Starting phenix.real_space_refine on Tue Apr 16 16:35:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6scj_10141/04_2024/6scj_10141.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6scj_10141/04_2024/6scj_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6scj_10141/04_2024/6scj_10141.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6scj_10141/04_2024/6scj_10141.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6scj_10141/04_2024/6scj_10141.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6scj_10141/04_2024/6scj_10141.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Residue "A ARG 38": "NH1" <-> "NH2" Residue "A ARG 88": "NH1" <-> "NH2" Residue "A ARG 167": "NH1" <-> "NH2" Residue "A ARG 169": "NH1" <-> "NH2" Residue "A ARG 170": "NH1" <-> "NH2" Residue "A ARG 294": "NH1" <-> "NH2" Residue "A ARG 305": "NH1" <-> "NH2" Residue "A ARG 320": "NH1" <-> "NH2" Residue "A ARG 350": "NH1" <-> "NH2" Residue "A ARG 423": "NH1" <-> "NH2" Residue "A ARG 466": "NH1" <-> "NH2" Residue "A ARG 614": "NH1" <-> "NH2" Residue "A ARG 657": "NH1" <-> "NH2" Residue "A ARG 666": "NH1" <-> "NH2" Residue "A ARG 668": "NH1" <-> "NH2" Residue "A PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 787": "NH1" <-> "NH2" Residue "A ARG 912": "NH1" <-> "NH2" Residue "A ARG 950": "NH1" <-> "NH2" Residue "A ARG 964": "NH1" <-> "NH2" Residue "A ARG 979": "NH1" <-> "NH2" Residue "A ARG 1009": "NH1" <-> "NH2" Residue "A ARG 1066": "NH1" <-> "NH2" Residue "A ARG 1081": "NH1" <-> "NH2" Residue "A ARG 1116": "NH1" <-> "NH2" Residue "A ARG 1136": "NH1" <-> "NH2" Residue "A ARG 1170": "NH1" <-> "NH2" Residue "A ARG 1214": "NH1" <-> "NH2" Residue "A ARG 1270": "NH1" <-> "NH2" Residue "A ARG 1328": "NH1" <-> "NH2" Residue "A ARG 1359": "NH1" <-> "NH2" Residue "A ARG 1361": "NH1" <-> "NH2" Residue "A PHE 1417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1423": "NH1" <-> "NH2" Residue "A ARG 1435": "NH1" <-> "NH2" Residue "A ARG 1497": "NH1" <-> "NH2" Residue "A ARG 1516": "NH1" <-> "NH2" Residue "A ARG 1536": "NH1" <-> "NH2" Residue "A ARG 1549": "NH1" <-> "NH2" Residue "A ARG 1550": "NH1" <-> "NH2" Residue "A ARG 1730": "NH1" <-> "NH2" Residue "A ARG 1792": "NH1" <-> "NH2" Residue "A ARG 1829": "NH1" <-> "NH2" Residue "A TYR 1916": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1967": "NH1" <-> "NH2" Residue "A ARG 1979": "NH1" <-> "NH2" Residue "A ARG 1999": "NH1" <-> "NH2" Residue "A PHE 2009": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2108": "NH1" <-> "NH2" Residue "A ARG 2127": "NH1" <-> "NH2" Residue "A ARG 2153": "NH1" <-> "NH2" Residue "A ARG 2173": "NH1" <-> "NH2" Residue "A ARG 2177": "NH1" <-> "NH2" Residue "A ARG 2185": "NH1" <-> "NH2" Residue "A ARG 2208": "NH1" <-> "NH2" Residue "A ARG 2212": "NH1" <-> "NH2" Residue "A PHE 2228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2261": "NH1" <-> "NH2" Residue "A ARG 2308": "NH1" <-> "NH2" Residue "A ARG 2378": "NH1" <-> "NH2" Residue "A ARG 2386": "NH1" <-> "NH2" Residue "A ARG 2400": "NH1" <-> "NH2" Residue "A PHE 2407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2408": "NH1" <-> "NH2" Residue "A ARG 2409": "NH1" <-> "NH2" Residue "A ARG 2455": "NH1" <-> "NH2" Residue "A ARG 2489": "NH1" <-> "NH2" Residue "A ARG 2494": "NH1" <-> "NH2" Residue "A ARG 2498": "NH1" <-> "NH2" Residue "A ARG 2519": "NH1" <-> "NH2" Residue "A ARG 2530": "NH1" <-> "NH2" Residue "A ARG 2532": "NH1" <-> "NH2" Residue "A ARG 2555": "NH1" <-> "NH2" Residue "A ARG 2578": "NH1" <-> "NH2" Residue "A ARG 2585": "NH1" <-> "NH2" Residue "A ARG 2603": "NH1" <-> "NH2" Residue "A ARG 2605": "NH1" <-> "NH2" Residue "A TYR 2611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2676": "NH1" <-> "NH2" Residue "A PHE 2681": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 38": "NH1" <-> "NH2" Residue "B ARG 88": "NH1" <-> "NH2" Residue "B ARG 167": "NH1" <-> "NH2" Residue "B ARG 169": "NH1" <-> "NH2" Residue "B ARG 170": "NH1" <-> "NH2" Residue "B ARG 294": "NH1" <-> "NH2" Residue "B ARG 305": "NH1" <-> "NH2" Residue "B ARG 320": "NH1" <-> "NH2" Residue "B ARG 350": "NH1" <-> "NH2" Residue "B ARG 423": "NH1" <-> "NH2" Residue "B ARG 466": "NH1" <-> "NH2" Residue "B ARG 614": "NH1" <-> "NH2" Residue "B ARG 657": "NH1" <-> "NH2" Residue "B ARG 666": "NH1" <-> "NH2" Residue "B ARG 668": "NH1" <-> "NH2" Residue "B PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 787": "NH1" <-> "NH2" Residue "B ARG 912": "NH1" <-> "NH2" Residue "B ARG 950": "NH1" <-> "NH2" Residue "B ARG 964": "NH1" <-> "NH2" Residue "B ARG 979": "NH1" <-> "NH2" Residue "B ARG 1009": "NH1" <-> "NH2" Residue "B ARG 1066": "NH1" <-> "NH2" Residue "B ARG 1081": "NH1" <-> "NH2" Residue "B ARG 1116": "NH1" <-> "NH2" Residue "B ARG 1136": "NH1" <-> "NH2" Residue "B ARG 1170": "NH1" <-> "NH2" Residue "B ARG 1214": "NH1" <-> "NH2" Residue "B ARG 1270": "NH1" <-> "NH2" Residue "B ARG 1328": "NH1" <-> "NH2" Residue "B ARG 1359": "NH1" <-> "NH2" Residue "B ARG 1361": "NH1" <-> "NH2" Residue "B PHE 1417": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1423": "NH1" <-> "NH2" Residue "B ARG 1435": "NH1" <-> "NH2" Residue "B ARG 1497": "NH1" <-> "NH2" Residue "B ARG 1516": "NH1" <-> "NH2" Residue "B ARG 1536": "NH1" <-> "NH2" Residue "B ARG 1549": "NH1" <-> "NH2" Residue "B ARG 1550": "NH1" <-> "NH2" Residue "B ARG 1730": "NH1" <-> "NH2" Residue "B ARG 1792": "NH1" <-> "NH2" Residue "B ARG 1829": "NH1" <-> "NH2" Residue "B TYR 1916": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1967": "NH1" <-> "NH2" Residue "B ARG 1979": "NH1" <-> "NH2" Residue "B ARG 1999": "NH1" <-> "NH2" Residue "B PHE 2009": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 2108": "NH1" <-> "NH2" Residue "B ARG 2127": "NH1" <-> "NH2" Residue "B ARG 2153": "NH1" <-> "NH2" Residue "B ARG 2173": "NH1" <-> "NH2" Residue "B ARG 2177": "NH1" <-> "NH2" Residue "B ARG 2185": "NH1" <-> "NH2" Residue "B ARG 2208": "NH1" <-> "NH2" Residue "B ARG 2212": "NH1" <-> "NH2" Residue "B PHE 2228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 2261": "NH1" <-> "NH2" Residue "B ARG 2308": "NH1" <-> "NH2" Residue "B ARG 2378": "NH1" <-> "NH2" Residue "B ARG 2386": "NH1" <-> "NH2" Residue "B ARG 2400": "NH1" <-> "NH2" Residue "B PHE 2407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 2408": "NH1" <-> "NH2" Residue "B ARG 2409": "NH1" <-> "NH2" Residue "B ARG 2455": "NH1" <-> "NH2" Residue "B ARG 2489": "NH1" <-> "NH2" Residue "B ARG 2494": "NH1" <-> "NH2" Residue "B ARG 2498": "NH1" <-> "NH2" Residue "B ARG 2519": "NH1" <-> "NH2" Residue "B ARG 2530": "NH1" <-> "NH2" Residue "B ARG 2532": "NH1" <-> "NH2" Residue "B ARG 2555": "NH1" <-> "NH2" Residue "B ARG 2578": "NH1" <-> "NH2" Residue "B ARG 2585": "NH1" <-> "NH2" Residue "B ARG 2603": "NH1" <-> "NH2" Residue "B ARG 2605": "NH1" <-> "NH2" Residue "B TYR 2611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 2676": "NH1" <-> "NH2" Residue "B PHE 2681": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 39884 Number of models: 1 Model: "" Number of chains: 6 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, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "B" 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, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} 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: "D" 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 Chain: "B" 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 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: 20.52, per 1000 atoms: 0.51 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 - 3.50 Amino acid : False - 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: 15.42 Conformation dependent library (CDL) restraints added in 6.9 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: 6.40 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: 26.38 Time building geometry restraints manager: 16.87 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: 97.56 - 106.05: 1334 106.05 - 114.55: 23180 114.55 - 123.05: 27585 123.05 - 131.55: 3178 131.55 - 140.04: 99 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 2.440 nonbonded pdb=" OG SER A 436 " pdb=" OD1 ASN A 438 " model vdw 2.244 2.440 nonbonded pdb=" OG SER B 436 " pdb=" OD1 ASN B 438 " model vdw 2.244 2.440 nonbonded pdb=" OE1 GLN A 99 " pdb=" OH TYR A 126 " model vdw 2.248 2.440 nonbonded pdb=" OE1 GLN B 99 " pdb=" OH TYR B 126 " model vdw 2.249 2.440 ... (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 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: 4.600 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: 0.030 Extract box with map and model: 15.120 Check model and map are aligned: 0.620 Set scattering table: 0.370 Process input model: 113.510 Find NCS groups from input model: 2.330 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 139.590 ------------------------------------------------------------------------------- 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 40806 Z= 0.303 Angle : 0.989 13.043 55376 Z= 0.523 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.055 0.003 TRP B2685 HIS 0.008 0.001 HIS A2303 PHE 0.032 0.003 PHE B2659 TYR 0.034 0.003 TYR A1819 ARG 0.014 0.001 ARG B 657 *********************** 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 fitting. rotamer outliers: 6 poor density : 743 time to evaluate : 4.530 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: 0.8756 (m-80) REVERT: A 582 GLN cc_start: 0.8833 (tt0) cc_final: 0.8585 (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 1068 LEU cc_start: 0.8745 (mt) cc_final: 0.8144 (tt) 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: 0.8089 (mmm160) REVERT: A 1369 LYS cc_start: 0.8859 (ptmt) cc_final: 0.8570 (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: 0.6533 (m-10) cc_final: 0.6277 (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: 0.8284 (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: 0.7573 (t0) REVERT: A 1937 GLN cc_start: 0.8517 (mm-40) cc_final: 0.8092 (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: 0.8331 (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: 0.9024 (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 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: 0.6213 (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: 0.8183 (m-10) REVERT: B 1323 ASP cc_start: 0.8331 (m-30) cc_final: 0.8036 (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: 0.8305 (m-30) cc_final: 0.7668 (t0) REVERT: B 1937 GLN cc_start: 0.8661 (mm-40) cc_final: 0.8430 (mm-40) REVERT: B 2286 VAL cc_start: 0.8660 (OUTLIER) cc_final: 0.8454 (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: 0.7704 (tpp-160) REVERT: B 2629 GLN cc_start: 0.8545 (pt0) cc_final: 0.8318 (mt0) REVERT: B 2646 LEU cc_start: 0.9337 (mt) cc_final: 0.8936 (mm) outliers start: 6 outliers final: 0 residues processed: 747 average time/residue: 0.6053 time to fit residues: 708.2078 Evaluate side-chains 379 residues out of total 4364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 377 time to evaluate : 5.022 ------------------------------------------------------------------------------- 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 430 optimal weight: 5.9990 chunk 386 optimal weight: 10.0000 chunk 214 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 260 optimal weight: 7.9990 chunk 206 optimal weight: 4.9990 chunk 399 optimal weight: 7.9990 chunk 154 optimal weight: 6.9990 chunk 243 optimal weight: 0.9990 chunk 297 optimal weight: 0.6980 chunk 463 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 331 GLN A 347 HIS A 369 GLN A 370 GLN A 468 GLN ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 967 ASN A1091 GLN A1207 GLN ** A1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1288 GLN A1295 HIS A1332 GLN A1348 ASN ** A1509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1526 ASN A1741 GLN ** A1787 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1971 GLN ** A2016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2266 GLN A2426 HIS A2456 GLN A2607 ASN ** A2657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2669 ASN B 331 GLN B 347 HIS B 369 GLN B 468 GLN B 563 ASN B 583 HIS ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1091 GLN ** B1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1288 GLN B1295 HIS B1332 GLN ** B1509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1526 ASN ** B1528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B2669 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.108 40806 Z= 0.330 Angle : 0.763 14.891 55376 Z= 0.395 Chirality : 0.046 0.343 6104 Planarity : 0.007 0.083 7290 Dihedral : 7.920 67.648 6244 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.68 % Favored : 88.28 % Rotamer: Outliers : 2.43 % Allowed : 8.99 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.92 (0.10), residues: 5058 helix: -2.62 (0.12), residues: 1156 sheet: -2.65 (0.18), residues: 622 loop : -2.73 (0.10), residues: 3280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A2685 HIS 0.006 0.001 HIS A2477 PHE 0.022 0.002 PHE B1723 TYR 0.039 0.002 TYR B1819 ARG 0.007 0.001 ARG B 492 *********************** 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 513 residues out of total 4364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 408 time to evaluate : 4.855 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 153 GLN cc_start: 0.8964 (mt0) cc_final: 0.8715 (pt0) REVERT: A 165 GLU cc_start: 0.8918 (mt-10) cc_final: 0.8637 (mt-10) REVERT: A 202 MET cc_start: 0.8671 (mmt) cc_final: 0.8464 (mmt) REVERT: A 226 ARG cc_start: 0.8590 (ptm-80) cc_final: 0.8086 (ptp90) REVERT: A 367 GLU cc_start: 0.8612 (tm-30) cc_final: 0.8355 (tm-30) REVERT: A 582 GLN cc_start: 0.8782 (tt0) cc_final: 0.8543 (tt0) REVERT: A 1254 TRP cc_start: 0.7891 (m100) cc_final: 0.7471 (m100) REVERT: A 1369 LYS cc_start: 0.9144 (ptmt) cc_final: 0.8745 (tttp) REVERT: A 1528 GLN cc_start: 0.8809 (tm-30) cc_final: 0.8534 (tm-30) REVERT: A 1570 LYS cc_start: 0.9234 (ttpt) cc_final: 0.8958 (ptpp) REVERT: A 1606 ASP cc_start: 0.7817 (t70) cc_final: 0.7389 (t0) REVERT: A 1609 GLU cc_start: 0.8975 (tt0) cc_final: 0.8309 (pp20) REVERT: A 1700 MET cc_start: 0.7837 (pmm) cc_final: 0.7511 (pmm) REVERT: A 1887 GLN cc_start: 0.7978 (mm-40) cc_final: 0.7597 (tp40) REVERT: A 1930 ASP cc_start: 0.8216 (m-30) cc_final: 0.7598 (t0) REVERT: A 1937 GLN cc_start: 0.8554 (mm-40) cc_final: 0.8202 (mm-40) REVERT: A 1960 LYS cc_start: 0.8305 (tmtt) cc_final: 0.7994 (tptt) REVERT: A 2540 TYR cc_start: 0.7435 (m-10) cc_final: 0.6967 (m-10) REVERT: A 2581 GLU cc_start: 0.7924 (tt0) cc_final: 0.7677 (tm-30) REVERT: A 2605 ARG cc_start: 0.8103 (mmm160) cc_final: 0.7559 (mmt-90) REVERT: A 2630 PHE cc_start: 0.8408 (m-10) cc_final: 0.8111 (m-10) REVERT: A 2647 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7617 (mm-30) REVERT: A 2702 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7580 (mp0) REVERT: B 165 GLU cc_start: 0.8807 (mt-10) cc_final: 0.8598 (mt-10) REVERT: B 203 MET cc_start: 0.7700 (mmm) cc_final: 0.7342 (mmm) REVERT: B 226 ARG cc_start: 0.8424 (ptm-80) cc_final: 0.7906 (ptp90) REVERT: B 460 PHE cc_start: 0.8771 (m-10) cc_final: 0.8447 (m-10) REVERT: B 469 GLN cc_start: 0.8636 (mt0) cc_final: 0.8411 (mt0) REVERT: B 492 ARG cc_start: 0.6331 (mtm110) cc_final: 0.6030 (mtm110) REVERT: B 661 ASP cc_start: 0.7988 (t70) cc_final: 0.7765 (t0) REVERT: B 886 PHE cc_start: 0.6638 (m-80) cc_final: 0.6318 (m-80) REVERT: B 985 GLN cc_start: 0.8747 (pp30) cc_final: 0.7991 (pp30) REVERT: B 1052 VAL cc_start: 0.8671 (t) cc_final: 0.8463 (p) REVERT: B 1305 MET cc_start: 0.3678 (OUTLIER) cc_final: 0.3360 (ttp) REVERT: B 1320 PHE cc_start: 0.8678 (m-10) cc_final: 0.8467 (m-10) REVERT: B 1513 ASP cc_start: 0.8473 (p0) cc_final: 0.7905 (t0) REVERT: B 1606 ASP cc_start: 0.8011 (t70) cc_final: 0.7602 (t0) REVERT: B 1609 GLU cc_start: 0.8996 (tt0) cc_final: 0.8519 (pp20) REVERT: B 1610 ASP cc_start: 0.7900 (t0) cc_final: 0.7571 (t70) REVERT: B 1700 MET cc_start: 0.7760 (pmm) cc_final: 0.7320 (pmm) REVERT: B 1887 GLN cc_start: 0.8135 (mm-40) cc_final: 0.7742 (tp40) REVERT: B 1930 ASP cc_start: 0.8281 (m-30) cc_final: 0.7597 (t0) REVERT: B 1937 GLN cc_start: 0.8649 (mm-40) cc_final: 0.8429 (mm-40) REVERT: B 1960 LYS cc_start: 0.8288 (tmtt) cc_final: 0.7981 (tptt) REVERT: B 1965 TYR cc_start: 0.8553 (m-80) cc_final: 0.8256 (m-80) REVERT: B 2241 ARG cc_start: 0.8244 (mtm-85) cc_final: 0.7831 (ttm110) REVERT: B 2290 GLN cc_start: 0.8806 (tt0) cc_final: 0.8427 (tt0) REVERT: B 2306 MET cc_start: 0.8072 (mmm) cc_final: 0.7848 (tpt) REVERT: B 2354 TRP cc_start: 0.7727 (m100) cc_final: 0.7306 (m100) REVERT: B 2540 TYR cc_start: 0.7647 (m-10) cc_final: 0.7371 (m-10) REVERT: B 2605 ARG cc_start: 0.8167 (mmm160) cc_final: 0.7584 (mmt-90) REVERT: B 2629 GLN cc_start: 0.8759 (pt0) cc_final: 0.8492 (pt0) outliers start: 105 outliers final: 54 residues processed: 486 average time/residue: 0.5266 time to fit residues: 425.8694 Evaluate side-chains 391 residues out of total 4364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 335 time to evaluate : 4.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 216 ASP 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 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 1059 ILE Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain A residue 1181 CYS Chi-restraints excluded: chain A residue 1348 ASN Chi-restraints excluded: chain A residue 1508 THR Chi-restraints excluded: chain A residue 1793 LEU Chi-restraints excluded: chain A residue 1966 THR Chi-restraints excluded: chain A residue 2034 MET Chi-restraints excluded: chain A residue 2286 VAL Chi-restraints excluded: chain A residue 2335 TYR Chi-restraints excluded: chain A residue 2339 VAL Chi-restraints excluded: chain A residue 2367 GLN Chi-restraints excluded: chain A residue 2418 LEU 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 2513 ASP Chi-restraints excluded: chain A residue 2593 ILE Chi-restraints excluded: chain A residue 2702 GLU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 216 ASP 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 456 LEU 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 720 ILE Chi-restraints excluded: chain B residue 741 THR Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1135 LEU Chi-restraints excluded: chain B residue 1181 CYS Chi-restraints excluded: chain B residue 1305 MET Chi-restraints excluded: chain B residue 1346 VAL Chi-restraints excluded: chain B residue 1687 THR Chi-restraints excluded: chain B residue 1876 LYS Chi-restraints excluded: chain B residue 1966 THR Chi-restraints excluded: chain B residue 2286 VAL Chi-restraints excluded: chain B residue 2304 ASN Chi-restraints excluded: chain B residue 2367 GLN Chi-restraints excluded: chain B residue 2423 VAL Chi-restraints excluded: chain B residue 2426 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 257 optimal weight: 0.9980 chunk 143 optimal weight: 9.9990 chunk 385 optimal weight: 3.9990 chunk 315 optimal weight: 0.9980 chunk 127 optimal weight: 9.9990 chunk 463 optimal weight: 3.9990 chunk 501 optimal weight: 0.6980 chunk 413 optimal weight: 8.9990 chunk 460 optimal weight: 1.9990 chunk 158 optimal weight: 9.9990 chunk 372 optimal weight: 0.0370 overall best weight: 0.9460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 ASN A 583 HIS A 630 GLN A 878 GLN A 985 GLN ** A1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1348 ASN ** A1509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2369 HIS ** A2463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 878 GLN B 967 ASN B1207 GLN ** B1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1706 ASN B2426 HIS ** B2629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2708 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 40806 Z= 0.206 Angle : 0.684 13.459 55376 Z= 0.350 Chirality : 0.044 0.336 6104 Planarity : 0.005 0.054 7290 Dihedral : 7.213 57.021 6244 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.11 % Favored : 88.85 % Rotamer: Outliers : 2.77 % Allowed : 9.96 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.41 (0.11), residues: 5058 helix: -1.77 (0.13), residues: 1192 sheet: -2.35 (0.19), residues: 610 loop : -2.57 (0.10), residues: 3256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B1254 HIS 0.009 0.001 HIS A2426 PHE 0.022 0.001 PHE A1320 TYR 0.035 0.002 TYR B1819 ARG 0.012 0.000 ARG A1530 *********************** 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 515 residues out of total 4364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 395 time to evaluate : 5.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ILE cc_start: 0.9032 (mm) cc_final: 0.8769 (mm) REVERT: A 226 ARG cc_start: 0.8524 (ptm-80) cc_final: 0.8038 (ptp90) REVERT: A 367 GLU cc_start: 0.8522 (tm-30) cc_final: 0.8213 (tm-30) REVERT: A 469 GLN cc_start: 0.8645 (mt0) cc_final: 0.8024 (mp10) REVERT: A 582 GLN cc_start: 0.8724 (tt0) cc_final: 0.8471 (tt0) REVERT: A 589 GLU cc_start: 0.8277 (tp30) cc_final: 0.7990 (tp30) REVERT: A 673 MET cc_start: 0.9350 (mmm) cc_final: 0.9077 (mmm) REVERT: A 1320 PHE cc_start: 0.8875 (m-80) cc_final: 0.8180 (m-80) REVERT: A 1323 ASP cc_start: 0.8612 (m-30) cc_final: 0.8405 (m-30) REVERT: A 1369 LYS cc_start: 0.9176 (ptmt) cc_final: 0.8753 (tttp) REVERT: A 1570 LYS cc_start: 0.9234 (ttpt) cc_final: 0.8922 (mttm) REVERT: A 1606 ASP cc_start: 0.7734 (t70) cc_final: 0.7195 (t0) REVERT: A 1609 GLU cc_start: 0.9004 (tt0) cc_final: 0.8306 (pp20) REVERT: A 1610 ASP cc_start: 0.7937 (t0) cc_final: 0.7677 (t0) REVERT: A 1870 GLN cc_start: 0.5970 (pm20) cc_final: 0.5713 (pm20) REVERT: A 1887 GLN cc_start: 0.7966 (mm-40) cc_final: 0.7585 (tp40) REVERT: A 1930 ASP cc_start: 0.8078 (m-30) cc_final: 0.7554 (t0) REVERT: A 1937 GLN cc_start: 0.8445 (mm-40) cc_final: 0.8063 (mm-40) REVERT: A 1960 LYS cc_start: 0.8280 (tmtt) cc_final: 0.7917 (tptt) REVERT: A 2382 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7710 (pt) REVERT: A 2423 VAL cc_start: 0.8373 (OUTLIER) cc_final: 0.8143 (m) REVERT: A 2540 TYR cc_start: 0.7359 (m-10) cc_final: 0.6955 (m-10) REVERT: A 2605 ARG cc_start: 0.8048 (mmm160) cc_final: 0.7473 (mmt-90) REVERT: A 2630 PHE cc_start: 0.8437 (m-10) cc_final: 0.8106 (m-10) REVERT: A 2647 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7492 (mm-30) REVERT: A 2702 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7515 (mp0) REVERT: B 81 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8127 (mm) REVERT: B 101 GLN cc_start: 0.8442 (mt0) cc_final: 0.8199 (mm-40) REVERT: B 203 MET cc_start: 0.7729 (mmm) cc_final: 0.7346 (mmm) REVERT: B 226 ARG cc_start: 0.8420 (ptm-80) cc_final: 0.7913 (ptp90) REVERT: B 460 PHE cc_start: 0.8835 (m-10) cc_final: 0.8619 (m-80) REVERT: B 492 ARG cc_start: 0.6466 (mtm110) cc_final: 0.6109 (mtm110) REVERT: B 886 PHE cc_start: 0.6623 (m-80) cc_final: 0.6261 (m-80) REVERT: B 985 GLN cc_start: 0.8706 (pp30) cc_final: 0.7981 (pp30) REVERT: B 1219 PHE cc_start: 0.8478 (m-80) cc_final: 0.8233 (m-80) REVERT: B 1320 PHE cc_start: 0.8631 (m-10) cc_final: 0.8419 (m-10) REVERT: B 1323 ASP cc_start: 0.8807 (m-30) cc_final: 0.8474 (m-30) REVERT: B 1568 MET cc_start: 0.7553 (tpt) cc_final: 0.7346 (tpt) REVERT: B 1606 ASP cc_start: 0.7955 (t70) cc_final: 0.7378 (t0) REVERT: B 1609 GLU cc_start: 0.9033 (tt0) cc_final: 0.8532 (pp20) REVERT: B 1610 ASP cc_start: 0.7871 (t0) cc_final: 0.7531 (t70) REVERT: B 1887 GLN cc_start: 0.8084 (mm-40) cc_final: 0.7660 (tp40) REVERT: B 1937 GLN cc_start: 0.8697 (mm-40) cc_final: 0.8449 (mm-40) REVERT: B 1960 LYS cc_start: 0.8321 (tmtt) cc_final: 0.8009 (tptt) REVERT: B 2241 ARG cc_start: 0.8201 (mtm-85) cc_final: 0.7978 (ttm110) REVERT: B 2290 GLN cc_start: 0.8781 (tt0) cc_final: 0.8291 (tt0) REVERT: B 2354 TRP cc_start: 0.7793 (m100) cc_final: 0.7443 (m100) REVERT: B 2382 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7981 (pt) REVERT: B 2605 ARG cc_start: 0.8088 (mmm160) cc_final: 0.7486 (mmt-90) REVERT: B 2646 LEU cc_start: 0.9345 (mm) cc_final: 0.9025 (tp) outliers start: 120 outliers final: 64 residues processed: 484 average time/residue: 0.5732 time to fit residues: 465.8790 Evaluate side-chains 407 residues out of total 4364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 338 time to evaluate : 5.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 216 ASP 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 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 746 LEU Chi-restraints excluded: chain A residue 751 MET Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 985 GLN Chi-restraints excluded: chain A residue 1059 ILE 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 1567 MET Chi-restraints excluded: chain A residue 1664 VAL Chi-restraints excluded: chain A residue 1687 THR Chi-restraints excluded: chain A residue 1793 LEU Chi-restraints excluded: chain A residue 1982 VAL Chi-restraints excluded: chain A residue 2201 VAL Chi-restraints excluded: chain A residue 2286 VAL Chi-restraints excluded: chain A residue 2335 TYR Chi-restraints excluded: chain A residue 2339 VAL Chi-restraints excluded: chain A residue 2380 VAL Chi-restraints excluded: chain A residue 2382 LEU 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 2513 ASP Chi-restraints excluded: chain A residue 2702 GLU Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 216 ASP 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 720 ILE Chi-restraints excluded: chain B residue 726 CYS Chi-restraints excluded: chain B residue 741 THR Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 1059 ILE Chi-restraints excluded: chain B residue 1148 LEU Chi-restraints excluded: chain B residue 1181 CYS 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 1982 VAL Chi-restraints excluded: chain B residue 1985 SER 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 2357 LEU Chi-restraints excluded: chain B residue 2380 VAL Chi-restraints excluded: chain B residue 2382 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 458 optimal weight: 0.8980 chunk 348 optimal weight: 0.7980 chunk 240 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 221 optimal weight: 3.9990 chunk 311 optimal weight: 0.0020 chunk 465 optimal weight: 5.9990 chunk 492 optimal weight: 0.8980 chunk 243 optimal weight: 2.9990 chunk 441 optimal weight: 0.3980 chunk 132 optimal weight: 0.9980 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 GLN ** A 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 892 HIS A 985 GLN ** A1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1348 ASN ** A1509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1963 ASN ** A2016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2426 HIS A2466 GLN ** A2629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2708 GLN ** B 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 892 HIS B1207 GLN ** B1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1288 GLN ** B1509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2369 HIS ** B2466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2708 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 40806 Z= 0.176 Angle : 0.654 13.962 55376 Z= 0.331 Chirality : 0.043 0.313 6104 Planarity : 0.005 0.049 7290 Dihedral : 6.675 56.376 6244 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.87 % Favored : 89.09 % Rotamer: Outliers : 2.75 % Allowed : 11.14 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.05 (0.11), residues: 5058 helix: -1.25 (0.14), residues: 1222 sheet: -2.06 (0.20), residues: 580 loop : -2.46 (0.10), residues: 3256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 788 HIS 0.018 0.001 HIS B2426 PHE 0.022 0.001 PHE B 976 TYR 0.028 0.001 TYR B1819 ARG 0.008 0.000 ARG A 492 *********************** 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 516 residues out of total 4364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 397 time to evaluate : 4.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ILE cc_start: 0.8997 (mm) cc_final: 0.8722 (mm) REVERT: A 226 ARG cc_start: 0.8613 (ptm-80) cc_final: 0.8084 (ptp90) REVERT: A 453 LEU cc_start: 0.9212 (mp) cc_final: 0.8919 (mp) REVERT: A 469 GLN cc_start: 0.8622 (mt0) cc_final: 0.8058 (mp10) REVERT: A 582 GLN cc_start: 0.8653 (tt0) cc_final: 0.8418 (tt0) REVERT: A 594 ASP cc_start: 0.8267 (t0) cc_final: 0.7980 (t0) REVERT: A 886 PHE cc_start: 0.6558 (m-80) cc_final: 0.6308 (m-80) REVERT: A 1152 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8489 (tp) REVERT: A 1283 ARG cc_start: 0.8152 (mmm160) cc_final: 0.7925 (mmm-85) REVERT: A 1320 PHE cc_start: 0.8851 (m-80) cc_final: 0.8212 (m-80) REVERT: A 1369 LYS cc_start: 0.9171 (ptmt) cc_final: 0.8940 (ptmm) REVERT: A 1530 ARG cc_start: 0.6820 (ttp-110) cc_final: 0.6039 (ptm160) REVERT: A 1570 LYS cc_start: 0.9218 (ttpt) cc_final: 0.8951 (ptpp) REVERT: A 1606 ASP cc_start: 0.7586 (t70) cc_final: 0.7120 (t0) REVERT: A 1609 GLU cc_start: 0.9042 (tt0) cc_final: 0.8329 (pp20) REVERT: A 1610 ASP cc_start: 0.7942 (t0) cc_final: 0.7646 (t0) REVERT: A 1870 GLN cc_start: 0.6036 (pm20) cc_final: 0.5782 (pm20) REVERT: A 1887 GLN cc_start: 0.7954 (mm-40) cc_final: 0.7559 (tp40) REVERT: A 1937 GLN cc_start: 0.8415 (mm-40) cc_final: 0.8107 (mm-40) REVERT: A 1960 LYS cc_start: 0.8276 (tmtt) cc_final: 0.7927 (tptt) REVERT: A 1965 TYR cc_start: 0.8462 (m-80) cc_final: 0.8141 (m-10) REVERT: A 2382 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7708 (pt) REVERT: A 2423 VAL cc_start: 0.8434 (OUTLIER) cc_final: 0.8194 (m) REVERT: A 2540 TYR cc_start: 0.7312 (m-10) cc_final: 0.6920 (m-10) REVERT: A 2605 ARG cc_start: 0.7995 (mmm160) cc_final: 0.7402 (mmt-90) REVERT: A 2630 PHE cc_start: 0.8386 (m-10) cc_final: 0.8078 (m-10) REVERT: B 81 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.8080 (mm) REVERT: B 101 GLN cc_start: 0.8415 (mt0) cc_final: 0.8206 (mm-40) REVERT: B 153 GLN cc_start: 0.8833 (mt0) cc_final: 0.8545 (pt0) REVERT: B 226 ARG cc_start: 0.8378 (ptm-80) cc_final: 0.7898 (ptp90) REVERT: B 460 PHE cc_start: 0.8840 (m-10) cc_final: 0.8597 (m-80) REVERT: B 469 GLN cc_start: 0.8557 (mt0) cc_final: 0.7874 (mp10) REVERT: B 492 ARG cc_start: 0.6601 (mtm110) cc_final: 0.6400 (mtm110) REVERT: B 731 GLN cc_start: 0.8794 (mt0) cc_final: 0.8225 (mt0) REVERT: B 886 PHE cc_start: 0.6563 (m-80) cc_final: 0.6195 (m-80) REVERT: B 1219 PHE cc_start: 0.8498 (m-80) cc_final: 0.8243 (m-80) REVERT: B 1305 MET cc_start: 0.3857 (OUTLIER) cc_final: 0.3361 (mtp) REVERT: B 1319 VAL cc_start: 0.7782 (OUTLIER) cc_final: 0.7492 (p) REVERT: B 1320 PHE cc_start: 0.8527 (m-10) cc_final: 0.8240 (m-10) REVERT: B 1323 ASP cc_start: 0.8864 (m-30) cc_final: 0.8529 (m-30) REVERT: B 1530 ARG cc_start: 0.7167 (ttp-110) cc_final: 0.6457 (ptm160) REVERT: B 1606 ASP cc_start: 0.7939 (t70) cc_final: 0.7387 (t0) REVERT: B 1609 GLU cc_start: 0.9068 (tt0) cc_final: 0.8540 (pp20) REVERT: B 1610 ASP cc_start: 0.7897 (t0) cc_final: 0.7553 (t70) REVERT: B 1908 GLU cc_start: 0.8397 (pt0) cc_final: 0.8130 (pt0) REVERT: B 1937 GLN cc_start: 0.8686 (mm-40) cc_final: 0.8397 (mm-40) REVERT: B 1960 LYS cc_start: 0.8319 (tmtt) cc_final: 0.8002 (tptt) REVERT: B 2241 ARG cc_start: 0.8117 (mtm-85) cc_final: 0.7894 (ttm110) REVERT: B 2290 GLN cc_start: 0.8749 (tt0) cc_final: 0.8255 (tt0) REVERT: B 2354 TRP cc_start: 0.7809 (m100) cc_final: 0.7505 (m100) REVERT: B 2423 VAL cc_start: 0.8308 (OUTLIER) cc_final: 0.8086 (m) REVERT: B 2540 TYR cc_start: 0.7166 (m-10) cc_final: 0.6659 (m-80) REVERT: B 2605 ARG cc_start: 0.8023 (mmm160) cc_final: 0.7632 (tpp-160) REVERT: B 2646 LEU cc_start: 0.9311 (mm) cc_final: 0.8982 (tp) outliers start: 119 outliers final: 76 residues processed: 491 average time/residue: 0.5306 time to fit residues: 434.5587 Evaluate side-chains 420 residues out of total 4364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 337 time to evaluate : 4.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 216 ASP 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 572 LEU Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 638 CYS 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 746 LEU Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 1059 ILE 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 1440 CYS 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 1752 LEU 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 1985 SER Chi-restraints excluded: chain A residue 2034 MET 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 2339 VAL Chi-restraints excluded: chain A residue 2380 VAL Chi-restraints excluded: chain A residue 2382 LEU Chi-restraints excluded: chain A residue 2423 VAL Chi-restraints excluded: chain A residue 2426 HIS Chi-restraints excluded: chain A residue 2504 VAL Chi-restraints excluded: chain A residue 2513 ASP Chi-restraints excluded: chain A residue 2566 LEU Chi-restraints excluded: chain A residue 2625 LEU Chi-restraints excluded: chain A residue 2702 GLU Chi-restraints excluded: chain B residue 66 ASP 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 216 ASP 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 638 CYS 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 762 GLN Chi-restraints excluded: chain B residue 1059 ILE 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 1440 CYS Chi-restraints excluded: chain B residue 1513 ASP 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 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 2091 ASP Chi-restraints excluded: chain B residue 2201 VAL Chi-restraints excluded: chain B residue 2286 VAL 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 2426 HIS Chi-restraints excluded: chain B residue 2625 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 410 optimal weight: 7.9990 chunk 279 optimal weight: 0.0970 chunk 7 optimal weight: 0.9980 chunk 367 optimal weight: 4.9990 chunk 203 optimal weight: 4.9990 chunk 420 optimal weight: 9.9990 chunk 340 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 251 optimal weight: 0.5980 chunk 442 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 985 GLN A1207 GLN ** A1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1348 ASN ** A1509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1706 ASN ** A2016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2426 HIS ** A2629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2708 GLN B 469 GLN ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 985 GLN B1207 GLN ** B1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1288 GLN ** B1348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2708 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 40806 Z= 0.200 Angle : 0.652 16.077 55376 Z= 0.329 Chirality : 0.043 0.321 6104 Planarity : 0.005 0.049 7290 Dihedral : 6.376 55.829 6244 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.99 % Favored : 88.95 % Rotamer: Outliers : 3.00 % Allowed : 11.95 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.11), residues: 5058 helix: -0.84 (0.14), residues: 1228 sheet: -1.92 (0.21), residues: 576 loop : -2.37 (0.11), residues: 3254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B2501 HIS 0.015 0.001 HIS A2426 PHE 0.020 0.001 PHE A 738 TYR 0.022 0.001 TYR A1819 ARG 0.013 0.000 ARG A1170 *********************** 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 502 residues out of total 4364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 372 time to evaluate : 4.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8073 (mm) REVERT: A 204 ILE cc_start: 0.9005 (mm) cc_final: 0.8726 (mm) REVERT: A 226 ARG cc_start: 0.8625 (ptm-80) cc_final: 0.8117 (ptp90) REVERT: A 453 LEU cc_start: 0.9277 (mp) cc_final: 0.8983 (mp) REVERT: A 469 GLN cc_start: 0.8611 (mt0) cc_final: 0.8040 (mp10) REVERT: A 582 GLN cc_start: 0.8646 (tt0) cc_final: 0.8405 (tt0) REVERT: A 589 GLU cc_start: 0.8385 (tp30) cc_final: 0.8110 (tp30) REVERT: A 594 ASP cc_start: 0.8284 (t0) cc_final: 0.7903 (t0) REVERT: A 886 PHE cc_start: 0.6592 (m-80) cc_final: 0.6348 (m-80) REVERT: A 1152 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8496 (tp) REVERT: A 1320 PHE cc_start: 0.8904 (m-80) cc_final: 0.8197 (m-80) REVERT: A 1323 ASP cc_start: 0.8828 (m-30) cc_final: 0.8361 (m-30) REVERT: A 1369 LYS cc_start: 0.9165 (ptmt) cc_final: 0.8929 (ptmm) REVERT: A 1530 ARG cc_start: 0.6760 (ttp-110) cc_final: 0.5950 (ptm160) REVERT: A 1570 LYS cc_start: 0.9289 (ttpt) cc_final: 0.8977 (ptpp) REVERT: A 1610 ASP cc_start: 0.8062 (t0) cc_final: 0.7777 (t70) REVERT: A 1870 GLN cc_start: 0.6228 (pm20) cc_final: 0.5846 (pm20) REVERT: A 1887 GLN cc_start: 0.7966 (mm-40) cc_final: 0.7564 (tp40) REVERT: A 1937 GLN cc_start: 0.8445 (mm-40) cc_final: 0.8131 (mm-40) REVERT: A 1960 LYS cc_start: 0.8305 (tmtt) cc_final: 0.7952 (tptt) REVERT: A 2382 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7705 (pt) REVERT: A 2423 VAL cc_start: 0.8494 (OUTLIER) cc_final: 0.8265 (m) REVERT: A 2540 TYR cc_start: 0.7392 (m-10) cc_final: 0.7014 (m-10) REVERT: A 2605 ARG cc_start: 0.7970 (mmm160) cc_final: 0.7378 (mmt-90) REVERT: A 2630 PHE cc_start: 0.8426 (m-10) cc_final: 0.8108 (m-10) REVERT: B 81 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.8073 (mm) REVERT: B 226 ARG cc_start: 0.8418 (ptm-80) cc_final: 0.7946 (ptp90) REVERT: B 460 PHE cc_start: 0.8841 (m-10) cc_final: 0.8611 (m-80) REVERT: B 469 GLN cc_start: 0.8562 (mt0) cc_final: 0.7983 (mp10) REVERT: B 492 ARG cc_start: 0.6641 (mtm110) cc_final: 0.6417 (mtm110) REVERT: B 594 ASP cc_start: 0.8303 (t0) cc_final: 0.8027 (t0) REVERT: B 731 GLN cc_start: 0.8798 (mt0) cc_final: 0.8256 (mt0) REVERT: B 886 PHE cc_start: 0.6563 (m-80) cc_final: 0.6183 (m-80) REVERT: B 1219 PHE cc_start: 0.8530 (m-80) cc_final: 0.8315 (m-80) REVERT: B 1305 MET cc_start: 0.3879 (OUTLIER) cc_final: 0.3381 (mtp) REVERT: B 1319 VAL cc_start: 0.7784 (OUTLIER) cc_final: 0.7507 (p) REVERT: B 1320 PHE cc_start: 0.8558 (m-10) cc_final: 0.8257 (m-10) REVERT: B 1323 ASP cc_start: 0.8898 (m-30) cc_final: 0.8550 (m-30) REVERT: B 1530 ARG cc_start: 0.7308 (ttp-110) cc_final: 0.6443 (ptm160) REVERT: B 1570 LYS cc_start: 0.9306 (ttpt) cc_final: 0.9067 (ptpt) REVERT: B 1606 ASP cc_start: 0.8064 (t70) cc_final: 0.7486 (t0) REVERT: B 1609 GLU cc_start: 0.9161 (tt0) cc_final: 0.8595 (pp20) REVERT: B 1610 ASP cc_start: 0.8068 (t0) cc_final: 0.7725 (t70) REVERT: B 1719 ASP cc_start: 0.8609 (m-30) cc_final: 0.8252 (t0) REVERT: B 1798 PHE cc_start: 0.8237 (t80) cc_final: 0.8000 (t80) REVERT: B 1819 TYR cc_start: 0.6630 (t80) cc_final: 0.6171 (t80) REVERT: B 1908 GLU cc_start: 0.8420 (pt0) cc_final: 0.8130 (pt0) REVERT: B 1937 GLN cc_start: 0.8667 (mm-40) cc_final: 0.8355 (mm-40) REVERT: B 1960 LYS cc_start: 0.8320 (tmtt) cc_final: 0.8000 (tptt) REVERT: B 2241 ARG cc_start: 0.8149 (mtm-85) cc_final: 0.7936 (ttm110) REVERT: B 2290 GLN cc_start: 0.8744 (tt0) cc_final: 0.8219 (tt0) REVERT: B 2354 TRP cc_start: 0.7852 (m100) cc_final: 0.7582 (m100) REVERT: B 2423 VAL cc_start: 0.8415 (OUTLIER) cc_final: 0.8184 (m) REVERT: B 2540 TYR cc_start: 0.7300 (m-10) cc_final: 0.6751 (m-80) REVERT: B 2605 ARG cc_start: 0.8022 (mmm160) cc_final: 0.7382 (mmt-90) REVERT: B 2646 LEU cc_start: 0.9346 (mm) cc_final: 0.9016 (tp) outliers start: 130 outliers final: 90 residues processed: 469 average time/residue: 0.5851 time to fit residues: 467.6760 Evaluate side-chains 432 residues out of total 4364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 334 time to evaluate : 4.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP 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 216 ASP 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 572 LEU Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 638 CYS Chi-restraints excluded: chain A residue 703 CYS Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 726 CYS Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 751 MET Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 1059 ILE 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 1364 VAL Chi-restraints excluded: chain A residue 1410 LEU Chi-restraints excluded: chain A residue 1440 CYS Chi-restraints excluded: chain A residue 1508 THR Chi-restraints excluded: chain A residue 1567 MET Chi-restraints excluded: chain A residue 1664 VAL Chi-restraints excluded: chain A residue 1752 LEU 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 2034 MET Chi-restraints excluded: chain A residue 2056 HIS 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 2339 VAL Chi-restraints excluded: chain A residue 2357 LEU Chi-restraints excluded: chain A residue 2380 VAL Chi-restraints excluded: chain A residue 2382 LEU Chi-restraints excluded: chain A residue 2423 VAL Chi-restraints excluded: chain A residue 2482 VAL Chi-restraints excluded: chain A residue 2504 VAL Chi-restraints excluded: chain A residue 2507 LEU Chi-restraints excluded: chain A residue 2513 ASP Chi-restraints excluded: chain A residue 2702 GLU Chi-restraints excluded: chain B residue 66 ASP 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 216 ASP 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 638 CYS Chi-restraints excluded: chain B residue 703 CYS Chi-restraints excluded: chain B residue 716 THR 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 762 GLN Chi-restraints excluded: chain B residue 991 ASP Chi-restraints excluded: chain B residue 1059 ILE 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 1364 VAL Chi-restraints excluded: chain B residue 1440 CYS Chi-restraints excluded: chain B residue 1513 ASP 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 1966 THR 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 2357 LEU 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 2482 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 165 optimal weight: 9.9990 chunk 443 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 289 optimal weight: 0.9990 chunk 121 optimal weight: 5.9990 chunk 493 optimal weight: 0.9980 chunk 409 optimal weight: 2.9990 chunk 228 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 163 optimal weight: 0.9980 chunk 259 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN ** A 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1348 ASN ** A1509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2016 GLN A2182 HIS A2629 GLN ** A2657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2708 GLN B 630 GLN B1207 GLN ** B1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1288 GLN ** B1348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1963 ASN B2426 HIS ** B2657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2708 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 40806 Z= 0.207 Angle : 0.651 16.463 55376 Z= 0.327 Chirality : 0.043 0.301 6104 Planarity : 0.005 0.047 7290 Dihedral : 6.233 55.734 6244 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.04 % Allowed : 11.17 % Favored : 88.79 % Rotamer: Outliers : 2.82 % Allowed : 12.52 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.11), residues: 5058 helix: -0.62 (0.15), residues: 1228 sheet: -1.90 (0.20), residues: 586 loop : -2.32 (0.11), residues: 3244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B2501 HIS 0.004 0.001 HIS B2477 PHE 0.022 0.001 PHE A1320 TYR 0.016 0.001 TYR B1819 ARG 0.010 0.000 ARG A 492 *********************** 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 482 residues out of total 4364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 360 time to evaluate : 4.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8063 (mm) REVERT: A 204 ILE cc_start: 0.9008 (mm) cc_final: 0.8744 (mm) REVERT: A 226 ARG cc_start: 0.8634 (ptm-80) cc_final: 0.8169 (ptp90) REVERT: A 453 LEU cc_start: 0.9284 (mp) cc_final: 0.8990 (mp) REVERT: A 469 GLN cc_start: 0.8447 (mt0) cc_final: 0.7922 (mp10) REVERT: A 582 GLN cc_start: 0.8670 (tt0) cc_final: 0.8429 (tt0) REVERT: A 589 GLU cc_start: 0.8383 (tp30) cc_final: 0.8093 (tp30) REVERT: A 594 ASP cc_start: 0.8296 (t0) cc_final: 0.7979 (t0) REVERT: A 886 PHE cc_start: 0.6548 (m-80) cc_final: 0.6291 (m-80) REVERT: A 1152 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8563 (tp) REVERT: A 1323 ASP cc_start: 0.8829 (m-30) cc_final: 0.8345 (m-30) REVERT: A 1369 LYS cc_start: 0.9139 (ptmt) cc_final: 0.8907 (ptmm) REVERT: A 1570 LYS cc_start: 0.9274 (ttpt) cc_final: 0.8948 (ptpt) REVERT: A 1610 ASP cc_start: 0.8106 (t0) cc_final: 0.7795 (t70) REVERT: A 1691 ARG cc_start: 0.7356 (ttp-170) cc_final: 0.6990 (ptt-90) REVERT: A 1887 GLN cc_start: 0.7971 (mm-40) cc_final: 0.7564 (tp40) REVERT: A 1937 GLN cc_start: 0.8485 (mm-40) cc_final: 0.8189 (mm-40) REVERT: A 1960 LYS cc_start: 0.8371 (tmtt) cc_final: 0.7782 (tptt) REVERT: A 2382 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7742 (pt) REVERT: A 2423 VAL cc_start: 0.8496 (OUTLIER) cc_final: 0.8265 (m) REVERT: A 2540 TYR cc_start: 0.7370 (m-10) cc_final: 0.6948 (m-10) REVERT: A 2605 ARG cc_start: 0.7990 (mmm160) cc_final: 0.7401 (mmt-90) REVERT: A 2630 PHE cc_start: 0.8428 (m-10) cc_final: 0.8120 (m-10) REVERT: B 81 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.8047 (mm) REVERT: B 102 GLN cc_start: 0.8750 (tm-30) cc_final: 0.8398 (tm-30) REVERT: B 226 ARG cc_start: 0.8419 (ptm-80) cc_final: 0.7978 (ptp90) REVERT: B 460 PHE cc_start: 0.8849 (m-10) cc_final: 0.8580 (m-10) REVERT: B 469 GLN cc_start: 0.8618 (mt0) cc_final: 0.7954 (mp10) REVERT: B 492 ARG cc_start: 0.6664 (mtm110) cc_final: 0.6402 (mtm110) REVERT: B 731 GLN cc_start: 0.8800 (mt0) cc_final: 0.8312 (mt0) REVERT: B 886 PHE cc_start: 0.6575 (m-80) cc_final: 0.6197 (m-80) REVERT: B 1219 PHE cc_start: 0.8527 (m-80) cc_final: 0.8300 (m-80) REVERT: B 1319 VAL cc_start: 0.7869 (OUTLIER) cc_final: 0.7594 (p) REVERT: B 1320 PHE cc_start: 0.8594 (m-10) cc_final: 0.8240 (m-10) REVERT: B 1323 ASP cc_start: 0.8914 (m-30) cc_final: 0.8572 (m-30) REVERT: B 1530 ARG cc_start: 0.7278 (ttp-110) cc_final: 0.6364 (ptm160) REVERT: B 1570 LYS cc_start: 0.9294 (ttpt) cc_final: 0.9055 (ptpt) REVERT: B 1606 ASP cc_start: 0.8100 (t70) cc_final: 0.7504 (t0) REVERT: B 1609 GLU cc_start: 0.9161 (tt0) cc_final: 0.8581 (pp20) REVERT: B 1610 ASP cc_start: 0.8107 (t0) cc_final: 0.7766 (t70) REVERT: B 1819 TYR cc_start: 0.6743 (OUTLIER) cc_final: 0.6339 (t80) REVERT: B 1937 GLN cc_start: 0.8665 (mm-40) cc_final: 0.8349 (mm-40) REVERT: B 1960 LYS cc_start: 0.8387 (tmtt) cc_final: 0.8058 (tptt) REVERT: B 2241 ARG cc_start: 0.8136 (mtm-85) cc_final: 0.7916 (ttm110) REVERT: B 2290 GLN cc_start: 0.8746 (tt0) cc_final: 0.8215 (tt0) REVERT: B 2354 TRP cc_start: 0.7856 (m100) cc_final: 0.7604 (m100) REVERT: B 2423 VAL cc_start: 0.8406 (OUTLIER) cc_final: 0.8175 (m) REVERT: B 2457 LYS cc_start: 0.8096 (mmtt) cc_final: 0.7877 (mmtm) REVERT: B 2540 TYR cc_start: 0.7348 (m-10) cc_final: 0.6850 (m-80) REVERT: B 2605 ARG cc_start: 0.8013 (mmm160) cc_final: 0.7352 (mmt-90) REVERT: B 2646 LEU cc_start: 0.9365 (mm) cc_final: 0.9039 (tp) outliers start: 122 outliers final: 91 residues processed: 455 average time/residue: 0.5372 time to fit residues: 414.9048 Evaluate side-chains 435 residues out of total 4364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 336 time to evaluate : 4.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP 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 198 ASN Chi-restraints excluded: chain A residue 216 ASP 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 572 LEU Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 638 CYS Chi-restraints excluded: chain A residue 703 CYS Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 726 CYS Chi-restraints excluded: chain A residue 741 THR Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 751 MET Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 1059 ILE 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 1364 VAL Chi-restraints excluded: chain A residue 1410 LEU 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 1687 THR Chi-restraints excluded: chain A residue 1719 ASP 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 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 2339 VAL Chi-restraints excluded: chain A residue 2380 VAL Chi-restraints excluded: chain A residue 2382 LEU Chi-restraints excluded: chain A residue 2423 VAL Chi-restraints excluded: chain A residue 2482 VAL Chi-restraints excluded: chain A residue 2504 VAL Chi-restraints excluded: chain A residue 2507 LEU Chi-restraints excluded: chain A residue 2513 ASP Chi-restraints excluded: chain A residue 2702 GLU Chi-restraints excluded: chain B residue 66 ASP Chi-restraints excluded: chain B residue 81 LEU 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 198 ASN Chi-restraints excluded: chain B residue 216 ASP 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 638 CYS Chi-restraints excluded: chain B residue 703 CYS Chi-restraints excluded: chain B residue 716 THR 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 762 GLN Chi-restraints excluded: chain B residue 991 ASP 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 1513 ASP 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 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 1966 THR 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 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 2625 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 510 random chunks: chunk 475 optimal weight: 0.4980 chunk 55 optimal weight: 3.9990 chunk 281 optimal weight: 3.9990 chunk 360 optimal weight: 7.9990 chunk 279 optimal weight: 0.0570 chunk 415 optimal weight: 1.9990 chunk 275 optimal weight: 0.7980 chunk 491 optimal weight: 1.9990 chunk 307 optimal weight: 1.9990 chunk 299 optimal weight: 0.0060 chunk 226 optimal weight: 1.9990 overall best weight: 0.6716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN ** A 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2708 GLN ** B1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1288 GLN ** B1348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2182 HIS ** B2657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2708 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.113 40806 Z= 0.188 Angle : 0.643 18.340 55376 Z= 0.323 Chirality : 0.043 0.336 6104 Planarity : 0.005 0.058 7290 Dihedral : 6.076 55.768 6244 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.91 % Favored : 89.05 % Rotamer: Outliers : 2.89 % Allowed : 13.01 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.62 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.12), residues: 5058 helix: -0.36 (0.15), residues: 1210 sheet: -1.81 (0.21), residues: 590 loop : -2.22 (0.11), residues: 3258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP B1632 HIS 0.004 0.001 HIS A1721 PHE 0.035 0.001 PHE A1320 TYR 0.025 0.001 TYR B1445 ARG 0.011 0.000 ARG A 492 *********************** 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 490 residues out of total 4364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 365 time to evaluate : 6.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8052 (mm) REVERT: A 204 ILE cc_start: 0.8953 (mm) cc_final: 0.8644 (mm) REVERT: A 226 ARG cc_start: 0.8610 (ptm-80) cc_final: 0.8115 (ptp90) REVERT: A 453 LEU cc_start: 0.9273 (mp) cc_final: 0.8998 (mp) REVERT: A 469 GLN cc_start: 0.8443 (mt0) cc_final: 0.7891 (mp10) REVERT: A 582 GLN cc_start: 0.8656 (tt0) cc_final: 0.8396 (tt0) REVERT: A 589 GLU cc_start: 0.8371 (tp30) cc_final: 0.8083 (tp30) REVERT: A 594 ASP cc_start: 0.8214 (t0) cc_final: 0.8001 (t0) REVERT: A 886 PHE cc_start: 0.6566 (m-80) cc_final: 0.6303 (m-80) REVERT: A 1152 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8587 (tp) REVERT: A 1323 ASP cc_start: 0.8835 (m-30) cc_final: 0.8304 (m-30) REVERT: A 1369 LYS cc_start: 0.9096 (ptmt) cc_final: 0.8861 (ptmm) REVERT: A 1530 ARG cc_start: 0.6901 (ttp-110) cc_final: 0.5956 (ptm160) REVERT: A 1570 LYS cc_start: 0.9240 (ttpt) cc_final: 0.8912 (ptpt) REVERT: A 1610 ASP cc_start: 0.8099 (t0) cc_final: 0.7763 (t70) REVERT: A 1819 TYR cc_start: 0.6920 (OUTLIER) cc_final: 0.6142 (t80) REVERT: A 1887 GLN cc_start: 0.7925 (mm-40) cc_final: 0.7556 (tp40) REVERT: A 1937 GLN cc_start: 0.8463 (mm-40) cc_final: 0.8157 (mm-40) REVERT: A 1960 LYS cc_start: 0.8325 (tmtt) cc_final: 0.7734 (tptt) REVERT: A 1965 TYR cc_start: 0.8652 (m-80) cc_final: 0.8002 (m-10) REVERT: A 2382 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7756 (pt) REVERT: A 2423 VAL cc_start: 0.8493 (OUTLIER) cc_final: 0.8264 (m) REVERT: A 2540 TYR cc_start: 0.7341 (m-10) cc_final: 0.6944 (m-10) REVERT: A 2605 ARG cc_start: 0.7931 (mmm160) cc_final: 0.7343 (mmt-90) REVERT: A 2630 PHE cc_start: 0.8404 (m-10) cc_final: 0.8071 (m-10) REVERT: B 81 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.8039 (mm) REVERT: B 102 GLN cc_start: 0.8770 (tm-30) cc_final: 0.8440 (tm-30) REVERT: B 144 GLU cc_start: 0.7959 (tm-30) cc_final: 0.7668 (tm-30) REVERT: B 226 ARG cc_start: 0.8377 (ptm-80) cc_final: 0.7963 (ptp90) REVERT: B 460 PHE cc_start: 0.8844 (m-10) cc_final: 0.8576 (m-10) REVERT: B 469 GLN cc_start: 0.8551 (mt0) cc_final: 0.7923 (mp10) REVERT: B 484 ASN cc_start: 0.8268 (m-40) cc_final: 0.8028 (m-40) REVERT: B 492 ARG cc_start: 0.6652 (mtm110) cc_final: 0.6389 (mtm110) REVERT: B 1219 PHE cc_start: 0.8530 (m-80) cc_final: 0.8285 (m-80) REVERT: B 1319 VAL cc_start: 0.7835 (OUTLIER) cc_final: 0.7560 (p) REVERT: B 1320 PHE cc_start: 0.8593 (m-10) cc_final: 0.8211 (m-10) REVERT: B 1323 ASP cc_start: 0.8926 (m-30) cc_final: 0.8578 (m-30) REVERT: B 1570 LYS cc_start: 0.9262 (ttpt) cc_final: 0.9033 (ptpt) REVERT: B 1606 ASP cc_start: 0.8184 (t70) cc_final: 0.7583 (t0) REVERT: B 1609 GLU cc_start: 0.9169 (tt0) cc_final: 0.8601 (pp20) REVERT: B 1610 ASP cc_start: 0.8163 (t0) cc_final: 0.7821 (t70) REVERT: B 1705 TYR cc_start: 0.6323 (m-10) cc_final: 0.6055 (m-10) REVERT: B 1819 TYR cc_start: 0.6839 (OUTLIER) cc_final: 0.6469 (t80) REVERT: B 1908 GLU cc_start: 0.8380 (pt0) cc_final: 0.7819 (pt0) REVERT: B 1937 GLN cc_start: 0.8770 (mm-40) cc_final: 0.8398 (mm-40) REVERT: B 1960 LYS cc_start: 0.8370 (tmtt) cc_final: 0.8043 (tptt) REVERT: B 2241 ARG cc_start: 0.8098 (mtm-85) cc_final: 0.7685 (ttm110) REVERT: B 2354 TRP cc_start: 0.7827 (m100) cc_final: 0.7604 (m100) REVERT: B 2423 VAL cc_start: 0.8400 (OUTLIER) cc_final: 0.8166 (m) REVERT: B 2457 LYS cc_start: 0.8064 (mmtt) cc_final: 0.7849 (mmtm) REVERT: B 2540 TYR cc_start: 0.7312 (m-10) cc_final: 0.6858 (m-10) REVERT: B 2605 ARG cc_start: 0.7962 (mmm160) cc_final: 0.7312 (mmt-90) REVERT: B 2646 LEU cc_start: 0.9363 (mm) cc_final: 0.9031 (tp) outliers start: 125 outliers final: 90 residues processed: 459 average time/residue: 0.5370 time to fit residues: 413.3157 Evaluate side-chains 433 residues out of total 4364 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 334 time to evaluate : 5.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 ASP 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 198 ASN Chi-restraints excluded: chain A residue 216 ASP 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 591 VAL Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 638 CYS Chi-restraints excluded: chain A residue 703 CYS Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 726 CYS Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 1059 ILE 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 1508 THR Chi-restraints excluded: chain A residue 1567 MET 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 1819 TYR 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 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 2339 VAL Chi-restraints excluded: chain A residue 2380 VAL Chi-restraints excluded: chain A residue 2382 LEU Chi-restraints excluded: chain A residue 2423 VAL Chi-restraints excluded: chain A residue 2504 VAL Chi-restraints excluded: chain A residue 2507 LEU Chi-restraints excluded: chain A residue 2513 ASP Chi-restraints excluded: chain A residue 2566 LEU Chi-restraints excluded: chain A residue 2625 LEU Chi-restraints excluded: chain A residue 2702 GLU Chi-restraints excluded: chain B residue 66 ASP 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 198 ASN Chi-restraints excluded: chain B residue 216 ASP 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 638 CYS Chi-restraints excluded: chain B residue 703 CYS Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 726 CYS Chi-restraints excluded: chain B residue 746 LEU Chi-restraints excluded: chain B residue 762 GLN 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 1508 THR Chi-restraints excluded: chain B residue 1513 ASP 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 1819 TYR 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 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 2201 VAL Chi-restraints excluded: chain B residue 2238 LEU 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 2482 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 304 optimal weight: 2.9990 chunk 196 optimal weight: 0.1980 chunk 293 optimal weight: 0.0050 chunk 148 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 95 optimal weight: 0.0030 chunk 312 optimal weight: 2.9990 chunk 334 optimal weight: 5.9990 chunk 243 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 386 optimal weight: 0.3980 overall best weight: 0.3204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 GLN A 331 GLN ** A 731 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2244 GLN ** A2463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2708 GLN B 331 GLN ** B1244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2224 GLN ** B2657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2708 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.3439 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: