 PHE cc_start: 0.8477 (m-10) cc_final: 0.8172 (m-10) REVERT: B 81 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7990 (mm) REVERT: B 101 GLN cc_start: 0.8470 (mt0) cc_final: 0.8240 (mm-40) REVERT: B 226 ARG cc_start: 0.8317 (ptm-80) cc_final: 0.7961 (ptp90) REVERT: B 460 PHE cc_start: 0.8829 (m-10) cc_final: 0.8586 (m-80) REVERT: B 469 GLN cc_start: 0.8282 (mt0) cc_final: 0.7813 (mp10) REVERT: B 492 ARG cc_start: 0.6305 (mtm110) cc_final: 0.6097 (mtm110) REVERT: B 582 GLN cc_start: 0.8672 (tt0) cc_final: 0.8417 (tt0) REVERT: B 731 GLN cc_start: 0.8817 (mt0) cc_final: 0.8330 (mt0) REVERT: B 886 PHE cc_start: 0.6637 (m-80) cc_final: 0.6279 (m-80) REVERT: B 1111 THR cc_start: 0.8219 (OUTLIER) cc_final: 0.7928 (p) REVERT: B 1319 VAL cc_start: 0.7920 (OUTLIER) cc_final: 0.7603 (p) REVERT: B 1323 ASP cc_start: 0.8838 (m-30) cc_final: 0.8468 (m-30) REVERT: B 1568 MET cc_start: 0.7720 (tpt) cc_final: 0.7508 (tpt) REVERT: B 1570 LYS cc_start: 0.9390 (ttpt) cc_final: 0.9189 (mttm) REVERT: B 1606 ASP cc_start: 0.7975 (t70) cc_final: 0.7410 (t0) REVERT: B 1609 GLU cc_start: 0.9143 (tt0) cc_final: 0.8614 (pp20) REVERT: B 1610 ASP cc_start: 0.8089 (t0) cc_final: 0.7750 (t70) REVERT: B 1908 GLU cc_start: 0.8419 (pt0) cc_final: 0.8184 (pt0) REVERT: B 1960 LYS cc_start: 0.8346 (tmtt) cc_final: 0.7943 (tptt) REVERT: B 1965 TYR cc_start: 0.8430 (m-80) cc_final: 0.8115 (m-80) REVERT: B 2354 TRP cc_start: 0.7829 (m100) cc_final: 0.7545 (m100) REVERT: B 2423 VAL cc_start: 0.8332 (OUTLIER) cc_final: 0.8102 (m) REVERT: B 2540 TYR cc_start: 0.7255 (m-10) cc_final: 0.6852 (m-10) REVERT: B 2605 ARG cc_start: 0.7843 (mmm160) cc_final: 0.7427 (mmt-90) REVERT: B 2646 LEU cc_start: 0.9383 (mm) cc_final: 0.9057 (tp) outliers start: 106 outliers final: 59 residues processed: 454 average time/residue: 0.2406 time to fit residues: 183.8999 Evaluate side-chains 389 residues out of total 4364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 322 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 703 CYS Chi-restraints excluded: chain A residue 726 CYS Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 1059 ILE Chi-restraints excluded: chain A residue 1068 LEU Chi-restraints excluded: chain A residue 1148 LEU Chi-restraints excluded: chain A residue 1152 LEU Chi-restraints excluded: chain A residue 1181 CYS Chi-restraints excluded: chain A residue 1348 ASN Chi-restraints excluded: chain A residue 1440 CYS Chi-restraints excluded: chain A residue 1533 GLN Chi-restraints excluded: chain A residue 1567 MET Chi-restraints excluded: chain A residue 1664 VAL Chi-restraints excluded: chain A residue 1687 THR Chi-restraints excluded: chain A residue 1894 LEU Chi-restraints excluded: chain A residue 1898 VAL Chi-restraints excluded: chain A residue 1982 VAL Chi-restraints excluded: chain A residue 2238 LEU Chi-restraints excluded: chain A residue 2286 VAL Chi-restraints excluded: chain A residue 2380 VAL Chi-restraints excluded: chain A residue 2423 VAL Chi-restraints excluded: chain A residue 2426 HIS Chi-restraints excluded: chain A residue 2702 GLU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 622 THR Chi-restraints excluded: chain B residue 703 CYS Chi-restraints excluded: chain B residue 726 CYS Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 1111 THR Chi-restraints excluded: chain B residue 1181 CYS Chi-restraints excluded: chain B residue 1319 VAL Chi-restraints excluded: chain B residue 1346 VAL Chi-restraints excluded: chain B residue 1440 CYS Chi-restraints excluded: chain B residue 1664 VAL Chi-restraints excluded: chain B residue 1687 THR Chi-restraints excluded: chain B residue 1864 VAL Chi-restraints excluded: chain B residue 1898 VAL Chi-restraints excluded: chain B residue 1957 LEU Chi-restraints excluded: chain B residue 1982 VAL Chi-restraints excluded: chain B residue 1985 SER Chi-restraints excluded: chain B residue 2056 HIS Chi-restraints excluded: chain B residue 2079 VAL Chi-restraints excluded: chain B residue 2091 ASP Chi-restraints excluded: chain B residue 2286 VAL Chi-restraints excluded: chain B residue 2304 ASN Chi-restraints excluded: chain B residue 2380 VAL Chi-restraints excluded: chain B residue 2423 VAL Chi-restraints excluded: chain B residue 2426 HIS Chi-restraints excluded: chain B residue 2625 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 487 optimal weight: 6.9990 chunk 501 optimal weight: 1.9990 chunk 369 optimal weight: 0.4980 chunk 252 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 332 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 153 optimal weight: 4.9990 chunk 447 optimal weight: 3.9990 chunk 328 optimal weight: 10.0000 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 985 GLN A1207 GLN ** A1509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1528 GLN A1706 ASN A1870 GLN A2426 HIS ** A2466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 GLN B1180 GLN B1288 GLN ** B1509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1528 GLN B2426 HIS ** B2466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.136025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.104730 restraints weight = 97126.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.108203 restraints weight = 50914.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.109759 restraints weight = 28575.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.109683 restraints weight = 24226.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.109966 restraints weight = 23293.878| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 40962 Z= 0.195 Angle : 0.728 18.264 55724 Z= 0.365 Chirality : 0.045 0.335 6104 Planarity : 0.005 0.056 7290 Dihedral : 6.358 56.493 6244 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.05 % Favored : 88.91 % Rotamer: Outliers : 2.59 % Allowed : 13.22 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % 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: -2.74 (0.11), residues: 5058 helix: -0.78 (0.14), residues: 1234 sheet: -2.05 (0.20), residues: 606 loop : -2.31 (0.11), residues: 3218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 492 TYR 0.026 0.002 TYR A1965 PHE 0.029 0.002 PHE B 738 TRP 0.024 0.002 TRP B2501 HIS 0.006 0.001 HIS B2477 Details of bonding type rmsd covalent geometry : bond 0.00448 (40806) covalent geometry : angle 0.71068 (55376) SS BOND : bond 0.00434 ( 120) SS BOND : angle 2.03133 ( 240) hydrogen bonds : bond 0.03256 ( 916) hydrogen bonds : angle 5.49622 ( 2472) link_BETA1-4 : bond 0.00326 ( 4) link_BETA1-4 : angle 2.41133 ( 12) link_NAG-ASN : bond 0.00279 ( 32) link_NAG-ASN : angle 2.26030 ( 96) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10116 Ramachandran restraints generated. 5058 Oldfield, 0 Emsley, 5058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10116 Ramachandran restraints generated. 5058 Oldfield, 0 Emsley, 5058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 4364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 337 time to evaluate : 1.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8084 (mm) REVERT: A 204 ILE cc_start: 0.9151 (mm) cc_final: 0.8882 (mm) REVERT: A 226 ARG cc_start: 0.8548 (ptm-80) cc_final: 0.8211 (ptp90) REVERT: A 469 GLN cc_start: 0.8630 (mt0) cc_final: 0.8064 (mp10) REVERT: A 582 GLN cc_start: 0.8712 (tt0) cc_final: 0.8482 (tt0) REVERT: A 589 GLU cc_start: 0.8323 (tp30) cc_final: 0.8089 (tp30) REVERT: A 886 PHE cc_start: 0.6622 (m-80) cc_final: 0.6343 (m-80) REVERT: A 1152 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8666 (tp) REVERT: A 1202 ARG cc_start: 0.8680 (mpp-170) cc_final: 0.8076 (mpp-170) REVERT: A 1320 PHE cc_start: 0.9082 (m-80) cc_final: 0.8143 (m-80) REVERT: A 1323 ASP cc_start: 0.8820 (m-30) cc_final: 0.8294 (m-30) REVERT: A 1533 GLN cc_start: 0.6396 (OUTLIER) cc_final: 0.5921 (tm-30) REVERT: A 1570 LYS cc_start: 0.9299 (ttpt) cc_final: 0.9012 (mttt) REVERT: A 1610 ASP cc_start: 0.8076 (t0) cc_final: 0.7708 (t0) REVERT: A 1819 TYR cc_start: 0.6785 (OUTLIER) cc_final: 0.5898 (t80) REVERT: A 1887 GLN cc_start: 0.7938 (mm-40) cc_final: 0.7587 (tp40) REVERT: A 1930 ASP cc_start: 0.8135 (m-30) cc_final: 0.7919 (t0) REVERT: A 1960 LYS cc_start: 0.8407 (tmtt) cc_final: 0.8062 (tptt) REVERT: A 2423 VAL cc_start: 0.8487 (OUTLIER) cc_final: 0.8245 (m) REVERT: A 2540 TYR cc_start: 0.7254 (m-10) cc_final: 0.6847 (m-10) REVERT: A 2605 ARG cc_start: 0.7867 (mmm160) cc_final: 0.7612 (mmt-90) REVERT: B 81 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.8039 (mm) REVERT: B 101 GLN cc_start: 0.8502 (mt0) cc_final: 0.8206 (mm-40) REVERT: B 226 ARG cc_start: 0.8329 (ptm-80) cc_final: 0.8006 (ptp90) REVERT: B 460 PHE cc_start: 0.8821 (m-10) cc_final: 0.8569 (m-80) REVERT: B 469 GLN cc_start: 0.8356 (mt0) cc_final: 0.7767 (mp10) REVERT: B 582 GLN cc_start: 0.8698 (tt0) cc_final: 0.8414 (tt0) REVERT: B 594 ASP cc_start: 0.8277 (t0) cc_final: 0.8074 (t0) REVERT: B 731 GLN cc_start: 0.8842 (mt0) cc_final: 0.8438 (mt0) REVERT: B 886 PHE cc_start: 0.6728 (m-80) cc_final: 0.6455 (m-80) REVERT: B 1111 THR cc_start: 0.8130 (OUTLIER) cc_final: 0.7864 (p) REVERT: B 1305 MET cc_start: 0.3387 (ttp) cc_final: 0.3180 (ttp) REVERT: B 1319 VAL cc_start: 0.7823 (OUTLIER) cc_final: 0.7466 (p) REVERT: B 1323 ASP cc_start: 0.8912 (m-30) cc_final: 0.8520 (m-30) REVERT: B 1568 MET cc_start: 0.7763 (tpt) cc_final: 0.7550 (tpt) REVERT: B 1606 ASP cc_start: 0.8022 (t70) cc_final: 0.7447 (t0) REVERT: B 1609 GLU cc_start: 0.9162 (tt0) cc_final: 0.8636 (pp20) REVERT: B 1610 ASP cc_start: 0.8180 (t0) cc_final: 0.7850 (t70) REVERT: B 1719 ASP cc_start: 0.8469 (OUTLIER) cc_final: 0.8208 (t0) REVERT: B 1819 TYR cc_start: 0.6803 (OUTLIER) cc_final: 0.6370 (t80) REVERT: B 1887 GLN cc_start: 0.8160 (mm-40) cc_final: 0.7883 (tp40) REVERT: B 1960 LYS cc_start: 0.8467 (tmtt) cc_final: 0.8139 (tptt) REVERT: B 2354 TRP cc_start: 0.7911 (m100) cc_final: 0.7638 (m100) REVERT: B 2423 VAL cc_start: 0.8393 (OUTLIER) cc_final: 0.8154 (m) REVERT: B 2540 TYR cc_start: 0.7341 (m-10) cc_final: 0.6967 (m-10) REVERT: B 2605 ARG cc_start: 0.7924 (mmm160) cc_final: 0.7485 (mmt-90) REVERT: B 2646 LEU cc_start: 0.9431 (mm) cc_final: 0.9130 (tp) outliers start: 112 outliers final: 77 residues processed: 424 average time/residue: 0.2386 time to fit residues: 170.0835 Evaluate side-chains 400 residues out of total 4364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 312 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 703 CYS Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 726 CYS Chi-restraints excluded: chain A residue 1059 ILE Chi-restraints excluded: chain A residue 1068 LEU Chi-restraints excluded: chain A residue 1111 THR Chi-restraints excluded: chain A residue 1148 LEU Chi-restraints excluded: chain A residue 1152 LEU Chi-restraints excluded: chain A residue 1181 CYS Chi-restraints excluded: chain A residue 1364 VAL Chi-restraints excluded: chain A residue 1410 LEU Chi-restraints excluded: chain A residue 1440 CYS Chi-restraints excluded: chain A residue 1533 GLN Chi-restraints excluded: chain A residue 1664 VAL Chi-restraints excluded: chain A residue 1687 THR Chi-restraints excluded: chain A residue 1724 CYS Chi-restraints excluded: chain A residue 1819 TYR Chi-restraints excluded: chain A residue 1894 LEU Chi-restraints excluded: chain A residue 1898 VAL Chi-restraints excluded: chain A residue 1982 VAL Chi-restraints excluded: chain A residue 2034 MET Chi-restraints excluded: chain A residue 2056 HIS Chi-restraints excluded: chain A residue 2091 ASP Chi-restraints excluded: chain A residue 2201 VAL Chi-restraints excluded: chain A residue 2238 LEU Chi-restraints excluded: chain A residue 2286 VAL Chi-restraints excluded: chain A residue 2335 TYR Chi-restraints excluded: chain A residue 2367 GLN Chi-restraints excluded: chain A residue 2380 VAL Chi-restraints excluded: chain A residue 2423 VAL Chi-restraints excluded: chain A residue 2482 VAL Chi-restraints excluded: chain A residue 2507 LEU Chi-restraints excluded: chain A residue 2702 GLU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 622 THR Chi-restraints excluded: chain B residue 703 CYS Chi-restraints excluded: chain B residue 720 ILE Chi-restraints excluded: chain B residue 726 CYS Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 1111 THR Chi-restraints excluded: chain B residue 1157 LEU Chi-restraints excluded: chain B residue 1181 CYS Chi-restraints excluded: chain B residue 1319 VAL Chi-restraints excluded: chain B residue 1364 VAL Chi-restraints excluded: chain B residue 1440 CYS Chi-restraints excluded: chain B residue 1664 VAL Chi-restraints excluded: chain B residue 1687 THR Chi-restraints excluded: chain B residue 1719 ASP Chi-restraints excluded: chain B residue 1752 LEU Chi-restraints excluded: chain B residue 1819 TYR Chi-restraints excluded: chain B residue 1864 VAL Chi-restraints excluded: chain B residue 1898 VAL Chi-restraints excluded: chain B residue 1957 LEU Chi-restraints excluded: chain B residue 1982 VAL Chi-restraints excluded: chain B residue 1985 SER Chi-restraints excluded: chain B residue 2012 LEU Chi-restraints excluded: chain B residue 2023 THR Chi-restraints excluded: chain B residue 2056 HIS Chi-restraints excluded: chain B residue 2079 VAL Chi-restraints excluded: chain B residue 2091 ASP Chi-restraints excluded: chain B residue 2201 VAL Chi-restraints excluded: chain B residue 2286 VAL Chi-restraints excluded: chain B residue 2304 ASN Chi-restraints excluded: chain B residue 2357 LEU Chi-restraints excluded: chain B residue 2380 VAL Chi-restraints excluded: chain B residue 2423 VAL Chi-restraints excluded: chain B residue 2507 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 285 optimal weight: 0.8980 chunk 458 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 376 optimal weight: 4.9990 chunk 217 optimal weight: 0.9980 chunk 77 optimal weight: 10.0000 chunk 174 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 303 optimal weight: 0.7980 chunk 176 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1528 GLN ** A2466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1288 GLN ** B1509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2182 HIS ** B2466 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 = 0.3958 r_free = 0.3958 target = 0.136883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.105689 restraints weight = 96738.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.108431 restraints weight = 47097.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.110178 restraints weight = 30496.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.111186 restraints weight = 23335.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.111774 restraints weight = 19963.801| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 40962 Z= 0.152 Angle : 0.700 15.757 55724 Z= 0.350 Chirality : 0.044 0.303 6104 Planarity : 0.005 0.050 7290 Dihedral : 6.229 56.614 6244 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.70 % Favored : 89.26 % Rotamer: Outliers : 2.45 % Allowed : 13.86 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % 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: -2.59 (0.11), residues: 5058 helix: -0.52 (0.15), residues: 1220 sheet: -2.00 (0.20), residues: 618 loop : -2.26 (0.11), residues: 3220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 492 TYR 0.020 0.001 TYR B1445 PHE 0.035 0.001 PHE B1697 TRP 0.026 0.001 TRP B2501 HIS 0.005 0.001 HIS A1721 Details of bonding type rmsd covalent geometry : bond 0.00350 (40806) covalent geometry : angle 0.68470 (55376) SS BOND : bond 0.00408 ( 120) SS BOND : angle 1.82844 ( 240) hydrogen bonds : bond 0.03015 ( 916) hydrogen bonds : angle 5.37144 ( 2472) link_BETA1-4 : bond 0.00280 ( 4) link_BETA1-4 : angle 2.19710 ( 12) link_NAG-ASN : bond 0.00228 ( 32) link_NAG-ASN : angle 2.23040 ( 96) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10116 Ramachandran restraints generated. 5058 Oldfield, 0 Emsley, 5058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10116 Ramachandran restraints generated. 5058 Oldfield, 0 Emsley, 5058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 4364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 339 time to evaluate : 1.280 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: A 81 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8054 (mm) REVERT: A 204 ILE cc_start: 0.9166 (mm) cc_final: 0.8890 (mm) REVERT: A 226 ARG cc_start: 0.8533 (ptm-80) cc_final: 0.8217 (ptp90) REVERT: A 469 GLN cc_start: 0.8592 (mt0) cc_final: 0.8059 (mp10) REVERT: A 582 GLN cc_start: 0.8734 (tt0) cc_final: 0.8506 (tt0) REVERT: A 589 GLU cc_start: 0.8358 (tp30) cc_final: 0.8100 (tp30) REVERT: A 886 PHE cc_start: 0.6742 (m-80) cc_final: 0.6469 (m-80) REVERT: A 1152 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8674 (tp) REVERT: A 1202 ARG cc_start: 0.8716 (mpp-170) cc_final: 0.8377 (mpp-170) REVERT: A 1320 PHE cc_start: 0.9077 (m-80) cc_final: 0.8254 (m-80) REVERT: A 1323 ASP cc_start: 0.8811 (m-30) cc_final: 0.8273 (m-30) REVERT: A 1533 GLN cc_start: 0.6500 (OUTLIER) cc_final: 0.6060 (tm-30) REVERT: A 1570 LYS cc_start: 0.9267 (ttpt) cc_final: 0.8967 (mttp) REVERT: A 1610 ASP cc_start: 0.8115 (t0) cc_final: 0.7685 (t70) REVERT: A 1819 TYR cc_start: 0.7029 (OUTLIER) cc_final: 0.6053 (t80) REVERT: A 1887 GLN cc_start: 0.7930 (mm-40) cc_final: 0.7572 (tp40) REVERT: A 1960 LYS cc_start: 0.8436 (tmtt) cc_final: 0.7982 (tptt) REVERT: A 2466 GLN cc_start: 0.6948 (mt0) cc_final: 0.6433 (mt0) REVERT: A 2540 TYR cc_start: 0.7215 (m-10) cc_final: 0.6834 (m-10) REVERT: A 2605 ARG cc_start: 0.7838 (mmm160) cc_final: 0.7510 (mmt-90) REVERT: B 81 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7994 (mm) REVERT: B 101 GLN cc_start: 0.8452 (mt0) cc_final: 0.8187 (mm-40) REVERT: B 226 ARG cc_start: 0.8322 (ptm-80) cc_final: 0.8074 (ptp90) REVERT: B 460 PHE cc_start: 0.8843 (m-10) cc_final: 0.8607 (m-80) REVERT: B 469 GLN cc_start: 0.8260 (mt0) cc_final: 0.7776 (mp10) REVERT: B 484 ASN cc_start: 0.8281 (m-40) cc_final: 0.8030 (m-40) REVERT: B 582 GLN cc_start: 0.8699 (tt0) cc_final: 0.8418 (tt0) REVERT: B 731 GLN cc_start: 0.8829 (mt0) cc_final: 0.8421 (mt0) REVERT: B 886 PHE cc_start: 0.6777 (m-80) cc_final: 0.6529 (m-80) REVERT: B 1111 THR cc_start: 0.8167 (OUTLIER) cc_final: 0.7909 (p) REVERT: B 1319 VAL cc_start: 0.7898 (OUTLIER) cc_final: 0.7482 (p) REVERT: B 1323 ASP cc_start: 0.8877 (m-30) cc_final: 0.8465 (m-30) REVERT: B 1568 MET cc_start: 0.7788 (tpt) cc_final: 0.7508 (tpt) REVERT: B 1606 ASP cc_start: 0.8107 (t70) cc_final: 0.7531 (t0) REVERT: B 1609 GLU cc_start: 0.9110 (tt0) cc_final: 0.8567 (pp20) REVERT: B 1610 ASP cc_start: 0.8168 (t0) cc_final: 0.7815 (t70) REVERT: B 1700 MET cc_start: 0.8572 (mpp) cc_final: 0.8256 (mpp) REVERT: B 1819 TYR cc_start: 0.6912 (OUTLIER) cc_final: 0.6557 (t80) REVERT: B 1887 GLN cc_start: 0.8157 (mm-40) cc_final: 0.7872 (tp40) REVERT: B 1908 GLU cc_start: 0.8362 (pt0) cc_final: 0.7797 (pt0) REVERT: B 1930 ASP cc_start: 0.8200 (m-30) cc_final: 0.7628 (t0) REVERT: B 1960 LYS cc_start: 0.8473 (tmtt) cc_final: 0.8154 (tptt) REVERT: B 2354 TRP cc_start: 0.7875 (m100) cc_final: 0.7647 (m100) REVERT: B 2540 TYR cc_start: 0.7212 (m-10) cc_final: 0.6914 (m-10) REVERT: B 2605 ARG cc_start: 0.7837 (mmm160) cc_final: 0.7436 (mmt-90) outliers start: 106 outliers final: 80 residues processed: 426 average time/residue: 0.2313 time to fit residues: 166.5542 Evaluate side-chains 409 residues out of total 4364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 321 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 703 CYS Chi-restraints excluded: chain A residue 726 CYS Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 1059 ILE Chi-restraints excluded: chain A residue 1068 LEU Chi-restraints excluded: chain A residue 1111 THR Chi-restraints excluded: chain A residue 1148 LEU Chi-restraints excluded: chain A residue 1152 LEU Chi-restraints excluded: chain A residue 1181 CYS Chi-restraints excluded: chain A residue 1364 VAL Chi-restraints excluded: chain A residue 1410 LEU Chi-restraints excluded: chain A residue 1440 CYS Chi-restraints excluded: chain A residue 1533 GLN Chi-restraints excluded: chain A residue 1607 CYS Chi-restraints excluded: chain A residue 1664 VAL Chi-restraints excluded: chain A residue 1687 THR Chi-restraints excluded: chain A residue 1719 ASP Chi-restraints excluded: chain A residue 1724 CYS Chi-restraints excluded: chain A residue 1819 TYR Chi-restraints excluded: chain A residue 1894 LEU Chi-restraints excluded: chain A residue 1898 VAL Chi-restraints excluded: chain A residue 1982 VAL Chi-restraints excluded: chain A residue 2034 MET Chi-restraints excluded: chain A residue 2056 HIS Chi-restraints excluded: chain A residue 2091 ASP Chi-restraints excluded: chain A residue 2201 VAL Chi-restraints excluded: chain A residue 2238 LEU Chi-restraints excluded: chain A residue 2286 VAL Chi-restraints excluded: chain A residue 2380 VAL Chi-restraints excluded: chain A residue 2423 VAL Chi-restraints excluded: chain A residue 2507 LEU Chi-restraints excluded: chain A residue 2625 LEU Chi-restraints excluded: chain A residue 2702 GLU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 622 THR Chi-restraints excluded: chain B residue 703 CYS Chi-restraints excluded: chain B residue 726 CYS Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 1111 THR Chi-restraints excluded: chain B residue 1181 CYS Chi-restraints excluded: chain B residue 1319 VAL Chi-restraints excluded: chain B residue 1346 VAL Chi-restraints excluded: chain B residue 1364 VAL Chi-restraints excluded: chain B residue 1440 CYS Chi-restraints excluded: chain B residue 1664 VAL Chi-restraints excluded: chain B residue 1687 THR Chi-restraints excluded: chain B residue 1752 LEU Chi-restraints excluded: chain B residue 1798 PHE Chi-restraints excluded: chain B residue 1819 TYR Chi-restraints excluded: chain B residue 1864 VAL Chi-restraints excluded: chain B residue 1898 VAL Chi-restraints excluded: chain B residue 1957 LEU Chi-restraints excluded: chain B residue 1982 VAL Chi-restraints excluded: chain B residue 1985 SER Chi-restraints excluded: chain B residue 2012 LEU Chi-restraints excluded: chain B residue 2056 HIS Chi-restraints excluded: chain B residue 2079 VAL Chi-restraints excluded: chain B residue 2091 ASP Chi-restraints excluded: chain B residue 2201 VAL Chi-restraints excluded: chain B residue 2286 VAL Chi-restraints excluded: chain B residue 2299 LEU Chi-restraints excluded: chain B residue 2304 ASN Chi-restraints excluded: chain B residue 2357 LEU Chi-restraints excluded: chain B residue 2367 GLN Chi-restraints excluded: chain B residue 2380 VAL Chi-restraints excluded: chain B residue 2625 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 398 optimal weight: 9.9990 chunk 279 optimal weight: 0.9990 chunk 464 optimal weight: 6.9990 chunk 373 optimal weight: 0.8980 chunk 322 optimal weight: 9.9990 chunk 8 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 216 optimal weight: 0.0070 chunk 280 optimal weight: 0.8980 chunk 297 optimal weight: 0.9990 chunk 403 optimal weight: 9.9990 overall best weight: 0.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 GLN ** A1509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1669 HIS A2182 HIS ** A2466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2607 ASN B1288 GLN ** B1509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.137613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.106505 restraints weight = 96085.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.110019 restraints weight = 50051.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.111361 restraints weight = 28269.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.111518 restraints weight = 24096.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.111757 restraints weight = 22982.429| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 40962 Z= 0.132 Angle : 0.699 19.299 55724 Z= 0.349 Chirality : 0.044 0.322 6104 Planarity : 0.005 0.069 7290 Dihedral : 6.117 56.527 6244 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.50 % Favored : 89.50 % Rotamer: Outliers : 2.26 % Allowed : 14.14 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % 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: -2.48 (0.12), residues: 5058 helix: -0.34 (0.15), residues: 1218 sheet: -2.04 (0.19), residues: 648 loop : -2.20 (0.11), residues: 3192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 492 TYR 0.018 0.001 TYR B1445 PHE 0.031 0.001 PHE B1697 TRP 0.025 0.001 TRP B2501 HIS 0.005 0.001 HIS A1721 Details of bonding type rmsd covalent geometry : bond 0.00308 (40806) covalent geometry : angle 0.68195 (55376) SS BOND : bond 0.00439 ( 120) SS BOND : angle 2.01375 ( 240) hydrogen bonds : bond 0.02983 ( 916) hydrogen bonds : angle 5.29184 ( 2472) link_BETA1-4 : bond 0.00360 ( 4) link_BETA1-4 : angle 2.07442 ( 12) link_NAG-ASN : bond 0.00230 ( 32) link_NAG-ASN : angle 2.12270 ( 96) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10116 Ramachandran restraints generated. 5058 Oldfield, 0 Emsley, 5058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10116 Ramachandran restraints generated. 5058 Oldfield, 0 Emsley, 5058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 4364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 349 time to evaluate : 1.504 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: A 81 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8056 (mm) REVERT: A 204 ILE cc_start: 0.9144 (mm) cc_final: 0.8872 (mm) REVERT: A 226 ARG cc_start: 0.8525 (ptm-80) cc_final: 0.8239 (ptp90) REVERT: A 469 GLN cc_start: 0.8611 (mt0) cc_final: 0.8060 (mp10) REVERT: A 582 GLN cc_start: 0.8690 (tt0) cc_final: 0.8457 (tt0) REVERT: A 589 GLU cc_start: 0.8326 (tp30) cc_final: 0.8083 (tp30) REVERT: A 886 PHE cc_start: 0.6725 (m-80) cc_final: 0.6463 (m-80) REVERT: A 1152 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8677 (tp) REVERT: A 1202 ARG cc_start: 0.8651 (mpp-170) cc_final: 0.8243 (mpp-170) REVERT: A 1320 PHE cc_start: 0.9106 (m-80) cc_final: 0.8293 (m-80) REVERT: A 1323 ASP cc_start: 0.8823 (m-30) cc_final: 0.8279 (m-30) REVERT: A 1408 PHE cc_start: 0.8379 (t80) cc_final: 0.8178 (t80) REVERT: A 1533 GLN cc_start: 0.6546 (OUTLIER) cc_final: 0.6153 (tm-30) REVERT: A 1570 LYS cc_start: 0.9267 (ttpt) cc_final: 0.8923 (ptpt) REVERT: A 1610 ASP cc_start: 0.8081 (t0) cc_final: 0.7626 (t70) REVERT: A 1819 TYR cc_start: 0.7073 (OUTLIER) cc_final: 0.6146 (t80) REVERT: A 1887 GLN cc_start: 0.7927 (mm-40) cc_final: 0.7560 (tp40) REVERT: A 1960 LYS cc_start: 0.8430 (tmtt) cc_final: 0.7960 (tptt) REVERT: A 2423 VAL cc_start: 0.8419 (OUTLIER) cc_final: 0.8184 (m) REVERT: A 2466 GLN cc_start: 0.6990 (mt0) cc_final: 0.6661 (mt0) REVERT: A 2540 TYR cc_start: 0.7150 (m-10) cc_final: 0.6878 (m-10) REVERT: A 2605 ARG cc_start: 0.7795 (mmm160) cc_final: 0.7434 (mmt-90) REVERT: B 81 LEU cc_start: 0.8197 (OUTLIER) cc_final: 0.7949 (mm) REVERT: B 101 GLN cc_start: 0.8466 (mt0) cc_final: 0.8166 (mm-40) REVERT: B 202 MET cc_start: 0.8345 (mmt) cc_final: 0.8023 (mmp) REVERT: B 226 ARG cc_start: 0.8366 (ptm-80) cc_final: 0.8091 (ptp90) REVERT: B 460 PHE cc_start: 0.8813 (m-10) cc_final: 0.8594 (m-10) REVERT: B 469 GLN cc_start: 0.8285 (mt0) cc_final: 0.7774 (mp10) REVERT: B 484 ASN cc_start: 0.8284 (m-40) cc_final: 0.8001 (m-40) REVERT: B 582 GLN cc_start: 0.8649 (tt0) cc_final: 0.8375 (tt0) REVERT: B 731 GLN cc_start: 0.8806 (mt0) cc_final: 0.8435 (mt0) REVERT: B 886 PHE cc_start: 0.6743 (m-80) cc_final: 0.6507 (m-80) REVERT: B 1111 THR cc_start: 0.8206 (OUTLIER) cc_final: 0.7980 (p) REVERT: B 1319 VAL cc_start: 0.7810 (OUTLIER) cc_final: 0.7377 (p) REVERT: B 1323 ASP cc_start: 0.8891 (m-30) cc_final: 0.8495 (m-30) REVERT: B 1568 MET cc_start: 0.7804 (tpt) cc_final: 0.7501 (tpt) REVERT: B 1606 ASP cc_start: 0.8127 (t70) cc_final: 0.7550 (t0) REVERT: B 1609 GLU cc_start: 0.9128 (tt0) cc_final: 0.8597 (pp20) REVERT: B 1610 ASP cc_start: 0.8171 (t0) cc_final: 0.7817 (t70) REVERT: B 1700 MET cc_start: 0.8520 (mpp) cc_final: 0.8221 (mpp) REVERT: B 1908 GLU cc_start: 0.8347 (pt0) cc_final: 0.7850 (pt0) REVERT: B 1930 ASP cc_start: 0.8194 (m-30) cc_final: 0.7690 (t0) REVERT: B 1960 LYS cc_start: 0.8482 (tmtt) cc_final: 0.8165 (tptt) REVERT: B 2354 TRP cc_start: 0.7807 (m100) cc_final: 0.7564 (m100) REVERT: B 2457 LYS cc_start: 0.7984 (mmtt) cc_final: 0.7755 (mmtm) REVERT: B 2540 TYR cc_start: 0.7160 (m-10) cc_final: 0.6905 (m-10) outliers start: 98 outliers final: 79 residues processed: 427 average time/residue: 0.2372 time to fit residues: 171.1283 Evaluate side-chains 402 residues out of total 4364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 315 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 703 CYS Chi-restraints excluded: chain A residue 726 CYS Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 1059 ILE Chi-restraints excluded: chain A residue 1068 LEU Chi-restraints excluded: chain A residue 1111 THR Chi-restraints excluded: chain A residue 1148 LEU Chi-restraints excluded: chain A residue 1152 LEU Chi-restraints excluded: chain A residue 1181 CYS Chi-restraints excluded: chain A residue 1364 VAL Chi-restraints excluded: chain A residue 1410 LEU Chi-restraints excluded: chain A residue 1440 CYS Chi-restraints excluded: chain A residue 1533 GLN Chi-restraints excluded: chain A residue 1607 CYS Chi-restraints excluded: chain A residue 1664 VAL Chi-restraints excluded: chain A residue 1687 THR Chi-restraints excluded: chain A residue 1719 ASP Chi-restraints excluded: chain A residue 1724 CYS Chi-restraints excluded: chain A residue 1752 LEU Chi-restraints excluded: chain A residue 1819 TYR Chi-restraints excluded: chain A residue 1894 LEU Chi-restraints excluded: chain A residue 1898 VAL Chi-restraints excluded: chain A residue 1982 VAL Chi-restraints excluded: chain A residue 2034 MET Chi-restraints excluded: chain A residue 2056 HIS Chi-restraints excluded: chain A residue 2091 ASP Chi-restraints excluded: chain A residue 2201 VAL Chi-restraints excluded: chain A residue 2238 LEU Chi-restraints excluded: chain A residue 2286 VAL Chi-restraints excluded: chain A residue 2380 VAL Chi-restraints excluded: chain A residue 2423 VAL Chi-restraints excluded: chain A residue 2625 LEU Chi-restraints excluded: chain A residue 2702 GLU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 622 THR Chi-restraints excluded: chain B residue 703 CYS Chi-restraints excluded: chain B residue 726 CYS Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 1111 THR Chi-restraints excluded: chain B residue 1181 CYS Chi-restraints excluded: chain B residue 1319 VAL Chi-restraints excluded: chain B residue 1364 VAL Chi-restraints excluded: chain B residue 1410 LEU Chi-restraints excluded: chain B residue 1440 CYS Chi-restraints excluded: chain B residue 1664 VAL Chi-restraints excluded: chain B residue 1687 THR Chi-restraints excluded: chain B residue 1752 LEU Chi-restraints excluded: chain B residue 1864 VAL Chi-restraints excluded: chain B residue 1898 VAL Chi-restraints excluded: chain B residue 1957 LEU Chi-restraints excluded: chain B residue 1982 VAL Chi-restraints excluded: chain B residue 1985 SER Chi-restraints excluded: chain B residue 2012 LEU Chi-restraints excluded: chain B residue 2034 MET Chi-restraints excluded: chain B residue 2056 HIS Chi-restraints excluded: chain B residue 2079 VAL Chi-restraints excluded: chain B residue 2091 ASP Chi-restraints excluded: chain B residue 2201 VAL Chi-restraints excluded: chain B residue 2286 VAL Chi-restraints excluded: chain B residue 2299 LEU Chi-restraints excluded: chain B residue 2304 ASN Chi-restraints excluded: chain B residue 2357 LEU Chi-restraints excluded: chain B residue 2380 VAL Chi-restraints excluded: chain B residue 2593 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 392 optimal weight: 3.9990 chunk 479 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 358 optimal weight: 5.9990 chunk 78 optimal weight: 10.0000 chunk 444 optimal weight: 5.9990 chunk 460 optimal weight: 0.0170 chunk 498 optimal weight: 2.9990 chunk 171 optimal weight: 1.9990 chunk 505 optimal weight: 0.6980 chunk 310 optimal weight: 4.9990 overall best weight: 1.2822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.136721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.105656 restraints weight = 96465.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.108378 restraints weight = 47120.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.110110 restraints weight = 30527.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.111050 restraints weight = 23353.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.111753 restraints weight = 20060.583| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 40962 Z= 0.164 Angle : 0.726 18.747 55724 Z= 0.362 Chirality : 0.044 0.317 6104 Planarity : 0.005 0.069 7290 Dihedral : 6.097 56.222 6244 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.87 % Favored : 89.13 % Rotamer: Outliers : 2.33 % Allowed : 14.63 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % 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: -2.43 (0.12), residues: 5058 helix: -0.29 (0.15), residues: 1232 sheet: -2.00 (0.20), residues: 628 loop : -2.19 (0.11), residues: 3198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 492 TYR 0.018 0.002 TYR B1445 PHE 0.035 0.001 PHE B1697 TRP 0.037 0.001 TRP A1632 HIS 0.008 0.001 HIS A1669 Details of bonding type rmsd covalent geometry : bond 0.00380 (40806) covalent geometry : angle 0.70936 (55376) SS BOND : bond 0.00454 ( 120) SS BOND : angle 2.01671 ( 240) hydrogen bonds : bond 0.03118 ( 916) hydrogen bonds : angle 5.33925 ( 2472) link_BETA1-4 : bond 0.00360 ( 4) link_BETA1-4 : angle 2.10240 ( 12) link_NAG-ASN : bond 0.00203 ( 32) link_NAG-ASN : angle 2.13854 ( 96) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10116 Ramachandran restraints generated. 5058 Oldfield, 0 Emsley, 5058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10116 Ramachandran restraints generated. 5058 Oldfield, 0 Emsley, 5058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 4364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 323 time to evaluate : 1.498 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: A 81 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8047 (mm) REVERT: A 226 ARG cc_start: 0.8512 (ptm-80) cc_final: 0.8303 (ptp90) REVERT: A 582 GLN cc_start: 0.8754 (tt0) cc_final: 0.8525 (tt0) REVERT: A 589 GLU cc_start: 0.8338 (tp30) cc_final: 0.8090 (tp30) REVERT: A 886 PHE cc_start: 0.6762 (m-80) cc_final: 0.6481 (m-80) REVERT: A 1152 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8688 (tp) REVERT: A 1202 ARG cc_start: 0.8698 (mpp-170) cc_final: 0.8370 (mpp-170) REVERT: A 1320 PHE cc_start: 0.9090 (m-80) cc_final: 0.8309 (m-80) REVERT: A 1323 ASP cc_start: 0.8824 (m-30) cc_final: 0.8223 (m-30) REVERT: A 1533 GLN cc_start: 0.6859 (OUTLIER) cc_final: 0.6149 (tm-30) REVERT: A 1570 LYS cc_start: 0.9242 (ttpt) cc_final: 0.8939 (mttp) REVERT: A 1610 ASP cc_start: 0.8108 (t0) cc_final: 0.7623 (t70) REVERT: A 1699 ASN cc_start: 0.8583 (t0) cc_final: 0.8274 (t0) REVERT: A 1700 MET cc_start: 0.8321 (mpp) cc_final: 0.8117 (mpp) REVERT: A 1819 TYR cc_start: 0.7169 (OUTLIER) cc_final: 0.6233 (t80) REVERT: A 1887 GLN cc_start: 0.7939 (mm-40) cc_final: 0.7561 (tp40) REVERT: A 1960 LYS cc_start: 0.8467 (tmtt) cc_final: 0.8063 (tptt) REVERT: A 2168 GLN cc_start: 0.7965 (pt0) cc_final: 0.7728 (pt0) REVERT: A 2423 VAL cc_start: 0.8410 (OUTLIER) cc_final: 0.8185 (m) REVERT: A 2540 TYR cc_start: 0.7213 (m-10) cc_final: 0.6915 (m-10) REVERT: A 2605 ARG cc_start: 0.7792 (mmm160) cc_final: 0.7467 (mmt-90) REVERT: B 81 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7965 (mm) REVERT: B 101 GLN cc_start: 0.8547 (mt0) cc_final: 0.8255 (mm-40) REVERT: B 226 ARG cc_start: 0.8368 (ptm-80) cc_final: 0.8136 (ptp90) REVERT: B 460 PHE cc_start: 0.8840 (m-10) cc_final: 0.8597 (m-80) REVERT: B 469 GLN cc_start: 0.8256 (mt0) cc_final: 0.7755 (mp10) REVERT: B 582 GLN cc_start: 0.8753 (tt0) cc_final: 0.8439 (tt0) REVERT: B 731 GLN cc_start: 0.8819 (mt0) cc_final: 0.8480 (mt0) REVERT: B 886 PHE cc_start: 0.6777 (m-80) cc_final: 0.6573 (m-80) REVERT: B 1111 THR cc_start: 0.8162 (OUTLIER) cc_final: 0.7930 (p) REVERT: B 1319 VAL cc_start: 0.7934 (OUTLIER) cc_final: 0.7375 (p) REVERT: B 1323 ASP cc_start: 0.8884 (m-30) cc_final: 0.8411 (m-30) REVERT: B 1568 MET cc_start: 0.7789 (tpt) cc_final: 0.7484 (tpt) REVERT: B 1606 ASP cc_start: 0.8152 (t70) cc_final: 0.7568 (t0) REVERT: B 1609 GLU cc_start: 0.9127 (tt0) cc_final: 0.8593 (pp20) REVERT: B 1610 ASP cc_start: 0.8192 (t0) cc_final: 0.7817 (t70) REVERT: B 1700 MET cc_start: 0.8564 (mpp) cc_final: 0.8244 (mpp) REVERT: B 1908 GLU cc_start: 0.8370 (pt0) cc_final: 0.7864 (pt0) REVERT: B 1930 ASP cc_start: 0.8158 (m-30) cc_final: 0.7651 (t0) REVERT: B 1960 LYS cc_start: 0.8506 (tmtt) cc_final: 0.8202 (tptt) REVERT: B 2354 TRP cc_start: 0.7865 (m100) cc_final: 0.7656 (m100) REVERT: B 2457 LYS cc_start: 0.7984 (mmtt) cc_final: 0.7748 (mmtm) REVERT: B 2540 TYR cc_start: 0.7237 (m-10) cc_final: 0.6942 (m-10) REVERT: B 2596 MET cc_start: 0.7801 (tpp) cc_final: 0.7451 (tpp) outliers start: 101 outliers final: 82 residues processed: 405 average time/residue: 0.2455 time to fit residues: 169.2607 Evaluate side-chains 400 residues out of total 4364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 310 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 703 CYS Chi-restraints excluded: chain A residue 726 CYS Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 1059 ILE Chi-restraints excluded: chain A residue 1068 LEU Chi-restraints excluded: chain A residue 1111 THR Chi-restraints excluded: chain A residue 1148 LEU Chi-restraints excluded: chain A residue 1152 LEU Chi-restraints excluded: chain A residue 1181 CYS Chi-restraints excluded: chain A residue 1364 VAL Chi-restraints excluded: chain A residue 1410 LEU Chi-restraints excluded: chain A residue 1440 CYS Chi-restraints excluded: chain A residue 1533 GLN Chi-restraints excluded: chain A residue 1607 CYS Chi-restraints excluded: chain A residue 1664 VAL Chi-restraints excluded: chain A residue 1687 THR Chi-restraints excluded: chain A residue 1724 CYS Chi-restraints excluded: chain A residue 1819 TYR Chi-restraints excluded: chain A residue 1894 LEU Chi-restraints excluded: chain A residue 1898 VAL Chi-restraints excluded: chain A residue 1982 VAL Chi-restraints excluded: chain A residue 2034 MET Chi-restraints excluded: chain A residue 2056 HIS Chi-restraints excluded: chain A residue 2091 ASP Chi-restraints excluded: chain A residue 2201 VAL Chi-restraints excluded: chain A residue 2238 LEU Chi-restraints excluded: chain A residue 2286 VAL Chi-restraints excluded: chain A residue 2380 VAL Chi-restraints excluded: chain A residue 2423 VAL Chi-restraints excluded: chain A residue 2507 LEU Chi-restraints excluded: chain A residue 2625 LEU Chi-restraints excluded: chain A residue 2702 GLU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 622 THR Chi-restraints excluded: chain B residue 703 CYS Chi-restraints excluded: chain B residue 726 CYS Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 1111 THR Chi-restraints excluded: chain B residue 1157 LEU Chi-restraints excluded: chain B residue 1181 CYS Chi-restraints excluded: chain B residue 1319 VAL Chi-restraints excluded: chain B residue 1364 VAL Chi-restraints excluded: chain B residue 1410 LEU Chi-restraints excluded: chain B residue 1440 CYS Chi-restraints excluded: chain B residue 1664 VAL Chi-restraints excluded: chain B residue 1687 THR Chi-restraints excluded: chain B residue 1752 LEU Chi-restraints excluded: chain B residue 1798 PHE Chi-restraints excluded: chain B residue 1864 VAL Chi-restraints excluded: chain B residue 1898 VAL Chi-restraints excluded: chain B residue 1957 LEU Chi-restraints excluded: chain B residue 1982 VAL Chi-restraints excluded: chain B residue 1985 SER Chi-restraints excluded: chain B residue 2012 LEU Chi-restraints excluded: chain B residue 2023 THR Chi-restraints excluded: chain B residue 2056 HIS Chi-restraints excluded: chain B residue 2079 VAL Chi-restraints excluded: chain B residue 2091 ASP Chi-restraints excluded: chain B residue 2201 VAL Chi-restraints excluded: chain B residue 2286 VAL Chi-restraints excluded: chain B residue 2299 LEU Chi-restraints excluded: chain B residue 2304 ASN Chi-restraints excluded: chain B residue 2357 LEU Chi-restraints excluded: chain B residue 2367 GLN Chi-restraints excluded: chain B residue 2380 VAL Chi-restraints excluded: chain B residue 2593 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 244 optimal weight: 1.9990 chunk 346 optimal weight: 0.9980 chunk 287 optimal weight: 6.9990 chunk 458 optimal weight: 1.9990 chunk 263 optimal weight: 3.9990 chunk 347 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 29 optimal weight: 0.3980 chunk 425 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1180 GLN ** A1509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1971 GLN ** A2466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.137362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.106363 restraints weight = 96156.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.109110 restraints weight = 46873.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.110864 restraints weight = 30255.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.111857 restraints weight = 23130.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.112517 restraints weight = 19792.756| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 40962 Z= 0.144 Angle : 0.716 18.341 55724 Z= 0.358 Chirality : 0.044 0.307 6104 Planarity : 0.005 0.071 7290 Dihedral : 6.027 56.279 6244 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.48 % Favored : 89.52 % Rotamer: Outliers : 2.20 % Allowed : 14.95 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % 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: -2.34 (0.12), residues: 5058 helix: -0.20 (0.15), residues: 1232 sheet: -2.00 (0.20), residues: 636 loop : -2.12 (0.11), residues: 3190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 492 TYR 0.022 0.001 TYR B1819 PHE 0.033 0.001 PHE B1697 TRP 0.051 0.001 TRP A2501 HIS 0.005 0.001 HIS A1721 Details of bonding type rmsd covalent geometry : bond 0.00333 (40806) covalent geometry : angle 0.70031 (55376) SS BOND : bond 0.00439 ( 120) SS BOND : angle 1.99215 ( 240) hydrogen bonds : bond 0.03100 ( 916) hydrogen bonds : angle 5.29369 ( 2472) link_BETA1-4 : bond 0.00359 ( 4) link_BETA1-4 : angle 1.99417 ( 12) link_NAG-ASN : bond 0.00233 ( 32) link_NAG-ASN : angle 2.13566 ( 96) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10116 Ramachandran restraints generated. 5058 Oldfield, 0 Emsley, 5058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10116 Ramachandran restraints generated. 5058 Oldfield, 0 Emsley, 5058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 4364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 336 time to evaluate : 1.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.8045 (mm) REVERT: A 469 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.7897 (mp10) REVERT: A 582 GLN cc_start: 0.8744 (tt0) cc_final: 0.8518 (tt0) REVERT: A 886 PHE cc_start: 0.6845 (m-80) cc_final: 0.6299 (m-80) REVERT: A 946 SER cc_start: 0.8847 (m) cc_final: 0.8610 (p) REVERT: A 1152 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8696 (tp) REVERT: A 1202 ARG cc_start: 0.8591 (mpp-170) cc_final: 0.8290 (mpp-170) REVERT: A 1320 PHE cc_start: 0.9074 (m-80) cc_final: 0.8281 (m-80) REVERT: A 1323 ASP cc_start: 0.8840 (m-30) cc_final: 0.8227 (m-30) REVERT: A 1533 GLN cc_start: 0.6880 (OUTLIER) cc_final: 0.6244 (tm-30) REVERT: A 1570 LYS cc_start: 0.9216 (ttpt) cc_final: 0.8954 (mttt) REVERT: A 1610 ASP cc_start: 0.8133 (t0) cc_final: 0.7718 (t0) REVERT: A 1819 TYR cc_start: 0.7182 (OUTLIER) cc_final: 0.6304 (t80) REVERT: A 1887 GLN cc_start: 0.7932 (mm-40) cc_final: 0.7547 (tp40) REVERT: A 1960 LYS cc_start: 0.8480 (tmtt) cc_final: 0.8106 (tptt) REVERT: A 2168 GLN cc_start: 0.7986 (pt0) cc_final: 0.7762 (pt0) REVERT: A 2466 GLN cc_start: 0.6865 (mt0) cc_final: 0.6597 (mt0) REVERT: A 2540 TYR cc_start: 0.7175 (m-10) cc_final: 0.6914 (m-10) REVERT: A 2605 ARG cc_start: 0.7739 (mmm160) cc_final: 0.7430 (mmt-90) REVERT: B 81 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7954 (mm) REVERT: B 101 GLN cc_start: 0.8517 (mt0) cc_final: 0.8246 (mm-40) REVERT: B 460 PHE cc_start: 0.8842 (m-10) cc_final: 0.8638 (m-10) REVERT: B 469 GLN cc_start: 0.8284 (mt0) cc_final: 0.7781 (mp10) REVERT: B 492 ARG cc_start: 0.6678 (mtm110) cc_final: 0.6402 (mtm110) REVERT: B 582 GLN cc_start: 0.8744 (tt0) cc_final: 0.8442 (tt0) REVERT: B 731 GLN cc_start: 0.8812 (mt0) cc_final: 0.8404 (mt0) REVERT: B 886 PHE cc_start: 0.6761 (m-80) cc_final: 0.6534 (m-80) REVERT: B 1111 THR cc_start: 0.8267 (OUTLIER) cc_final: 0.8041 (p) REVERT: B 1319 VAL cc_start: 0.7927 (OUTLIER) cc_final: 0.7303 (p) REVERT: B 1320 PHE cc_start: 0.8254 (m-80) cc_final: 0.7499 (m-80) REVERT: B 1323 ASP cc_start: 0.8844 (m-30) cc_final: 0.8338 (m-30) REVERT: B 1568 MET cc_start: 0.7773 (tpt) cc_final: 0.7324 (tpt) REVERT: B 1606 ASP cc_start: 0.8160 (t70) cc_final: 0.7548 (t0) REVERT: B 1609 GLU cc_start: 0.9159 (tt0) cc_final: 0.8590 (pp20) REVERT: B 1610 ASP cc_start: 0.8202 (t0) cc_final: 0.7812 (t70) REVERT: B 1700 MET cc_start: 0.8590 (mpp) cc_final: 0.8284 (mpp) REVERT: B 1908 GLU cc_start: 0.8393 (pt0) cc_final: 0.7853 (pt0) REVERT: B 1930 ASP cc_start: 0.8163 (m-30) cc_final: 0.7720 (t0) REVERT: B 1960 LYS cc_start: 0.8498 (tmtt) cc_final: 0.8190 (tptt) REVERT: B 2354 TRP cc_start: 0.7837 (m100) cc_final: 0.7633 (m100) REVERT: B 2457 LYS cc_start: 0.8015 (mmtt) cc_final: 0.7776 (mmtm) REVERT: B 2466 GLN cc_start: 0.6857 (mt0) cc_final: 0.6396 (mt0) REVERT: B 2540 TYR cc_start: 0.7161 (m-10) cc_final: 0.6892 (m-10) REVERT: B 2596 MET cc_start: 0.7805 (tpp) cc_final: 0.7469 (tpp) outliers start: 95 outliers final: 82 residues processed: 412 average time/residue: 0.2281 time to fit residues: 159.0487 Evaluate side-chains 409 residues out of total 4364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 319 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 96 CYS Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 585 ILE Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 703 CYS Chi-restraints excluded: chain A residue 726 CYS Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 1068 LEU Chi-restraints excluded: chain A residue 1111 THR Chi-restraints excluded: chain A residue 1148 LEU Chi-restraints excluded: chain A residue 1152 LEU Chi-restraints excluded: chain A residue 1181 CYS Chi-restraints excluded: chain A residue 1364 VAL Chi-restraints excluded: chain A residue 1410 LEU Chi-restraints excluded: chain A residue 1440 CYS Chi-restraints excluded: chain A residue 1533 GLN Chi-restraints excluded: chain A residue 1607 CYS Chi-restraints excluded: chain A residue 1664 VAL Chi-restraints excluded: chain A residue 1687 THR Chi-restraints excluded: chain A residue 1724 CYS Chi-restraints excluded: chain A residue 1819 TYR Chi-restraints excluded: chain A residue 1894 LEU Chi-restraints excluded: chain A residue 1898 VAL Chi-restraints excluded: chain A residue 1982 VAL Chi-restraints excluded: chain A residue 2034 MET Chi-restraints excluded: chain A residue 2056 HIS Chi-restraints excluded: chain A residue 2091 ASP Chi-restraints excluded: chain A residue 2201 VAL Chi-restraints excluded: chain A residue 2238 LEU Chi-restraints excluded: chain A residue 2286 VAL Chi-restraints excluded: chain A residue 2380 VAL Chi-restraints excluded: chain A residue 2423 VAL Chi-restraints excluded: chain A residue 2625 LEU Chi-restraints excluded: chain A residue 2702 GLU Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 96 CYS Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 622 THR Chi-restraints excluded: chain B residue 703 CYS Chi-restraints excluded: chain B residue 726 CYS Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 1111 THR Chi-restraints excluded: chain B residue 1157 LEU Chi-restraints excluded: chain B residue 1181 CYS Chi-restraints excluded: chain B residue 1319 VAL Chi-restraints excluded: chain B residue 1364 VAL Chi-restraints excluded: chain B residue 1410 LEU Chi-restraints excluded: chain B residue 1440 CYS Chi-restraints excluded: chain B residue 1607 CYS Chi-restraints excluded: chain B residue 1664 VAL Chi-restraints excluded: chain B residue 1687 THR Chi-restraints excluded: chain B residue 1752 LEU Chi-restraints excluded: chain B residue 1798 PHE Chi-restraints excluded: chain B residue 1864 VAL Chi-restraints excluded: chain B residue 1898 VAL Chi-restraints excluded: chain B residue 1957 LEU Chi-restraints excluded: chain B residue 1982 VAL Chi-restraints excluded: chain B residue 1985 SER Chi-restraints excluded: chain B residue 2012 LEU Chi-restraints excluded: chain B residue 2023 THR Chi-restraints excluded: chain B residue 2056 HIS Chi-restraints excluded: chain B residue 2079 VAL Chi-restraints excluded: chain B residue 2091 ASP Chi-restraints excluded: chain B residue 2201 VAL Chi-restraints excluded: chain B residue 2286 VAL Chi-restraints excluded: chain B residue 2299 LEU Chi-restraints excluded: chain B residue 2304 ASN Chi-restraints excluded: chain B residue 2357 LEU Chi-restraints excluded: chain B residue 2367 GLN Chi-restraints excluded: chain B residue 2380 VAL Chi-restraints excluded: chain B residue 2593 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 476 optimal weight: 2.9990 chunk 3 optimal weight: 7.9990 chunk 357 optimal weight: 2.9990 chunk 167 optimal weight: 6.9990 chunk 295 optimal weight: 1.9990 chunk 198 optimal weight: 1.9990 chunk 216 optimal weight: 1.9990 chunk 46 optimal weight: 0.0060 chunk 225 optimal weight: 1.9990 chunk 292 optimal weight: 1.9990 chunk 439 optimal weight: 5.9990 overall best weight: 1.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.136125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.105106 restraints weight = 96820.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.107783 restraints weight = 48177.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.109465 restraints weight = 31422.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.110423 restraints weight = 24206.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.111061 restraints weight = 20832.147| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.3824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 40962 Z= 0.187 Angle : 0.735 18.105 55724 Z= 0.367 Chirality : 0.045 0.311 6104 Planarity : 0.005 0.089 7290 Dihedral : 6.091 56.059 6244 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.85 % Favored : 89.13 % Rotamer: Outliers : 2.31 % Allowed : 14.72 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % 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: -2.33 (0.12), residues: 5058 helix: -0.18 (0.15), residues: 1240 sheet: -1.96 (0.20), residues: 632 loop : -2.13 (0.11), residues: 3186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 492 TYR 0.022 0.002 TYR B1965 PHE 0.042 0.002 PHE B1320 TRP 0.043 0.002 TRP A2501 HIS 0.005 0.001 HIS B2477 Details of bonding type rmsd covalent geometry : bond 0.00431 (40806) covalent geometry : angle 0.71820 (55376) SS BOND : bond 0.00464 ( 120) SS BOND : angle 2.03529 ( 240) hydrogen bonds : bond 0.03227 ( 916) hydrogen bonds : angle 5.35250 ( 2472) link_BETA1-4 : bond 0.00362 ( 4) link_BETA1-4 : angle 2.14078 ( 12) link_NAG-ASN : bond 0.00200 ( 32) link_NAG-ASN : angle 2.18371 ( 96) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7736.60 seconds wall clock time: 134 minutes 11.41 seconds (8051.41 seconds total)